UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C.  20549

FORM 10-Q

x
QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 
For the quarterly period ended September 30, 2013March 31, 2014
or

oTRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 
For the transition period from                    to

Commission file number 000-26422

DISCOVERY LABORATORIES, INC.
(Exact name of registrant as specified in its charter)

Delaware
 
94-3171943
(State or other jurisdiction of incorporation or organization)
 
(I.R.S. Employer Identification Number)

2600 Kelly Road, Suite 100
Warrington, Pennsylvania 18976-3622
(Address of principal executive offices)
2600 Kelly Road, Suite 100
Warrington, Pennsylvania 18976-3622
(Address of principal executive offices)

(215) 488-9300
(Registrant’s telephone number, including area code)
__________________


Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.   YES x     NO o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    YES x      NO o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company.  See definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

Large accelerated filero
o
Accelerated filerx
Non-accelerated filer  o (Do not check if a smaller reporting company)
Smaller reporting company
o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).  YES o NO x

As of November 8, 2013, 80,749,022April 30, 2014, 85,052,281 shares of the registrant’s common stock, par value $0.001 per share, were outstanding.



Table of Contents

PART I - FINANCIAL INFORMATION

Page
Item 1.1
 
 
 
 
1
 
 
 
 
2
 
 
 
 
3
 
 
 
 
4
Item 2.
14
Item 3.2624
Item 4.2624
 
 
 
PART II - OTHER INFORMATION
Item 1.2725
Item 1A.2725
Item 2.3125
Item 6.3125
3226

Unless the context otherwise requires, all references to “we,” “us,” “our,” and the “Company” include Discovery Laboratories, Inc., and its wholly owned, presently inactive subsidiary, Acute Therapeutics, Inc.

FORWARD-LOOKING STATEMENTS
 
This Quarterly Report on Form 10-Q contains “forward-looking statements” within the meaning of Section 27A of the Securities Act of 1933 and Section 21E of the Securities Exchange Act of 1934.  The forward-looking statements representare only estimates and provide our current expectations aboutor forecasts of future events and financial performance and may be identified by the use of forward-looking terminology, including thesuch terms as “believes,” “estimates,” “anticipates,” “expects,” “plans,” “intends,” “may,” “will” or “should” or, in each case, their negative, or other variations or comparable terminology, though the absence of these words does not necessarily mean that a statement is not forward-looking.  Forward-looking statements include all matters that are not historical facts and include, without limitation, statements concerningconcerning: our business strategy, outlook, objectives, future milestones, plans, intentions, goals, and future financial condition, including the period of time forduring which our existing resources will enable usare expected to fund our operations.  Forward-looking statements also include our financial, clinical, manufacturing and distribution plans, and our expectations and timing related to the commercialization of SURFAXIN®, the AFECTAIR® device  and our development, potential regulatory plans and expected timing to secure marketing authorization for infants and our products under development, starting with AEROSURF®, if approved; our expectations, timing and anticipated outcomes of submitting regulatory filings for our products under development; our research and development programs, including planning for development activities, anticipated timing of and design of clinical trials and potential development milestones;milestones, for our KL4 surfactant pipeline product candidates and our capillary aerosol generator (CAG) for delivery of aerosolized medications; plans for the manufacture of drug products, active pharmaceutical ingredients (APIs) and materials, and medical devices;devices and related components; and plans regarding potential strategic alliances and other collaborative arrangements to develop, manufacture and market our products.

We intend that all forward-looking statements be subject to the safe-harbor provisions of the Private Securities Litigation Reform Act of 1995.  Forward-looking statements are subject to many risks and uncertainties that could cause actual results to differ materially from any future results expressed or implied by the forward-looking statements.  We caution you therefore against relying on any of these forward-looking statements.  They are neither statements of historical fact nor guarantees or assurances of future performance.  Examples of the risks and uncertainties include, but are not limited to:

risks relating to the ability of our sales and marketing organization to effectively introduce SURFAXINrisk that we will require in the U.S.near term, but may be unable to secure, significant additional capital to continue our operations, fund our debt service and support our research and development activities, including expensive and time-consuming clinical trials, until such time, if approved,ever, that our other product candidates, in a timely manner, if at all; andrevenues from all sources are sufficient to offset our cash outflows. To the extent that we may not succeedraise such capital through additional financings, such additional financings could result in developing a sufficient market awareness of our products or that our product candidates may not gain market acceptance by physicians, patients, healthcare payers and others in the medical community;equity dilution;

the risk that, if we fail to successfully commercialize SURFAXIN as planned, and if we do notare unable to achieve revenues over the next several years that are consistent with our expectations, our revenues would be limited, and weit may be unablemore difficult to secure the additional capital we will require when needed, if at all, whether from strategic alliances or other sources, to continue our commercial and medical affairs activities, as well as our research and development programs and our operations would be impaired, which ultimately could have a material adverse effect on our business, financial condition and results of operations;

the risks that, although the U.S. Food
risks relating to the ability of our sales and marketing organization to effectively introduce SURFAXIN in the United States (U.S.) and, if approved, our other product candidates, in a timely manner, if at all; and Drug Administration (FDA) has completed its review and cleared our investigational new drug (IND) application for our AEROSURF® phase 2 clinical program, and we expect to initiate our phase 2 clinical program in the fourth quarter of 2013, our clinical program may be delayed, or fail, which will harm our business;

the risk that we may be unable to enter into strategic alliances and/or collaboration agreements that would assist and support usnot succeed in markets outside the U.S. with the developmentdeveloping sufficient market awareness of our KL4 surfactant pipeline products beginning with AEROSURF (our combination drug-deviceor that our product based on our aerosolized KL4 surfactantcandidates may not gain market acceptance by physicians, patients, healthcare payers and our capillary aerosol generator (CAG) technology that we are developing to address RDS in premature infants), and including the development of our lyophilized KL4 surfactant, and, if approved, commercialization of AEROSURF in markets outside the U.S.; and support the commercialization of SURFAXIN in countries where regulatory approval is facilitated by the information containedothers in the SURFAXIN new drug application (NDA) approved by the FDA; and potentially support the development and, if approved, commercialization, of our other pipeline products;
medical community;

risks relating to our ability to timely modify our business strategy to respond to changing circumstances, assumptions and forecasts, and otherwise as needed to manage growth effectively and respond to developments in our commercial operations and research and development activities, which amongas well as our business, our industry and other things involve time-consuming and expensive preclinical studies and potentially multiple clinical trials that may be subject to potentially significant delays or regulatory holds or fail;factors;

risks related tothe risk that the initial and later phases of our efforts to gain regulatory approval, inAEROSURF phase 2 clinical program may be interrupted, delayed, or fail, which will harm our business;

the risk that we and the U.S. Food and elsewhere, for our drug product and medical device candidates, including AEROSURF, a drug-device combination productDrug Administration (FDA) or other regulatory authorities will not be able to agree on matters raised during the regulatory review process, or that we are developingmay be required to address RDS in premature infants, andconduct significant additional activities to potentially gain approval of our lyophilized KL4 surfactant that we expect will be the drug component of AEROSURF and potentially be developed as a life cycle extension of SURFAXIN under the name SURFAXIN LS™ ;
product candidates, if ever;

risks relating to the transfer of our manufacturing technology to contract manufacturing organizations (CMOs) and assemblers;

risks relating to our and our CMOs' ability to manufacture our KL4 surfactant, in liquid and lyophilized dosage forms, which must be processed in an aseptic environment and tested using sophisticated and extensive analytical methodologies and quality control release and stability tests, for both commercial and research and development activities;

risks relating to our and our CMOs’ ability to develop and manufacture combination drug/device products based on our CAG technology, for preclinical and clinical studies of our product candidates and, if approved, for commercialization;

the risk that we, our CMOs or any of our third-party suppliers, many of which are single-source providers, may encounter problems or delays in manufacturing our KL4 surfactant drug products and the APIs used in the manufacture of our drug product,products, CAG devices and other materials on a timely basis or in an amount sufficient to support the commercial introduction of SURFAXIN and the AFECTAIR device for infants, our aerosol-conducting airway connector, as well as our research and development activities for AEROSURF and our other product candidates;
needs;

the risk that we may not succeed in implementing our long-term manufacturing strategy to assure continuity of SURFAXIN commercial drug product supply, which could expose us to risks that even if we succeed with the commercial introductionmay affect our ability to maintain sufficient supplies of SURFAXIN we nevertheless in commercial drug product;

the future will require, butrisk that we may be unable to secure, significant additional capital to continue our operations, fund our debt serviceenter into strategic alliances and/or collaboration agreements that would assist and support us in markets outside the U.S. with the development of our researchKL4 surfactant pipeline products, beginning with AEROSURF, including development of our lyophilized KL4 surfactant, and, if approved, commercialization of AEROSURF in markets outside the U.S.; support the commercialization of SURFAXIN in countries where regulatory approval is facilitated by the information contained in the SURFAXIN new drug application (NDA) approved by the FDA; and potentially support the development activities until such time,and, if ever,approved, commercialization, of our other pipeline products;

risks relating to our plans potentially  to secure marketing and distribution capabilities in certain markets through third-party strategic alliances and/or marketing alliances and/or distribution arrangements, that could require us to give up rights to our revenues from all sources are sufficient to offset our cash outflows. To the extent that we raise such capital through additional financings, such additional financings could result in equity dilution;drug products, drug product candidates and drug delivery technologies;

risks relating to our pledge of substantially all of our assets to secure our obligations under our loan facility (Deerfield Facility)Loan) with affiliates of Deerfield Management Company, L.P., which could make it more difficult for us to secure additional capital to satisfy our obligations and require us to dedicate cash flow to payments for debt service, which would reduce the availability of our cash flow to fund working capital, capital expenditures and other investment; and

other risks and uncertainties as detailed in “Risk Factors” in our most recent Annual Report on Form 10‑K filed with the Securities and Exchange Commission (SEC) on March 15, 2013,17, 2014, and our other filings with the SEC and any amendments thereto, and in the documents incorporated by reference in this report.
Pharmaceutical, biotechnology and medical device technology companies have suffered significant setbacks inconducting clinical trials, even after obtaining promising earlier trial results.  Datapreclinical and clinical data.  Moreover, data obtained from such clinical trials are susceptible to varying interpretations, which could delay, limit or prevent regulatory approval.  After gaining approval of a drug product, pharmaceutical and biotechnology companies face considerable challenges in marketing and distributing their products, and may never become profitable.

The forward-looking statements contained in this report or the documents incorporated by reference herein speak only as of their respective dates.  Factors or events that could cause our actual results to differ may emerge from time to time and it is not possible for us to predict them all.  Except to the extent required by applicable laws, rules or regulations, we do not undertake any obligation to publicly update any forward-looking statements or to publicly announce revisions to any of the forward-looking statements, whether as a result of new information, future events or otherwise.

Trademark Notice
AEROSURF®, AFECTAIR®, DISCOVERYLABS®, INSPIRED INNOVATION®, SURFAXIN®, andWARMING CRADLE® are registered trademarks of Discovery Laboratories, Inc. (Warrington, PA).

PART I - FINANCIAL INFORMATION

ITEM 1.
FINANCIAL STATEMENTS

DISCOVERY LABORATORIES, INC. AND SUBSIDIARY
Consolidated Balance Sheets
(in thousands, except per share data)
(in thousands, except per share data)
 March 31,  December 31, 
 
September 30,
2013
  
December 31,
2012
  2014  2013 
 (Unaudited)  
  (Unaudited)  
 
ASSETS 
  
  
  
 
Current Assets: 
  
  
  
 
Cash and cash equivalents $21,177  $26,892  $75,942  $86,283 
Inventory  117   195 
Accounts receivable     67 
Inventory, net  173   112 
Prepaid expenses and other current assets  418   719   702   777 
Total Current Assets  21,712   27,806 
Total current assets  76,817   87,239 
Property and equipment, net  1,417   1,737   2,007   1,656 
Restricted cash  400   400   325   325 
Other assets  102      349   97 
Total Assets $23,631  $29,943 
Total assets $79,498  $89,317 
LIABILITIES & STOCKHOLDERS’ EQUITY                
Current Liabilities:                
Accounts payable $1,489  $1,166  $2,578  $1,433 
Accrued expenses  5,071   4,159   3,726   4,785 
Deferred revenue  85   139 
Common stock warrant liability  4,678   6,305   4,672   5,425 
Equipment loans and capitalized leases, current portion  72   69 
Total Current Liabilities  11,310   11,699 
Equipment loans, current portion  74   73 
Total current liabilities  11,135   11,855 
                
Long-term debt, net of discount of $3,674 at September 30, 2013 and $0 at December 31, 2012  6,326    
Equipment loans and capitalized leases, non-current portion  89   148 
Long-term debt, $30,000 net of discount of $11,207 at March 31, 2014 and $11,646 at December 31, 2013  18,793   18,354 
Equipment loans, non-current portion  49   69 
Other liabilities  431   443   714   538 
Total Liabilities  18,156   12,290 
Total liabilities  30,691   30,816 
Stockholders’ Equity:                
Preferred stock, $0.001 par value; 5,000,000 shares authorized; no shares issued or outstanding            
Common stock, $0.001 par value; 150,000,000 shares authorized at September 30, 2013, 100,000,000 shares authorized at December 31, 2012; 54,946,327 and 43,673,636 shares issued, 54,925,435 and 43,652,744 shares outstanding at September 30, 2013 and December 31, 2012, respectively  55   44 
Common stock, $0.001 par value; 150,000,000 shares authorized; 85,073,173 and 84,659,111 shares issued at March 31, 2014 and December 31, 2013, respectively; 85,052,281 and 84,638,219 shares outstanding at March 31, 2014 and December 31, 2013, respectively  85   85 
Additional paid-in capital  476,695   455,398   543,202   541,420 
Accumulated deficit  (468,221)  (434,735)  (491,426)  (479,950)
Treasury stock (at cost); 20,892 shares  (3,054)  (3,054)  (3,054)  (3,054)
Total Stockholders’ Equity  5,475   17,653 
Total Liabilities & Stockholders’ Equity $23,631  $29,943 
Total stockholders’ equity  48,807   58,501 
Total liabilities & stockholders’ equity $79,498  $89,317 

See notes to consolidated financial statements.
1

DISCOVERY LABORATORIES, INC. AND SUBSIDIARY
Consolidated Statements of Operations
(Unaudited)

(in thousands, except per share data) 
 
 
 Three Months Ended 
 
 March 31, 
 
 2014  2013 
 
 
  
 
 
 
  
 
Revenues: 
  
 
Product sales $28  $ 
Grant revenue  3   72 
 
  31   72 
Expenses:        
Cost of product sales  781    
Research and development  5,590   8,472 
Selling, general and administrative  4,423   4,220 
 
  10,794   12,692 
Operating loss  (10,763)  (12,620)
 
        
Change in fair value of common stock warrant liability  378   162 
 
        
Other income / (expense):        
Interest and other income  2   1 
Interest and other expense  (1,093)  (178)
Other income / (expense), net  (1,091)  (177)
Net loss $(11,476) $(12,635)
Net loss per common share – Basic and diluted $(0.14) $(0.29)
Weighted-average number of common shares outstanding – basic and diluted  84,728   43,657 
(in thousands, except per share data)
 
 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
 
 
 2013  2012  2013  2012 
 
 
  
  
  
 
 
 
  
  
  
 
Grant revenue $60  $  $315  $ 
Expenses:                
Research and development  6,574   5,743   21,909   15,482 
Selling, general and administrative  4,299   4,255   12,648   9,912 
Total expenses  10,873   9,998   34,557   25,394 
Operating loss  (10,813)  (9,998)  (34,242)  (25,394)
 
                
Change in fair value of common stock warrant liability  (1,059)  (3,309)  1,627   (5,063)
Interest income  1   1   2   5 
Interest expense  (353)  (4)  (873)  (12)
Other expense  -   (36)  -   (36)
Net loss $(12,224) $(13,346) $(33,486) $(30,500)
 
Net loss per common share –
                
Basic $(0.22) $(0.31) $(0.68) $(0.80)
Diluted $(0.22) $(0.31) $(0.69) $(0.80)
 
Weighted average number of common shares outstanding
                
Basic  54,792   43,444   49,235   38,061 
Diluted  54,792   43,444   50,377   38,061 
See notes to consolidated financial statements.
2

DISCOVERY LABORATORIES, INC. AND SUBSIDIARY
Consolidated Statements of Cash Flows
(Unaudited)

(in thousands)
 Three Months Ended 
 
Nine Months Ended
September 30,
  March 31, 
 2013  2012  2014  2013 
 
  
  
  
 
Cash flows from operating activities: 
  
  
  
 
Net loss $(33,486) $(30,500) $(11,476) $(12,635)
Adjustments to reconcile net loss to net cash used in operating activities:                
Depreciation and amortization  537   855   149   197 
Stock-based compensation and 401(k) match  2,367   1,805 
Provision for excess inventory  766    
Stock-based compensation and 401(k) Plan employer match  954   612 
Fair value adjustment of common stock warrants  (1,627)  5,063   (378)  (162)
Loss on sale or disposal of equipment     36 
Amortization of discount on long-term debt  302      439   59 
Changes in:                
Inventory  78   (128)  (1,083)  195 
Accounts receivable  67    
Prepaid expenses and other current assets  301   (723)  75   98 
Accounts payable  323   (903)  1,145   659 
Accrued expenses  912   693   (1,059)  814 
Deferred revenue  (54)   
Other assets  (115)        (111)
Other liabilities  (12)  (19)  176   39 
Net cash used in operating activities  (30,420)  (23,821)  (10,279)  (10,235)
Cash flows from investing activities:                
Purchase of property and equipment  (204)  (593)  (497)  (120)
Net cash used in investing activities  (204)  (593)  (497)  (120)
Cash flows from financing activities:                
Proceeds from issuance of securities, net of expenses  15,114   43,605 
Proceeds from issuance of long-term debt, net of expenses  9,850         9,850 
Proceeds from exercise of common stock warrants and options  1   6,741 
Repayment of equipment loans and capital lease obligations  (56)  (57)
Proceeds from exercise of common stock options  31   1 
Proceeds from exercise of common stock warrants  423    
Repayment of equipment loans  (19)  (18)
Net cash provided by financing activities  24,909   50,289   435   9,833 
Net (decrease) / increase in cash and cash equivalents  (5,715)  25,875 
Net decrease in cash and cash equivalents  (10,341)  (522)
Cash and cash equivalents – beginning of period  26,892   10,189   86,283   26,892 
Cash and cash equivalents – end of period $21,177  $36,064  $75,942  $26,370 
Supplementary disclosure of cash flows information:                
Interest paid $559  $10  $649  $116 
See notes to consolidated financial statements.
3


Notes to Consolidated Financial Statements (unaudited)

Note 1 – Organization and Business

Discovery Laboratories, Inc. (referred to as “we,” “us,” or the “Company”) is a specialty biotechnology company focused on creating life-saving products for critical carecritical-care patients with respiratory disease and improving the standard of care in pulmonary medicine.  Our proprietary drug technology produces a synthetic, peptide-containing surfactant (KL4 surfactant) that is structurally similar to pulmonary surfactant, a substance produced naturally in the lung and essential for normal respiratory function and survival.  We are developing our KL4 surfactant in liquid, lyophilized and aerosolized dosage forms.  We are also developing novel drug delivery technologies potentially to enable the efficient delivery of our aerosolized KL4 surfactant, and potentially other aerosolized drugs and inhaled therapies.surfactant.  We believe that our proprietary technologies may make it possible, for the first time, to develop a significant pipeline of products to address a variety of respiratory diseases for which there frequently are few or no approved therapies.

