Shan Lu, Ph.D. - US grants

DNA vaccination is a novel approach to immunization and offers new hope for the development of a vaccine against human immunodeficiency virus-1 (HIV-1). HIV-1 DNA vaccines use direct inoculation of DNA plasmids to express HIV-1 antigens in vivo and to raise immune responses. We propose studies focusing on the immunogenicity of HIV-1 DNA vaccines. Preliminary studies with DNA vaccines expressing envelope (Env) protein of HIV-1 in vivo demonstrated that different forms of Env (gp120, gp140 or full- length gp160) had different levels of immunogenicity as determined by their ability to raise anti-Env antibody responses. The full-length Env was the least immunogenic. New strategies aimed at raising high neutralizing antibody responses against this form of Env will provide fundamental information useful for the ultimate development of effective HIV-1 vaccines. With the ability to express antigens in vivo and to preserve their native conformation, DNA vaccination is an ideal candidate for this task. We propose to study the immunological mechanisms which determine the types and levels of anti-Env antibody responses by using newly improved and existing HIV-1 DNA vaccines. The isotype and affinity profile of serum antibody responses will be measured. The trafficking of Env-specific, antibody forming cells will be analyzed. The levels of specific cytokine-secreting cells will be assayed following immunizations to determine the nature of the elicited immune responses. More importantly, we propose to test the roles of cytokines and adjuvants on Env-specific antibody responses. Finally, co-inoculation of DNA plasmids which express highly immunogenic, non-HIV proteins will be studied to see if they can provide additional T-helper functions to enhance HIV-1 Env- specific antibody responses. The information generated from these studies will not only help us develop a viable DNA vaccine against AIDS but also provide valuable information regarding the critical interactions between HIV-1 and the immune system.

gene targeting; genetic techniques; simian immunodeficiency virus; virus infection mechanism; provirus; disease /disorder model; mucosa; model design /development; vector vaccine; AIDS vaccines; virus DNA; vaccine development; polymerase chain reaction; Macaca;

DESCRIPTION (provided by applicant): The overall objective of this application is to rapidly develop much needed alternative plague vaccine candidate formulations based on our recent discovery that a modified Y. pestis V antigen (LcrV) based DNA vaccine was highly effective in protecting experimental mice against lethal intranasal challenge with Y. pestis. Our preliminary data suggested that good protection resulted from improved antigen presentation and possibly through improved Th1 type immune responses. This is the first time a DNA-based plague vaccine induced complete protection against lethal mucosal challenge in any animal model. We now propose to conduct vigorous validation and testing in the first 18-24 months to develop a subunit plague vaccine formulation using this novel modified V antigen as the core protective component. The protection efficacy of this subunit vaccine, delivered in the forms of DNA, protein, or a combination of both, will be evaluated against lethal Y. pestis challenge via the airway mucosa. Additional immunological studies will be conducted to confirm the improved efficacy of this modified V antigen. We also propose to continue our search for additional protective Y. pestis antigens to be incorporated into the above primary formulation so that a true multi-gene plague vaccine can be developed to achieve broader protection to discourage attempts to engineer vaccine resistant Y. pestis strains. This search will focus primarily on antigens involved in the function of the Y. pestis Type III secretion apparatus including YopB, YopD and YscF. A variety of combination formulations will be tested among these candidates and the modified V antigen to identify the formulation that can provide the most effective protection. This project will employ the most advanced DNA immunization technology in combination with small-scale protein production to quickly develop potential subunit-based plague vaccine products.

vaccine evaluation; immune response; hepatitis G virus; vector vaccine; Callithricidae; hepatitis vaccine; animal colony;

