William Robinson - US grants

Three years ago we discovered a hepatitis virus in Beechey ground squirrels (GSHV) with ultrastructural, antigenic, molecular and biological properties similar to those of hepatitis B virus (HBV) of man and woodchuck hepatitis virus (WHV). In the past 3 years we have studied the host range of GSHV, its antigenic and polypeptide structure, its DNA structure and the viral DNA forms in infected liver. Little or no hepatitis and no hepatomas have been observed in chronically GSHV infected ground squirrels in contrast to moderately severe hepatitis and hepatomas frequently observed in WHV infected woodchucks and HBV infected humans. We propose to investigate the basis for the difference in incidence and severity of liver disease in the different virus-host systems. We will investigate the infectivity and pathogenicity of GSHV for woodchucks and WHV for ground squirrels to attempt to determine whether a difference in pathogenicity of the two virus, or a difference in response of the two hosts accounts for the observed difference in disease incidence. We will examine the viral DNA forms in GSHV infected ground squirrel liver and determine whether viral DNA becomes integrated in cellular DNA, and compare these findings with results in woodchuck and human systems. We will study the effects of environmental conditions and aflatoxin B1 on the pathogenic effects of GSHV in ground squirrels. We will study replication of GSHV DNA in infected liver and in tissue culture cells if they can be successfully infected. Finally, we will study the effect of antivirals on the high titer persistent infection seen in GSHV.

We propose to continue our efforts to characterize the polypeptides and DNA of hepatitis B virus (HBV) and to study its relationship to hepatocellular carcinoma. We have recently discovered a virus with similar ultrastructural, antigenic, molecular and biological features in wild Beechey ground squirrels (ground squirrel hepatitis virus or GSHV) trapped in Northern California. We propose to develop this animal model of infection with a virus similar to HBV and determine the natural history of infections and the associated diseases. We will compare the antigenic and molecular structures of the two viruses and attempt to infect cells in culture with both viruses and the viral DNAs. We will attempt to produce hepatitis B surface antigen (HBsAg) in large quantities in cell culture by introducing the gene for the major HBsAg polypeptide into cells as part of a plasmid vector with SV 40 promotors. HBsAg produced in this way will be tested for immunogenicity and assessed as a potential HBV vaccine. This approach will be used to attempt to identify coding regions in HBV DNA for other viral gene products. Attempts will be made to produce monoclonal human anti-HBs as a potential source for passive immunization against HBV.

We propose to continue our studies of duck hepatitis B virus (DHBV) infection of domestic ducks as an animal model of hepatitis B virus, which is associated with hepatitis, hepatomas, and immune complex disease in man. DHBV is present in 5-10% of the Peking ducks of many domestic flocks in the U.S. We plan to investigate the long-term course of DHBV-infection and document the associated disease. Hepatomas have been observed in areas of China where DHBV is endemic. We will study duck hepatomas from China and any that might appear in our flock for the presence of DHBV. Tumors will be analyzed for viral DNA by Southern blotting and integrated viral DNA will be cloned for further characterization. We will continue our analysis of DHBV surface and core antigen polypeptides, and will produce monoclonal as well as polyvalent antibodies to them to provide sensitive serological tests. We will study the appearance and relationship of different viral DNA forms during the course of infection in embryonated eggs, and attempt to grow virus in culture of duck embryo cells. Finally we will study the host range of DHBV by injection of the virus into different varieties of ducks, other species of fowl, and non-avian species. This virus-host system may offer certain advantages over other hepadna virus-host systems. Among these is the ease with which ducks and embryonated duck eggs can be obtained and experimentally manipulated, the ease with which embryos can be infected, the ease with which embryonic tissues can be cultured in vitro, the apparent difference in disease manifestations in different hosts (acute hepatitis in Khaki Campbell and not in Peking ducklings) and the possible association of the virus and hepatomas in ducks in China. These advantages justify the further development of the duck virus system in order to understand the mechanism of virus replication and the pathogenesis of diseases associated with infection.

Hepatitis B virus (HBV) is an important cause of liver disease including liver cancer in man. It is a member of a family of viruses which have interesting structure, mode of replication and biological properties. We propose to study the role of HBV in liver cancer by analyzing integrated viral DNA sequences with flanking cellular DNA cloned from two hepatocellular carcinomas (HCC), each with single integration sites. We will also further investigate NIH 3T3 cell transformation observed with a cloned HBV DNA dimer, an 1850 bp BamHI fragment of HBV DNA and DNA from HCC. We will also investigate the effect of liver regeneration on viral integration and HCC formation. We will further characterize high molecular weight HBV DNA forms (5 and 9 kd) found in virions from plasma. A final goal is to investigate a viral vaccine strategy by which relevant viral antigens are expressed by enteric bacterial strains which result in immune responses but not disease when live bacteria are ingested by mouth. Although this approach might offer a particular advantage for enteric pathogens such as rotavirus for which local enteric immunity is important, the approach could be equally effective for other agents such as HBV for which only systemic immunity is important. We have introduced genes for hepatitis B surface (HBsAg) and core (HBcAg) antigens and rotavirus VP7 into plasmid expression vectors and have achieved expression of HBsAg and rotavirus VP7 as fusion proteins and HBcAg as a discrete polypeptide in E. coli. We propose to optimize expression of these antigens in E. coli; introduce the hybrid plasmids into Salmonella typhi strain Ty 21a and S. typhimurine 1479 (mutants with attenuated virulence and successfully used as live, oral Salmonella vaccines); and test the transformed Salmonella for viral antigen expression and ability to induce immune responses in mice. The long-term goal is live oral vaccines for rotavirus and HBV in man.

We propose to continue our studies of disease and infection in 2 animal models of hepatitis B virus, which is associated with hepatitis and hepatocellular carcinoma (HCC) in man. In 1 of the models, ground squirrels infected with ground squirrel hepatitis virus (GSHV), we have seen developed of HCC significantly associated with virus infection, and propose to continue study of the long term effects of virus infection in the animals remaining the colony. We will continue to study the effects of environmental factors such as aflatoxin B1 and antivirals on HCC development. We will determined what common and differentiating characteristics exist between the integrated and unintegrated forms of GSHV DNA in the 8 HCC observed in carrier squirrels and those from studies of WHV- and HBV-related HCC. We will clone and sequence single integrations of GSHV DNA in HCC and study whether c-myc or other oncogenes are rearranged or amplified. We will continue to sequence virus-virus junction areas in the "novel" DNA forms cloned from chronically- infected ground squirrels to determine if these forms reveal a mechanism for integration of viral DNA into chromosomal DNA. In the other animal model, duck hepatitis B virus (DHBV) infection of ducks, we will study what factors influence the type and amount of hepatitis that we have observed in ducklings experimentally injected with DHBV, but absent in congentially- infected animals and uninjected controls. We will follow experimentally-infected ducklings to see if these ducks develop HCC, unlike the congenitally-infected ducklings that we have studied so far. We will use DHBV infection of primary duck hepatocyte cultures to study early events in viral infection, to test monoclonal antibodies to DHBV for neutralizing ability, and to establish a rapid test for antiviral effectiveness. We will attempt to develop alternate cell culture systems for growing DHBV by culturing yolk sac endodermal cells or their precursors and by culturing hepatocytes from ducklings treated with diethylnitrosamine. We will use electroporation-aided transfection of DHBV DNA into both susceptible and non- susceptible cells to study the mechanism of host specificity.