Our near-term focus is to develop our KL4 surfactant and drug delivery technologies to improveWe are initially focused on improving the management of respiratory distress syndrome (RDS) in premature infants.  RDS is a serious respiratory condition caused by insufficient surfactant production in underdeveloped lungs of premature infants, andinfants.  RDS is the most prevalent respiratory disease in the neonatal intensive care unitNeonatal Intensive Care Unit (NICU).  RDS and can result in long-term respiratory problems, developmental delay and death.  Currently,Our first KL4 surfactant drug product, SURFAXIN® (lucinactant) Intratracheal Suspension for the prevention of RDS in premature infants at high risk for RDS, was approved by the United States Food and Drug Administration (FDA) in 2012.  SURFAXIN is our KL4 surfactant in liquid form, and is the first synthetic, peptide-containing surfactant approved by the FDA and the only alternative to animal-derived surfactants currently used in the United States (U.S.).  SURFAXIN has been commercially available in the U.S. since November 2013.

Premature infants with severe RDS currently are treated with surfactants that can only be administered by endotracheal intubation supported with mechanical ventilation, both invasive procedures that may each result in serious respiratory conditions and other complications.  To avoid such adverse results,complications, many neonatologists generally provide surfactants as initial therapy only to premature infants with severe RDS where the potential benefits of surfactant therapy outweigh the risks associated with endotracheal intubation and mechanical ventilation.  Fortreat infants with less severe RDS neonatologists first attempt to provide respiratory support using aby less invasive means, such astypically nasal continuous positive airway pressure (nCPAP).  Unfortunately, a significant number of thesepremature infants doon nCPAP will not respond adequately to nCPAP, anwell (an outcome referred to as nCPAP failure,failure) and thereafter may require subsequentdelayed surfactant administration via intubation and mechanical ventilation.therapy.  Since it is not possible to ascertainneonatologists currently cannot predict which patientsinfants will experience nCPAP failure, neonatologists treating less severe RDS are faced with a dilemma,difficult choices in treating infants with less severe RDS.  This is because the outcomemedical outcomes for those infants who experience nCPAP failure and receive delayed surfactant therapy may not be asless favorable asthan the outcomeoutcomes for those infants who receive surfactant therapy as initial therapy.

With mortality and morbidity rates that have not meaningfully improved over the last decade, we believe that the RDS market is presently underserved.  We also believe that our RDS programs, including SURFAXIN® and, if approved, AEROSURF®, have the potential to greatly improve the management of RDS and, over time, become a new standard of care for premature infants with RDS.  Moreover, we believe that the neonatal community is increasingly recognizing the potential benefits of (i) a synthetic, peptide-containing surfactant, and more importantly, (ii) a less-invasive method of delivering aerosolized surfactant to treat premature infants at risk of suffering from respiratory disorders.

In 2012, the U.S. Food and Drug Administration (FDA) approved our first KL4 surfactant drug product, SURFAXIN (lucinactant) Intratracheal Suspension for the prevention of RDS in premature infants at high risk for RDS.  SURFAXIN is the first synthetic, peptide-containing surfactant approved by the FDA and the only alternative to animal-derived surfactants currently used in the U.S.  On October 4, 2013, we announced that the FDA agreed to updated product specifications that we previously submitted for SURFAXIN.  On November 8, 2013, we announced that we have initiated the commercial introductionhours of SURFAXIN.  Our commercial and medical affairs organizations currently are advancing initiatives to communicate that SURFAXIN is available and to secure formulary acceptance from our target hospitals.  We are also preparing to support hospitals that order SURFAXIN with in-service training, medical information and other activities intended to promote and enable a deliberate and orderly introduction of SURFAXIN to the neonatal community.life.

AEROSURF® is anour investigational combination drug-devicedrug/device product that combines our KL4 surfactant with our proprietary capillary aerosol generator (CAG).  We are developing AEROSURF potentially will enable administration of aerosolized KL4 surfactant to deliverpremature infants supported with nCPAP, without invasive intubation and mechanical ventilation.  By enabling delivery of our KL4 surfactant in aerosolized form to premature infants with RDS.  AEROSURF potentially will provide neonatologists with the ability to avoid theusing less invasive procedures, currently required to administer surfactant therapy and deliver our KL4 surfactant in aerosolized form to premature infants supported with nCPAP.  For this reason, we believe that AEROSURF if approved, may address a serious unmet medical need and potentially enable the treatment of a significantly greater number of premature infants with RDS who could benefit from surfactant therapy but are currently not treated.

On October 17, 2013, we announced that we have submitted an Investigational New Drug (IND) Application to the FDA for our initial AEROSURF phase 2 clinical trial.  The FDA has completed its review and cleared our IND and we expect to initiate our phase 2 clinical program in the fourth quarter of 2013.

4

We are also developing a lyophilized (freeze-dried) dosage form of our KL4 surfactant whichthat is stored as a powder and resuspendedreconstituted to liquid form prior to use and is being developed with the objective of improving ease of use for healthcare practitioners, as well as potentially prolongingto prolong shelf life and eliminatingeliminate the need for cold-chain storage.  We are planning initially todeveloping this dosage form for use lyophilized KL4 surfactant in our AEROSURF development program.  We are also assessing a potential development plan intendedplanning to seek regulatory advice to determine if we could gain regulatory approvalmarketing authorization for SURFAXIN LS™, a lyophilized dosage form of SURFAXIN under a development plan that would be both capital efficient and capable of implementation within a reasonable time.  If feasible, we would likely implement such a development plan and would plan to introduce it commercially as a life-cycle extension of SURFAXIN under the name SURFAXIN LS™, in the U.S. and potentially in other markets.
4

WithTo support the assistancecommercial introduction of Battelle Memorial Institute (Battelle),SURFAXIN in the U.S. and our other KL4 surfactant pipeline products, if approved, we have completedestablished our own specialty respiratory critical care commercial and medical affairs team.  This team includes medical professionals with experience in neonatal/pediatric respiratory critical care, and has focused on products that address neonatal indications, beginning with SURFAXIN.  We believe that this team will be positioned to efficiently introduce our other KL4 surfactant products under development, if approved, including AEROSURF and potentially SURFAXIN LS and future applications of our aerosolized KL4 surfactant.

In addition, we recognize that our commercial and medical affairs team could potentially support introductions of other synergistic pipeline products, including products owned or developed by third parties for the NICU/PICU.  To that end, we would consider potential transactions focused on securing commercial rights to such synergistic products, including in the form of product acquisitions, in-licensing agreements or distribution, marketing or co-marketing arrangements.

In the future, we expect that we may be able to leverage the information, data and know-how that we gain from our development efforts with SURFAXIN and AEROSURF to support development of a clinic-ready CAG device, which has passed a rigorous design verification testing program,product pipeline to address serious critical care respiratory conditions in larger children and have manufactured a sufficient numberadults in pediatric and adult intensive care units (PICUs and ICUs), including potentially acute lung injury (ALI), chronic obstructive pulmonary disorder (COPD) and cystic fibrosis (CF).  At the present time, however, we are focusing our resources primarily on the commercial introduction of clinic-ready CAGs to support the initial phaseSURFAXIN and development of our AEROSURF through phase 2 clinical program.  We plan to continue development of our CAG andtrials.  Once we have advanced these objectives, we expect to manufacture additional devicesbe in a better position to support completionassess the potential of our phase 2 clinical programother development programs to address the critical care needs of patients in the PICU and potentially our phase 3 clinical program.  The CAG has been designed to produce aerosolized KL4 surfactant in volumes up to 10 times the output produced by currently available aerosol devices.ICU.

AFECTAIR®We also have developed a disposable aerosol-conducting airway connector for infants that is our novel disposable device intended to simplify the delivery of aerosolized medications (including our aerosolized KL4 surfactant,surfactant) and other aerosolized medications and inhaled therapies to infants in NICUs and pediatric intensive care units (PICUs) who requirecritical-care patients requiring ventilatory support by introducing thesupport.  This device introduces aerosolized medicationmedications directly at the patient interface and minimizingminimizes the number of connections in the ventilator circuit.  To gain information and assess the use ofWe have registered this device in different clinical settings, we are continuingthe U.S. as a national user experience program at a number of institutions, including leading neonatal thought centers, acrossClass I, exempt medical device under the name AFECTAIR® and it is currently commercially available in the U.S.

We have established our own specialty commercial and medical affairs organizations to focus on neonatal/pediatric respiratory critical care in hospitals across the U.S.  These organizations are primarily responsible for the commercial introduction of SURFAXIN and the AFECTAIR device.  In the future, we expect that these teams will be able to leverage the experience and relationships gained from the introduction of SURFAXIN to support the potential introductions of our own future pipeline products, beginning with, if approved, AEROSURF and potentially SURFAXIN LS.  In addition, we will consider opportunities to leverage our experience and relationships to market and support other synergistic products that could be of benefit in the NICU/PICU.

Our objectives for 2013 include initiating the commercial introduction of SURFAXIN and advancing the AEROSURF phase 2 clinical program.  In the future, we expect that we will be able to apply the knowledge and experience gained from these activities to develop a pipeline of innovative products based on our technologies and intended to address other critical care respiratory conditions in the NICU, PICU and intensive care units (ICUs).

An important priority for us is to secure strategic and financial resources to advance our KL4 surfactant and aerosol device development programs and the commercial introduction of our approved RDS products in markets outside the U.S.  See, Note 2, “Liquidity Risks and Management’s Plans.”  While we currently intend to retain all rights and commercialize our approved products in the U.S., we are focused on identifying potential strategic alliances to assist us with our development  programs in markets outside the U.S.  We seek strategic partners that have broad experience in the designated markets, including regulatory and product development expertise as well as an ability to commercialize our products.  In addition to development and commercial support, such alliances typically also would provide us with financial resources to support our activities, potentially in the form of upfront payments, milestone payments, commercialization royalties and a sharing of research and development expenses.  We are focused on securing a significant strategic alliance predominantly to support our activities in the European Union (EU).  To date, the primary focus of our discussions has been on AEROSURF.  In the future, we may also seek strategic alliances and/or collaboration arrangements to support the potential commercial introduction of SURFAXIN and, if approved, SURFAXIN LS, in countries where regulatory approval is facilitated by the information contained in our SURFAXIN new drug application (NDA) approved by the FDA.

There can be no assurance that we will be successful in securing the necessary capital, or concluding any strategic alliance, collaboration arrangement or other similar transaction.  See, Note 2, “Liquidity Risks and Management’s Plans.”

Note 2 – Liquidity Risks and Management’s Plans

We have incurred substantial losses since inception, due to investments in research and development, manufacturing, and, potentialmore recently, commercialization and medical affairs activities, and we expect to continue to incur substantial losses over the next several years.  Historically, we have funded our business operations through various sources, including public and private securities offerings, debt facilities, strategic alliances, the use of Committed Equity Financing Facilitiescommitted equity financing facilities (CEFFs) and at-the-market equity programs, and capital equipment financings.

5

As of September 30, 2013,March 31, 2014, we had cash and cash equivalents of $21.2$75.9 million approximately $6.6and long-term debt of $30 million ($18.8 million net of accounts payable and accrued expenses, and $10 million of long-term debtdiscount) under our Deerfield FacilityLoan with affiliates of Deerfield Management  Company, L.P. (Deerfield).

On October 15, 2013, we completed an offering under our At-the-Market Program (ATM Program) (see,, Note 4, “Stockholders’ Equity7Common Stock Offerings – At-the-Market Program”“Deerfield Loan”) with Stifel, Nicolaus & Company, Incorporated (Stifel) and issued 713,920 shares of our common stock resulting in net proceeds to us (after deducting commissions due to Stifel) of approximately $1.9 million.  Through our ATM Program, subject to market conditions, we have the ability to sell up to approximately $23 million of common stock at such times and in such amounts that we deem appropriate.  However, use of the ATM Program is subject to market and other conditions and the ATM Program can be cancelled at any time by either party.  There can be no assurance that the ATM Program will be available when needed, if at all.

On November 5, 2013, we completed a public offering of 25 million shares of common stock, at a price of $2.00 per share resulting in gross proceeds of $50.0 million ($46.8 million net after commissions, discounts and expenses)In addition, we also granted the underwriters a 30-day option to purchase up to an additional 3.75 million shares of common stock (over-allotment) at an offering price of $2.00 per share.  On November 8, 2013, we received notification that the underwriters have exercised the full over-allotment and will purchase an additional 3.75 million shares.  This transaction is expected to close on or about November 14, 2013 and result in additional net proceeds to us of approximately $7.1 million.

We also have met the conditions for, and expect in early December to receive, an additional advance of $20 million under the Deerfield Facility, which became due upon the first commercial sale of SURFAXIN drug product.  See, Note 6, “Long-Term Debt – Loan Facility with Deerfield.”

Before any additional financings, including under our ATM Program and taking into account(see, Note 11, “At-the-Market Program (ATM Program),” to the additional approximately $7.1 million expected from the underwriters’ exercise of the over-allotmentconsolidated financial statements in our November public offering andAnnual Report on Form 10-K for the expected $20 million advance under the Deerfield Facility,year ended December 31, 2013 (2013 Form 10‑K)), we anticipate that we will have sufficient cash available to supportfund our operations and debt service obligations through the third quarter of 2015.

Our future capital requirements depend upon many factors, primarily the success of our efforts to (i) execute the commercial introduction of SURFAXIN and AFECTAIR in the U.S., as planned;; (ii) advance the AEROSURF development program to completion of the phase 2 clinical program as planned in mid-2015;the second half of 2015; and (iii) secure one or more strategic alliances or other collaboration arrangements (a) to support the development and, if approved, commercial introduction of AEROSURF in markets outside the U.S., including potentially in the European Union, and (b) to support the regulatory approval process and commercial introduction of SURFAXIN AEROSURF, AFECTAIR and potentially SURFAXIN LS, in certain markets outside the U.S.  We believe that, if we are successful with the commercial introduction of SURFAXIN and if we are able to complete the AEROSURF phase 2 clinical program on a timely basis and obtain encouraging results, and if we are able to advance the commercial introduction of SURFAXIN, our ability to enter into a significant strategic alliance will be enhanced.  There can be no assurance, however, that our efforts will be successful, or that, even if successful, we will be able to obtain additional capital to support our activities when needed on acceptable terms, if at all.
5

Even if we succeed with
For the commercial introduction of SURFAXIN and the AFECTAIR device as planned, given the time required to secure formulary acceptance of SURFAXIN at our target hospitals,next several years, we expect our revenues from SURFAXIN and AFECTAIR to be modest in the first 12-18 months and then increase over time as our products gain hospital acceptance.  As a result,that our cash outflows for marketing, commercial and medical activities, development programs, operations and debt service and development programs are expected towill outpace the rate at which we may generate revenues for several years.revenues.  To execute our business strategy and fund our operations over the long term,next several years, we will require significant additional infusions of capital until such time as the net revenues from SURFAXIN, AFECTAIR and, ifthe sale of approved AEROSURF, from potential strategic alliancesproducts and from other sources are sufficient to offset our cash flow requirements.  ToWhile we currently intend to retain all rights and commercialize our approved products in the U.S., an important priority for us is to secure additional capital and strategic resources to support the necessary capital,continued development and commercial introduction of our RDS products in markets outside the U.S. For our AEROSURF development program, we would prefer to enter intoare seeking a significant strategic alliances or collaboration agreements with partnersalliance that potentially could provide development, regulatory and commercial market expertise as well as financial resources, (potentiallyand, if approved, support the commercial introduction of AEROSURF in the EU and other selected markets outside the U.S.  Such alliances typically also would provide financial resources, in the form of upfront payments, milestone payments, commercialization royalties and a sharing of research and development expenses) and introduce our approved productsexpenses.  To advance SURFAXIN in various markets outside the U.S. where regulatory marketing authorization is facilitated by the information contained in our new drug application (NDA) approved by the FDA, we would consider various financing or collaboration arrangements that could provide regulatory expertise, support the commercial introduction of SURFAXIN in markets outside the U.S., and potentially provide a sharing of revenues.  Such countries could potentially include those in Latin America, North Africa and the Middle East.  We also plan to consider other public and private equity offerings, including under our ATM Program, which currently may allow for the sale of up to approximately $23 million of our commons stock (see, Note 11, “At-the-Market Program (ATM Program)”), as well as other financing transactions, such as secured equipment financing facilities or other similar transactions.

As of September 30, 2013,March 31, 2014, we had outstanding warrants to purchase approximately 10.314.5 million shares of our common stock at various prices, exercisable on different dates throughinto 2019.  Of these warrants, approximately 2.3warrants to purchase 7 million warrantsshares were issued to Deerfield in connection with the first advance under the Deerfield Facility.  Upon receipt of the final $20 million advance under the Deerfield Facility, which is anticipated on or about December 3, 2013, we will issue warrants to purchase an additional 4.66 million shares of our common stockLoan at an exercise price of $2.81 per share (we refer to these warrants and the warrants previously issued to Deerfield as the Deerfield Warrants).share.  The Deerfield Warrants may be exercised for cash or on a cashless basis.  In lieu of paying cash upon exercise, the holders also may elect to reduce the principal amount of the Deerfield loanLoan in an amount sufficient to satisfy the exercise price of the Deerfield Warrants.  In addition to the Deerfield Warrants, we have outstanding five-year warrants issued in February 2011 to purchase approximately 4.94.6 million shares of common stock that were issued in February 2011, are exercisable for five-years, and contain anti-dilution provisions that adjust the exercise price if we issue any common stock, securities convertible into common stock, or other securities (subject to certain exceptions) at a value below the then-existing exercise price of the warrants.  These warrants were originally issued withcurrently have an exercise price of $3.20 per share and thereafter adjusted downward, first to $2.80 per share following a public offering in March 2012 and then to $1.50 per share following a public offering in May 2013.share.  Although we believe that, in the future, we will secure additional capital from the exercise of at least a portion of our outstanding warrants, there can be no assurance that the market price of our common stock will equal or exceed price levels that would make exercise of outstanding warrants likely, or, even if the price levels are sufficient, that holders of the Deerfield Warrants would choose to exercise their warrants for cash, or that holders of any of our outstanding warrants willwould choose to exercise any or all of their warrants prior to the applicable warrant expiration date.dates.  Moreover, if our outstanding warrants are exercised, such exercises likely will be at a discount to the then-market value of our common stock and have a dilutive effect on the value of our shares of common stock at the time of exercise.

As of September 30, 2013,March 31, 2014, 150 million shares of common stock were authorized under our Amended and Restated Certificate of Incorporation, and approximately 71.7 million shares of common stock were available for issuance and not otherwise reserved.  As of November 8, 2013, following the financings under our ATM Program, our public offering, and establishment of additional reserves for the shares expected to be issued in connection with the underwriters’ exercise of the over-allotment in our November public offering and with respect to the warrants expected to be issued to Deerfield upon receipt of the $20 million advance in early December, approximately 4242.1 million shares of common stock were available for issuance and not otherwise reserved.

Although we currently believe that we will be able to successfully execute our business plan and accomplish our objectives,strategy, there can be no assurance that our AEROSURF development program will be successful within our anticipated time frame, if at all, that we will succeed in obtaining the necessary regulatory approvals in the U.S. and other markets, that any approved product, including SURFAXIN, will be commercially viable, that the ATM Program will be available when needed, if at all, or that we will be able to obtain additional capital when needed on acceptable terms, if at all, that we will be successful.  There can be no assurance that weWe will be successful in securingrequire significant additional capital to satisfy debt obligations and sustain operations, and to complete the needed capital, through strategic alliances, collaboration arrangements, financings, debt arrangementsdevelopment and, other transactions.if they are approved, support the commercial introduction of our products.  Failure to secure the necessary additional capital would have a material adverse effect on our business, financial condition and results of operations.  Even if we succeed in raising additional capital and developing and subsequently commercializing product candidates, we may never achieve sufficient sales revenue to achieve or maintain profitability.
Note 3 – Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim unaudited consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the U.S. for interim financial information in accordance with the instructions to Form 10‑Q.  Accordingly, they do not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete consolidated financial statements.  In the opinion of management, all adjustments (consisting of normally recurring accruals) considered for fair presentation have been included.  Operating results for the three and nine months ended September 30, 2013March 31, 2014 are not necessarily indicative of the results that may be expected for the year ending December 31, 2013.2014.  There have been no changes to our critical accounting policies since December 31, 2012.2013.  For further information, refer toa discussion of our accounting policies, see, the consolidated financial statements and footnotesnotes thereto included in our Annual Report on2013 Form 10-K for the year ended December 31, 2012 that we filed with the Securities and Exchange Commission (SEC) on March 15, 2013 (2012 Form 10-K).10-K.  Readers are encouraged to review those disclosures in conjunction with this Quarterly Report on Form 10-Q.