[unreadable] DESCRIPTION (provided by applicant): The goal of this revised R01 application is to further optimize the DNA prime and protein boost approach for the development of improved polyvalent HIV vaccine formulations that can generate broad neutralizing antibodies against targeted HIV-1 viruses. This application is based on our recent results that the DNA prime plus protein boost immunization approach was effective in eliciting neutralizing antibody responses against certain primary HIV isolates across multiple clades from both preclinical animal and early phase human clinical studies. This was achieved when the Env antigens from primary HIV-1 isolates were used in this prime/boost vaccination approach. It is believed that DNA priming contributes to the quality of the final antibody responses while the protein boost leads to a quick production of high level antibody responses. Because DNA immunization has been traditionally used for cell mediated immune responses rather than antibody responses, this unexpected finding will bring novel applications to DNA immunization in eliciting neutralizing antibodies against HIV-1. Therefore our approach has exciting potential in human HIV vaccine development. Aim 1. To further expand the breadth of neutralizing antibodies against additional primary viral isolates especially those resistant to our pilot polyvalent formulations. Aim 2. To develop the next generation DNA prime and protein boost HIV vaccines by using optimized forms of Env antigen designs and optimized immunization schedules. Aim 3. To study the immunological mechanism and the antibody affinity maturation process that may contribute to the efficacy of DNA prime plus protein boost strategy so that more effective polyvalent DNA plus protein vaccines can be developed. The current application combines two important technologies in HIV vaccine development: the DNA prime plus protein boost vaccination approach which has been shown promise in generating neutralizing antibodies against primary HIV-1 isolates and the high throughput neutralization assays with standardized primary viral panels. This will allows us to effectively screen a large number of unique primary Env antigens to formulate the effective polyvalent HIV vaccines for the next phase of clinical testing. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): Elevated androgen receptor (AR) activity and PI3K-Akt signaling are involved in prostate cancer development and progression. The mechanisms responsible for elevation of these two key signaling pathways in prostate cancer, however, have not fully elucidated. We found that Vav3 oncogene, a quanine nucleotide exchange factor (GEF) for Rac/Rho GTPases, is overexpressed in androgen-independent prostate cancer cells and in 32% of human prostate cancer. Further analysis revealed that Vav3 stimulates growth of prostate cancer cells, interacts with AR via the DH domain, and activates AR as a coactivator. Vav3, as a signal transducer, also upregulates PI3K-Akt signaling leading to AR activation. Furthermore, targeted overexpression of Vav3 in the prostate epithelium induces prostatic intraepithelial neoplasia (mPIN) in young adult mice as early as two months old. We hypothesize that overexpression of Vav3 inappropriately activates AR and promotes prostate cancer development and that further elevated Vav3 activity stimulates prostate cancer progression to the androgen-independent status. Three Specific Aims are proposed to test the hypothesis. Specific Aim 1: To determine the role of Vav3 overexpression in prostate cancer development and progression to the androgen-independent status in mouse prostate cancer models. We will investigate whether forced overexpression of Vav3 stimulates androgen-independent growth in prostate tumor and whether targeted overexpression of Vav3 in the prostate epithelium induces prostate cancer development and stimulates progression to the androgen-independent status in transgenic mice. Specific Aim 2: To elucidate the signaling pathways of Vav3 in prostate cancer. We will determine the underlying molecular mechanisms of Vav3 coactivation for AR and Vav3 signaling via the conventional Vav3-Rho-PI3K-Akt pathway leading AR activation in prostate cancer cells. We will also build up the whole Vav3-mediated signaling pathways that connect extracellular stimuli to AR signaling axis as well as cell growth and survival pathway by GST-pull down and Mass Spectrometry-based proteomics analysis. Specific Aim 3: To associate Vav3 overexpression with Gleason score, pathologic stage, PI3K-Akt signaling, and androgen-independent status in human prostate cancers. Once completed, these studies from the preclinical mouse model to the clinical study in human prostate cancer specimens will further our understanding of the mechanisms of prostate cancer development and its androgen-independent growth and provide targets and animal models for the rational development of novel therapies against prostate cancer.

DESCRIPTION (provided by applicant): The overall goal of this application is to develop improved plague vaccines. Our proposal was developed based on our recent progress in plague vaccine studies which includes 1.) the use of a DNA immunization approach to search for additional protective antigens and 2.) the discovery of cell mediated immune responses in the protection of Y. pestis infection. Support for the current proposal will allow us to develop a unique technological platform which can combine antigen discovery, optimization of vaccine formulation, and efficient needle free intradermal delivery of subunit-based multi-gene plague vaccines into one system. Specific Aim 1: To continue our work using DNA immunization as a tool to screen for additional protective antigens against plague, including both the study of individual candidate antigens and the high throughput screening of animal sera which has been immunized with specialized Y. pestis strains deficient for the dominant antigens LcrV and F1. This approach exploits the availability of a newly constructed Y. pestis expression library and protein microarray techniques. Specific Aim 2: To study the cellular immunological mechanisms that are important for improving the protective efficacy of plague vaccines which includes the use of the DNA prime plus protein boost approach to increase the level and longevity of protective antibody responses induced by subunit plague vaccines. Specific Aim 3: To conduct late-phase preclinical immunogenicity and protection studies in non-human primates to prepare for a clinical study with optimized plague vaccine formulation and DNA delivery device that has been proven effective in humans. Plain, lay language summary: This study is designed to produce effective biodefense vaccines against Y. pestis, the highly lethal bacteria that causes plague, an infection that has the potential to cause a high percentage of human fatalities. This study is part of the broad biodefense effort to protect against such agents if they were to be used for bioterrorism purposes.

DESCRIPTION (provided by applicant): The overall objective of this multi-project HIVRAD program application is to elicit neutralizing antibodies that target the CD4 binding site (CD4bs) of primary HIV-1 envelope (Env) glycoproteins. This P01 program proposal consists of three major projects, plus two cores to support the activities of major projects. The following is a summary of major activities as proposed in different Projects/Cores of this program. Goal 1: To organize and manage a highly interactive and productive research team (Core B). Goal 2: To understand how the variation in HIV-1 R5 Envs affect tropism, neutralization and vaccine development (Project 1). HIV-1 R5 envelopes vary extensively in their capacity to infect macrophages. We propose to investigate the impact of variation in macrophage tropism (mac-tropism) on other biological properties associated with Env including neutralization sensitivity. Goal 3: To study how the variation of antigenicity of CD4bs will affect the neutralization sensitivity and immunogenicity of primary Env proteins (Project 2). The CD4bs antigenicity of several panels of primary Envs, each with their own unique biological features, will be probed by mAbs. We will examine whether high CD4bs antigenicity and high sensitivity to CD4bs mAb mediated neutralization will lead to high immunogenicity for key representative Env using the DMA prime-protein boost immunization approach. Goal 4: To study the modification of receptor binding site as an approach to HIV-1 vaccine design (Project 3). We will test whether changes resulting from specific glycan modifications will lead to increased stability or accessibility of conserved epitopes in the receptor binding site and whether greater accessibility of these conserved sites will enhance their function as immunogen to elicit cross-reactive NAb responses. Goal 5: To provide support to major projects on structure analysis of Env and to study the structure of novel antigens, and antigen-antibody interactions (Core A).