Hepatitis B virus (HBV) is an important cause of liver disease including liver cancer in man. It is a member of a family of viruses which have interesting structure, mode of replication and biological properties. We propose to study the role of HBV in liver cancer by analyzing integrated viral DNA sequences with flanking cellular DNA cloned from two hepatocellular carcinomas (HCC), each with single integration sites. We will also further investigate NIH 3T3 cell transformation observed with a cloned HBV DNA dimer, an 1850 bp BamHI fragment of HBV DNA and DNA from HCC. We will also investigate the effect of liver regeneration on viral integration and HCC formation. We will further characterize high molecular weight HBV DNA forms (5 and 9 kd) found in virions from plasma. A final goal is to investigate a viral vaccine strategy by which relevant viral antigens are expressed by enteric bacterial strains which result in immune responses but not disease when live bacteria are ingested by mouth. Although this approach might offer a particular advantage for enteric pathogens such as rotavirus for which local enteric immunity is important, the approach could be equally effective for other agents such as HBV for which only systemic immunity is important. We have introduced genes for hepatitis B surface (HBsAg) and core (HBcAg) antigens and rotavirus VP7 into plasmid expression vectors and have achieved expression of HBsAg and rotavirus VP7 as fusion proteins and HBcAg as a discrete polypeptide in E. coli. We propose to optimize expression of these antigens in E. coli; introduce the hybrid plasmids into Salmonella typhi strain Ty 21a and S. typhimurine 1479 (mutants with attenuated virulence and successfully used as live, oral Salmonella vaccines); and test the transformed Salmonella for viral antigen expression and ability to induce immune responses in mice. The long-term goal is live oral vaccines for rotavirus and HBV in man.

We propose to continue our studies of disease and infection in 2 animal models of hepatitis B virus, which is associated with hepatitis and hepatocellular carcinoma (HCC) in man. In 1 of the models, ground squirrels infected with ground squirrel hepatitis virus (GSHV), we have seen developed of HCC significantly associated with virus infection, and propose to continue study of the long term effects of virus infection in the animals remaining the colony. We will continue to study the effects of environmental factors such as aflatoxin B1 and antivirals on HCC development. We will determined what common and differentiating characteristics exist between the integrated and unintegrated forms of GSHV DNA in the 8 HCC observed in carrier squirrels and those from studies of WHV- and HBV-related HCC. We will clone and sequence single integrations of GSHV DNA in HCC and study whether c-myc or other oncogenes are rearranged or amplified. We will continue to sequence virus-virus junction areas in the "novel" DNA forms cloned from chronically- infected ground squirrels to determine if these forms reveal a mechanism for integration of viral DNA into chromosomal DNA. In the other animal model, duck hepatitis B virus (DHBV) infection of ducks, we will study what factors influence the type and amount of hepatitis that we have observed in ducklings experimentally injected with DHBV, but absent in congentially- infected animals and uninjected controls. We will follow experimentally-infected ducklings to see if these ducks develop HCC, unlike the congenitally-infected ducklings that we have studied so far. We will use DHBV infection of primary duck hepatocyte cultures to study early events in viral infection, to test monoclonal antibodies to DHBV for neutralizing ability, and to establish a rapid test for antiviral effectiveness. We will attempt to develop alternate cell culture systems for growing DHBV by culturing yolk sac endodermal cells or their precursors and by culturing hepatocytes from ducklings treated with diethylnitrosamine. We will use electroporation-aided transfection of DHBV DNA into both susceptible and non- susceptible cells to study the mechanism of host specificity.

DESCRIPTION: (Adapted from Applicant's Abstract). In this proposal, it is demonstrated that several aqueous and organic fractions from plants used in Bolivian folk medicine have anti-HIV activity. These fractions will be further purified using various chemical techniques. Compounds will be partitioned against organic solvents based on polarity and acid/base properties. Groups of similar compounds will be further purified by chromatographic means until pure compounds are obtained. Chemical structures will be determined by nuclear magnetic resonance, mass spectrometry, or other chemical or instrumental means. The methods of action of anti-HIV compounds will be characterized in in vitro assays. Assays for the inhibition of the gp120-CD4 interaction (receptor binding), uncoating, or reverse transcriptase activity will be performed. Additional studies to evaluate whether the compounds induce the production of interferon or inhibit cellular processes, such as glycosylation, will be examined. Once purified compounds are discovered and their modes of action have been defined, the drugs will be tested for anti-HIV activity in human mononuclear cells in vitro and in an animal model for HIV infection in vivo. The investigators claim that these studies have already lead to the discovery of anti-HIV activity in several crude fractions. Further, the applicants believe that with further purification, it is possible that medicinally important anti-HIV agents may be discovered thus improving our ability to treat HIV infections in humans.

Melatonin is being given in a standard dose to patients with malignant melanoma and brain metastasis with and without radiation therapy.

We propose to continue our studies of disease and infection in 2 animal models of hepatitis B virus, which is associated with hepatitis and hepatocellular carcinoma (HCC) in man. In 1 of the models, ground squirrels infected with ground squirrel hepatitis virus (GSHV), we have seen developed of HCC significantly associated with virus infection, and propose to continue study of the long term effects of virus infection in the animals remaining the colony. We will continue to study the effects of environmental factors such as aflatoxin B1 and antivirals on HCC development. We will determined what common and differentiating characteristics exist between the integrated and unintegrated forms of GSHV DNA in the 8 HCC observed in carrier squirrels and those from studies of WHV- and HBV-related HCC. We will clone and sequence single integrations of GSHV DNA in HCC and study whether c-myc or other oncogenes are rearranged or amplified. We will continue to sequence virus-virus junction areas in the "novel" DNA forms cloned from chronically- infected ground squirrels to determine if these forms reveal a mechanism for integration of viral DNA into chromosomal DNA. In the other animal model, duck hepatitis B virus (DHBV) infection of ducks, we will study what factors influence the type and amount of hepatitis that we have observed in ducklings experimentally injected with DHBV, but absent in congentially- infected animals and uninjected controls. We will follow experimentally-infected ducklings to see if these ducks develop HCC, unlike the congenitally-infected ducklings that we have studied so far. We will use DHBV infection of primary duck hepatocyte cultures to study early events in viral infection, to test monoclonal antibodies to DHBV for neutralizing ability, and to establish a rapid test for antiviral effectiveness. We will attempt to develop alternate cell culture systems for growing DHBV by culturing yolk sac endodermal cells or their precursors and by culturing hepatocytes from ducklings treated with diethylnitrosamine. We will use electroporation-aided transfection of DHBV DNA into both susceptible and non- susceptible cells to study the mechanism of host specificity.