Inventory

Inventories, which are determinedrecorded at the lower of cost or market, value withinclude materials, labor, and other direct and indirect costs and are valued at cost determined underusing the specific identificationfirst-in, first-out method. We assess the potential capitalization of inventory and the timing ofcapitalize inventories produced in preparation for commercial launches when the related product candidates receive regulatory approval and that the related costs are expected towill be recoverable through the commercializationcommercial sale of our products.the product.  Costs incurred prior to FDA approval of SURFAXIN drug productproducts and registration of our initial AFECTAIR device have beenmedical devices are recorded in our statement of operations as research and development expense.  DueInventory is evaluated for impairment through consideration of factors such as the net realizable value, lower of cost or market, obsolescence, and expiry. Inventories do not have carrying values that exceed either cost or net realizable value.

We evaluate our expiry risk by evaluating current and future product demand relative to product shelf life. We build demand forecasts by considering factors such as, but not limited to, overall market potential, market share, market acceptance and hospital ordering practices.

Accrued Severance and Retention Costs

A liability for employee severance and retention benefits is recognized when (1) management has committed to a delayplan of termination; (2) the plan provides sufficient details, such as the employees affected, amounts to be paid, and expected dates of termination and payment; (3) it is unlikely that significant changes to the plan will be made or that the plan will be withdrawn; and (4) the plan has been communicated to employees.  The cost of such benefits are accrued over the remaining service period.

In September 2013, we implemented an employee severance and retention plan for employees at our manufacturing facility in commercial availabilityTotowa, NJ (“Totowa Facility”) to minimize employee turnover and encourage employees to remain with us through any potential plant closing.  The plan provides for severance for non-union employees and retention bonuses for management.  If we succeed in our efforts to secure longer-term utilization of SURFAXIN drug product, previously capitalized raw material costs of $195,072 were chargedthe Totowa Facility, the severance plan and retention bonuses will remain in effect.  The total cash amount expected to be paid for severance and retention under this plan through June 2016, assuming a June 2015 plant closing, is approximately $1.1 million.  The plan-related expense incurred for the quarter ended March 31, 2014 is $0.1 million and is included in research and development expense.  The related accrued liability is $0.2 million as of March 31, 2014.
In addition, at the Totowa Facility, there are 14 employees who are subject to a collective bargaining agreement under which they would be eligible to receive severance payments if the Totowa Facility were closed.  The plan-related expense incurred for the quarter ended March 31, 2014 is $33,000 and is included in research and development expense.  The related accrued liability is $0.4 million as of March 31, 2014.

Product Sales

Revenues from product sales are recognized when (1) persuasive evidence of an arrangement exists, (2) delivery has occurred or services have been rendered, (3) the price is fixed or determinable and (4) collectability is reasonably assured.

Our products are distributed in the firstU.S. using a specialty distributor.  Under this model, the specialty distributor purchases and takes physical delivery and title of product, and then sells to hospitals.  We began the commercial introduction of SURFAXIN in the fourth quarter of 2013 as these raw materials were no longerand, for that reason, we currently cannot make a reasonable estimate of future product returns when product is delivered to the specialty distributor.  Therefore, we currently do not recognize revenue upon product shipment to the specialty distributor, even though the distributor is invoiced upon product shipment.  Instead, we recognize revenue once product has been sold through to the hospital and all revenue recognition criteria have been met.  Once product has been delivered to the hospital, the risk of material returns is significantly mitigated.  We will begin to recognize revenue at the time of shipment of product to our specialty distributor when we can reasonably estimate expected to be useddistributor sales deductions and returns.  In developing estimates for commercial production.sales returns, we consider the shelf life of the product, expected demand based on market data and return rates of other surfactant products.

Inventory asProduct sales are recorded net of September 30, 2013 consists of AFECTAIR devices availableaccruals for commercial sale.  Inventory costs for our AFECTAIR device consist primarily of third-party manufacturing fees, freight,estimated chargebacks, discounts, specialty distributor deductions and indirect personnel overhead costs.returns.

·Chargebacks.  Chargebacks are discounts that occur when contracted customers purchase directly from our specialty distributor.  Contracted customers, which currently consist primarily of member hospitals of Group Purchasing Organizations, generally purchase the product at a discounted price.  Our specialty distributor, in turn, charges back the difference between the price initially paid by the specialty distributor and the discounted price paid to the specialty distributor by the customer.  The allowance for specialty distributor chargebacks is based on known sales to contracted customers.
7


·Sales discounts:  Sales discounts are offered to certain contracted customers based upon a customer’s historical volume of surfactant product purchases.  Customers must enter into a Letter of Participation (LOP) with us to receive sales discounts.  Sales discounts are periodically adjusted on a prospective basis based upon the customer’s purchases of SURFAXIN, as provided in the LOP.  The allowance for sales discounts is based on known sales to contracted customers.

·Specialty distributor deductions. Our specialty distributor is offered various forms of consideration including allowances, service fees and prompt payment discounts. Specialty distributor allowances and service fees are provided in our contractual agreement and are generally a percentage of the purchase price paid by the specialty distributor. The specialty distributor is offered a prompt pay discount for payment within a specified period.

·Returns.  Sales of our products are not subject to a general right of return; however, we will accept product that is damaged or defective when shipped or for expired product up to six months subsequent to its expiry date.  Product that has been administered to patients is no longer subject to any right of return.

Research and development expense

We track research and development expense by activity, as follows: (a) product development and manufacturing, (b) medical and regulatory operations, and (c) direct preclinical and clinical programs.   Research and development expense includes personnel, facilities, manufacturing and quality operations, pharmaceutical and device development, research, clinical, regulatory, other preclinical and clinical activities and medical affairs.  Research and development costs are charged to operations as incurred.  For the nine months ended September 30, 2012, research and development expense includes a $0.5 million charge related to a milestone payment that became payable to Johnson & Johnson (J&J) upon FDA approval

Net loss per common share

Basic net loss per common share is computed by dividing net loss by the weighted average number of common shares outstanding for the period.  Diluted net loss per common share is computed by giving effect to all potentially dilutive securities outstanding for the period.  For the quarters ended March 31, 2014 and 2013, the number of shares of common stock potentially issuable upon the exercise of certain stock options and warrants was 21.3 million and 15.8 million shares, respectively.

In accordance with Accounting Standards Codification (ASC) Topic 260, “Earnings per Share,” when calculating diluted net loss per common share, a gain associated with the decrease in the fair value of certain warrants classified as derivative liabilities results in an adjustment to the net loss; and the dilutive impact of the assumed exercise of the warrants results in an adjustment to the weighted average common shares outstanding.  We utilize the treasury stock method to calculate the dilutive impact of the assumed exercise of the warrants.  For the nine monthsquarters ended September 30,March 31, 2014 and 2013, the effect of the adjustments for warrants issued in February 2011 was dilutive.  For the three months ended September 30, 2013 and for the three and nine months ended September 30, 2012, the effect of the adjustments for all warrants classified as derivative liabilities was non-dilutive.

The table below provides information pertaining toFor the calculation of diluted net loss per common share for the periods presented:
(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
 
 
 2013  2012  2013  2012 
Numerator:        
Net loss as reported $(12,224) $(13,346) $(33,486) $(30,500)
Less: income from change in fair value of warrant liability        (1,525)   
Numerator for diluted net loss per common share $(12,224) $(13,346) $(35,011) $(30,500)
 
                
Denominator:                
Basic weighted average common shares outstanding  54,792   43,444   49,235   38,061 
Dilutive common shares from assumed warrant exercises        1,142    
Diluted weighted average common shares outstanding  54,792   43,444   50,377   38,061 

As of September 30,quarters ended March 31, 2014 and 2013, all potentially dilutive securities were anti-dilutive and 2012, 10.7 million and 12.0 million shares of common stock potentially issuable upon the exercise of certain stock options and warrants weretherefore have been excluded from the computation of diluted net loss per common share because their impact would have been anti-dilutive.share.

We do not have any components of other comprehensive income (loss).

Recent accounting pronouncements

There were no new accounting pronouncements issued during the ninethree months ended September 30, 2013March 31, 2014 that are expected to have a material impact on the Company’s financial position, operating results cash flows or disclosures.

Note 4 Stockholders’ Equity

Registered Public Offerings

On May 15, 2013, we completed a registered public offering of 9.5 million shares of our common stock, at a price of $1.50 per share resulting in gross proceeds of $14.3 million ($13.2 million net).  We also granted the underwriter a 30-day option to purchase up to an additional 1.425 million shares of common stock at an offering price of $1.50 per share.  On May 31, 2013, the underwriter exercised its option and purchased 1.347 million additional shares of common stock for net proceeds to us (after underwriter fees) of $1.9 million.  In connection with this offering, we agreed not to issue or sell (with certain limited exceptions) securities for a period of 90 days after the date of the prospectus supplement ending August 8, 2013.  Regarding our ATM Program, we agreed not to issue or sell securities for a period of 30 days after the date of the underwriting agreement ending on June 9, 2013.

At-the-Market Program

In February 2013, we entered into an At-the-Market Equity Offering Sales Agreement with Stifel, under which Stifel, as our exclusive agent, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $25 million of our common stock over a three-year period.  We are not required to sell any shares at any time during the term of the ATM Program.  We have agreed to pay Stifel a commission of 3% of gross proceeds of any sales of shares.  See, Note 17, “Subsequent Events – ATM Program,” to the consolidated financial statements in our 2012 Form 10-K.

Committed Equity Financing Facility (CEFF)

We had a CEFF dated June 11, 2010 with Kingsbridge Capital Limited (Kingsbridge), under which, for a period of up to three years, Kingsbridge was committed to purchase, subject to certain conditions, newly issued shares of our common stock.  Our ability to access the CEFF was subject to certain covenants and conditions, including stock price and volume limitations.  For a detailed description of our CEFF, see, Note 10, “Stockholders’ Equity – Registered Public Offerings – Committed Equity Financing Facility (CEFF),” to the consolidated financial statements in our 2012 Form 10-K.

The CEFF expired on June 11, 2013 with approximately 1.1 million available shares not issued.

Note 54 – Fair Value of Financial Instruments

Fair value is defined as the exchange price that would be received for an asset or paid to transfer a liability in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date.

Valuation techniques used to measure fair value must maximize the use of observable inputs and minimize the use of unobservable inputs.  The fair value hierarchy is based on three levels of inputs, of which the first two are considered observable and the last unobservable, as follows:

·Level 1 – Quoted prices in active markets for identical assets and liabilities.
·Level 2 – Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities, quoted prices in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.
·Level 3 – Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Fair Value on a Recurring Basis

The tabletables below categorizescategorize assets and liabilities measured at fair value on a recurring basis as of September 30, 2013March 31, 2014 and December 31, 2012:2013:
 
 Fair Value  Fair value measurement using 
 
 September 30, 2013  Level 1  Level 2  Level 3 
 
 
  
  
  
 
Assets: 
  
  
  
 
Money Market $19,877  $19,877  $  $ 
Certificate of Deposit  400   400       
Total Assets $20,277  $20,277  $  $ 
 
                
Liabilities:                
Common stock warrant liability $4,678  $  $  $4,678 

 Fair Value  Fair value measurement using  Fair Value  Fair value measurement using 
 December 31, 2012  Level 1  Level 2  Level 3  March 31, 2014  Level 1  Level 2  Level 3 
 
  
  
  
  
  
  
  
 
Assets: 
  
  
  
  
  
  
  
 
Money Market $23,377  $23,377  $  $ 
Cash and cash equivalents $75,942  $75,942  $  $ 
Certificate of Deposit  400   400         325   325       
Total Assets $23,777  $23,777  $  $  $76,267  $76,267  $  $ 
                                
Liabilities:                                
Common stock warrant liability $6,305  $  $  $6,305  $4,672  $  $  $4,672 

 
 Fair Value  Fair value measurement using 
 
 
December 31,
2013
  
 
Level 1
  
 
Level 2
  
 
Level 3
 
 
  
  
  
 
Assets: 
  
  
  
 
Cash and cash equivalents $86,283  $86,283  $  $ 
Certificate of Deposit  325   325       
Total Assets $86,608  $86,608  $  $ 
 
                
Liabilities:                
Common stock warrant liability $5,425  $  $  $5,425 

The tablestable below summarizes the activity of Level 3 inputs measured on a recurring basis for the ninethree months ended September 30, 2013March 31, 2014 and 2012:
(in thousands) 
Fair Value Measurements of
Common Stock Warrants Using
 Significant Unobservable Inputs
(Level 3)
 
 
  
Balance at December 31, 2012 $6,305 
Change in fair value of common stock warrant liability  (1,627)
Balance at September 30, 2013 $4,678 

2013:

(in thousands) 
Fair Value Measurements of
 Common Stock Warrants Using
 Significant Unobservable Inputs
(Level 3)
  
Fair Value Measurements of
Common Stock Warrants Using
Significant Unobservable Inputs
(Level 3)
 
    
Balance at December 31, 2011 $6,996 
Balance at December 31, 2013 $5,425 
Exercise of warrants  (136)  (375)
Change in fair value of common stock warrant liability  5,063   (378)
Balance at September 30, 2012 $11,923 
Balance at March 31, 2014 $4,672 
(in thousands) 
Fair Value Measurements of
Common Stock Warrants Using
Significant Unobservable Inputs
(Level 3)
 
 
  
Balance at December 31, 2012 $6,305 
Change in fair value of common stock warrant liability  (162)
Balance at March 31, 2013 $6,143 

The significant unobservable inputs used in the fair value measurement of the common stock warrants measured on a recurring basis are the historical volatility of our common stock market price, expected term of the applicable warrants, and the risk-free interest rate based on the U.S. Treasury yield curve in effect at the measurement date.  In addition to the significant unobservable inputs noted above, thecertain fair value measurement of certain five-year warrants issued in February 2011measurements also takestake into account an assumption of the likelihood and timing of the occurrence of an event that would result in an adjustment to the exercise price in accordance with the anti-dilutive pricing provisions in the warrant.  Any significant increases or decreases in the unobservable inputs, with the exception of the risk-free interest rate, wouldmay result in significantly higher or lower fair value measurements.

Significant Unobservable Input
Assumptions of Level 3 Valuations
 September 30, 2013March 31, 2014  December 31, 20122013 
 
 
  
 
Historical Volatility  55% - 6160%-62%  56% -8062% -76%
Expected Term (in years)  0.60.12.41.9   1.40.43.22.1 
Risk-free interest rate  0.05%0.03% - 0.450.41%  0.16%0.08% - 0.360.44%

Fair Value of Long-Term Debt

As of September 30, 2013,At March 31, 2014, the carrying value of our long-term debt, net of discounts, approximates fair value.  We had no long-term debt as of December 31, 2012.  We estimate theestimated fair value of the Deerfield Facility usingLoan was $23.7 million compared to a discountedcarrying value, net of discounts, of $18.8 million.  At December 31, 2013, the estimated fair value of the Deerfield Loan was $23.6 million compared to a carrying value, net of discounts, of $18.4 million.  The estimated fair value of the Deerfield Loan was based on discounting the future contractual cash flow analysis.flows to the present value.  This analysis utilizes certain Level 3 unobservable inputs, including the effective interest rate and current cost of capital.  Considerable judgment is required to interpret market data and to develop estimates of fair value.  The estimates presented are not necessarily indicative of amounts we could realize in a current market exchange.  The use of alternative market assumptions and estimation methodologies could have a material effect on these estimates of fair value.

Note 65 –  Long-term DebtInventory

Loan Facility with Deerfield

On February 13, 2013, we entered into a secured loan facility (Deerfield Facility) with affiliates of Deerfield Management Company, L.P. (Deerfield) for up to $30 million in secured financing in 2013.  Deerfield advanced to us $10 million upon executionInventory is comprised of the agreement and agreed to advance an additional $20 million, subject to certain conditions, on or about the date of the first commercial sale of SURFAXIN drug product (Milestone Date), if the Milestone Date occurs on or before December 31, 2013.  On November 8, 2013, we notified Deerfield that the first commercial sale of SURFAXIN has occurred, and anticipate receipt of the $20 million advance on or about December 3, 2013.

The loan may be prepaid in whole or in part without penalty at any time.  In addition, the principal amount of the loan may be reduced to the extent that holders of the notes elect to apply all or a portion of the principal amount outstanding under the loan to satisfy the exercise price of all or a portion of the Deerfield Warrants upon exercise.  The principal amount of the loan is payable in equal annual installments on the fourth, fifth and sixth anniversaries of the Deerfield Facility agreement, provided that the amount payable on the fourth anniversary shall be deferred for one year if either (i) our “Net Sales” (defined below) for the immediately preceding 12-month period are at least $20 million, or (ii) our “Equity Value” (defined below) is at least $200 million; and provided further, that the amount payable on the fifth anniversary (together with any amount deferred on the fourth anniversary) shall be deferred until the sixth anniversary if either (i) our “Net Sales” for the immediately preceding 12 month period are at least $30 million, or (ii) our “Equity Value” is at least $250 million.  For the purposes of the foregoing deferrals of principal, “Net Sales” means, without duplication, the gross amount invoiced by us or on our behalf, any of our subsidiaries or any direct or indirect assignee or licensee for products, sold globally in bona fide, arm’s length transactions, less customary deductions determined without duplication in accordance with generally accepted accounting principles; and “Equity Value” means, with respect to each measurement date, the product of (x) the number of issued and outstanding shares of our common stock on such measurement date multiplied by (y) the per share closing price of our common stock on such measurement date.  Accordingly, if the milestones are achieved in each year, payment of the principal amount could be deferred until the sixth anniversary date of the loan on February 13, 2019.

Any amounts received and outstanding under the Deerfield Facility will accrue interest at a rate of 8.75%, payable quarterly in cash.  The Deerfield Facility agreement contains customary terms and conditions but does not require us to meet minimum financial and revenue performance covenants.  In connection with each advance, Deerfield has received and, upon advance of the additional $20 million, will receive, a transaction fee equal to 1.5% of the amount disbursed.  The facility agreement also contains various representations and warranties and affirmative and negative covenants customary for financings of this type, including restrictions on our ability to incur additional indebtedness and grant additional liens on our assets.  In addition, all amounts outstanding under the Deerfield Facility may become immediately due and payable upon (i) an “Event of Default,” as defined in the Deerfield Facility agreement, in which case Deerfield would have the right to require us to repay the outstanding principal amount of the loan, plus any accrued and unpaid interest thereon, or (ii) the occurrence of certain events as defined in the facility agreement, including, among other things, the consummation of a change of control transaction or the sale of more than 50% of our assets (a Major Transaction).

In connection with the execution of the Deerfield Facility and receipt of the initial disbursement of $10 million, we issued to Deerfield warrants to purchase approximately 2.3 million shares of our common stock at an exercise price of $2.81.  Upon disbursement of the additional $20 million loan under the facility agreement, we will issue additional warrants to Deerfield to purchase an additional 4.66 million shares of our common stock at an exercise price of $2.81 per share of common stock.  The number of shares of common stock into which the Deerfield Warrants are exercisable and the exercise price of any Deerfield Warrant will be adjusted to reflect any stock splits, recapitalizations or similar adjustments in the number of outstanding shares of common stock.