The main objectives of Project 2 are to identify primary HIV-1 envelope protein (Env) that have high ability in eliciting antibodies against the CD4 binding site (CD4bs) and, if successful, to further select those Env antigens that can also elicit broad neutralizing activities through the induction of anti-CD4bs antibodies. Aim 1 To Identify variation in the antigenicity of the CD4bs for primary Envs of HIV-1. CD4bs is a key target for eliciting broad neutralizing antibodies (NAbs) against HIV-1, as shown by previous studies that had used mAb b12, and more recently, using sera from HIV infected individuals. Our recent studies have shown that not every HIV primary Env antigen is equally effective in inducing NAb responses. In Aim 1, we will test whether Envs from primary isolates of different backgrounds, phenotypes, and clades may have varying antigenicity for both neutralizing and non-neutralizing CD4bs antibodies. Aim 2 To understand the consequences of CD4bs antigenic variation on the neutralization sensitivity of primary HIV-1 isolates. It is well known that heavy glycosylation and epitope masking play a key role in resistance to neutralization. Beyond these generalizations however, specific determinants of neutralization sensitivity or resistance are difficult to identify due to the complexity of the Env and the often unknown interactions and changes in conformation that occur as a result of trimerization of Env. In Aim 2, we intend to determine if there is a link between CD4bs antigenicity and neutralization sensitivity. Aim 3 To determine the immunogenicity of primary envelopes with varying levels of CD4bs antigencity and to select Env antigens that can elicit anti-CD4bs mediated neutralizing activities. The precise characteristics of a good HIV immunogen have yet to be identified. Previous studies have made a number of attempts to increase the immunogenicity of the HIV Env with limited success. In Aim 3, we will test whether the CD4bs antigenicity may be one, as of yet unidentified, determinant of a good immunogen. Immunogenicity studies will be conducted with the DMA prime-protein boost approach to identify those primary Env antigens that can elicit strong anti-CD4bs antibodies, possibly with broad neutralizing activities as well. RELEVANCE (Seeinstructions): We plan to study the unique structure of HIV outside coat to find a common pattern on the coat that will allow scientists to use them as part of the vaccine components to induce good protective immune responses.

The Administrative Core will be responsible for the overall management of this HIVRAD P01 program according to PAR 06-285. Specific Aim 1 To coordinate overall interactions a) among scientists from the different institutions that are included in the current program and b) between our team and NIH personnel regarding efficient implementation of proposed research plans; Specific Aim 2 To establish and implement milestones for the entire HIVRAD program and each project/core, and to prioritize and coordinate studies to be conducted by subcontractors; Specific Aim 3 To oversee all budgetary matters, including the review and funding of studies to be conducted by subcontractors, to monitor regular expenses and to prepare for various financial reports; Specific Aim 4 Information management: to provide bioinformatics and statistical support, to develop an Intellectual Property plan as needed, and to promote data standardization, and data and resource sharing. RELEVANCE (See instructions): Core B (Administrative Core) will be responsible for the daily operation of this NIH funded HIV Vaccine Research and Development (HIVRAD) Program and will coordinate activitiesto be conducted by individual projects and cores.