A materials-oriented approach to chemistry is being developed through the preparation of "A Materials Chemistry Companion to General Chemistry", by an ad hoc committee of two dozen leading chemistry researchers and teachers. Consisting of text, problem sets, model kits, software, videotapes, demonstration and laboratory experiments, the "Companion" is scheduled for publication by the American Chemical Society in 1993. The "Companion" will demonstrate how virtually every topic typically covered in introductory chemistry courses can be illustrated with solids such as polymers, semiconductors, metals, superconductors, and ceramics. The project focuses both on innovation - the completion of material for the "Companion" - and on change - the implementation of a national strategy for assimilating materials chemistry into introductory chemistry courses. Strategies for effecting change include national testing of the "Companion" at over two dozen volunteering college test sites (more than 15,000 students); development of modules based on the "Companion" and their use in workshops for college and pre-college teachers; and critical evaluation of the instructional materials. The "Companion" and supporting activities will revitalize general chemistry courses, enhance the scientific literacy of students and teachers, and increase the number and diversity of high-quality students electing to pursue careers as chemists, chemistry teachers, scientists and engineers.

The human immunodeficiency virus (HIV) is the retrovirus associated with the acquired immune deficiency syndrome (AIDS). Like all retroviruses, integration of a complementary DNA copy of the viral RNA genome into a host chromosome is absolutely required for productive and stable infection of cells by HIV. The integration function is carried out by a viral enzyme, integrase, which is an attractive target for the development of novel anti-HIV therapies. To date, the search for HIV integrase inhibitors has been somewhat disappointing: the majority of compounds described that inhibit HIV integrase in biochemical reactions fail to interfere with HIV replication in tissue culture. The dicaffeoylquinic acids and L- chicoric acid represent the first small molecule integrase inhibitors with activity against HIV in tissue culture. These compounds block HIV replication at concentrations ranging from 2 uM to 10uM while the doses that inhibit cellular growth (toxic concentrations) are fully 50-100 times greater. Their activity against HIV integrase in biochemical reactions range from 100nM to approximately 800nM, making them the most potent small molecule integrase inhibitors yet reported. With the identification of these inhibitors, it is now possible to perform in-depth structure activity relationship studies thus making synthesis of more potent and more selective integrase inhibitors not just a goal but a likely possibility. This project would achieve that goal through the following specific aims: 1) Synthesize more potent and less toxic HIV integrase inhibitors. 2) Perform biochemical and mechanistic analyses of existing and new integrase inhibitors. 3) Optimize integrase inhibitors in combination drug therapy. 4) Develop more sensitive and quantitative measures of viral integration within cells. At the least, these studies should offer significant information about the function of HIV integrase and the role of triple therapy targeted against three different HIV enzymes: reverse transcriptase, integrase, and protease. The successful completion of these specific aims may result in a new class of anti-HIV agents that could be evaluated for use in HIV infected individuals both alone and in combination with other anti HIV agents.

The purpose of this study is to determine how effective treatment with tirapamine and cisplatin is in treating advanced cervical cancer. At present, cervical cancer is the fourth most common malignancy in American women, and the second leading cause of death from gynecologic malignancy. Therapeutic outcome for cervical carcinoma which is refractory or recurrent following primary therapy remains disappointing. Thus, research is ongoing to identify more effective chemotherapeutic regimens for this disease. This cancer is a relatively chemoresistant tumor, and the efficaicy is often further diminished by complications of prior radiation therapy. Additionally, the contribution of bulky tumor masses and poor blood supply often results in a hypoxic environment for a large percentage of tumor cells which limits the efficacy of most standard chemotherapeutic agents. Tirapazamine is an investigational chemotherapeutic agent which was specifically developed to have increased activity against hypoxic cells. The present study has been designed to study the efficacy and toxicities associated with a combination of cisplatin plus tirapazamine administered every 21 days in patients with recurrent or refractory cervix cancer.

There is no standard treatment for advanced endometrial cancer. Once the tumor has spread beyond the uterus, treatment with surgery ad pelvic radiation may not be sufficient to control the disease and additional therapy may be helpful. In a previous GOG (Gynecologic Oncology Group) study the chemotherapy agents, doxorubicin and cisplatin, have been given to patients with advanced endometrial cancer and over 40% of patients had a response to this combination of drugs. Another chemotherapy agent, paclitaxel, has been shown to reduce the tumor size in some patients with endometrial cancer. The purpose of this study is to determine whether treatment with paclitaxel and doxorubicin is more effective than treatment with doxorubicin and cisplatin in patients with primary Stage III and IV or recurrent endometrial cancer.

The standard treatment for optimally debulked Stage III ovarian or primary peritoneal carcinoma is chemotherapy with intravenous Cisplatin and Paclitaxel. The purpose of this study is to determine the effectiveness of administration of chemotherapy into the abdominal cavity in addition to intravenous chemotherapy compared to the current standard intravenous chemotherapy. Because ovarian cancer spreads in the abdominal cavity, giving chemotherapy by infusion into the abdominal cavity may result in a greater dose of the drugs reaching tumor cells. This study will evaluate the patient's response, and survival/disease free interval when treated with standard intravenous Cisplatin and Paclitaxel compared to intravenous Paclitaxel and intraperitoneal Cisplatin and Paclitaxel. The study will also evaluate the impact of treatment on the patient's quality of life.

My career goal is to develop treatments for patients with devastating clinical immune disorders. During the time of this award, with Dr. Lawrence Steinman as my mentor I propose to develop selective immune therapy for an animal model of rheumatoid arthritis (RA). RA is a chronic autoimmune inflammatory synovitis affecting 1 percent of the world population. Using collagen-induced arthritis (CIA) in mice as a model for RA and DNA vaccination as a tool for generating and modulating immune responses, I propose to answer several questions pertaining to therapeutic immunization against CIA. I will also develop and study peptide pulsed peripheral monocytes for therapy of CIA and autoimmunity. I will address the following specific aims: (1) Can we protect against CIA by injection of DNA encoding: (a) the Vbeta8.2 region of the T-cell receptor, (b) collagen or collagen peptide, and (c) tandem DNA constructs encoding collagen, collagen peptide, or Vbeta8 TCR plus Th2 promoting cytokines including IL-4, IL-10, and TGF-beta? (2) We will examine the mechanisms of DNA vaccine-mediated protection against CIA using (a) cytokine assays, (b) flow cytometry, (c) soluble tetrameric major histocompatibility complex class II-peptide complexes, (d) T cell proliferation assays, (e) bone marrow chimeric mice, and (f) DNA microarrays. (3) Can we protect against CIA by injection of collagen peptide pulsed peripheral monocytes? These experiments will be carried out at the Stanford University Beckman Center. During the course of the proposed award period the candidate will continue to practice clinical Rheumatology on a 10 percent basis and take formal coursework in immunology and the ethical conduct of research. The overall goal of the proposed training program is to prepare this candidate to establish an independent laboratory in an academic division of Rheumatology.