The Deerfield Warrants will expire on the sixth anniversary of the facility agreement and contain certain limitations that generally prevent the holder from acquiring shares upon exercise of a Deerfield Warrant that would result in the number of shares beneficially owned by it to exceed 9.985% of the total number of shares of common stock then issued and outstanding.  The holder of a Deerfield Warrant may exercise all or a portion of such Deerfield Warrant either for cash or on a cashless basis.  In connection with a Major Transaction, as defined in the Deerfield Warrants, to the extent of consideration payable to stockholders in cash in connection with such Major Transaction, the holder may have the option to redeem the Deerfield Warrant or that portion of the Deerfield Warrant for cash in an amount equal to the Black-Scholes value (as defined in the Deerfield Warrant) of the Deerfield Warrant or that portion of the Deerfield Warrant redeemed.  In addition, in connection with a Major Transaction, to the extent of any consideration payable to stockholders in securities, or in the event of an Event of Default, the holder may have the option to exercise the Deerfield Warrant and receive therefor that number of shares of Common Stock that equals the Black-Scholes value of the Deerfield Warrant or that portion of the Deerfield Warrant exercised.  Prior to the holder exercising the Deerfield Warrant for shares in such transactions, the Company may elect to terminate the Deerfield Warrant or that portion of the Deerfield Warrant and pay the holder cash in an amount equal to the Black-Scholes value of the Deerfield Warrant.

We have recorded the loan as long-term debt at its face value of $10.0 million less debt discounts and issuance costs consisting of (i) $3.8 million fair value of the Deerfield Warrants issued upon the advance of the $10 million initial disbursement, and (ii) a $150,000 transaction fee.  The discount is being accreted to the $10 million loan over its term using the effective interest method.  The Deerfield Warrants are derivatives that qualify for an exemption from liability accounting as provided for in ASC Topic 815 “Derivatives and Hedging – Contracts in Entity’s Own Equity” (ASC 815) and have been classified as equity.

The fair value of the Deerfield Warrants at issuance was calculated using the Black-Scholes option-pricing model.  The significant Level 3 unobservable inputs used in valuing the Deerfield Warrants are the historical volatility of our common stock market price, expected term of the warrants, and the risk-free interest rate based on the U.S. Treasury yield curve in effect at the measurement date.  Any significant increases or decreases in the unobservable inputs, with the exception of the risk-free interest rate, would have resulted in a significantly higher or lower fair value measurement.

Significant Unobservable Input
 Assumptions of Level 3 Valuations
Historical Volatility101%
Expected Term (in years)6.0
Risk-free interest rate1.175%

Long-term debt as of September 30, 2013 consists solely of amounts due under the Deerfield Facility as follows:

Note Payable $10,000 
Unamortized discount  (3,674)
Long-term debt, net of discount $6,326 

The following amounts comprise the Deerfield Facility interest expense for the periods presented:

(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
 
 
 2013  2012  2013  2012 
 
        
Cash interest expense $221  $  $551  $ 
Non-cash amortization of debt discounts  125      302    
Amortization of debt costs  5      13    
Total Deerfield Facility interest expenses $351  $  $866  $ 
 March 31,  December 31, 
(in thousands) 2014  2013 
 
    
Inventories, current:    
Raw materials $52  $52 
Finished goods, net of reserves  121   60 
 
  173   112 
Inventories, non-current:        
Raw materials  256    
Total inventories, net $429  $112 

Raw materials inventory that is not expected to be used in commercial production until more than 12 months from the balance sheet date is classified as a non-current other asset on the balance sheet.  The shelf life of our raw materials is 2‑5 years.  Since the commercial introduction of SURFAXIN in the fourth quarter of 2013, we have made investments to increase our raw materials inventory to support future commercial production.
12
In addition, as of March 31, 2014, we had $1.0 million of raw materials that were purchased prior to October 4, 2013, the date the FDA approved updated SURFAXIN product specifications, which enabled the commercial introduction of SURFAXIN.  These raw materials have a carrying value of zero, as the costs to purchase this material were expensed in the period of purchase as research and development expense, and accordingly are not reflected in the inventory balances shown above.  These raw materials are anticipated to be used in manufacturing development, research and development activities and in the manufacture of commercial product.

Inventory reserves as of March 31, 2014 and December 31, 2013 were $1.3 million and $0.5 million, respectively.  Inventory reserves reflect costs of SURFAXIN finished goods inventories that are not anticipated to be recoverable through the commercial sale of the product during the initial launch period due to product expiration.  These reserves ensure that the inventory carrying values do not exceed net realizable value.
Cash interest expense represents interest of 8.75% on the outstanding principal amount for the period, paid in cash on a quarterly basis.  Non-cash amortization of debt discount represents the amortization of transaction fees and the fair value of the warrants issued in connection with the Deerfield Facility.  The amortization of debt costs represents legal costs incurred in connection with the Deerfield Facility.

Note 76 – Common Stock Warrant Liability

We account for common stock warrants in accordance with applicable accounting guidance provided in ASC Topic 815“Derivatives and Hedging – Contracts in Entity’s Own Equity” (ASC 815), either as derivative liabilities or as equity instruments depending on the specific terms of the warrant agreement.

The form of warrant agreement for the registered warrants that we issued in our May 2009 and February 2010 public offerings generally provide that, in the event a related registration statement or an exemption from registration is not available for the issuance or resale of the warrant shares upon exercise of the warrant, the holder may exercise the warrant on a cashless basis.  Notwithstanding the availability of cashless exercise, generally accepted accounting principles (GAAP) provide that these registered warrants are deemed to be subject to potential net cash settlement and must be classified as derivative liabilities because (i) under federal securities laws, providing freely-tradable shares upon exercise of the warrants may not be within our control in all circumstances, and (ii) the warrant agreements do not expressly provide that there is no circumstance in which we may be required to effect a net cash settlement of the warrants.  The accounting guidance expressly precludes an evaluation of the likelihood that cash settlement could occur.  Accordingly, the May 2009 and February 2010 warrants have been classified as derivative liabilities and reported, at each balance sheet date, at estimated fair value determined using the Black-Scholes option-pricing model.

The form of warrant agreement for the registered five-year warrants that we issued in the February 2011 public offering (February 2011 five-year warrants) contain anti-dilutive provisions that adjust the exercise price if we issue any common stock, securities convertible into common stock, or other securities (subject to certain exceptions) at a value below the then-existing exercise price of the February 2011 five-year warrants.  Although by their express terms, these warrants are not subject to potential cash settlement, due to the nature of the anti-dilution provisions, these warrants have been classified as derivative liabilities and reported, at each balance sheet date, at estimated fair value determined using a trinomial pricing model.See, Note 8, “Common Stock Warrant Liability,” to the consolidated financial statements in our 2012 Form 10-K for a discussion of common stock warrant liability.

Selected terms and estimated fair value of warrants accounted for as derivative liabilities at September 30, 2013 are as follows:

 
  
 
   
 
Fair Value of Warrants
(in thousands)
Issuance
Date
 
Number of
Warrant Shares
Issuable
  
Exercise
Price
 
Warrant
Expiration
Date
 
Value at
Issuance
Date
  
 
March 31,
2014
  
December 31,
2013
 
 
 
  
 
 
 
  
  
 
5/13/2009  466,667  $17.25 5/13/2014 $3,360  $  $ 
2/23/2010  916,669   12.75 2/23/2015  5,701   1   6 
2/22/2011  4,552,600   1.50 2/22/2016  8,004   4,671   5,419 
 
        
 
     $4,672  $5,425 

 
 
   
Fair Value of Warrants
(in thousands)
 
 
Issuance
Date
Number of
Warrant
 Shares
 
 
Exercise
Price
 
Warrant
Expiration
 Date
 
Issuance
Date
 
 
September 30,
2013
 
 
 
 
 
 
5/13/2009 466,667  $17.25 5/13/2014$3,360 $ 
2/23/2010 916,669   12.75 2/23/2015 5,701  2 
2/22/2011 4,948,750   1.50 2/22/2016 8,004  4,676 
During the three months ended March 31, 2014, holders of the February 2011 five-year warrants exercised warrants to purchase 282,350 shares of common stock for total proceeds of $0.4 million.  There were no February 2011 five-year warrants exercised during the three months ended March 31, 2013.

Changes in the estimated fair value of warrants classified as derivative liabilities are reported in the accompanying Consolidated Statement of Operations as the “Change in fair value of common stock warrants.”
Note 7 –Deerfield Loan

Long-term debt consists solely of amounts due under a $30 million loan (Deerfield Loan) with affiliates of Deerfield Management Company, L.P. (Deerfield) for the periods presented:

 March 31,  December 31, 
(in thousands) 2014  2013 
 
    
Note Payable $30,000  $30,000 
Unamortized discount  (11,207)  (11,646)
Long-term debt, net of discount $18,793  $18,354 

The principal amount of the loan is payable in equal annual installments on the fourth, fifth and sixth anniversaries of the Deerfield Loan agreement, provided that the amount payable on the fourth anniversary shall be deferred for one year if either (i) our “Net Sales” for the immediately preceding 12-month period are at least $20 million, or (ii) our “Equity Value” is at least $200 million; and provided further, that the amount payable on the fifth anniversary (together with any amount deferred on the fourth anniversary) shall be deferred until the sixth anniversary if either (i) our “Net Sales” for the immediately preceding 12-month period are at least $30 million, or (ii) our “Equity Value” is at least $250 million.  Accordingly, if the milestones are achieved in each year, payment of the principal amount could be deferred until the sixth anniversary date of the loan, on February 13, 2019.

The following amounts comprise the Deerfield Loan interest expense for the periods presented:

 Three months ended 
(in thousands) March 31, 
 
 2014  2013 
 
 
  
 
Cash interest expense $647  $113 
Non-cash amortization of debt discount  439   57 
Amortization of debt costs  5   5 
Total interest expense $1,091  $175 

Cash interest expense represents interest at an annual rate of 8.75% on the outstanding principal amount for the period, payable quarterly in cash.  Non-cash amortization of debt discount represents the amortization of transaction fees and the fair value of the warrants issued in connection with the Deerfield Loan.  The amortization of debt costs represents legal costs incurred in connection with the Deerfield Loan.

In connection with the loan, we issued to Deerfield warrants to purchase 7.0 million shares of our common stock at an exercise price of $2.81 per share that expire on February 13, 2019.  The Deerfield warrants are derivatives that qualify for an exemption from liability accounting as provided for in ASC Topic 815 “Derivatives and Hedging – Contracts in Entity’s Own Equity” (ASC 815) and are classified as equity.  See, Note 9, “Deerfield Loan,” to the Consolidated Financial Statements in our 2013 Form 10-K.

Note 8 – Stock Options and Stock-Based Employee Compensation

We recognize in our consolidated financial statements all stock-based awards to employees and non-employee directors based on their fair value on the date of grant, calculated using the Black-Scholes option-pricing model.  Compensation expense related to stock-based awards is recognized ratably over the vesting period, which for employees is typically three years.
The fair value of each option award is estimated on the date of grant using the Black-Scholes option-pricing formula that uses weighted-average assumptions noted in the following table:table.

 March 31, 
 2013  2012  2014  2013 
        
Weighted-average expected volatility  110%  110%  100%  110%
Weighted-average expected term (in years) 4.7  4.8 
Weighted-average expected term 5.4 years  4.8 years 
Weighted-average risk-free interest rate  0.74%  0.79%  1.6%  0.74%
Expected dividends            

The table below summarizes the total stock-based compensation expense included in the statements of operations for the periods presented:

 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
  Three Months Ended 
(in thousands) March 31, 
 2013  2012  2013  2012  2014  2013 
Research & Development $210  $150  $551  $388  $248  $141 
Selling, General & Administrative  431   324   1,053   889   455   215 
Total $641  $474  $1,604  $1,277  $703  $356 
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ITEM 2.
MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Some of the information contained in this discussion and analysis or set forth elsewhere in this Quarterly Report on Form 10‑Q, including information with respect to our plans and strategy for our business and related financing activities, includes forward-looking statements that involve risks and uncertainties.  You should review the “Forward-Looking Statements” section, and the risk factors discussed in the “Risk Factors” section and elsewhere in this Quarterly Report on Form 10-Q, as well as in our Annual Report on Form 10-K for the year ended December 31, 20122013 that we filed with the Securities and Exchange Commission (SEC) on March 15, 2013 (201217, 2014 (2013 Form 10-K ) and our other filings with the SEC, and any amendments thereto, for a discussion of important factors that could cause actual results to differ materially from the results described in or implied by the forward-looking statements contained in the following discussion and analysis or elsewhere in this Quarterly Report on Form 10-Q.

Management’s Discussion and Analysis of Financial Condition and Results of Operations (MD&A) is provided as a supplement to the accompanying interim unaudited consolidated financial statements and footnotes to help provide an understanding of our financial condition, the changes in our financial condition and our results of operations.  This item should be read in connection with our accompanying interim unaudited consolidated financial statements (including the notes thereto).

OVERVIEW

Discovery Laboratories, Inc. (referred to as “we,” “us,” or the “Company”) is a specialty biotechnology company focused on creating life-saving products for critical carecritical-care patients with respiratory disease and improving the standard of care in pulmonary medicine.  Our proprietary drug technology produces a synthetic, peptide-containing surfactant (KL4 surfactant) that is structurally similar to pulmonary surfactant, a substance produced naturally in the lung and essential for normal respiratory function and survival.  We are developing our KL4 surfactant in liquid, lyophilized and aerosolized dosage forms.  We are also developing novel drug delivery technologies potentially to enable the efficient delivery of our aerosolized KL4 surfactant, and potentially other aerosolized drugs and inhaled therapies.surfactant.  We believe that our proprietary technologies may make it possible, for the first time, to develop a significant pipeline of products to address a variety of respiratory diseases for which there frequently are few or no approved therapies.
Our near-term focus is to develop our KL4 surfactant and drug delivery technologies to improveWe are initially focused on improving the management of respiratory distress syndrome (RDS) in premature infants.  RDS is a serious respiratory condition caused by insufficient surfactant production in underdeveloped lungs of premature infants, andinfants.  RDS is the most prevalent respiratory disease in the neonatal intensive care unitNeonatal Intensive Care Unit (NICU).  RDS and can result in long-term respiratory problems, developmental delay and death.  Currently,Our first KL4 surfactant drug product, SURFAXIN® (lucinactant) Intratracheal Suspension for the prevention of RDS in premature infants at high risk for RDS, was approved by the United States Food and Drug Administration (FDA) in 2012.  SURFAXIN is our KL4 surfactant in liquid form, and is the first synthetic, peptide-containing surfactant approved by the FDA and the only alternative to animal-derived surfactants currently used in the United States (U.S.).  SURFAXIN has been commercially available in the U.S. since November 2013.

Premature infants with severe RDS currently are treated with surfactants that can only be administered by endotracheal intubation supported with mechanical ventilation, both invasive procedures that may each result in serious respiratory conditions and other complications.  To avoid such adverse results,complications, many neonatologists generally provide surfactants as initial therapy only to premature infants with severe RDS where the potential benefits of surfactant therapy outweigh the risks associated with endotracheal intubation and mechanical ventilation.  Fortreat infants with less severe RDS neonatologists first attempt to provide respiratory support using aby less invasive means, such astypically nasal continuous positive airway pressure (nCPAP).  Unfortunately, a significant number of thesepremature infants doon nCPAP will not respond adequately to nCPAP, anwell (an outcome referred to as nCPAP failure,failure) and thereafter may require subsequentdelayed surfactant administration via intubation and mechanical ventilation.therapy.  Since it is not possible to ascertainneonatologists currently cannot predict which patientsinfants will experience nCPAP failure, neonatologists treating less severe RDS are faced with a dilemma,difficult choices in treating infants with less severe RDS.  This is because the outcomemedical outcomes for those infants who experience nCPAP failure and receive delayed surfactant therapy may not be asless favorable asthan the outcomeoutcomes for those infants who receive surfactant therapy as initial therapy.in the first hours of life.

With mortality and morbidity rates that have not meaningfully improved over the last decade, we believe that the RDS marketAEROSURF® is presently underserved.  We also believe that our RDS programs, including SURFAXIN® and, if approved, AEROSURF®, have the potential to greatly improve the management of RDS and, over time, become a new standard of care for premature infants with RDS.  Moreover, we believe that the neonatal community is increasingly recognizing the potential benefits of (i) a synthetic, peptide-containing surfactant, and more importantly, (ii) a less-invasive method of delivering aerosolized surfactant to treat premature infants at risk of suffering from respiratory disorders.

In 2012, the U.S. Food and Drug Administration (FDA) approved our first KL4 surfactant drug product, SURFAXIN (lucinactant) Intratracheal Suspension for the prevention of RDS in premature infants at high risk for RDS.  SURFAXIN is the first synthetic, peptide-containing surfactant approved by the FDA and the only alternative to animal-derived surfactants currently used in the U.S.  On October 4, 2013, we announced that the FDA agreed to updated product specifications that we previously submitted for SURFAXIN.  On November 8, 2013, we announced that we have initiated the commercial introduction of SURFAXIN.  Our commercial and medical affairs organizations currently are advancing initiatives to communicate that SURFAXIN is available and to secure formulary acceptance from our target hospitals.  We are also preparing to support hospitals that order SURFAXIN with in-service training, medical information and other activities intended to promote and enable a deliberate and orderly introduction of SURFAXIN to the neonatal community.

AEROSURF is an investigational combination drug-devicedrug/device product that combines our KL4 surfactant with our proprietary capillary aerosol generator (CAG).  We are developing AEROSURF potentially will enable administration of aerosolized KL4 surfactant to deliverpremature infants supported with nCPAP, without invasive intubation and mechanical ventilation.  By enabling delivery of our KL4 surfactant in aerosolized form to premature infants with RDS.  AEROSURF potentially will provide neonatologists with the ability to avoid theusing less invasive procedures, currently required to administer surfactant therapy and deliver our KL4 surfactant in aerosolized form to premature infants supported with nCPAP.  For this reason, we believe that AEROSURF if approved, may address a serious unmet medical need and potentially enable the treatment of a significantly greater number of premature infants with RDS who could benefit from surfactant therapy but are currently not treated.

We are also developing a lyophilized (freeze-dried) dosage form of our KL4 surfactant whichthat is stored as a powder and resuspendedreconstituted to liquid form prior to use and is being developed with the objective of improving ease of use for healthcare practitioners, as well as potentially prolongingto prolong shelf life and eliminatingeliminate the need for cold-chain storage.  We are planning initially todeveloping this dosage form for use lyophilized KL4 surfactant in our AEROSURF development program.  We are also assessing a potential development plan intendedplanning to seek regulatory advice to determine if we could gain regulatory approvalmarketing authorization for SURFAXIN LS™, a lyophilized dosage form of SURFAXIN under a development plan that would be both capital efficient and capable of implementation within a reasonable time.  If feasible, we would likely implement such a development plan and would plan to introduce it commercially as a life-cycle extension of SURFAXIN under the name SURFAXIN LS™, in the U.S. and potentially in other markets.

AFECTAIR®To support the commercial introduction of SURFAXIN in the U.S. and our other KL4 surfactant pipeline products, if approved, we have established our own specialty respiratory critical care commercial and medical affairs team.  This team includes medical professionals with experience in neonatal/pediatric respiratory critical care, and has focused on products that address neonatal indications, beginning with SURFAXIN.  We believe that this team will be positioned to efficiently introduce our other KL4 surfactant products under development, if approved, including AEROSURF and potentially SURFAXIN LS and future applications of our aerosolized KL4 surfactant.