DESCRIPTION (provided by applicant): The goal of this U19 application is to further advance the DNA prime/protein boost approach to focus on the development of broadly reactive antibody responses. This proposal is developed based on our recent phase 1 study result that, for the first time, a candidate AIDS vaccine induced both cell-mediated immunity and neutralizing antibody responses against selected primary HIV-1 isolates in the same human clinical trial. It was also the first time that DNA immunization was effective in priming high level antibody responses in human volunteers. The current proposal represents a key progress that we are able to use a highly reproducible vaccination technology platform to conduct incremental improvements on the components of actual vaccine formulations. By using the current IPCAVD program, we propose to conduct advanced vaccine optimization studies in order to address two key issues: 1) to conduct a rational selection of Env antigens in order to improve the breadth of neutralizing antibody responses, and 2) to optimize the selection of adjuvants to reduce any potential high reactogenicity in those volunteers who received the one protein boost after the high dose DNA prime in our previous clinical trial. Specifically, the following aims are proposed: Objective 1: To assemble and manage a highly productive research and development team. Objective 2: To develop the next generation polyvalent Env formulation by including Env antigens that were selected based on a well controlled rational screening system. Objective 3: To improve the safety profile by testing different adjuvants and using alternative DNA vaccine delivery method to reduce any potential reactogenicity. Objective 4: To conduct GMP manufacturing of DNA and protein vaccine components, definitive toxicology studies, and regulatory reviews of the next generation polyvalent HIV vaccine formulation. Objective 5: To plan for a Phase 1 safety and immunogenicity clinical trial and transfer GMP products to be tested in humans to NIH's HIV Vaccine Trial Network (HVTN). RELEVANCE: Developing a further improved candidate AIDS vaccine to control HIV virus transmission in the world. An early version of this vaccine design showed promising results in its first human study. PROJECT 1 Project Title: Optimizing the Immunogenicity of Next Generation Polyvalent HIV Vaccine Formulations Project Leader: Shan Lu, MD, PhD PROJECT 1 DESCRIPTION (provided by applicant): Project 1 will focus on the optimization of the next generation polyvalent Env HIV vaccine formulations using the multi-gene, polyvalent DNA prime/protein boost technology platform. Our first HIV vaccine formulation, DP6-001, was developed several years ago for a proof-of-concept trial to demonstrate the immunogenicity of the DNA prime/protein boost approach in human volunteers. The primary Env antigens isolated from HIV infected patients in mid-1990s were selected randomly based on their genetic clades. Rapid progress in the HIV vaccine field now provides us with a much larger selection of primary Env antigens, especially those Env proteins from clades less studied in the past and those Env proteins with more detailed information about the patients from whom the viruses were isolated. In addition, the recently developed pseudotyped neutralization assay and newly established target HIV-1 primary virus panel (the Tiers System) provides a measurable standard to guide our selection of more relevant primary Env antigens for the development of HIV vaccines focusing on the induction of neutralizing antibody responses. By taking advantage of the above progress, we have identified a group of primary Env antigens that were able to elicit much broader neutralizing antibodies than those included in our previous formulation DP6-001. In the current Project 1 of this IPCAVD program, the following studies will be conducted: Aim 1 To finalize the selection of next generation polyvalent Env formulation to further improve the quality of neutralizing antibody activities. Aim 2 To select an immunogenic adjuvant to be used as part of the protein boost for the next generation polyvalent Env formulation. Aim 3 To test the immunogenicity of next generation polyvalent Env formulation when the DNA priming is delivered by the electroporation method. Aim 4 To examine the epitope profiles in immune sera elicited by DNA prime-protein boost approach and identify the epitope specificities of antibodies responsible for the neutralizing activities. RELEVANCE: To optimize the next generation polyvalent Env HIV vaccine formulations using the multi-gene, polyvalent DNA prime - protein boost technology platform.

Project 1 will focus on the optimization of the next generation polyvalent Env HIV vaccine formulations using the multi-gene, polyvalent DMA prime - protein boost technology platform. Our first HIV vaccine formulation, DP6-001, was developed several years ago for a proof-of-concept trial to demonstrate the immunogenicity of the DMA prime - protein boost approach in human volunteers. The primary Env antigens isolated from HIV infected patients in mid-1990s were selected randomly based on their genetic clades. Rapid progress in the HIV vaccine field now provides us with a much larger selection of primary Env antigens, especially those Env proteins from clades less studied in the past and those Env proteins with more detailed information about the patients from whom the viruses were isolated. In addition, the recently developed pseudotyped neutralization assay and newly established target HIV-1 primary virus panel ("the Tiers System") provides a measurable standard to guide our selection of more relevant primary Env antigens for the development of HIV vaccines focusing on the induction of neutralizing antibody responses. By taking advantage of the above progress, we have identified a group of primary Env antigens that were able to elicit much broader neutralizing antibodies than those included in our previous formulation DP6-001. In the current Project 1 of this IPCAVD program, the following studies will be conducted: Aim 1 To finalize the selection of next generation polyvalent Env formulation to further improve the quality of neutralizing antibody activities. Aim 2 To select an immunogenic adjuvant to be used as part of the protein boost for the next generation polyvalent Env formulation. Aim 3 To test the immunogenicity of next generation polyvalent Env formulation when the DMA priming is delivered by the electroporation method. Aim 4 To examine the epitope profiles in immune sera elicited by DMA prime-protein boost approach and identify the epitope specificities of antibodies responsible for the neutralizing activities.

Among all types of software bugs, concurrency bugs in multi-threaded parallel programs are especially troublesome. They widely exist and are becoming increasingly severe due to the pervasiveness of multi-core machines. Existing approaches to detecting concurrency bugs mostly struggle at the complicated cause of concurrency bugs --- non-deterministic interaction among multiple threads in concurrent programs.

This project aims to address the concurrency bug problem through an effect-oriented approach. Specifically, it will provide (1) a characteristic study and a deep understanding of the error propagation process of real-world concurrency bugs; (2) an effect-oriented bug detection and testing framework that can identify potential failures in a program and search for concurrency bugs leading to these failures through backward analysis; (3) a bug-fixing tool that leverages the error propagation information identified above and suggests patches to software developers; (4) a general effect-oriented philosophy that can guide other tools related to multi-threaded parallel programs. This research will improve our understanding of the dependability problem of concurrent software, provide substantial tool support to help lower software development and maintenance costs, and improve software users' everyday experience through faster and more reliable software on a wide spectrum of platforms.

Performance bugs cause unintended performance degradation and energy waste in mainstream software. These bugs can easily slow down production software for several times and are posing increasing threat to software quality with the meager increases in single threaded performance in multi-core era and an increasing emphasis on energy efficiency.

Previous works for performance bugs, including testing and profiling, mostly treat software as a black-box, and are usually too late or ineffective in preventing the damage of performance bugs. This NSF CAREER research project seeks to develop systems and tools that take a white-box approach to addressing the open problem of performance bugs. First, it conducts an empirical study to enrich the understanding of performance bugs in real-world. Second, it develops tools that can automatically detect performance bugs before, during, and after bug manifestation. Third, it designs a testing framework to expose performance bugs before software release. Finally, it also looks at the performance bug issue in multi-threaded programs.