This project brings together a team of ecologists and physiologists to investigate how physiological mechanisms constrain the evolution of parental investment and self-maintenance in tropical and temperate environments. Life-history theory predicts that long-lived organisms should allocate more resources to enhancing survival, thereby protecting future reproduction, at the expense of current reproduction. Many of the predicted responses of physiology and behavior are controlled by endocrine and immune system mechanisms that establish incompatible physiological states and limit individual responses of organisms and evolved responses of populations. This collaborative study will compare related species of birds living in contrasting tropical and temperate environments to determine population parameters (adult survival and reproductive rate) and physiological and behavioral responses. Incorporating a strongly developed student-training component in the project, measurements will include activity, metabolism, health status, and endocrine profiles in the field, and metabolism, hormonal stress response, and immune system response in the laboratory. Analysis and interpretation of these data will relate variation in life-history attributes to phylogenetic relationship, region, and ecological measures of habitat, diet, and predator environment. This project is unique in that it integrates studies in ecology, physiology, and demography to focus on major patterns of diversification of life histories.

PROJECT SUMMARY

Teacher-Fellow teams in seven Middle Schools (Harbor, McCormack, Woodrow Wilson, Lewis, and Gavin Middle Schools in the Boston Public Schools; Pierce Middle School in the Milton Public Schools; Dedham Middle School in the Dedham Public Schools) located within the Neponset River watershed are adapting existing instructional materials such as FOSS kits to use a study of the local watershed as a unifying theme for middle school science. Data is being gathered from the school playground, the students' backyards and the larger community surrounding the participating schools. Inter-school information exchange enables the students at each school to relate their situation to the larger picture and the community of schools can collaborate to gain a sense of conditions within the entire watershed. Quantitative examples and activities are being emphasized in order to hone students' mathematics skills, reinforce the existing mathematics curriculum, and demonstrate mathematics' relevance to science and everyday life. Fellows receive a Summer Teacher Training workshop in pedagogy, state and national frameworks, and effective classroom management. Each Fellow is then teamed with a middle school Teacher in a weeklong Summer Environmental Science Content Institute that uses specific examples and hands-on activities within the watershed to strengthen the Teachers' and Fellows' science content knowledge and concept understanding. In addition to their classroom duties, Fellows are required to take a specially developed course, Teaching Environmental Sciences and Technology. (TEST), that provides continuing pedagogical and content training. Five daylong workshops are held for all Fellows and Teachers during the school year to exchange information and experiences and provide additional content and pedagogical material. A 1-credit spring seminar is used as a base to allow one cohort of Fellows to pass on their experiences and knowledge to the next. Special events such as canoe trips, river cleanups, Boston Harbor cruises, and citizen science activities help foster a sense of connectedness across municipal boundaries. WISP will be evaluated internally by a science pedagogy faculty member and externally by the Educational Development Center, Inc. of Newton, MA. The broader benefits of the program accrue to the Fellows, the teachers, the middle school students and the institutions involved. The Fellows are developing the interest, skills, and commitment necessary to be actively engaged in K-12 education throughout their scientific careers. Teachers are gaining environmental science content knowledge and enhancing their ability to teach science curricula and to reflect on their teaching practices. Middle school students are gaining a deeper understanding and appreciation for science and mathematics. A set of school districts diverse in size, ethnicity and socio-economics and the University of Massachusetts, Boston are developing a shared learning community focused on common needs and shared resources.

Title: A Watershed-Integrated Sciences Partnership (WISP)
Institution: The University of Massachusetts--Boston
PI/co-PI: Robert F. Chen, William E. Robinson, Michael Shiaris, Clara Jennings, and Marilyn Decker,
Partner School Districts: Boston Public, Milton Public, Dedham Public
Funding: $1,497,458 total for 3 years
Number of Fellows/year: 10 Graduate and 3-5 Undergraduate
Grade Band: Middle School
Setting: Urban, suburban
Disciplines: Geosciences, Biology, Chemistry, Computer Sciences

Habitat fragmentation is the process by which large areas of continuous habitat are divided into smaller pieces (i.e. "habitat islands" or "patches"), usually due to human activity. Understanding why some species are intolerant of habitat fragmentation and disappear from isolated patches, whereas other species are widely distributed and maintain a presence even in remote fragments is a central issue in both basic community ecological research and conservation biology. A key hypothesis is that differences in dispersal abilities among species strongly influence distribution patterns. The connection between how easily species move between patches and their presence in isolated communities has often been hypothesized but rarely experimentally evaluated. The goal of this project is to uncover the relationship between dispersal ability and community composition for tropical understory forest birds in an archipelago of forested islands. This will be accomplished by evaluating the Restricted Dispersal Hypothesis, which states: Variation in behavioral or physiological traits among species of forest understory birds, such as willingness or ability to cross a habitat gap, explains biogeographic patterns of island occupancy. To assess dispersal ability, I will conduct a series of simple experiments where birds are transported by boat to various distances away from mainland forest and released to document their abilities to fly successfully back to mainland. Preliminary results show a strong positive correlation between the maximum distance flown in release trials and the distance to the most isolated island inhabited by each species. Broader scientific impacts are clear: connectivity of fragments in tropical landscapes is critical to ensure persistence of entire regional avifaunas. Without corridors of habitat through which birds may move among patches, fragmented landscapes will lack the subset of avifaunas which are poor dispersers.

DESCRIPTION (provided by applicant): The human immunodeficiency virus type 1 (HIV-1) is the causative agent in the acquired immune deficiency syndrome (AIDS). Despite breakthroughs in therapy, there is an urgent need for novel anti- HIV agents that are targeted at new sites of the viral replication cycle. One such target is integrase (IN), an enzyme essential for HIV replication. Several classes of IN inhibitor have been identified and a proposed inhibitor-binding pocket for three such classes of inhibitor has been described. The nature of the inhibitor-binding pocket and the role each amino acid within the pocket plays in inhibitor binding, on the enzymatic activities of the protein, and on HIV replication will be investigated. Furthermore, the mechanisms by which HIV becomes resistant to such inhibitors will be explored. To accomplish this task, the following specific aims are proposed: 1. Map an HIV IN inhibitor-binding pocket or pockets. 2. Determine the biological effects of mutations within a proposed IN inhibitor-binding pocket. 3. Determine the nature of resistance to IN inhibitors. 4. Co-crystallize IN with inhibitors. Through the successful completion of these aims, the nature of the inhibitor-binding pocket on HIV IN will be determined. Ultimately, these findings will be used to synthesize more potent inhibitors of HIV IN that may prove useful in the treatment of HIV infection. Specifically, molecules will be synthesized that interact maximally with each residue within the inhibitor-binding pocket based on chemical interactions, size, and charge within the pocket. Moreover, by understanding the nature of inhibitor resistance, new molecules with activity against inhibitor-resistant HIV can be designed and synthesized.