In addition, we recognize that our commercial and medical affairs team could potentially support introductions of other synergistic pipeline products, including products owned or developed by third parties for the NICU/PICU.  To that end, we would consider potential transactions focused on securing commercial rights to such synergistic products, including in the form of product acquisitions, in-licensing agreements or distribution, marketing or co-marketing arrangements.
In the future, we expect that we may be able to leverage the information, data and know-how that we gain from our development efforts with SURFAXIN and AEROSURF to support development of a product pipeline to address serious critical care respiratory conditions in larger children and adults in pediatric and adult intensive care units (PICUs and ICUs), including potentially acute lung injury (ALI), chronic obstructive pulmonary disorder (COPD) and cystic fibrosis (CF).  At the present time, however, we are focusing our resources primarily on the commercial introduction of SURFAXIN and development of AEROSURF through phase 2 clinical trials.  Once we have advanced these objectives, we expect to be in a better position to assess the potential of other development programs to address the critical care needs of patients in the PICU and ICU.

We also have developed a disposable aerosol-conducting airway connector for infants that is our novel disposable device intended to simplify the delivery of aerosolized medications (including our aerosolized KL4 surfactant, surfactant) and other aerosolized medications and inhaled therapies to infants in NICUs and pediatric intensive care units (PICUs) who requirecritical-care patients requiring ventilatory support by introducing thesupport.  This device introduces aerosolized medicationmedications directly at the patient interface and minimizingminimizes the number of connections in the ventilator circuit.  To gain information and assess the use ofWe have registered this device in different clinical settings, we are continuing a national user experience program at a number of institutions, including leading neonatal thought centers, across the U.S.

We have established our own specialty commercial and medical affairs organizations to focus on neonatal/pediatric respiratory critical care in hospitals across the U.S. These organizations are primarily responsible foras a Class I, exempt medical device under the commercial introduction of SURFAXINname AFECTAIR® and the AFECTAIR device.  In the future, we expect that these teams will be able to leverage the experience and relationships gained from the introduction of SURFAXIN to support the potential introductions of our own future pipeline products, beginning with, if approved, AEROSURF and potentially SURFAXIN LS.  In addition, we will consider opportunities to leverage our experience and relationships to market and support other synergistic products that could be of benefit in the NICU/PICU.

Our objectives for 2013 include initiating the commercial introduction of SURFAXIN and advancing the AEROSURF phase 2 clinical program.  In the future, we expect that we will be able to apply the knowledge and experience gained from these activities to develop a pipeline of innovative products based on our technologies and intended to address other critical care respiratory conditions in the NICU, PICU and intensive care units (ICUs).

An important priority for usit is to secure strategic and financial resources to advance our KL4 surfactant and aerosol device development programs and the commercial introduction of our approved RDS products in markets outside the U.S.  See, “– Liquidity and Capital Resources – Overview.”  While we currently intend to retain all rights and commercialize our approved productscommercially available in the U.S., we are focused on identifying potential strategic alliances to assist us with our development programs in markets outside the U.S.  We seek strategic partners that have broad experience in the designated markets, including regulatory and product development expertise as well as an ability to commercialize our products.  In addition to development and commercial support, such alliances typically also would provide us with financial resources to support our activities, potentially in the form of upfront payments, milestone payments, commercialization royalties and a sharing of research and development expenses.  We are focused on securing a significant strategic alliance predominantly to support our activities in the European Union (EU).  To date, the primary focus of our discussions has been on AEROSURF.  In the future, we may also seek strategic alliances and/or collaboration arrangements to support the potential commercial introduction of SURFAXIN and, if approved, SURFAXIN LS, in countries where regulatory approval is facilitated by the information contained in our SURFAXIN new drug application (NDA) approved by the FDA.

There can be no assurance that we will be successful in securing the necessary capital, or concluding any strategic alliance, collaboration arrangement or other similar transaction.  See, “– Liquidity and Capital Resources.”

Business and Pipeline Programs Update

The reader is referred to, and encouraged to read in its entirety “Item 1 – Business,” in our 20122013 Form 10-K, which contains a discussion of our Business and Business Strategy, as well as information concerning our proprietary technologies and our current and planned KL4 pipeline programs.

Following are updates to our pipeline programs since the filing of our 20122013 Form 10-K:

·With the commercial introduction of SURFAXIN forunderway, our commercial and medical teams are focused on forming relationships with key constituents in our target hospitals, including neonatologists, pharmacists, respiratory therapists, NICU nurses and other staff in the PreventionNICU with the goal of Respiratory Distress Syndrome (RDS)obtaining formulary acceptance and, ultimately, product utilization in Premature Infants at High Risk for RDSour target hospitals.  We also are focused on conducting in-service training to assure that SURFAXIN is administered in a safe and consistent manner.

In April 2013, we received a response from the FDA to a submission we made in the fourth quarter of 2012 concerning our improved analytical chemistry method and updated product specifications for SURFAXIN drug product.  The April FDA correspondence included a request for specific information and documents, recommendations regarding documentation of product specifications generally and for the upper limit of a single product specification, and a request for supporting data using the improved and revalidated analytical chemistry method.  We completed the required work and submitted our response to the FDA on June 7, 2013.  On October 4, 2013, we received confirmation that the FDA has agreed with our updated product specifications.  We have now manufactured new drug product and have initiated the commercial introduction of SURFAXIN.
Although not an indicator or predictor of revenue, formulary acceptance for SURFAXIN is a necessary prerequisite to be able to sell SURFAXIN drug product to a hospital and realize revenues.  In the brief period that SURFAXIN has been available, our early experience suggests that the time required to have SURFAXIN reviewed by hospital committees, accepted on hospital formulary, purchased by the hospital pharmacy, and ultimately used in the NICU is considerably longer than expected.  As a result, while we continue to believe that we will be able to meet our long term objectives for SURFAXIN, we anticipate that our short term revenues will be modest in the next several years.

On August 7, 2013, we entered into a Pharmaceutical Manufacturing and Supply Agreement with our contract manufacturer, DSM Pharmaceuticals, Inc. (DSM) providing for the manufacture of SURFAXIN drug product.  We anticipate that DSM will become our principal manufacturer of SURFAXIN upon expiration of the lease for our manufacturing operations in Totowa, NJ, currently in mid-2015.  See, “– Results of Operations – Research and Development Expenses – Product Development and Manufacturing.”SURFAXIN is the first synthetic, peptide-containing alternative to the previously available animal-derived surfactants.  Our experience to date indicates that, to properly explain the method of administration  and the potential benefits of SURFAXIN, including both potential medical and pharmacoeconomic benefits, it is important to emphasize medical education and scientific discussions with formulary committees to better inform their process.  Accordingly, in the second quarter of 2014, we are resizing and realigning our commercial and medical affairs teams to emphasize medical education balanced with an appropriate sales effort, and to focus on securing formulary acceptance with hospitals that we believe are centers of excellence whose reputation and influence is strong both regionally and nationally.  We expect that this realignment could result in a reduction in expense in the second half of 2014 of approximately $1.0 million per quarter compared to our recent historical expense.  As we monitor our progress, our strategy is to routinely assess and adjust our tactical plan and make appropriate additional investments if needed to assure that we maximize potential formulary uptake and SURFAXIN sales revenue.
·AEROSURF

On October 17, 2013, we announced that we have submitted an Investigational New Drug (IND) Application to the FDA for ourOur AEROSURF phase 2 clinical program. is underway.  The FDA has completed its review and cleared our IND, and we expectinitial phase 2a clinical trial is designed to initiate our phase 2 clinical program in the fourth quarter of 2013.

The primary goal of the study (phase 2a) of the AEROSURF clinical program is to evaluateassess the safety and tolerability of a single exposure of aerosolized KL4 surfactant drug product. This study is planned as an escalating dose study evaluating three dose levels of aerosolized KL4 surfactant.  The comparator isin premature infants 29 to 32 weeks gestational age receiving nCPAP alone.  The study will be conducted in three centersfor RDS.  Results are expected in the U.S.third quarter of 2014.  We currently are planning for, and is expectedexpect to be completed by mid-2014.  The design ofinitiate, a phase 2b clinical study in the second study (phase 2b) will be informed byhalf of 2014 and expect to complete it in the resultssecond half of the phase 2a study. The primary objective of this study will be to determine the optimal dose and to estimate the efficacy margin, information that will inform the design of the phase 3 efficacy and safety study. Phase 2b is expected to be conducted in multiple centers and completed by mid-2015.
2015.

·
DSM has manufacturedWe are progressing with our long-term manufacturing strategy.  We are continuing to explore possible alternatives that could enable longer-term utilization of our Totowa Facility, the clinical lyophilizedlease for which currently is scheduled to expire on June 30, 2015.  We are also pursuing potentially manufacturing KL4 surfactant drug product neededusing third-party CMOs.  Since 2012, we having been working with DSM to conduct the phase 2a studycomplete a technology transfer of our AEROSURF clinical program.  On October 24, 2013,liquid KL4 surfactant manufacturing process to DSM and we have entered into a Master Services Agreementsupply agreement with DSM providingthat provides for the furthermanufacture of commercial supply of SURFAXIN drug product through December 31, 2015, with such potential extensions as we may agree.  We also are working to identify a second CMO to manufacture SURFAXIN drug product.  Although we believe that we will successfully execute our plan to provide for the long-term availability of SURFAXIN drug product, there can be no assurance that we will be successful.    See our 2013 Form 10-K "Item – 1A – Risk Factors – Our manufacturing strategy includes relying, at least in part in the future, on third parties to manufacture our current approved products as well as certain of our drug product candidates and medical devices, which exposes us to risks that may affect our ability to maintain supplies of our commercial products and/or delay our research and development activities, regulatory approval and commercialization of our drug product candidates."
·We recently announced that we have secured three additional patents in the U.S., including two patents containing composition of matter and method of making claims for our lyophilized KL4 surfactant, which extend to 2033, and manufacture of additional drug supply neededone related to complete our phase 2 clinical program, and potentially for our phase 3 clinical program and, if approved, commercial supply.

With the assistance of Battelle Memorial Institute (Battelle), we have completed development of a clinic-ready CAG device, which has passed a rigorous design verification testing program, and have manufactured a sufficient number of clinic-ready CAGsnovel AFECTAIR aerosol-conducting airway connector that extends to support the initial phaseApril 2029.  These patents are indicative of our AEROSURF clinical program.  We planefforts to continue developmentprotect the long-term commercial potential of our CAG and expect to manufacture additional devices to support completion of our phase 2 clinical program and potentially our phase 3 clinical program.  The CAG has been designed to produce aerosolized KL4 surfactant  in volumes upand aerosol delivery technologies. our lyophilized KL4 surfactant is being developed initially for our AEROSURF development program. Our longer term goal is to 10 times the output produced by currently available aerosol devices.
develop our technologies to address other potential indications that could benefit from our proprietary KL4 surfactant.
16


CRITICAL ACCOUNTING POLICIES

There have been no changes to our critical accounting policies since December 31, 2012.2013.  For more information on critical accounting policies, see, Note 3, “Summary of Significant Accounting Policies and Recent Accounting Pronouncements,” to the consolidated financial statements included in our 20122013 Form 10-K.  Readers are encouraged to review those disclosures in conjunction with this Quarterly Report on Form 10-Q.

RESULTS OF OPERATIONS

Net Loss and Operating Loss

The net loss for the three months ended September 30,March 31, 2014 and 2013 and 2012 was $12.2$11.5 million (or $0.22 basic$0.14 net loss per share) and $13.3$12.6 million (or $0.31 basic$0.29 net loss per share), respectively.  IncludedThe decrease in the net loss isfrom 2013 to 2014 was due to the changedecrease in fair value of certain common stock warrants classified as derivative liabilities, resultingoperating loss, partially offset by a $0.9 million increase in non-cashinterest expense of $1.1 million and $3.3 million for 2013 and 2012, respectively.

The net loss forassociated with the nine months ended September 30, 2013 and 2012 was $33.5 million (or $0.68 basic net loss per share) and $30.5 million (or $0.80 basic net loss per share), respectively.  Included in the net loss is the change in fair value of certain common stock warrants classified as derivative liabilities, resulting in non-cash income of $1.6 million and non-cash expense of $5.1 million in 2013 and 2012, respectively.Deerfield Loan.

The operating loss for the three months ended September 30,March 31, 2014 and 2013 and 2012 was $10.8 million and $10.0$12.6 million, respectively.  The increasedecrease in operating loss from 20122013 to 2013 is primarily2014 was due to (i) a $0.6$1.2 million increasedecrease in investment in the AEROSURF development program, primarilycosts to develop and manufacture ourclinic-ready CAG devices for clinical use in the AEROSURF phase 2a clinical study, and further development of our lyophilized KL4 surfactant manufacturing process at DSM.

The operating loss for the nine months ended September 30, 2013 and 2012 was $34.2 million and $25.4 million, respectively.  The increase in operating loss from 2012 to 2013 is primarily due to (i) a $3.3 million increase in investment in our own specialty commercial and medical affairs organizations that are focused on neonatal/pediatric respiratory critical care in NICUs/PICUs across the U.S., (ii) a $4.0$1.2 million increase in investment in the AEROSURF development program, primarily to develop and manufacture our CAG for clinical use in our AEROSURF phase 2 clinical studies, and completion of the technology transfer and further development of our lyophilized KL4 surfactant manufacturing process at DSM, and (iii) a $1.5 million increasedecrease in purchases of raw materials to manufacture drug product forof active pharmaceutical ingredients (APIs) used in the manufacture of SURFAXIN and our AEROSURF development program.

Grant Revenue

For the three and nine months ended September 30, 2013, we recognized $0.1 million and $0.3 million, respectively, of grant revenue.  The grant revenue represents funds received and expended under a Small Business Innovation Research (SBIR) Phase I award from National Institute of Health’s (NIH) National Institute of Allergy and Infectious Diseases (NIAID) Center for Medical Counter Measures Against Radiation and Nuclear Threats to assess the ability of KL4 surfactant to mitigate the effects of acute radiation exposure to the lung, including acute pneumonitis and delayed lung injury.  The total amount of the award is $0.6 million and funds received and expended from inception of the award through September 30, 2013 have totaled $0.5 million.  The remainder of the award is expected to be received and expended in 2013.  We did not recognize any grant revenues for the comparable periods in 2012.

We believe that our aerosolized KL4 surfactant mayfor AEROSURF development program.

Product Sales

In accordance with our revenue recognition policy, we recognize revenue once product has been sold through to the hospital and all revenue recognition criteria have been met.  For the three months ended March 31, 2014, we recognized revenue in the amount of $28,000.

Cost of product sales

Cost of product sales for the three months ended March 31, 2014 includes an increase of $766,000 in inventory reserves for SURFAXIN finished goods inventories that are not anticipated to be an effective intervention for people at risk for, or with, Acute Lung Injury (ALI), and that our development work with AEROSURF for RDS may formrecoverable through the basis for a potential pipelinecommercial sale of productsthe product during the initial launch period due to address ALI.  We are collaborating with leading research institutions in a series of preclinical studies funded through various U.S. government-sponsored, biodefense-related initiatives, including NIAID.product expiration.

Research and Development Expenses

Our research and development expenses are charged to operations as incurred and we track such costsare tracked by category rather than by development project.  As many of our research and development activities form a foundation for the development of our KL4 surfactant and drug delivery technologies, they are expected to benefit more than a single project.  For that reason, we cannot reasonably estimate the costs of our research and development activities on a project-by-project basis.  We believe that tracking our expenses by category is a more accurate method of accounting for these activities.  Our research and development costs consist primarily of expenses associated with (a) product development and manufacturing, (b) medical and regulatory operations, and (c) direct preclinical and clinical programs.programs, and (d) other related expenses.

The table below summarizes research and development expenses for the periods presented:

(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
  
Three Months Ended
March 31,
 
 2013  2012  2013  2012 
Research and Development Expenses 2014  2013 
            
Product development and manufacturing $4,769  $4,258  $16,591  $11,298  $3,623  $6,824 
Medical and regulatory operations  1,506   1,400   4,416   3,475   1,633   1,451 
Direct preclinical and clinical programs  299   85   902   709   333   197 
Total Research & Development Expenses $6,574  $5,743  $21,909  $15,482  $5,590  $8,472 

Research and development expenses for the three months ended March 31, 2014 and 2013 include non-cash charges associated with stock-based compensation and depreciation of $0.4 million for each of the three months ended September 30, 2013 and 2012, respectively; and $1.1$0.3 million, and $1.2 million for the nine months ended September 30, 2013 and 2012, respectively.

Product Development and Manufacturing

Product development and manufacturing includes (i) the cost of our manufacturing operations, both in-house and with our CMO,CMOs, validation activities and quality assurance and analytical chemistry capabilities to support production of drug supply for our KL4 surfactant products in conformance with current good manufacturing practices (cGMP);, and of medical devices, including AFECTAIR, WARMING CRADLE® and CAG, in accordance with Quality System Regulations (QSR), (ii) design and development activities related to our CAG devicesdevice for use in our planned AEROSURF phase 2 clinical program;  (iii) design and development activities related to our AFECTAIR aerosol-conducting airway connector; and (iv)(iii) pharmaceutical development activities, including development of a lyophilized dosage form of our KL4 surfactant.  These costs include employee expenses, facility-related costs, depreciation, costs of drug substances (including raw materials), supplies, quality control and assurance activities, analytical services, and expert consultants and outside services to support pharmaceutical and device development activities.

Product development and manufacturing expenses for the three months ended September 30, 2013 increased $0.5March 31, 2014 decreased $3.2 million as compared to the same period in 2012, primarily2013, due to costs associated(i) investments of $1.2 million in 2013 to complete development activities for our clinic-ready CAG device for use in our AEROSURF phase 2 clinical trials, including work that began in June 2012 with Battelle Memorial Institute (Battelle), which assisted with the design and testing, and manufactured a supply of clinic-ready CAG devices for use in the initial AEROSURF phase 2a clinical trial; (ii) a reduction of $1.2 million in purchases of APIs used in the manufacture of SURFAXIN commercial drug product, and our lyophilized KL4 surfactant for use in preclinical and clinical development activities, including to complete the technology transfer of, and further development ofdevelop our KL4 surfactant manufacturing process at DSM.

Product developmentDSM Pharmaceuticals, Inc. (DSM), and manufacturing expenses for the nine months ended September 30, 2013 increased $5.3 million from the comparable period in 2012 primarily dueactivities to (i) costs of design and development activities related to our CAG for use in our planned AEROSURF phase 2 clinical trials,  including work with third party device experts and work that we began in June 2012 with Battelle, which is assisting with design, testing, and manufacture ofdevelop a clinic-ready CAG devices; (ii) costs associated with the technical transfer and further development of our KL4 surfactant manufacturing processes at DSM; and (iii) purchases of active pharmaceutical ingredients (APIs) used in the production of SURFAXIN and our lyophilized KL4 surfactant, development activities, including preparation of our CAGprepare for use in our anticipated AEROSURF phase 2 clinical program, and to support completion of the technical transfer and further development of our KL4 surfactant manufacturing process at DSM.
We have invested, from the beginning of 2012 through September 2013, approximately $7 million to develop the CAG and complete the technology transfer and further develop our lyophilized KL4 surfactant process at DSM, in preparation for initiation of the AEROSURF clinical program.
We believe that our RDS product portfolio, based on our novel synthetic, peptide-containing KL4 surfactant, has the potential to greatly improve the management of RDS and, over time, may enable the treatment of a significantly greater number of premature infants at risk for RDS who could benefit from surfactant therapy but are currently not treated.  We are implementing a long-term manufacturing strategy intended to assure that we have and maintain the capabilities and resources needed to give meaning to this vision.

As we undertake the commercial introduction of SURFAXIN and initiate our phase 2 clinical program for AEROSURF in the fourth quarter of 2013, we are planning for long-term continuity of supply and continued integrity and reliability of our manufacturing and quality assurance processes.  We seek to build a foundation to support our anticipated long-term needs, and intend to make appropriate capital investments in the near-term, balance the use of our available resources against our short-term revenue expectations, and maintain flexibility in planning our manufacturing activities and goals.
We have secured an extension of the lease for our manufacturing operations at Totowa, NJ, which was scheduled to expire in December 2014, until to June 30, 2015.  We continue to explore possible alternatives that potentially may enable longer-term utilization of that facility.  In addition, in 2012, to secure an additional source to manufacture commercial supply of SURFAXIN, we initiated a technology transfer of our SURFAXIN manufacturing process to DSM.  We also entered into a supply agreement with DSM that provides for the manufacture of commercial supply of SURFAXIN drug product through December 31, 2015, with such further extensions at that time as may be agreed by the parties.  We currently plan to complete the technology transfer to DSM and manufacture process validation batches of SURFAXIN in the fourth quarter of 2013.  After time for stability assessment and FDA review, we expect that DSM may be approved for commercial production of SURFAXIN in the fourth quarter of 2014.