The education focus of this project is to broaden the software curriculum to bring students more awareness and exercise of performance and correctness issues in software, especially multi-threaded software.

This research will improve the understanding of performance waste problem in software, provide substantial tool support to help lower software development and performance testing costs, and improve software users' everyday experience through faster software. It will also help improve the energy efficiency of production-run software and protect environment in the field.

Bug fixing is time-consuming and error-prone. In the current multi-core era, widespread multi-threaded software and concurrency bugs make things even worse. Developers struggle to release correct patches for concurrency bugs on time. Much progress has been made in detecting concurrency bugs. Unfortunately, software reliability does not improve until the detected bugs are actually fixed.

This project aims to build an automated bug-fixing framework that enables self-healing multi-threaded software by combining the strengths of concurrency-bug detection, static analysis, and multi-threaded software testing. Specifically, the proposed framework will include four automated components: (1) a testing and bug-detection component that helps understand concurrency bugs and designs fix strategies; (2) a static analysis and code transformation component that inserts synchronization into software and generates high-quality patches; (3) a component that evaluates and refines patches; (4) a component that provides ad-hoc patches for bugs with incomplete information. This research will help lower the costs of software development, failure diagnosis, and bug repair. It will also improve software users everyday experience through faster and more reliable software on a wide spectrum of platforms.

DESCRIPTION (provided by applicant): The membrane proximal external region (MPER) of HIV gp41 comprises a highly conserved region involved in HIV viral fusion. It is an important target of antibody (Ab)-mediated neutralization as it contains epitopes for two broadly (b) neutralizing (Nt) monoclonal (M) Abs (2F5 and 4E10) and two MAbs that neutralize a significant, but not truly broad, range of HIV isolates (Z13 and m66.6), making the MPER an obvious target for an AIDS vaccine. However, all attempts to produce an MPER-targeting vaccine have failed. Most of these vaccines have been of three types: (i) synthetic peptides; (ii) MPER sequence grafted onto protein scaffolds; or (iii) onto proteins displayed on virus-like particles. In explaiing these failures, we hypothesize that previous vaccines have not faithfully mimicked the neutralization competent structure (NCS) of the MPER. Our preliminary work has shown that the gp41 transmembrane domain (TMD) is required for the full exposure of the MPER, since its replacement with the TMD from another membrane protein, decreases binding by MAb 4E10. Drs. Scott and Lu previously collaborated on producing a DNA vaccine that expresses a gp41 fragment comprising the MPER and TMD, so as to present the MPER in the context of the cell membrane. However, repeated immunization of rabbits with this DNA vaccine elicited low titer Abs that cross-reacted weakly with MPER peptides and did not neutralize virus; boosting immunizations with a virus-like particle vaccine did not improve anti-MPER titers, probably because of low MPER copy number. We propose to design more effective protein-boost immunogens that will mimic the NCS. In specific aim 1 we plan to design liposome and nanoparticle immunogens that present the gp41 MPER+TMD in high copy number in lipid bilayers, so as to better mimic the NCS of the MPER without added proteins that might distract the Ab response. We will produce DNA, liposome and nanoparticle candidates that have optimized the: (i) MPER, (ii) TMD, and (iii) composition of the lipid environment, based on relative binding affinity by bNt MAbs, the absence of binding by non-Nt mutants of the bNt MAbs, their behavior in a novel membrane leakage assay, and structural stabilization. In specific aim 2 optimized DNA, liposome and nanoparticle candidates will be produced and tested for their ability to elicit MPER-binding activities and Nt Abs. The optimized liposome and nanoparticle vaccines will then be tested as protein boosts (i.e., following DNA priming) with the goal of maximizing MPER-specific Ab titers and Nt potency and breadth. In addition, antigenicity, immunogenicity and structural data will be used to develop a molecular model of the MPER NCS, which should support future vaccine design. PUBLIC HEALTH RELEVANCE: The membrane proximal external region of the envelope protein gp41 (MPER) is a highly conserved region on the trimeric spike of infectious HIV-1, and a target of antibodies that neutralize a broad range of HIV-1 isolates. When used as a passive vaccine in monkeys, these antibodies protect against infection by HIV-like viruses; however so far there is no vaccine that can elicit such antibodies. Our goal is to produce a vaccine that will mimic the structure of the MPER on the infectious spike, and in so doing, will elicit antibodies that prevent infection by a broad spectrum of HIV-1 isolates; providing the important first steps in achieving a successful AIDS vaccine.

Title: XPS: FULL: CCA: Production-Run Failure Recovery Based Approach to Reliable Parallel Software

Concurrency bugs are a severe threat to system reliability in the multi-core era. Approaches to handling concurrency bugs and improving the reliability of production-run parallel software are sorely needed. This project aims to create a new parallel computing paradigm. The intellectual merits are that the project will pioneer treating run-time failure recovery as default for parallel programs, and reshaping every aspect of parallel-program development and maintenance. The project's broader significance and importance are that it will help lower the costs of software development, in-house testing, failure diagnosis, and bug repair, broadly benefiting society through better-performing parallel software.