The mechanisms underlying the generation of tropical diversity have eluded biologists for centuries. This project tests the hypothesis that variation in mobility across taxa will promote or retard long-distance gene flow and thereby drive differences in population subdivision, divergence, and ultimately speciation. This SGER will generate preliminary estimates of gene flow across a sampling transect and demonstrate the degree of spatial pattern in genetic structure within our target taxa.

This study will be the first to quantify experimentally the potential mobility of Neotropical birds and similarly will be the first to compare estimates of mobility with long-term patterns of gene flow. The resulting clarification of the links between behavior and population subdivision have far-reaching implications for our understanding of the historical processes of population differentiation, lineage divergence, and speciation. The results will have important and direct conservation applications for the many taxa (avian and otherwise) that occur in rapidly fragmenting tropical forests and will provide insight into the consequences of population (dis)connectivity in tropical landscapes.

A grant has been awarded to the University of Massachusetts Boston under the direction of Dr. Sarah Oktay-Quigley for partial support for the acquisition of broadband internet capability for the Nantucket Field Station (NFS) facility. In addition, funds granted will be used to purchase much needed computer and data transfer equipment to enrich research and instructional programs, archive decades of environmental and biological data, provide real-time web data feeds, and expand the usage of the facility. This grant will significantly increase the NFS' ability to support research use and to maintain its high quality of instruction.

The multidisciplinary nature of the programs supported by the NFS is reflected in the topics of current courses taught on site: coastal ecology, salt marsh ecology, marine invertebrate ecology, environmental geology, oceanography, hydrogeology, art, ornithology, linguistics, instructional design, and medical counseling. Examples of research and educational programs that will benefit from this grant include the following: NFS participation in an island-wide Biodiversity Assessment Initiative, collaboration on water quality surveys with the Town of Nantucket, a citizen beach profiling project, and funded projects investigating coastal circulation, fisheries management, groundwater flow, and salt marsh remediation. The NFS also provides laboratory space for many visiting scientists funded through the NSF on studies ranging from gray seal repopulation surveys to the reintroduction of the American Burying Beetle. The Research Experience for Undergraduates (REU) Program in Ecology and Conservation Biology at UMass Boston culminates their annual summer program with a retreat to the Field Station to present their summer research projects and conduct field trips. The research facility is available for use by all scientific, local government, and environmental organizations on Nantucket.

The NFS' unique location on Nantucket enables research addressing a wide range of environmental concerns such as habitat protection of endangered species like the northern harrier to identification of pollution threats to sole source aquifers. The NFS is closely linked with the town of Nantucket, local environmental and land conservation non-governmental agencies, citizen scientists and naturalists, the arts community, and the educational system. As such, we have a great responsibility to inspire environmental stewardship and provide scientific data that can be used in environmental management decisions. This award will benefit a rapidly growing research community, enable the dissemination of large amounts of data between area ecological stations, and provide a storehouse of educational materials available to the community. The NFS is open to the public and provides educational outreach through an interpretive nature trail and interactive research demonstrations. Hosting school groups, senior citizen trips, organic landscaping forums, poetry performances, and Native American Heritage programs are among its many contributions to the community.

This award supports the development of a miniature radio tag capable of communicating with cell tower receivers normally used by cellular phones. The device is essentially a stripped-down version of a cell phone with low enough mass (2 grams) to permit its attachment to migratory birds or other small animals. To conserve power, a timer in the unit will keep it dormant until preprogrammed dates when the transmitter will activate and attempt to make contact with a nearby cell phone tower. Because the device will remain off during an extended period, and then activate for only long enough to make contact with the nearest receiver, a tiny battery is expected to provide sufficient power for several contacts over a period as long as 2 years. Each unit will communicate a unique identifying number, so that individual tagged birds can be linked to a specific location. Following the contact, the PI will receive notification of the tag identity and location from the cellular network provider by email. The tag will be useful in studies of migration and dispersal, both of which are nearly universal behaviors among animals, particularly birds. Despite their importance, the impact of these behaviors on population dynamics remain major unanswered questions in biology, in large part because of our inability to track Individual animals throughout their annual cycle. The strategy is expected to locate birds to within a 5 km radius, a completely unprecedented level of precision for locating individual small migratory animals. The project is a collaboration of ecologists and electrical engineering researchers that will involve undergraduate and graduate students in collaborative learning opportunities, including both design and field testing of the instrument.

Software evolution, through maintenance or updates, requires the greatest effort in the software industry's product life-cycle. This effort is increasing with the industry's desire to be more responsive to customer needs. Mass customization, and related theories, provides guidance for producing high quality, low cost, mass-produced craft products. The design theories, however, provide no guidance for post-purchase customization, as required of software evolution. This project contributes to a Science of Design by addressing how to keep a software application's behavior in line with the requirements. The Requirements Monitoring (ReqMon) approach taken in this research provides guidance on when and what aspects of software should be evolved by dynamically monitoring individual user goals.

Assistive technologies (AT), which support individuals with disabilities such as cognitive impairments (CI), are in the vanguard of those that require individually personalized software. Monitoring individual user goals during their use of AT may mitigate the commonplace abandonment of AT, by providing clinicians and designers the necessary and timely feedback for continuous adaptation and redesign of software-intensive AT. A new, personalized design science is needed to improve the design, use, function and stability of AT systems to assist the large and growing population of individuals that required AT to fully participation in society.

This research is developing user goal monitoring tools and theory in support of dynamically personalizing AT specifically, and software evolution more generally. This research will offer two contributions. First, the monitoring method provides an approximate solution to understanding the dynamically changing needs of software users. Second, the mass-personalized software development (MPSD) theory provides a framework for analyzing continuously personalized designs in mass markets. MPSD suggests strategies for post-purchase customization of digital products.