For our lyophilized KL4 surfactant, as noted above (see, “– Overview – Business and Pipeline Programs Update – AEROSURF,”  and “– SURFAXIN LS”), we completed the technology transfer  of our lyophilized KL4 surfactant manufacturing process to DSM and have manufactured a supply of KL4 surfactant for use in the initial phase of our AEROSURF clinical program.  We have entered into a Master Services Agreement for the further development of KL4 surfactant, potentially to complete our AEROSURF phase 2 clinical program,program; and potentially our AEROSURF phase 3 clinical program, as well as other pipeline programs.  For the life cycle management(iii) $0.9 million of SURFAXIN, we are assessing a potential development plan that will allow for the conversion of our liquid formulationcosts capitalized to a lyophilized dosage form, SURFAXIN LS, and gain regulatory approval inventory in the U.S. and potentially in other markets.

Consistent with our long-term manufacturing strategy, we have initiated a project to identify a potential second CMO to manufacture clinical and commercial supply and assure a continuous and back up supply of our KL42014. surfactant drug product.  We are in preliminary discussions with several CMOs with a plan to initiate activities in the fourth quarter of 2013.  We believe that, by manufacturing our drug product at our Totowa operations and with CMOs, we improve our ability to manage the level of our capital investments, maintain an appropriate balance between our fixed costs and variable expense while maintaining flexibility and reducing the risk profile of meeting the long-term requirements for development and commercial supply of our drug products.

We believe we have executive management and manufacturing capabilities to assure and support our long-term success.  Our executive team includes leaders in pharmaceutical and biopharmaceutical drug product manufacturing, with extensive experience in manufacturing both small and large molecules, biological and sterile drug/device combination products in both domestic and overseas operations, and supply chain; as well as in worldwide quality operations to assure consistent and continued quality and cGMP compliance for our products, whether manufactured on our own or with a CMO.  Our manufacturing operations are lead by seasoned professionals with broad technical and managerial skills in all facets of our KL4 surfactant manufacturing process, expertise built on many years of accumulated knowledge in biopharmaceutical manufacturing, facility management, process and cleaning validation, sterility assurance and microbiological analyses, clean room operation and direction of formulation and aseptic filling of our drug product.  We believe we can leverage the extensive experience that we have gained from having owned our own manufacturing operations since 2005 to flexibly respond over time and provide for the continued manufacture of our KL4 surfactant drug product, on our own or with our CMO.

Medical and Regulatory Operations

Medical and regulatory operations includes (i) medical, scientific, clinical, regulatory, data management and biostatistics activities in support of our research and development programs; and (ii) medical affairs activities to provide scientific and medical education support related to both SURFAXIN, and AFECTAIR as well as our other KL4 surfactant and aerosol delivery products under development.  These costs include personnel, expert consultants, outside services to support regulatory and data management, symposiums at key medical meetings, facilities-related costs, and other costs for the management of clinical trials.

Medical and regulatory operations costs for the ninethree months ended September 30, 2013March 31, 2014 increased $0.9$0.2 million compared to the same period in 2012, primarily2013, due to an increased investment in our medical affairs organization to support the commercial introductionexecute our AEROSURF phase 2 clinical program.
18

Direct Preclinical and Clinical Programs

Direct preclinical and clinical programs include: (i) development activities, including for the anticipated AEROSURF clinical program, toxicology studies and other preclinical studies to obtain data to support our Investigational New Druginvestigational new drug (IND) Applicationapplications and, potentially, our New Drug Application (NDA) filings for AEROSURF, potentially SURFAXIN LS, and our other product candidates;filings; and (ii) activities if any, associated with conducting clinical trials, including patient enrollment costs, external site costs, clinical device and drug supply, and related external costs, such as research consultant fees and expenses.

Direct preclinical and clinical programs expenseexpenses for the three and nine months ended September 30, 2013March 31, 2014 increased $0.2$0.1 million as compared to the same periodsperiod in 2012 primarily due2013.  Costs for the three months ended March 31, 2014 consisted of AEROSURF Phase 2a clinical trial and related activities.  Costs for the three months ended March 31, 2013 consisted of pre-clinical activities to preparatory activities forsupport our planned AEROSURF phase 2 clinical trials.  Such preparatory activities include the manufacture of clinic-ready CAG devices, implementation of clinical data management systemsdevelopment program and selection of clinical site locations.  Costs in 2012 included a $0.5 million charge related to a milestone payment that became payable to Johnson and Johnson (J&J) upon FDA approval of SURFAXIN in March 2012.activities.

We anticipate that direct clinical program costs associated with conducting the AEROSURF phase 2 clinical program will be approximately $8 -10$10 - 11 million for 2014 and through the anticipated completion of phase 2b in 2015.

Our drug research and development activities are focused on the management of RDS in premature infants.  To prepare for our AEROSURF clinical program, we previously conducted preliminary meetings with the FDA and we have engaged regulatory consultants to assist us in implementing and, as needed, refining our development plan.  We also plan to retain regulatory consultants to assist us in engaging with international regulatory authorities regarding the AEROSURF development plan.  We filed an IND with the FDA in October 2013.  The FDA has completed its review and cleared our IND, and we expect to initiate our phase 2 program in the fourth quarter of 2013.  We are also assessing a potential development plan intended to gain marketing authorization for SURFAXIN LS, a lyophilized dosage form of SURFAXIN, in the U.S. and potentially other major markets.  We previously discussed with the FDA potential development activities that may be needed to support regulatory approval of SURFAXIN LS and expect to engage in further discussions with the FDA in this regard.  For future development plans, we plan to leverage the development investments to date in our KL4 surfactant and aerosol technology programs to address respiratory critical care conditions in older children and adults, including potentially ALI.2015.

Research and Development Projects – Updates

Due to the significant risks and uncertainties inherent in the clinical development and regulatory approval processes, the nature, timing and costs of the efforts necessary to complete individual projects in development are not reasonably estimable.  With every phase of a development project, there are unknowns that may significantly affect cost projections and timelines.  As a resultIn view of the number and nature of these factors, many of which are outside our control, the success, timing of completion and ultimate cost of development of any of our product candidates is highly uncertain and cannot be estimated with any degree of certainty.  Certain of the risks and uncertainties affecting our ability to estimate projections and timelines are discussed in the Risk Factors Section and elsewhere in this Quarterly Report on Form 10-Q and in our 20122013 Form 10-K, including in “Item 1 – Business – Government Regulation,” “Item 1A – Risk Factors,” and “Management’s Discussion and Analysis of Financial Condition and Results of Operations – Results of Operations – Research and Development Expenses.”

Our leadresearch and development projects have been focused initially focused on the management of RDS in premature infants, includingand include (i) SURFAXIN liquid instillate, andwhich was approved by the FDA in 2012, (ii) our lyophilized KL4 surfactant, which we are developing initially for use in our AEROSURF development program and, if we are able to undertake a development plan that would be both capital efficient and capable of implementation within a reasonable time,potentially, in a SURFAXIN LS development program; and (ii)(iii) our aerosol delivery technology, including preparationin particular the development of a clinic-ready CAG device to support our planned AEROSURF phase 2 clinical program.  These and our other productdevelopment programs are described in “– Overview – Business and Pipeline Programs Update,” and in our other periodic filings with the SEC, including our 20122013 Form 10-K, “Item 1 – Business – Proprietary Platform – Surfactant and Aerosol Technologies,” and “‑ Surfactant Replacement Therapy for Respiratory Medicine.Medicine, and in our other periodic filings with the SEC.

With respect to activities in supportTo prepare for initiation of ourthe AEROSURF developmentphase 2 clinical program, from the beginning ofduring 2012 through September 2013, we invested approximately $7 million to develop thea clinic-ready CAG device and complete the technology transfer and further develop our lyophilized KL4 surfactant manufacturing process at DSM, in preparation for initiation of the phase 2 AEROSURF program.  In addition, asDSM.  As noted above, we anticipate that direct clinical program costs associated with conducting the AEROSURF phase 2 clinical program will be approximately $8 -10$10 - 11 million for 2014 and through the completion of phase 2b in 2015.  We also plan to continue securing appropriate capabilities to support the further advancement of AEROSURF, including for manufacturing development of our lyophilized KL4 surfactant, the conduct of a phase 3 clinical program, and the further development of a CAG device suitable for use in a phase 3 clinical program and, if successful, commercial use.
At the present time, we are focusing our efforts primarily on the commercial introduction of SURFAXIN and development of AEROSURF through the phase 2 clinical trials.  We also believe that, we may be able to leverage the information, data and know-how that we gain from our work with SURFAXIN and AEROSURF to support development of a robust product pipeline that could address serious critical care respiratory conditions in larger children and adults in pediatric intensive care units (PICUs) and adult intensive care units (ICUs), including potentially acute lung injury (ALI), chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF).

The reader is referred to and encouraged to review updates to the Pipeline Programs Update in “– Overview,” and “–Business and Pipeline Programs Update” at the beginning of this MD&A, which contain information necessary and important to this discussion.  See also, “– Overview,” and “– Liquidity and Capital Resources.”

Selling, General and Administrative Expenses

(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
  
Three Months Ended
March 31,
 
 2013  2012  2013  2012  2014  2013 
Selling, General and Administrative Expenses $4,299  $4,255  $12,648  $9,912  $4,423  $4,220 

Selling, general and administrative expenses consist primarily of the costs of sales and marketing activities, executive management, commercial development, including marketing and field-based sales, business development, intellectual property, finance and accounting, legal, human resources, information technology, facilityfacilities and other administrative costs.

Selling, general and administrative expenses for the ninethree months ended September 30, 2013March 31, 2014 increased $2.7$0.2 million compared to the same periodsperiod in 2012, primarily2013 due to an increased investmentsinvestment in our marketing and field-based sales organization and related marketing expenses in preparation forforce to execute the commercial introduction of SURFAXIN and the AFECTAIR device for infants.

In addition to developing our commercial marketing and sales organization, we have made additional investments to enhance certain of our general and administrative resources, including in legal, finance and accounting, and information technologies, to support the commercial introduction of our products.

Change in Fair Value of Common Stock Warrant Liability

(in thousands) Three Months Ended
September 30,
  Nine Months Ended
September 30,
  Three Months Ended
March 31,
 
 2013  2012  2013  2012  2014  2013 
Change in fair value of common stock warrant liability (Income / (Expense)) $(1,059) $(3,309) $1,627  $(5,063)
Change in fair value of common stock warrant liability $378  $162 

We account for common stock warrants in accordance with applicable accounting guidance provided in Accounting Standards Codification (ASC)ASC Topic 815 “Derivatives and Hedging – Contracts in Entity’s Own Equity” (ASC 815), either as either derivative liabilities or as equity instruments depending on the specific terms of the warrant agreement.  Derivative warrant liabilities are valued at the date of initial issuance and as of each subsequent balance sheet date using the Black-Scholes or trinomial pricing models, depending on the terms of the applicable warrant agreement.  Changes in the fair value of the warrants are reflected in the consolidated statement of operations as “Change in the fair value of common stock warrant liability.”  See, Notes 5 and 7Note 6 to our Consolidated Financial Statements in this Quarterly Report on Form 10-Q, and our 20122013 Form 10-K, “Item 7 – Management’s Discussion and Analysis of Financial Condition and Results of Operations – Results of Operations – Change in Fair Value of Common Stock Warrant Liability.”

Changes in the fair value of common stock warrant liability generally are due primarily to changes in our common stock share price during the periods.
Other Income and (Expense)

 Three months ended 
(in thousands) March 31, 
 
 2014  2013 
 
 
  
 
Interest income $2  $1 
Interest expense  (1,093)  (178)
Other income / (expense), net $(1,091) $(177)

Interest Expenseincome consists of interest earned on our cash and cash equivalents.  To ensure preservation of capital, we invest our cash in an interest bearing operating cash account and a U.S. treasury-based money market fund.

The table below summarizes interest expense for the periods presented:
(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
 
 
 2013  2012  2013  2012 
Interest Expense $(353) $(4) $(873) $(12)

Interest expense in 2013 consists of interest expense associated with the Deerfield FacilityLoan (see, “– Liquidity and Capital Resources – Loan Facility with Deerfield”) Note 7 to our Consolidated Financial Statements in this Quarterly Report on Form 10-Q) and interest expense incurred under our equipment financing facilities.  Interest expense for 2012 consists of interest expense incurred under our equipment financing facilities.

The following amounts comprise the Deerfield FacilityLoan interest expense for the periods presented:

 Three months ended 
(in thousands) 
Three Months Ended
September 30,
  
Nine Months Ended
September 30,
  March 31, 
 2013  2012  2013  2012  2014  2013 
         
  
 
Cash interest expense $221  $  $551  $  $647  $113 
Non-cash amortization of debt discounts  125      302    
Non-cash amortization of debt discount  439   57 
Amortization of debt costs  5      13      5   5 
Total Deerfield Facility interest expenses $351  $  $866  $ 
Total interest expense $1,091  $175 

Cash interest expense represents interest at an annual rate of 8.75% calculated on the outstanding principal amount for the period, paid in cash on a quarterly basis.  Non-cash amortization of debt discount represents the amortization of transaction fees and the fair value of the Deerfield Warrants.  The amortization of debt costs represents legal costsprofessional fees incurred in connection with the Deerfield Facility.Loan.

LIQUIDITY AND CAPITAL RESOURCES

Overview

We have incurred substantial losses since inception, due to investments in research and development, manufacturing, and, potentialmore recently, commercialization and medical affairs activities, and we expect to continue to incur substantial losses over the next several years.  Historically, we have funded our business operations through various sources, including public and private securities offerings, debt facilities, strategic alliances, the use of Committed Equity Financing Facilitiescommitted equity financing facilities (CEFFs) and at-the-market equity programs, and capital equipment financings.

As of September 30, 2013,March 31, 2014, we had cash and cash equivalents of $21.2$75.9 million approximately $6.6and long-term debt of $30 million ($18.8 million net of accounts payable and accrued expenses, and $10 million of long-term debtdiscount) under our Deerfield FacilityLoan with affiliates of Deerfield Management  Company, L.P. (Deerfield).

On October 15, 2013, we completed an offering under (see, Note 7, “ – Deerfield Loan,” to our At-the-Market Program (ATM Program) (Consolidated Financial Statements in this Quarterly Report on Form 10-Qsee, “– Common Stock Offerings – At-the-Market Program”) with Stifel, Nicolaus & Company, Incorporated (Stifel) and issued 713,920 shares of our common stock resulting in net proceeds to us (after deducting commissions due to Stifel) of approximately $1.9 million.  Through our ATM Program, subject to market conditions, we have the ability to sell up to approximately $23 million of common stock at such times and in such amounts that we deem appropriate.  However, use of the ATM Program is subject to market and other conditions and the ATM Program can be cancelled at any time by either party.  There can be no assurance that the ATM Program will be available when needed, if at all.

On November 5, 2013, we completed a public offering of 25 million shares of common stock, at a price of $2.00 per share resulting in gross proceeds of $50.0 million ($46.8 million net after commissions, discounts and expenses)In addition, we also granted the underwriters a 30-day option to purchase up to an additional 3.75 million shares of common stock (over-allotment) at an offering price of $2.00 per share.  On November 8, 2013, we received notification that the underwriters have exercised the full over-allotment and will purchase an additional 3.75 million shares.  This transaction is expected to close on or about November 14, 2013 and result in additional net proceeds to us of approximately $7.1 million.

We also have met the conditions for, and expect in early December to receive, an additional advance of $20 million under the Deerfield Facility, which became due upon the first commercial sale of SURFAXIN drug product.  See, “– Loan Facility with Deerfield.”

Before any additional financings, including under our ATM Program (see, “– Common Stock Offerings – At-the-Market Program (ATM Program),” and taking into accountNote 11, “Stockholders’ Equity – ATM Program,” to the additional approximately $7.1 million expected from the underwriters’ exercise of the over-allotmentconsolidated financial statements in our November public offering and the expected $20 million advance under the Deerfield Facility,2013 Form 10-K), we anticipate that we will have sufficient cash available to supportfund our operations and debt service obligations through the third quarter of 2015.
Our future capital requirements depend upon many factors, primarily the success of our efforts to (i) execute the commercial introduction of SURFAXIN and AFECTAIR in the U.S., as planned;; (ii) advance the AEROSURF development program to completion of the phase 2 clinical program as planned in mid-2015;the second half of 2015; and (iii) secure one or more strategic alliances or other collaboration arrangements (a) to support the development and, if approved, commercial introduction of AEROSURF in markets outside the U.S., including potentially in the European Union, and (b) to support the regulatory approval process and commercial introduction of SURFAXIN AEROSURF, AFECTAIR and potentially SURFAXIN LS, in certain markets outside the U.S.  We believe that, if we are successful with the commercial introduction of SURFAXIN and if we are able to complete the AEROSURF phase 2 clinical program on a timely basis and obtain encouraging results, and if we are able to advance the commercial introduction of SURFAXIN, our ability to enter into a significant strategic alliance will be enhanced.  There can be no assurance, however, that our efforts will be successful, or that, even if successful, we will be able to obtain additional capital to support our activities when needed on acceptable terms, if at all.

Even if we succeed withFor the commercial introduction of SURFAXIN and the AFECTAIR device as planned, given the time required to secure formulary acceptance of SURFAXIN at our target hospitals,next several years, we expect our revenues from SURFAXIN and AFECTAIR to be modest in the first 12-18 months and then increase over time as our products gain hospital acceptance.  As a result,that our cash outflows for marketing, commercial and medical activities, development programs, operations and debt service and development programs are expected towill outpace the rate at which we may generate revenues for several years.revenues.  To execute our business strategy and fund our operations over the long term,next several years, we will require significant additional infusions of capital until such time as the net revenues from SURFAXIN, AFECTAIR and, ifthe sale of approved AEROSURF, from potential strategic alliancesproducts and from other sources are sufficient to offset our cash flow requirements.  ToWhile we currently intend to retain all rights and commercialize our approved products in the U.S., an important priority for us is to secure additional capital and strategic resources to support the necessary capital,continued development and commercial introduction of our RDS products in markets outside the U.S. For our AEROSURF development program, we would prefer to enter intoare seeking a significant strategic alliances or collaboration agreements with partnersalliance that potentially could provide development, regulatory and commercial market expertise as well as financial resources, (potentiallyand, if approved, support the commercial introduction of AEROSURF in the EU and other selected markets outside the U.S.  Such alliances typically also would provide financial resources, in the form of upfront payments, milestone payments, commercialization royalties and a sharing of research and development expenses) and introduce our approved productsexpenses.  To advance SURFAXIN in various markets outside the U.S. where regulatory marketing authorization is facilitated by the information contained in our new drug application (NDA) approved by the FDA, we would consider various financing or collaboration arrangements that could provide regulatory expertise, support the commercial introduction of SURFAXIN in markets outside the U.S., and potentially provide a sharing of revenues.  Such countries could potentially include those in Latin America, North Africa and the Middle East.  We also plan to consider other public and private equity offerings, including under our ATM Program, which currently may allow for the sale of up to approximately $23 million of our commons stock (see, “– At-the-Market Program (ATM Program)”), as well as other financing transactions, such as secured equipment financing facilities or other similar transactions.