Specifically, the proposed framework will include five components: (1) a feather-weight run-time recovery framework that utilize natural program idempotence to obtain natural concurrency-bug failure recovery; (2) a new code-development system that guide developers to write software with improved recoverability; (3) a new in-house testing system, where the testing focus is shifted towards hard-to-recover code; (4) a new on-demand run-time monitoring system that leverages on-demand run-time monitoring for run-time recovery; (5) a new off-line failure diagnosis system that leverages the feedback from recovery for failure diagnosis and fixing. These five components will work together to significantly improve the reliability and lower the development cost of parallel software.

Core B ? Abstract In this adjuvant-enhanced and electroporation-delivered DNA prime-protein boost HIV vaccine development program, the availability of high-quality and well-developed recombinant Env protein vaccine components are critical to the success of entire program. Core B is designed to provide non-GMP recombinant Env proteins for proposed pre-clinical animal studies, including non-human primate studies, and to advise on scientific and technical issues related to the production of GMP-grade recombinant Env proteins for planned phase I clinical studies. The PI of Core B, Dr. Shan Lu, has developed a polyvalent gp120 protein formulation from his previous NIH-funded programs. That formulation includes four recombinant gp120 proteins (covering HIV-1 subtypes A, B, C, and AE) produced using the CHO system under GMP conditions.

Large-scale shared hosting infrastructures such as multi-tenant cloud computing systems have become increasingly popular by allowing users to lease resources on-demand in a cost-effective way. As multiple tenants may share computing resources, hosting infrastructures are complex systems and prone to various system anomalies. Although software developers often perform rigorous offline testing, many subtle bugs only manifest themselves during large-scale production run. Many anomalies such as those where the system does not crash but fails to behave as expected are hard to reproduce and diagnose using existing techniques. Existing system anomaly diagnosis work can be broadly classified into two categories: 1) the black-box schemes which do not require source code and are suitable for online production-site diagnosis, and 2) the white-box schemes which require source code and expensive code instrumentation and are suitable for development site, offline diagnosis. Although white-box schemes provide fine-grained diagnosis, large-scale production hosting infrastructures are reluctant to adopt them due to their high-overhead and intrusive system recording approaches.

The overarching objective of this project is to explore an innovative cross-site system anomaly debugging approach that intelligently integrates production-site black-box diagnosis with development-site white-box debugging into a more powerful hosting infrastructure debugging framework. This project will develop techniques for development-site, offline white-box debugging that takes the production-site fault inference results as guidance to find the exact anomaly causes. The project will focus on diagnosing non-crashing system anomalies (e.g., performance degradation, service outage, software hang, unexpected halt) that are common in real world hosting infrastructures but are difficult to debug using existing techniques.

Techniques developed in this project will generate significant impact on improving the robustness of real world hosting infrastructures. The PIs will develop new course modules on the hosting infrastructure debugging for both graduate and undergraduate classes they regularly teaches. This project will develop programming courseware based on the research prototypes developed in this project. The PIs will use their power of role model and a set of outreach activities to recruit more female students to pursue systems research. The PIs will disseminate their results and collected data broadly through publication and technology transfer. Developed software artifacts and experimental datasets will be released for public use.

We interact with online shopping and banking websites on a daily basis. Many of these websites are powered by data-driven applications. Such application often consists of two parts: an application hosted on an application server, and a database management system (DBMS) hosted on a separate server from the application server that maintains persistent data. Unfortunately, many data-driven applications suffer from performance problems, such as taking a long time to load a page or inability to scale up to serve large number of clients simultaneously. The state of the art in discovering and fixing performance problems in data-driven applications is to examine the two parts of the application separately, and doing so misses many opportunities in discovering and fixing such problems. Unlike prior approaches, in this project we will treat the DBMS and the application in tandem. In particular, we will devise new techniques and tools to help identify performance problems, understand the cause of such problems, and fix them automatically. This project will open up new opportunities in cross-layer program compilation and optimization, with the practical goal of improving the performance of data-driven applications that will have a significant impact in many aspects of our daily lives. The findings from this project will be incorporated into undergraduate and graduate software engineering, introduction to data management, and compiler classes to be offered at the University of Chicago and the University of Washington. The outreach activities of this project will include engaging and advising students through special programs geared toward under-represented groups such as the Distributed Research Experiences for Undergraduates (DREU) organized by CRA-W (Computing Research Association -- Women) and Diversity Workshops organized by CRA-W.

Specifically, the proposed research consists of three thrusts: (1) a new cross-layer program analysis framework that produces an end-to-end profile of data-driven applications by understanding the application code, the queries that the application sends to the DBMS, and how the DBMS processes such queries; (2) a program analysis and testing framework that identify performance problems in data-driven applications by leveraging the end-to-end profile created from (1); and (3) new means to optimize data-driven applications by transforming both the application code and the queries that are issued. These three thrusts will work together to improve the performance of data-driven applications and help programmers detect performance problems during development. Software developed by this project, benchmarks used for evaluation, and performance comparison with existing techniques will be released to public domain through the project website. Further information will be available at the project website (http://db.cs.washington.edu/projects/coopt.html).

This award supports student travel for US-based graduate students to attend the 2016 USENIX Annual Technical Conference (ATC16). ATC is considered one of the premier forums for advanced professionals from academic and industrial backgrounds to meet and discuss the latest research in systems software. USENIX ATC16 will be held in Denver, CO from June 22-24, 2016 and will consist of 3 days of the expanded ATC technical program. Co-located workshops available for student participation include: HotStorage, HotCloud, and SOUPs.