AIDS education /prevention; meeting /conference /symposium

[unreadable] DESCRIPTION (provided by applicant): With increasing resistance and toxicity to existing anti-retroviral agents, it is imperative that inhibitors targeted at steps in the life cycle of the human immunodeficiency virus (HIV) other than protease and reverse transcriptase be developed. Integrase (IN) inhibitors have moved into clinical trials. Therefore, resistance to IN inhibitors will arise. Specifically, it is hypothesized that resistance to IN inhibitors will adversely affect the biochemistry and structure of IN and the interactions between IN and its inhibitors. Second, through synthesis of analogues derived from existing IN inhibitors, the nature of the interactions between IN and its inhibitors can be probed. Ultimately, this will lead to inhibitors of the integration reaction that enter into animal and human testing. To test these hypotheses we propose the following specific aims: 1. Select for IN inhibitor resistant HIV and map resistance mutations. 2. Determine the effects resistance mutations have on IN, HIV replication, and integration. 3. Synthesize analogues of the DCTA's and DKA's to identify compounds with improved anti-HIV activity, improved activity against IN, and improved cellular entry. 4. Map amino acids that bind inhibitors in solution. These studies will determine the mechanisms by which IN becomes resistant to inhibitors and the cost such resistance has on viral fitness. Additionally, the NMR studies will map an inhibitor-binding pocket on the HIV IN protein and identify the specific residues that interact with IN inhibitors. The long-term aim of these studies will be to obtain information critical for the rational synthesis of second generation, clinically-useful inhibitors of HIV IN with activity against both IN inhibitor-sensitive and inhibitor-resistant isolates of HIV. One HIV protein, integrase, is critical for HIV replication and thus progression to AIDS. Inhibitors of integrase are in clinical testing. Understanding how HIV becomes resistant to these compounds and how such compounds interact with integrase are fundamental to the synthesis of better anti-HIV drugs. [unreadable] [unreadable] [unreadable]

0608934
Park

The goal of the project is to develop an on-chip spectroscopy system for cancer detection. The project can have impact on treating melanoma, which is the cancer that the investigators have focused on for early detection. The proposed goal is to use nanoprobes attached to DNA probes as a tool for biomarker detection which will enable a compact on-chip detection system that will provide a highly accurate and inexpensive blood test. The planned device will be suitable for use in physicians' offices rather than only at hospitals. The important component of the system will be a tunable negative refractive index photonic crystal. Tunability will be achieved in Si nano-rods PC assembly embedded in polymeric medium by mechanical stretching of the film. The broader impacts will be in terms of nanotechnology and student training, especially in involvement of underrepresented minorities.

[unreadable] DESCRIPTION (provided by applicant): The broad, long-range objective of this proposal is to identify pathogenic autoantigens in and to develop diagnostics and therapeutics for rheumatoid arthritis (RA). Recent studies identified citrullinated fibrin as a candidate autoantigen in RA, and native fibrinogen was previously described as a candidate autoantigen. Citrullination (deimination) results from the conversion of peptidyl-arginine to peptidyl-citrulline by peptidyl arginine deiminase (PAD). To assess B cell reactivity against fibrinogen in RA we synthesized overlapping native and citrulline-substituted peptides representing the a- and b- chains of fibrinogen for inclusion on synovial protein microarrays. Synovial mircroarray analysis demonstrated autoantibodies targeting epitopes derived from predominantly native, and to a lesser extent citrullinated, fibrinogen in 20% of RA patients. Based on these results we developed a fibrinogen-induced arthritis (FIA) mouse model using native human fibrinogen as the immunizing antigen. Mice with FIA exhibit erythema and swelling encompassing the digits and midfoot, and histophathology demonstrates mononuclear cell infiltrates and synoviocyte proliferation. In this model we demonstrate strong T cell reactivity to native fibrinogen. Synovial protein microarray analysis demonstrated strong autoreactive B cell responses to epitopes representing native fibrinogen, and spreading to citrullinated fibrinogen, gp39 and collagen type V. We propose to investigate the mechanisms underlying FIA including the role of T cells, antibodies and immune complexes in mediating arthritis (Aims 1 and 2). We also propose to apply synovial micoarrays to survey autoantibody reactivity against native and citrullinated fibrinogen in established and pre-disease serum samples derived from RA patients (Aim 3). Our overriding hypothesis is that native and/or citrullinated fibrinogen/fibrin is a pathogenic autoantigen in RA, and that autoimmunity against fibrinogen/fibrin defines a molecular subtype of RA (representing approximately 20% of RA patients). Relevance to public health: RA affects 0.6% of the world population, yet the triggering antigens remain poorly understood. We propose to investigate the potential role for the clotting protein fibrinogen as a pathogenic autoantigen in RA. The success of the proposed studies could lead to development of novel diagnostic tests and therapeutics for RA. [unreadable] [unreadable] [unreadable]

Changes in tropical forests worldwide are a real and urgent problem. Many of these changes are attributed to obvious destructive interventions such as logging and burning. The influences of global climate change on tropical forests have been documented also. Trees grow more slowly in hot years and many tropical streams are more acidic in El Niño years. Evidence suggests there are other factors that may play a significant role as well. Extinction of tropical frog species is probably due to a complex interaction of climate change and susceptibility to a fatal fungal disease. The overarching goal of this project is the creation of an interdisciplinary network of scientists from tropical field sites with long-term data sets to test hypotheses about the causes of ongoing changes in tropical forests. The network meetings and the resultant research will enable the project to evaluate the likely effects of changes in forest dynamics, project these impacts into future decades, and plan ways to lessen the destructive impact of the changes.

The broader importance of this project concerns how the health of the tropical environment is connected to the condition of the entire planet and to the health and economic well-being of its human inhabitants through mechanisms such as the spread of disease vectors like ticks and mosquitoes and disruption of crop pollination. This compelling scientific importance is coupled with the integration of outreach to K-12 and adult learning groups in the network activities to facilitate greater understanding about how changes in tropical forests have world-wide implications.

One of today?s most challenging design issues is the threat of radiation-induced soft errors in CMOS digital systems. In nanometer technologies, the frequency of soft errors affects the markets of consumer electronics and networking, not just aerospace or military applications. This research aims to develop mitigation strategies that reduce the overall soft error rate while minimizing traditional cost metrics such as silicon area, power consumption, and performance degradation. Both technology scaling and system complexity have motivated designers to rely upon cell libraries and reusable cores in their design flow. This work investigates the fundamental fault generation and fault transport of radiation-induced soft errors within those building blocks. By identifying the fundamental characteristics of soft errors, design principles can be developed to improve the starting point for reliability of all types of integrated circuits, from avionics and space applications to enterprise servers, network routers, and control systems. This work includes simulation of irradiated individual circuits as well as experimentation to analyze the full hardware implementation of a microprocessor. The research leverages and integrates traditional domains such as computer architecture, VLSI design, fault tolerance, and radiation effects. Another critical component of this effort is the recruitment and retention of students in science and engineering from traditionally underrepresented groups. The PI has partnered with the Tennessee Louis Stokes Alliance for Minority Participation program at Vanderbilt University to provide summer undergraduate research opportunities and professional development seminars to help students prepare for and succeed in graduate school.