As of September 30, 2013,March 31, 2014, we had outstanding warrants to purchase approximately 10.314.5 million shares of our common stock at various prices, exercisable on different dates throughinto 2019.  Of these warrants, approximately 2.3warrants to purchase 7 million warrantsshares were issued to Deerfield in connection with the first advance under the Deerfield Facility.  Upon receipt of the final $20 million advance under the Deerfield Facility, which is anticipated on or about December 3, 2013, we will issue warrants to purchase an additional 4.66 million shares of our common stockLoan at an exercise price of $2.81 per share (we refer to these warrants and the warrants previously issued to Deerfield as the Deerfield Warrants).share.  The Deerfield Warrants may be exercised for cash or on a cashless basis.  In lieu of paying cash upon exercise, the holders also may elect to reduce the principal amount of the Deerfield loanLoan in an amount sufficient to satisfy the exercise price of the Deerfield Warrants.  In addition to the Deerfield Warrants, we have outstanding five-year warrants issued in February 2011 to purchase approximately 4.94.6 million shares of common stock that were issued in February 2011, are exercisable for five-years, and contain anti-dilution provisions that adjust the exercise price if we issue any common stock, securities convertible into common stock, or other securities (subject to certain exceptions) at a value below the then-existing exercise price of the warrants.  These warrants were originally issued withcurrently have an exercise price of $3.20 per share and thereafter adjusted downward, first to $2.80 per share following a public offering in March 2012 and then to $1.50 per share following a public offering in May 2013.share.  Although we believe that, in the future, we will secure additional capital from the exercise of at least a portion of our outstanding warrants, there can be no assurance that the market price of our common stock will equal or exceed price levels that would make exercise of outstanding warrants likely, or, even if the price levels are sufficient, that holders of the Deerfield Warrants would choose to exercise their warrants for cash, or that holders of any of our outstanding warrants willwould choose to exercise any or all of their warrants prior to the applicable warrant expiration date.dates.  Moreover, if our outstanding warrants are exercised, such exercises likely will be at a discount to the then-market value of our common stock and have a dilutive effect on the value of our shares of common stock at the time of exercise.
As of September 30, 2013,March 31, 2014, 150 million shares of common stock were authorized under our Amended and Restated Certificate of Incorporation, and approximately 71.7 million shares of common stock were available for issuance and not otherwise reserved.  As of November 8,  2013, following the financings under our ATM Program, our public offering, and establishment of additional reserves for the shares expected to be issued in connection with the underwriters’ exercise of the over-allotment in our November public offering and with respect to the warrants expected to be issued to Deerfield upon receipt of the $20 million advance in early December, approximately 4242.1 million shares of common stock were available for issuance and not otherwise reserved.

Although we currently believe that we will be able to successfully execute our business plan and accomplish our objectives,strategy, there can be no assurance that our AEROSURF development program will be successful within our anticipated time frame, if at all, that we will succeed in obtaining the necessary regulatory approvals in the U.S. and other markets, that any approved product, including SURFAXIN, will be commercially viable, that the ATM Program will be available when needed, if at all, or that we will be able to obtain additional capital when needed on acceptable terms, if at all, that we will be successful.  There can be no assurance that weWe will be successful in securingrequire significant additional capital to satisfy debt obligations and sustain operations, and to complete the needed capital, through strategic alliances, collaboration arrangements, financings, debt arrangementsdevelopment and, other transactions.if they are approved, support the commercial introduction of our products.  Failure to secure the necessary additional capital would have a material adverse effect on our business, financial condition and results of operations.  Even if we succeed in raising additional capital and developing and subsequently commercializing product candidates, we may never achieve sufficient sales revenue to achieve or maintain profitability.

Cash Flows

As of September 30, 2013,March 31, 2014, we had cash and cash equivalents of $21.2$75.9 million compared to $26.9$86.3 million as of December 31, 2012.2013.  Cash outflows before financingsfinancing activities for the ninethree months ended September 30, 2013March 31, 2014 consisted of $30.4$10.3 million used for ongoing operating activities and $0.2$0.5 million for purchases of property and equipment.  Cash outflows before financingsprovided by financing activities were offset by a $10 million ($9.9 million net of expenses) advance in February 2013 under the Deerfield Facility and $15.1$0.4 million of net proceeds from a registered public offering that we completed in May 2013.the exercise of warrants and stock options.

Operating Activities

Net cash used in operating activities for the three months ended March 31, 2014 and 2013 was $30.4$10.3 million and $23.8$10.2 million, for the nine months ended September 30, 2013 and 2012, respectively.

Net cash used in operating activities is thea result of our net losslosses for the period, adjusted for non-cash items associated with the change in fair value of common stock warrants (income of $1.6 million in 2013 and expense of $5.1 million in 2012), stock-based compensation, including our 401(k) match, and depreciation and amortization expenses ($2.9 million in 2013 and $2.7 million in 2012); and changes in working capital.

The increase in net cash used in operating activities from 2012 to 2013 is primarily due to (i) investment in our own specialty commercial and medical affairs organizations that are specialized in neonatal/pediatric respiratory critical care in NICUs/PICUs across the U.S., and manufacturing and quality activities in preparation for the commercial introduction of SURFAXIN and the AFECTAIR device for infants; (ii) costs to develop and manufacture clinic-ready CAGs for use in our planned AEROSURF phase 2a clinical study, including work with third party device experts and work that we began in June 2012 with Battelle, which is assisting with design, testing, and manufacture of clinic-ready CAG devices; and (iii) purchases of APIs used in the production of SURFAXIN and our lyophilized KL4 surfactant, for commercial purposes, development activities, including preparation of our CAG for use in our anticipated AEROSURF phase 2 clinicalprogram, and to support the technical transfer of our manufacturing processes to our CMO.

Investing Activities

Net cash used in investing activities for the three months ended March 31, 2014 and 2013 represents capital expenditures of $0.2$0.5 million and $0.6$0.1 million, for the nine months ended September 30, 2013 and 2012, respectively.  The increase in capital expenditures is due to timing of routine equipment purchases.

Financing Activities

Net cash provided by financing activities for the three months ended March 31, 2014 and 2013 was $24.9$0.4 million and $50.3$9.9 million, respectively.   Net cash provided by financing activities for the ninethree months ended September 30,March 31, 2014 represents proceeds from the exercise of warrants and stock options.  Net cash provided by financing activities for the three months ended March 31, 2013 and 2012, respectively, summarized as follows:represents the first advance of $10.0 million ($9.9 million, net) under the Deerfield Loan upon execution of the agreement in February 2013.
(in thousands) Nine Months Ended
September 30,
 
 
 2013  2012 
 
    
Financings pursuant to common stock offerings $15,114  $42,145 
Issuance of long-term debt, net of expenses  9,850    
Financings under the ATM Program     1,460 
Repayment of equipment loans and capital lease obligations  (56)  (57)
Exercise of stock options and warrants  1   6,741 
Cash flows from financing activities, net $24,909  $50,289 

The following sections provide a more detailed discussion of our available financing facilities.

Common Stock Offerings

Historically, we have funded, and expect that we will continue to fund, our business operations through various sources, including financings in the form of common stock offerings.  In June 2011, we filed a universal shelf registration statement on Form S-3 (No.  333-174786) (2011 Universal Shelf) with the SEC for the proposed offering from time to time of up to $200 million of our securities, including common stock, preferred stock, varying forms of debt and warrant securities, or any combination of the foregoing, on terms and conditions that will be determined at that time.  The 2011 Universal Shelf replaced an earlier shelf registration statement that was declared effective by the SEC on June 21, 2008.  As of September 30, 2013,March 31, 2014, after reserves for unexercised warrants and amounts remaining under our ATM Program, approximately $68.5$11.0 million remained available under the 2011 Universal Shelf.  As of November 8, 2013, following the financings under our ATM Program and our public offering and establishment of a reserve related to the anticipated issuance of shares in connection with the underwriters’ exercise of the over-allotment, we had approximately $11 million available under theThe 2011 Universal Shelf.Shelf will expire in June 2014.

Registered Public OfferingsAt-the-Market Program (ATM Program)

On May 15, 2013, we completed a registered public offering of 9.5 million shares of our common stock, at a price of $1.50 per share resulting in gross proceeds of $14.3 million ($13.2 million net).  We also granted the underwriter a 30-day option to purchase up to an additional 1.425 million shares of common stock at an offering price of $1.50 per share.  On May 31, 2013, the underwriter exercised its option and purchased 1.347 million additional shares of common stock for net proceeds to us (after underwriter fees) of $1.9 million.  In connection with this offering, we agreed not to issue or sell (with certain limited exceptions) securities for a period of 90 days after the date of the prospectus supplement ending August 8, 2013.  Regarding our ATM Program, we agreed not to issue or sell securities for a period of 30 days after the date of the underwriting agreement ending on June 9, 2013.

On November 5, 2013, we completed a registered public offering of 25 million shares of our common stock, at a price of $2.00 per share resulting in gross proceeds of $50.0 million ($46.8 million net after commissions, discounts and expenses).  In addition, we also granted the underwriters a 30-day option to purchase up to an additional 3.75 million shares of our common stock at a public offering price of $2.00 per share.  In connection with this offering, we agreed not to issue or sell (with certain limited exceptions) securities for a period of 90 days after the date of the prospectus supplement ending February 3, 2014.  Regarding our ATM Program, we agreed not to issue or sell securities for a period of 30 days after the date of the underwriting agreement ending on December 5, 2013.  On November 8, 2013, we received notification that the underwriters have exercised the full over-allotment and will purchase an additional 3.75 million shares.  This transaction is expected to close on or about November 14, 2013 and result in additional net proceeds to us of approximately $7.1 million.

At-the-Market Program

In February 2013, we entered into an At-the-Market Equity Offering Sales Agreement with Stifel, under which Stifel, as our exclusive agent, at our discretion and at such times that we may determine from time to time, may sell up to a maximum of $25 million of our common stock over a three-year period.  We are not required to sell any shares at any time during the term of the ATM Program.  We have agreed to pay Stifel a commission of 3% of gross proceeds of any sales of shares.  See, Note 17, “Subsequent Events11, “Stockholders’ Equity – ATM Program,” to the consolidated financial statements in our 20122013 Form 10-K.

On October 15, 2013, we completed an offering under our ATM Program and issued 713,920 shares of our common stock for an aggregate purchase price of approximately $2.0 million, resulting in net proceeds to us of approximately $1.9 million, after deducting commissions due to Stifel.  As of November 8, 2013,March 31, 2014, approximately $23 million shares of common stock remained available under the ATM Program.

Committed Equity Financing Facility (CEFF)

We had a Stock Purchase Agreement dated June 11, 2010 (CEFF) with Kingsbridge Capital Limited (Kingsbridge) that provided initially for the purchase by Kingsbridge of the lesser of up to 2.1 million shares of our common stock or a maximum of $35 million in shares.  We were not obligated to issue shares at any time.  This CEFF expired on June 11, 2013 with 1.1 million shares available but not issued.  See, “2012 Form 10-K – Item 7 – Management’s Discussion and Analysis of Financial Condition and Results of Operations – Liquidity and Capital Resources – Committed Equity Financing Facility (CEFF).”

Loan Facility with Deerfield

On February 13, 2013, we entered into a secured loan facility (Deerfield Facility) with affiliates of Deerfield Management Company, L.P. (Deerfield) for up to $30 million in secured financing in 2013.  Deerfield advanced to us $10 million upon execution of the agreement and agreed to advance an additional $20 million, subject to certain conditions, on or about the date of the first commercial sale of SURFAXIN drug product (Milestone Date), if the Milestone Date occurs on or before December 31, 2013.  On November 8 2013, we notified Deerfield that the first commercial sale of SURFAXIN has occurred, and anticipate receipt of the $20 million advance on or about December 3, 2013.

The loan may be prepaid in whole or in part without penalty at any time.  Any amounts received and outstanding under the Deerfield Facility will accrue interest at a rate of 8.75%, payable quarterly in cash.  See, “– Note 6, Long-term Debt – Loan Facility with Deerfield,” to the Consolidated Financial Statements (unaudited) in this Quarterly Report on Form 10‑Q, for a description of the terms and conditions of the Deerfield Facility agreement and terms of the Deerfield Warrants.

We have recorded the loan as long-term debt at its face value of $10.0 million less debt discounts and issuance costs consisting of (i) $3.8 million fair value of warrants that we issued to Deerfield in connection with the $10 million initial advance, to purchase approximately 2.3 million shares at an exercise price of $2.81, and (ii) a $150,000 transaction fee.  The discount is being accreted to the $10 million loan over its term using the effective interest method.  The Deerfield Warrants are derivatives that qualify for an exemption from liability accounting as provided for in ASC 815 and are classified as equity.

Long-term debt as of September 30, 2013 consists solely of amounts due under the Deerfield Facility as follows:

Note Payable $10,000 
Unamortized discount  (3,674)
Long-term debt, net of discount $6,326 

Contractual Obligations and Commitments

Future payments due under contractual obligations at September 30, 2013 are as follows:

(in thousands) 2013  2014  2015  2016  2017  
There-
after
  Total 
Operating lease obligations $272  $1,087  $1,024  $934  $935  $158  $4,410 
Deerfield Loan Facility(1)
              3,330   6,670   10,000 
Equipment loan obligations  13   79   69            161 
Total $285  $1,166  $1,093  $934  $4,265  $6,828  $14,571 

(1)  See, “– Loan Facility with Deerfield”
ITEM 3.
QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Our exposure to market risk is confined to our cash and cash equivalents.  We place our investments with high quality issuers and, by policy, we have limits as to the amount of credit exposure to any one issuer.  We do not hedge interest rate or currency exchange exposure and do not use derivative financial instruments for speculation or trading purposes.  We classify highly liquid investments purchased with a maturity of three months or less as “cash equivalents.”  Loans under our Deerfield Facility have a fixed interest rate of 8.75%.  Because of the fixed rate, a change in market interest rates would not have a material impact on interest expense associated with the loan.Not applicable.

ITEM 4.
CONTROLS AND PROCEDURES

Evaluation of disclosure controls and procedures

Our management, including our President and Chief Executive Officer (principal executive officer) and our Chief Financial Officer (principal executive officer and financial officer), does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent all error and all fraud.  Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, have been detected.  These inherent limitations include the realities that judgments in decision-making can be faulty and that breakdowns can occur because of simple error or mistake.  Controls can also be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the controls.  The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions.  Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures.  Because of the inherent limitations in a cost-effective control system, misstatements due to error or fraud may occur and not be detected.  In designing and evaluating the disclosure controls and procedures, our management recognized that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives and our management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Our President and Chief Executive Officer and our Chief Financial Officer hashave evaluated the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Rule 13a-15(e) and Rule 15d-15(e) of the Exchange Act) as of the end of the period covered by this Quarterly Report on Form 10-Q.  Based on this evaluation, our President and Chief Executive Officer and our Chief Financial Officer concluded that, as of the end of the period covered by this report, our disclosure controls and procedures were effective to ensure that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is accumulated and communicated to our management, including our President and Chief Executive Officer and our Chief Financial Officer, to allow for timely decisions regarding required disclosures, and recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms.

Changes in internal controls

There were no changes in our internal controlscontrol over financial reporting identified in connection with the evaluation required by Rule 13a-15(d) under the Exchange Actdescribed above that occurred during the quarter ended September 30, 2013,March 31, 2014 that havehas materially affected, or areis reasonably likely to materially affect, our internal control over financial reporting.
PART II – OTHER INFORMATION

ITEM 1.
ITEM 1.
LEGAL PROCEEDINGS

We are not aware of any pending or threatened legal actions that would, if determined adversely to us, have a material adverse effect on our business and operations.

We have from time to time been involved in disputes and proceedings arising in the ordinary course of business, including in connection with the conduct of our clinical trials.  In addition, as a public company, we are also potentially susceptible to litigation, such as claims asserting violations of securities laws.  Any such claims, with or without merit, if not resolved, could be time-consuming and result in costly litigation.  There can be no assurance that an adverse result in any future proceeding would not have a potentially material adverse effect on our business, results of operations and financial condition.

ITEM 1A.
RISK FACTORS

Investing in our securities involves risks. In addition to the other information in this Quarterly Report on Form 10-Q, stockholdersStockholders and potential investors should carefully consider the risks and uncertainties discussed in the section "Item 1A. Risk Factors" in our 20122013 Form 10-K, as supplemented by the risks and uncertainties discussed below and elsewhere in this Quarterly Report on Form 10-Q. The risks and uncertainties discussed in this Quarterly Report on Form 10-Q and described in our 2013 Form 10-K are not the only ones that may materialize. Additional risks and uncertainties not presently known to us or that we currently consider immaterial may also impair our business operations. If any of the risks and uncertainties set forth belowdiscussed in this Quarterly Report on Form 10-Q or in our 20122013 Form 10-K actually materialize, our business, financial condition and/or results of operations could be materially adversely affected, the trading price of our common stock could decline and a stockholder could lose all or part of his or her investment.  The risks and uncertainties set forth below and discussed elsewhere in this Quarterly Report on Form 10-Q and described in our 2012 Form 10‑K are not the only ones that may materialize.  Additional risks and uncertainties not presently known to us or that we currently consider immaterial may also impair our business operations.

Even if we succeed with the commercial introduction of SURFAXIN® as planned, we nevertheless in the future will require, but may be unable to secure when needed, significant additional capital to continue our operations, pay our debt service, and commercialize our approved products and develop our products under development, including our AEROSURF® phase 2 clinical program, and to continue our other research and development programs.  Moreover, any financings could result in substantial dilution to our stockholders, cause our stock price to fall and adversely affect our ability to raise capital.

Our operations have consumed substantial amounts of cash since inception.  As of September 30, 2013, we have an accumulated deficit of approximately $468.2 million and we expect to continue to incur significant, increasing operating losses over the next several years.  As of September 30, 2013, we had cash and cash equivalents of approximately $21.2 million and approximately $6.6 million of accounts payable and accrued expenses and $10 million of long-term debt under the Deerfield Facility.  In October, we completed an offering under our ATM Program that resulted in net proceeds to us of approximately $1.9 million.  On November 5, 2013, we completed a public offering that resulted in net proceeds to us of approximately $46.8 million and granted the underwriters an option to purchase an additional 3.75 million shares (the over-allotment).  The over-allotment was exercised in full and, on or about November 14, 2013, we anticipate receipt of an additional approximately $7.1 million.  On November 8, 2013, we announced that we have initiated the commercial launch of SURFAXIN and notified Deerfield that we had met the requirements to receive the additional $20 million available under the Deerfield Facility.  Before any additional financings, including under our ATM Program and taking into account the expected $20 million advance under the Deerfield Facility and the $7.1 million expected in connection with the over-allotment, we anticipate that we will have sufficient cash available to support our operations and debt service obligations through 2015.

We expect to continue to spend substantial amounts to execute our business strategy and will require significant additional infusions of capital until such time as the net revenues from SURFAXIN and, if approved, AEROSURF, and from potential strategic alliance and collaboration arrangements and other sources, are sufficient to offset our cash flow requirements.  Given the time required to secure formulary acceptance of SURFAXIN, we expect our revenues from SURFAXIN to be modest in the first 12-18 months and then increase over time.  Our investments in our operations, debt service and development programs are expected to outpace the rate at which we may generate revenues for several years.  See, “Part 1, Item 2 – Management’s Discussion and Analysis of Financial Condition and Results of Operations – Liquidity and Capital Resources.”
 
We cannot be certain that additional funding will be available on acceptable terms, or at all.  If we are unable to raise additional capital in sufficient amounts or on terms acceptable to us, we may have to significantly delay, scale back or discontinue the development or commercialization of our products or our research and development programs.  We also could be required to:
seek collaborators for one or more of our development programs for territories that we had planned to retain or on terms that are less favorable than might otherwise be available; and/or
relinquish or license on unfavorable terms our rights to technologies or product candidates that we otherwise would seek to develop or commercialize ourselves.