In addition to attending the conference events, students receiving assistance may serve as scribes for the conference sessions to write summaries for a later issue of ;login: magazine, will be invited to sessions to interact with senior members of the research community specifically interested in meeting students in a casual and informal atmosphere, and will be strongly encouraged to present posters and works in progress as part of the selection process.

Participation in conferences is a valuable and important part of the graduate school experience providing students exposure to senior researchers and leading edge work in the field.

DCBA: Distributed Concurrency Bugs Annihilation

Software systems are getting more complex, creating reliability issues that cause millions of dollars in economic loss. Beyond local software, distributed cloud software infrastructures (i.e., cloud systems) have emerged as a dominant backbone for many modern applications. Users expect high reliability from these systems, but guaranteeing their reliability proves to be challenging. Cloud systems run on hundreds/thousands of machines, execute complicated distributed protocols, and face a variety of hardware faults. This combination makes cloud systems prone to distributed concurrency bugs, which can cause catastrophic failures such as data loss, downtimes, and data loss/inconsistencies. This Distributed Concurrency Bugs Annihilation (DCBA) project will address this important issue and bring many direct benefits to the society; users from many areas (science, healthcare, business, education, military, and government) increasingly use cloud computing services and demand high availability and predictability. Combating distributed concurrency bugs is an important ingredient to such success.

Distributed concurrency bugs are caused by non-deterministic order of distributed events such as message arrivals, faults, and reboots. This project, Distributed Concurrency Bugs Annihilation (DCBA), will find, remove, and prevent buggy interleavings of concurrent distributed events with the development of four approaches: (1) full, automated, and deep distributed system model checkers, (2) fast inference, detection, testing and fixing of order violations, (3) runtime statistical debugging, prevention, and recovery, and (4) design advancements that reduce the possibilities of distributed concurrency bugs to appear. This DCBA project will advance the state of cloud dependability research. Existing literature on distributed systems reliability focuses on monitoring, post-mortem debugging, deterministic record and replay, and verifiable programming language frameworks. The DCBA project will introduce advancements to approaches related to model checking, bug detection, bug fixing, runtime debugging, prevention and recovery.

As more organizations build more distributed systems on farms of machines and services in cloud era, it is time for the dependability community to address distributed concurrency bugs in systematic and comprehensive manners. The DCBA initiative will have a profound impact to future distributed cloud systems.

Modern data-centric systems, ranging from Internet-of-Things devices to online services, can benefit from helping people make clear their intent for how their devices and services should behave and interact with each other. Generally, this requires people to engage in some amount of end-user programming, or programming by people who are not typically trained in programming. Common examples of this include specifying that a light should only turn on when a room is occupied or that emails with certain words in the subject line should be routed into a particular folder. Trigger-action programming (TAP), which consists of "if-this-then-that" rules, is the most common model for end-user programming because it is relatively easy to write simple TAP programs. However, as the number and complexity of both rules and devices increases, TAP programs increasingly suffer from bugs and dependability problems and are hard to correct for inexperienced and trained programmers alike. This project's goal is to make TAP programming, and thus people's ability to interact with devices that act on their behalf, more robust through developing a better understanding of end users' needs and abilities to write and debug TAP programs, computational techniques to both better model user intents and suggest TAP programs that meet them, and tools that use those techniques to help people more easily create correct TAP programs. Apart from the potential benefits to people's well-being, the project will also provide educational benefits by developing course materials that increase awareness of both human aspects of, and formal methods for, programming. Further, the tangible nature of such devices and the familiarity of popular online services are a fertile domain for engaging the public and training undergraduate students, K-12 students, and early-career graduate students in the computer science research lifecycle.

To accomplish these goals, the work combines techniques from formal methods, human-computer interaction, and machine learning. Contributions to formal methods include the design of systematic solutions to unique program repair, synthesis, and specification-refinement problems in the context of end-user programming. Contributions to cyber human systems include empirical studies and the design of data-driven interfaces for more accurately expressing intent. Specifically, the empirical human subjects studies seek to understand and improve the debugging process for trigger-action programming, create and distribute needed data sets of user-centric collections of trigger-action programs, and comparatively evaluate proposed interfaces. The interfaces developed in this work use data-driven methods to help users pinpoint and understand bugs in trigger-action programs, as well as to choose among candidates for automatically repaired trigger-action programs. Underlying these interfaces will be formal models of trigger-action programs, which are verified against specified properties written in linear temporal logic. The system developed will systematically synthesize program repairs, taking into account users' experiences and preferences. The system will also use a combination of machine learning and formal methods to automatically generate trigger-action programs and summarize specifications based on historical traces of user interaction with the system. In sum, helping non-technical users accurately communicate their intent through trigger-action programming benefits widely deployed end-user-programming systems for integrating internet-connected devices and online services.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