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (03) Biomarker Discovery and Validation and specific Challenge Topic, 03-AR-103 Biomarkers: Bench to Bedside for Autoimmune and Inflammatory Skin and Rheumatic Diseases. Title: Proteomic Identification of Actionable Biomarkers in Rheumatoid Arthritis Project Summary/Abstract Rheumatoid arthritis (RA) is the most common inflammatory joint disease of autoimmune etiology and remains a cause of substantial morbidity and mortality. Effective treatment of RA has been impeded by a paucity of diagnostic/predictive biomarkers of RA, largely as a result of the heterogeneity of the disease and a lack of insight into the mechanisms that underlie the onset and progression of RA. Nevertheless, the advent of biological therapeutics has led to significant advances in the treatment of RA. Promising findings from several placebo-controlled trials support the concept of treating patients in the early stages of RA (early RA) with combination therapies (e.g., methotrexate in concert with an anti-TNF agent) in order to slow and prevent joint damage. Furthermore, recent data suggest that it might be possible to induce disease remission in patients with early RA, such that anti-TNF therapy could then be withdrawn. At present, however, RA is diagnosed once arthritis is already established, a time at which the window of opportunity for effective treatment may have been missed. A test for the early diagnosis of RA is therefore warranted, as early diagnosis would enable the identification of patients with asymptomatic and/or early arthritis for their enrollment in primary RA prevention trials, and could ultimately be used by primary care physicians and rheumatologists to identify pre-disease RA patients that would benefit from early therapeutic intervention. A corollary of this is the need to determine what specific therapy an RA patient should receive, given that approximately one-third of RA patients exhibit robust responses to anti-TNF therapeutics - currently a mainstay of RA therapy - while one-third do not exhibit clinical improvement. Thus, a test that enables prediction of whether or not an RA patient will respond to anti- TNF and other disease-modifying therapies would be of great value to rheumatologists and patients alike. For this Challenge Grant application we propose the development of tests for (i) the early diagnosis of RA, (ii) predicting the severity of RA, and (iii) guiding the selection of RA patients that should receive anti-TNF or small molecule therapies. Robust biomarkers are directly related to the mechanisms underlying disease, and this proposal will provide insights into the mechanisms that underpin the development of autoimmunity in RA, the progression of RA, and the response to anti-TNF therapy. Our laboratory developed RA antigen microarrays to profile the specificity of autoantibody responses in RA. RA antigen microarray analysis revealed the targeting of a variety of candidate native and citrullinated antigens by autoantibodies in established RA. In addition, through the use of optimized BioPlex bead-array methods for the analysis of cytokines in RA sera, we demonstrated that blood cytokine levels are elevated in one-third of patients with early RA, and that elevated blood cytokines are associated with autoantibody targeting of citrullinated proteins. Furthermore, we identified autoantibody and cytokine signatures that differentiate between distinct subsets of RA patients, thus providing insight into the heterogeneity of RA. In Aim 1, we will expand and apply RA antigen arrays and bead array cytokine assays to characterize serial pre-arthritis samples to determine the specificity and titers of autoantibodies, as well as the levels of serum cytokines, and to define their temporal relationships to the onset of clinical RA. Our overriding hypothesis is that asymptomatic individuals that ultimately develop clinical RA exhibit a series of pre-arthritis phenotypes characterized initially by the production of autoantibodies, subsequently by an increase in cytokine and chemokine levels, and finally by epitope spreading of the autoantibody response, which results in progression to clinical arthritis. Elucidation of the hierarchy of epitope spreading and cytokine elevations will provide insights into the events that trigger progression to clinical RA. Such findings could lead to development of an early RA diagnostic that could provide the basis for preventive interventions in RA. The proposed studies will also identify biomarkers associated with progression to severe RA, and these biomarkers will provide insights into the mechanisms underlying progression of disease. We will further apply these proteomic technologies to identify biomarkers that are (i) predictive of and (ii) pharmacodynamic markers for response to anti-TNF and small molecule therapies. In Aim 2, we will extend our efforts to convert these biomarkers onto the clinical-grade BioPlex assay format, and we will use BioPlex technology for the high-throughput characterization of all samples in the pre-disease, disease progression, and response to therapy cohorts. The success of this proposal would result in the development of novel clinical diagnostic tests that would transform the care for patients with RA. Rheumatoid arthritis (RA) is a chronic autoimmune arthritis that affects 0.6% of the world population. This proposal will identify novel autoantibody and cytokine biomarkers for (i) early diagnosis, (ii) predicting disease severity, and (iii) guiding therapeutic decision making for the treatment of RA.

DESCRIPTION (provided by applicant): The human immunodeficiency virus (HIV) is the causative agent for the acquired immune deficiency syndrome (AIDS). It is predicted that globally approximately 33,000,000 individuals are currently infected with HIV. Although a number of significant advances have been made to our understanding of the molecular and cellular biology of HIV, our understanding of the pathogenesis of AIDS remains less well understood. Despite numerous efforts, vaccination attempts have largely failed. Likewise, although therapy is highly effective, the mechanisms by which HIV becomes resistant to drugs are less clearly defined. For fourteen years the Palm Springs Symposium on HIV/AIDS has been one of the leading national meetings bringing together experts and young investigators to discuss research on HIV and on AIDS. The symposium offers evolving topics on an annual basis that cover pathogenesis, vaccines, and drug development. The topics for 2009-2011 are proposed as "HIV and the Immune System: Back to Basics", "Novel Drug Targets and Mechanisms of Resistance", and "Molecular Mechanisms Leading to AIDS", respectively. Twenty invited speakers have been identified and have accepted their invitations for the 2009 meeting. A similar number of speakers will be invited to subsequent meetings. Continuing this intimate meeting is important for the community of HIV/AIDS investigators to share data, to form collaborations, and to make progress on the elimination of AIDS as an illness.

This grant provides support for travel, conference registration fees, and accommodation costs for students selected to attend the Doctoral Symposium being held at the 2009 International Conference on Requirements Engineering (RE?09) in Atlanta, USA, 31 August ? 4 September 2009. The International Requirements Engineering Conference is sponsored by the IEEE and is the premier academic and industrial event in the field of Requirements Engineering. The Doctoral Symposium at RE?09 provides a venue for young researchers to access worldwide expertise in software engineering. The Symposium is a one-day closed RE?09 event that provides a forum for Ph.D. students to publicly discuss their research goals, methods, and results at an early stage in their research. The Symposium aims to provide useful guidance to the students from a panel of experts, for completion of the dissertation research and initiation of a research career.