If we are unable to secure such financing, we may seek additional capital from the public markets, which could have a dilutive impact on our stockholders and the issuance, or even potential issuance, of shares could have a negative effect on the market price of our common stock.

Depending on conditions in the global financial markets, we may face significant challenges accessing the capital markets at a time when we would like or require, and at an increased cost of capital.  Except for our ATM Program, we do not have arrangements to obtain additional financing.  Any such financing could be difficult to obtain or only available on unattractive terms and could result in significant dilution of stockholders’ interests.  In any such event, the market price of our common stock may decline.  In addition, failure to secure any necessary financing in a timely manner and on favorable terms could have a material adverse effect on our business plan, financial performance and stock price and could delay new product development and clinical trial plans.

Our near-term prospects are highly dependent on the success of SURFAXIN.  To the extent we fail to successfully commercialize SURFAXIN, or if our efforts to commercialize SURFAXIN are significantly delayed, our business, financial condition and results of operations would be materially adversely affected and the price of our common stock would likely decline.

In March 2012, the FDA approved SURFAXIN.  Following a period in which we updated product specifications and improved an analytical chemistry method, in October 2013, we received a communication from the FDA that it agreed with our updates.  We immediately manufactured SURFAXIN drug product and have initiated the commercial introduction of SURFAXIN in our target hospitals.  We believe that SURFAXIN product sales may constitute substantially all or most of our total revenue over the next several years.

We currently believe that we will successfully execute the commercial introduction of SURFAXIN within our anticipated timeframe.  However, our efforts are subject to a variety of risks and uncertainties that could cause actual results to be materially different.

If we successfully make our products commercially available, the commercial success of SURFAXIN and our ability to generate and increase revenues will depend on a number of factors, including the following:
the number of hospitals and critical care centers that agree to place SURFAXIN drug product on their formulary lists and the length of time required to achieve broad formulary acceptance;
the willingness of the target hospitals to accept and employ WARMING CRADLE® dry-block heater;
the effectiveness of our marketing, sales and medical affairs organizations and their ability to (a) accurately describe SURFAXIN consistent with its approved labeling, and (b) educate and provide critical care providers and hospitals with medical and scientific education and information concerning our products;
our ability to gain access to the entire market with our commercial organizations;
the safety and efficacy of SURFAXIN, our ability to provide hospitals acceptable evidence of the safety and efficacy of SURFAXIN, and the perceived advantages of SURFAXIN over alternative treatment methods;
the pharmacoeconomic benefits (which are determined by comparing, among other things, the cost and effects of a product when compared to different treatment options) and cost-effectiveness of our products;
the budget impact of adding our products and devices to relevant formulary and medical device hospital lists and the availability, cost and potential advantages of alternative treatments, including less expensive generic drugs and other competitive products;
the availability of different size drug vials and medical devices to meet the specific needs of healthcare practitioners;
the claims, limitations, warnings and other information that appear in the package insert and labeling of SURFAXIN drug product;
the willingness of third-party payers, including government payers, to provide coverage and reimbursements to patients, physicians and other providers who wish to prescribe and use our products;
our ability to secure and maintain regulatory marketing approvals from the U.S. and foreign regulatory authorities;
the rate of preterm births;
the number of infants who are diagnosed with RDS and the number treated with SURFAXIN;
the growth of commercial sales;
our ability to meet commercial demand for SURFAXIN, including through maintenance of commercial supplies of our active drug substances and other excipients, and manufacturing capabilities, by ourselves and through third-party manufacturers; and commercial inventory supplies of our medical device products; and
the sufficiency of coverage or reimbursement by third parties.

Our efforts to achieve formulary acceptance of SURFAXIN, and to educate the medical community and third-party payers regarding the benefits of SURFAXIN will require significant, focused and competent resources and we may not be successful in achieving our objectives.  SURFAXIN is approved for marketing only in the U.S.  We cannot predict whether physicians, healthcare insurers or maintenance organizations, or the medical community in general, will accept or utilize SURFAXIN and our other products and devices, if approved.  If we are not successful in our efforts to gain broad acceptance of SURFAXIN in our target hospitals, the revenues we generate from sales will be limited and our business may not be profitable.

Our clinical development program for AEROSURF involves significant risks and uncertainties that are inherent in the clinical development and regulatory approval processes.  Our clinical trials may be delayed, or fail, which will harm our business.

The FDA has completed its review and cleared our IND for our AEROSURF® phase 2 clinical program. This initial clinical study is the first in a series of clinical studies that will be needed to gain marketing authorization for AEROSURF.  Such clinical programs generally take two to five years or more to complete and may be delayed by a number of factors.  We may not reach agreement with the FDA or a foreign regulator on the design of any one or more of the clinical studies necessary for approval, or we may be unable to reach agreement on a single study design that would permit us to conduct a single clinical program.  Conditions imposed by the FDA and foreign regulators on our clinical studies could significantly increase the time required for completion of such clinical studies and the costs of conducting the clinical studies.  For example, we may not be successful in achieving a study design that is acceptable to the FDA and regulators in other countries, which would cause us to greatly increase our investment or limit the scope of our activities.  Like many biotechnology companies, even after obtaining promising results in earlier studies or in preliminary findings for such clinical studies, we may suffer significant setbacks in late-stage clinical studies. Data obtained from clinical studies are susceptible to varying interpretations that may delay, limit or prevent regulatory approval.  In addition, we may be unable to enroll patients quickly enough to meet our expectations for completing any or all of these studies.  The timing and completion of current and planned clinical studies of our product candidates depend on many factors, including the rate at which patients are enrolled.  Delays in patient enrollment in clinical studies may occur, which would be likely to result in increased costs, program delays, or both.

Patient enrollment is a function of many factors, including:
the number of clinical sites;
the size of the patient population;
the eligibility and enrollment criteria for the study;
the willingness of patients’ parents or guardians to participate in the clinical trial;
the existence of competing clinical studies;
the existence of alternative available products; and
geographical and geopolitical considerations.

If we succeed in achieving our patient enrollment targets, patients that enroll in our clinical studies could suffer adverse medical events or side effects that are known, such as a decrease in the oxygen level of the blood upon administration, or currently unknown to us.  It is also possible that we, our AEROSURF Clinical Trial (ACT) Steering Committee, the Safety Review Committee (SRC), or the FDA could interrupt, delay or halt any one or more of our clinical studies for any of our product candidates.  If our ACT Steering Committee, the SRC, any regulator or we believe that study participants face unacceptable health risks, any one or more of our studies could be suspended or terminated.  In addition, clinical studies may be interrupted, delayed or halted, in whole or in part, for reasons other than health and safety concerns, including, among other things, matters related to the design of the study, drug availability, ACT Steering Committee and/or SRC recommendation, or business reasons.

In addition to our planned clinical programs to support AEROSURF, in the future, we also may initiate or support clinical studies evaluating other KL4 surfactant pipeline products.  All of these clinical studies will be time-consuming and potentially costly.  Should we fail to complete our clinical development programs or should such programs yield unacceptable results, such failures would have a material adverse effect on our business.

Our manufacturing strategy includes relying, at least in part in the future, on third parties to manufacture our current approved products as well as certain of our drug product candidates and medical devices, which exposes us to risks that may affect our ability to maintain supplies of our commercial products and/or delay our research and development activities, regulatory approval and commercialization of our drug product candidates.

We currently manufacture our SURFAXIN liquid instillate at our operations located in Totowa, New Jersey.  Our strategy includes potentially manufacturing SURFAXIN drug product in the future and our lyophilized dosage form of our KL4 surfactant, as well as our CAG and AFECTAIR devices, using third-party contract manufacturing organizations (CMOs).  Our planned future reliance on CMOs exposes us, among other things, to the following risks:
we may be unable to successfully identify manufacturers with whom we might establish appropriate arrangements on acceptable terms, if at all, because the number of potential manufacturers is limited and the FDA must approve any replacement CMO.  This approval could take as long as a year and would require new testing and compliance inspections as well as a potentially lengthy qualification process;
CMOs might be unable to manufacture our products in the volume and to our specifications to meet our commercial and clinical needs, or we may have difficulty scheduling the production of drug product and devices in a timely manner to meet our timing requirements;
CMOs may not perform as agreed, or may not remain in the CMO business for a lengthy time, or may refuse to renew an expiring agreement as expected, or may fail to product a sufficient supply to meet our commercial and/or clinical needs;
CMOs are subject to ongoing periodic unannounced inspection by the FDA, the Drug Enforcement Administration, and corresponding state agencies to ensure strict compliance with cGMP and/or quality system regulations (QSR) and other government regulations and corresponding foreign standards.  We do not have control over CMO’s compliance with these regulations and standards;
moreover, if we desire to make our drug products and/or devices available outside the U.S. for commercial or clinical purposes, our CMOs would become subject to, and may not be able to comply with, corresponding manufacturing and quality system regulations of the various foreign regulators having jurisdiction over our activities abroad.  Such failures could restrict our ability to execute our business strategies;
if any third-party manufacturer makes improvements in the manufacturing process for our products, we may not have rights to, or may have to share, the intellectual property rights to any such innovation.  We may be required to pay fees or other costs for access to such improvements; and
each of these risks could delay our commercial manufacturing plans and our development programs, the approval, if any, of our product candidates by the FDA or result in higher costs or deprive us of potential product revenues.

We depend upon key employees and consultants in a competitive market for skilled personnel.  If we are unable to attract and retain key personnel, it could adversely affect our ability to develop and market our products.

As we prepared for the commercial introduction of SURFAXIN, we implemented a plan to hire additional qualified personnel to support (i) the commercial introduction of SURFAXIN and AFECTAIR, and (ii) the advancement of our AEROSURF and SURFAXIN LS development programs.  In particular, we established our field-based sales and marketing and medical affairs organizations, and continue to invest in our regulatory affairs, quality control and assurance and administrative capabilities.  We compete for qualified individuals with numerous biopharmaceutical companies, universities and other research institutions.  Competition for such individuals is significant and attracting and retaining qualified personnel will be critical to our success, and any failure to do so successfully may have a material adverse effect on us.

We are highly dependent upon the members of our executive management team and our directors, as well as our scientific advisory board members, consultants and collaborating scientists.  Many of these individuals have been involved with us for many years, have played integral roles in our progress and we believe that they continue to provide value to us.  A loss of any of our key personnel may have a material adverse effect on aspects of our business and clinical development and regulatory programs.

In March 2013, we entered into employment agreements with five executive officers, including the President and Chief Executive Officer and Chief Financial Officer; the Senior Vice President and Chief Operating Officer; the Senior Vice President, General Counsel and Corporate Secretary; the Senior Vice President, Human Resources; and the Senior Vice President, Research and Development.  These agreements expire on March 31, 2015, subject to automatic renewal for additional one-year periods, unless a party provides notice of non-renewal at least 90 days in advance.  In addition, we recently entered into new agreements with five other officers that also expire on March 31, 2015.  The loss of services from any of our executives could significantly adversely affect our ability to develop and market our products and obtain necessary regulatory approvals.  Further, we do not maintain key man life insurance.

As we prepare for the commercial introduction of our approved products and to initiate our AEROSURF phase 2 clinical program, we need to attract and retain highly-qualified personnel to join our management, commercial, medical affairs and development teams, although there can be no assurances that we will be successful in that endeavor.  We may be unable to attract and retain necessary executive talent.

Our future success also will depend in part on the continued service of our key scientific and management personnel and our ability to identify, hire and retain additional personnel.  While we attempt to provide competitive compensation packages to attract and retain key personnel at all levels in our organization, many of our competitors have greater resources and more experience than we do, making it difficult for us to compete successfully for key personnel.  We may experience intense competition for qualified personnel and the existence of non-competition agreements between prospective employees and their former employers may prevent us from hiring those individuals or subject us to lawsuits brought by their former employers.

ITEM 2.UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

During the ninethree months ended September 30, 2013,March 31, 2014, we issued an aggregate of 23,7508,750 unregistered shares of common stock to a consultant as compensation for management consulting services rendered during 2013.  The shares were issued as follows: 7,500 shares on each of February 28, 2013, and May 31, 2013, and 8,750 shares on August 31, 2013.2014.  The shares were issued in reliance upon the exemption from securities registration provided by Section 4(2) of the Act.

ITEM 6.
EXHIBITS

Exhibits are listed on the Index to Exhibits at the end of this Quarterly Report.  The exhibits required by Item 601 of Regulation S-K, listed on such Index in response to this Item, are incorporated herein by reference.
SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.
 
 
Discovery Laboratories, Inc.
(Registrant)
(Registrant)
 
 
 
Date: NovemberMay 12, 2013
2014
By:
/s/ John G. Cooper
John G. Cooper
President and Chief Executive Officer
 
 
Date: May 12, 2014By:/s/ John G. CooperTattory
 
 
President and Chief Executive Officer and Chief Financial Officer
John Tattory
 
 
(Principal Executive andChief Financial Officer)Officer
INDEX TO EXHIBITS

The following exhibits are included with this Quarterly Report on Form 10-Q.

Exhibit No.
Description
Method of Filing
 
 
 
3.1Amended and Restated Certificate of Incorporation of Discovery Laboratories, Inc. (Discovery) filed as of August 1, 2013, including amendments reflected in a Certificate of Amendment to the Restated Certificate of Incorporation of Discovery filed on December 27, 2010, and in a Certificate of Amendment to the Restated Certificate of Incorporation of Discovery filed on October 3, 2011Incorporated by reference to Exhibit 3.1 to Discovery’s Quarterly Report on Form 10-Q, for the quarter ended June 30, 2013, as filed with the SEC on August 8, 2013.
 
 
 
3.2Certificate of Designations, Preferences and Rights of Series A Junior Participating Cumulative Preferred Stock of Discovery, dated February 6, 2004Incorporated by reference to Exhibit 2.2 to Discovery’s Form 8-A, as filed with the SEC on February 6, 2004.
 
 
 
3.3Amended and Restated By-Laws of Discovery, as amended effective September 3, 2009Incorporated by reference to Exhibit 3.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on September 4, 2009.
 
 
 
4.1Shareholder Rights Agreement, dated as of February 6, 2004, by and between Discovery and Continental Stock Transfer & Trust CompanyIncorporated by reference to Exhibit 10.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on February 6, 2004.
 
 
 
4.2Warrant Agreement dated May 22, 2008 by and between Kingsbridge Capital Limited and DiscoveryIncorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K as filed with the SEC on May 28, 2008.
4.3Warrant Agreement dated December 12, 2008 by and between Kingsbridge Capital Limited and DiscoveryIncorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on December 15, 2008.
 
 
 
4.44.3Form of StockWarrant to Purchase WarrantCommon Stock issued in May 2009Incorporated by reference to Exhibit 10.3 to Discovery’s Current Report on Form 8-K, as filed with the SEC on May 8, 2009.
 
 
 
4.54.4Form of StockWarrant to Purchase WarrantCommon Stock issued in February 2010Incorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on February 18, 2010.
 
 
 
4.64.5Warrant Agreement, dated as of April 30, 2010, by and between Discovery and PharmaBioIncorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on April 28, 2010.
 
 
 
4.74.6Warrant Agreement dated June 11, 2010 by and between Kingsbridge Capital Limited and DiscoveryIncorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on June 14, 2010.
Exhibit No.
Description
Method of Filing
 
 
 
4.84.7Form of Series I Warrant to Purchase Common Stock issued on June 22, 2010 (Five-Year Warrant)Incorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on June 17, 2010.

Exhibit No.
Description
Method of Filing
4.9
4.8Warrant Agreement, dated as of October 12, 2010, by and between Discovery and PharmaBio
Incorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on October 13, 2010.
 
 
 
4.104.9Form of Series I Warrant to Purchase Common Stock issued on February 22, 2011 (Five-Year Warrant)Incorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K, as filed with the SEC on February 16, 2011.
 
 
 
4.11Form of Series II Warrant to Purchase Common Stock issued on February 22, 2011Incorporated by reference to Exhibit 4.2 to Discovery’s Current Report on Form 8-K, as filed with the SEC on February 16, 2011.
4.12+4.10+Form of Warrant dated February 13, 2013, issued to affiliates of Deerfield Private Design Fund II, L.P.Management Co., Deerfield Private Design International II, L.P., Deerfield Special Situations Fund, L.P. and Deerfield Special Situations International Master Fund, L.P. (collectively, Deerfield)LLP (Deerfield) under a Facility Agreement dated as of February 13, 20132012 between Discovery and Deerfield (Deerfield Facility)Incorporated by reference to Exhibit 4.1 to Discovery’s Current Report on Form 8-K/A,8-K, as filed with the SEC on March 15,June 14, 2013.
 
 
 
4.134.11+Form of NotesWarrant dated December 3, 2013, issued to affiliates of Deerfield evidencing loanManagement Co., LLP (Deerfield) on December 3, 2013 under a Facility Agreement dated as of February 13, 2012 between Discovery and Deerfield FacilityIncorporated by reference to Exhibit 4.24.1 to Discovery’s Current Report on Form 8-K/A,8-K, as filed with the SEC on March 15, 2013.
10.1Extension, dated as of July 16, 2013, of Lease dated as of December 3, 2004, between Discovery, as successor-in-interest to Laureate Pharma, Inc. (Tenant), and Norwell Land Company (“Landlord”), with respect to property at 710 Union Blvd., Totowa, NJ 07512Incorporated by reference to Exhibit 10.1 to Discovery’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2013, as filed with the SEC on August 8, 2013.
10.2+Pharmaceutical Manufacturing and Supply Agreement dated August 7, 2013 between Discovery and DSM Pharmaceuticals, Inc. (DSM)Incorporated by reference to Exhibit 10.2 to Discovery’s Quarterly Report on Form 10-Q for the quarter ended June 30, 2013, as filed with the SEC on August 8,6, 2013.
 
 
 
Master ServicesEmployment Agreement dated October 24, 2013as of March 21, 2014 between Discovery and DSMJohn TattoryFiled herewith.
 
 
 
Certification of Chief Executive Officer andpursuant to Rule 13a-14(a) of the Exchange ActFiled herewith.
Certification of Chief Financial Officer pursuant to Rule 13a-14(a) of the Exchange ActFiled herewith.
 
 
 
Certification of Chief Executive Officer and Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002Filed herewith.
Exhibit No.
Description
Method of Filing
 
 
 
101.1The following consolidated financial statements from the Discovery Laboratories, Inc. QuarterlyAnnual Report on Form 10-Q for the quarter ended September 30, 2013,March 31, 2014, formatted in Extensive Business Reporting Language (“XBRL”): (i) Balance Sheets as of September 30, 2013March 31, 2014 (unaudited) and December 31, 2012,2013, (ii) Statements of Operations (unaudited) for the three and nine months ended September 30,March 31, 2014 and March 31, 2013, and September 30, 2012, (iii) Statements of Cash Flows (unaudited) for the ninethree months ended September 30,March 31, 2014 and March 31, 2013, and September 30, 2012, and (v) Notes to consolidated financial statements.
 
Exhibit No.
Description
Method of Filing
101.INSInstance DocumentFiled herewith.
 
 
 
101.SCHXBRL Taxonomy Extension Schema DocumentFiled herewith.
 
 
 
101.CALXBRL Taxonomy Extension Calculation Linkbase DocumentFiled herewith.
 
 
 
101.DEFXBRL Taxonomy Extension Definition Linkbase DocumentFiled herewith.
 
 
 
101.LABXBRL Taxonomy Extension Label Linkbase DocumentFiled herewith.
 
 
 
101.PREXBRL Taxonomy Extension Presentation Linkbase DocumentFiled herewith.
 
+Confidential treatment requested as to certain portions of these exhibits.  Such portions have been redacted and filed separately with the Commission.

*A management contract or compensatory plan or arrangement required to be filed as an exhibit to this quarterly report pursuant to Item 6 of Form 10-Q.Confidential treatment requested as to certain portions of this exhibit.  Such portions have been redacted and filed separately with the Commission.
 
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