As a critical backend for many of today's applications and services, large-scale distributed systems must be highly reliable. In the last couple of years the field witnessed a phenomenal scale of deployment; Google is known to run clusters with thousands of machines each, Apple deploys over 100,000 database machines, and Netflix runs tens of database clusters with 500 nodes each. This new era of cloud-scale distributed systems has given birth to a new class of faults, scalability faults---faults whose symptoms surface in large-scale deployments but not necessarily in small/medium-scale deployments. The CP2 project is proposed to solve the problem of correctness checkability and performance predictability of systems at extreme scale. Specifically the project will analyze over 500 real-world scalability faults in over a dozen large-scale systems, develop a single-machine scale-checking framework that allows developers to test large distributed code on one or a few machines, and provide groundwork for compute- and I/O-performance predictability of large-scale jobs on both existing and future architectures. These tasks will advance debugging, testing, learning, and prediction methods both on traditional hardware platforms and emerging ones and ultimately lead to correct-by-construction development methods. The CP2 project will have impact in multiple disciplines including systems (cloud/datacenter systems reliability), programming languages/compilers (new static/dynamic analysis techniques), architecture (compute/storage prediction for heterogeneous hardware), algorithms (the use of learning methods), and high-performance computing (benchmarking of HPC systems/applications).

In terms of societal benefits, the CP2 project addresses paramount issues mentioned in the NSF Strategic Plan for 2018-2022. More specifically, society increasingly depends on complicated systems that are products of human ingenuity, including ecosystems of large and complex software with millions of lines of code running on thousands of machines. CP2 will address the challenges of understanding and predicting the behavior of such systems. Furthermore, as society?s reliance on complex systems grows, learning about their robustness and understanding how to strengthen them are of increasing importance. In terms of education, the CP2 project gives unique hands-on research and education with cutting-edge systems technology in which students will be trained to operate software on a large number of machines and analyze their performance and correctness. The results of the CP2 project will be released through the classic medium of publication, through the development of numerous software artifacts which will be open-sourced, and finally through collaboration with various industry partners to help shape the next generation of large-scale systems.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

This proposal is for support of a travel to the 25th ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), to be held in Lausanne, Switzerland, March 16-20, 2020. ASPLOS is a leading forum for multidisciplinary systems research spanning computer architecture and hardware, programming languages and compilers, and operating systems. Research papers selected for ASPLOS often target a wide spectrum of important goals such as performance, energy and thermal efficiency, reliability, security, and sustainability. The funds requested from NSF will help support 20 students who currently study in US universities and institutes to attend the ASPLOS conference, and hence get chances to presenting their research ideas and to get advice from leaders in the community. Moreover, part of the funds will be reserved to support undergraduate student applicants and students belonging to under-represented groups.

The importance of forum such as ASPLOS continues to grow as we come to the end of Moore's Law, experiencing the explosion of big data, the wide spectrum of computing scales from ultra-low power wearable devices to exascale parallel and cloud computers, and the need for sustainability. ASPLOS embraces systems research that directly targets these new problems in new ways. Historically, the conference has attracted top research papers from both academia and industry, and many innovations published in the proceedings have been influential in the history of the systems and hardware industry.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

In light of the limits of Moore's Law and Dennard scaling and the ever increasing computing demand, the last decade has seen unprecedented deployment scales; Google is known to run clusters with thousands of machines each, Apple deploys a total of 100,000 database machines, and Netflix runs tens of database clusters with 500 nodes each. This era of extreme-scale distributed systems has given birth to a new class of faults, "scalability faults" -- complex latent faults that are scale-dependent, whose symptoms surface in large-scale deployments but not necessarily in small/medium-scale deployments. Many fundamental research questions are not answerable today. On correctness: How to detect bugs that only manifest under large scale through program analysis? How to test and reproduce various dimensions of system scales efficiently on one machine? How to prevent and fix scalability-related faults? On performance: How to reason about software performance on various heterogeneous devices? How to accurately predict performance of fine-grained tasks to reduce inaccuracies at the aggregate level and project performance to future architectures? Finally, in combination: How to answer all these questions for the larger connected ecosystem -- not just the individual software and hardware components -- and to eventually build future-generation systems that are reproducible and verifiable by construction with respect to correctness and performance at scale?

The ScaleStuds project involves a team of ten researchers to develop the foundations of correctness checkability (CC) and performance predictability (PP) of systems at scale. The key principle of this project is to "check large with large" -- check large-scale systems with a large fleet of data, analysis, tests, learning, models, and proofs. The vision is to build an ecosystem of distributed "CC+PP-certified" software-software and -hardware interactions. The project is paving the vision one "floor" at a time, creating composable building blocks ("the studs"). The project first builds new mechanisms such as a scale-testing platform and a unified database of software program properties and hardware performance profiles exposing clear APIs. These studs then enable multi-dimensional automated scalability tests and program analysis and performance learning and prediction at various levels of the software/hardware stack. Ultimately all of these experiences are intended to lead to correct and performant cross-layer/service interactions and future design principles including reproducible- and verified-by-construction development methods. The project novelties include the advancement of debugging, testing, learning, and prediction methods to ensure correctness checkability and performance predictability of extreme-scale systems and applications both on classical hardware platforms and emerging ones; a unified data ecosystem of software/hardware properties and profiles that facilitates automated analyses via clear APIs; a multi-dimensional scale-testing framework that empowers the development of new large-scale unit-tests and program analysis; detailed device profiling and observation to enable large-scale performance learning/prediction and deliver lessons for learning/predicting the behavior of other devices and layers in an end-to-end hardware/software stack; and ultimately a clear definition of CC+PP-certifiability for today's systems and future verifiable/reproducible-by-construction development methods.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.