DESCRIPTION (provided by applicant): Rheumatoid arthritis (RA) is the most common inflammatory joint disease of autoimmune etiology. Characteristic histologic features in RA joints are synovial hyperplasia, inflammatory cell infiltrates, bone erosions and fibrin deposits. Carboxypeptidase B (CPB) is well established to play an anti-fibrinolytic role by removing C-terminal lysine residues from fibrin, thereby preventing its cleavage by plasmin. Recently, C3a, C5a, thrombin-cleaved osteopontin (OPN-R) and bradykinin were identified as additional substrates of CPB. These substrates are involved in inflammatory pathways including chemotaxis and T cell activation. CPB removes arginine residues from the C-terminus of these substrates and is thereby postulated to modulate biologic function of these inflammatory mediators. We discovered that CPB deficient mice developed dramatically more severe arthritis as compared to wild type (WT) controls following transfer of anti-collagen antibodies. C5 deficient mice were also protected from arthritis, while bradykinin B2 receptor deficient mice developed arthritis equivalent in severity to that in WT mice. CPB deficient mice exhibited increased leukocyte chemotaxis in an acute peritonitis model, and in vitro chemotaxis assays showed that thrombin-cleaved OPN and C5a act as chemoattractants. Genetic association studies using tag single nuclear polymorphisms (SNPs) representing the CPB2 gene showed that the minor allele SNP rs1409433 was associated with a reduced RA disease susceptibility. The non- synonymous C1064T CPB SNP is in strong linkage disequilibrium with rs1409433, and the C1064T variant encoding CPB Thr325Ile has been reported to possess a longer half-life (Schneider et al, 2002). Our overriding hypothesis is that CPB plays a central role in down- regulating inflammatory responses in RA. We hypothesize that CPB cleaves C5a and OPN-R to inactivate their chemotactic properties, and thereby reduces inflammatory responses that contribute to the development and progression of RA. Finally, we hypothesize that individuals possessing the C1064T CPB variant express CPB Thr325Ile which possesses a longer half- life, and that long half-life CPB is associated with reduced incidence and severity of RA. This proposal is to investigate the role of CPB in RA: Aim 1 will utilize murine models of RA to further characterize the mechanisms by which CPB modulates inflammatory arthritis;Aim 2 will determine if CPB cleavage of C5a and OPN-R inactivates their chemotactic properties;Aim 3 will investigate the genetic influence of CPB in human RA;and Aim 4 will characterize CPB protein expression in human RA. PUBLIC HEALTH RELEVANCE: Rheumatoid arthritis (RA) is a chronic autoimmune arthritis that affects 0.6% of the world population. Current therapies are only partially effective, and there is great need for more effective therapeutic approaches. Success of the proposed experiments would demonstrate that CPB is a natural down-regulator of inflammation in RA. The proposed experiments will provide insights into pathogenesis, and could lead to development of new therapeutic approaches for RA.

Most plant species depend on animals for successful reproduction. However, many plants and their associated pollinators are declining for reasons that are not well known. This project examines the extent to which pollen limitation is due to reduced movements of pollinators caused by landscape fragmentation and habitat loss. Since most pollinators are very small, the effects of habitat fragmentation on their movement has never before been tested. A large-scale experiment designed to disentangle the effects of tropical forest landscape connectivity, patch size, and habitat loss on plant pollination will test this idea. The study will be conducted in a tropical forest; this forest type is declining rapidly and plant-pollinator interactions in tropical forests is often highly specialized.

The project will capitalize on the charisma and diversity of tropical hummingbirds to transmit ideas about the importance of biodiversity conservation and ecosystem services to the general public. Results will be transferred to over 10,000 school children and undergraduates annually. School children in Oregon and Costa Rica will take part in a citizen-based monitoring effort to test whether landscape fragmentation affects hummingbirds.

DESCRIPTION (provided by applicant): New Orleans (NO), Louisiana is a city of 343,000, based on 2010 Census data (60% Black, 33% Caucasian, 5% Hispanic, 3% Asian). Tulane Medical Center {including the medical school, hospital and clinic) has provided health care In NO since 1834. In 2005, Hurricane Katrina struck and destroyed most of the city with high winds and/or flood waters that took weeks to subside. Since then, many local institutions have rebuilt, including Tulane's cancer research program, which exclusively provides services to several large segments of the community. These include: 1) the Tulane Medical Center/Hospital and Clinic System, including the Tulane Comprehensive Cancer Clinic, the Tulane Medical Center of Louisiana/New Orleans (MCLNO) clinic, and the Tulane Lakeside Clinic; 2) the Medical Homes program, based on a series of neighborhood clinics in NO; 3) the local Veterans Administration (VA) Hospital; and 4) Tulane Oncology Affiliates, a group of regional private oncology practices. These facts have prompted the leadership of Tulane Cancer Center (TCC) to seek an MB-CCOP grant in order to expand access to clinical research in these populations. Dr, William Robinson, Maxwell E. Lapham Professor of Gynecologic Oncology will serve as PD/PI and has a long record of clinical cancer research success as a Study Coordinator and site PI with GOG, SWOG and ACTG. Dr Marcelo Blaya, Assistant Professor, Medical Oncology, will serve as co-PI, and has extensive experience with NCl cooperative group research as well. Dr Eboni Price, Assistant Professor, Internal Medicine, will serve as Co-PD/PI for Cancer Prevention studies. Dr Roy Weiner, Associate Dean of Clinical Research, will serve as Associate PD, and provide senior leadership and advice. Dr Aniko Vigh is the Director of the TCC Clinical Research Office and will serve as Administrator/Manager. This team is well prepared to successfully manage an MB-CCOP in the NO community it serves.

I/UCRC for Integrated Design-for-Reliability for Electronics (iDRE)

1160865 University of California-Riverside; Albert Wang
1160870 Vanderbilt University; Bharat Bhuva

The University of California-Riverside (UC-R) and Vanderbilt University (VU) are collaborating to establish the proposed center, with UC-R as the lead institution.

The Center for Integrated Design-for-Reliability for Electronics (iDRE) will conduct research on investigating radiation and transient electrostatic discharge (ESD) induced failures to integrated circuits (IC), multi-chip nodules (MCM) and system-in-package (SiP), and microelectronics systems; as well as developing reliability solutions by integrated designs for industrial electronics. An additional objective of the planning grant proposal is to hold a meeting with potential industrial partners to discuss the research needs for integrated design-for-reliability (DfR) and center operation mechanisms.

If successful, research activities at the iDRE Center will reveal fundamentals and mechanisms of ESD and soft error failures, as well as deliver ESD protection and soft error mitigation solutions to advanced ICs and systems. The research outcomes will cast huge impacts on modern microelectronics and system products, and will have significant benefits to the electronic industry and the nation's economy. The proposed integrated DfR reliability solutions will affect all aspects of human lives, from communications and entertainment, to information processing and storage, to life-threatening devices and mission-critical tasks, and so on. The PIs also propose a diversity plan to promote involvement of female and underrepresented minority students in engineering education and research.

This research seeks to uncover explanations and principles about how requirements for information systems evolve and how they are managed across project contexts. It will enumerate project design workflows and practices to determine how different forms of artifact and process distribution affect requirements engineering goals and project success. Currently there are no rigorous, theory-based approaches to understanding and explaining large-scale distribution of requirements, though there is evidence of its success. Requirements engineering approaches address spatial and social distribution, and to a lesser extent, structural and temporal distribution. Most importantly, the combination of these issues, in total, has not been considered. Consequently, we cannot say which configuration of practices is best suited to achieve specified development goals, such as reduced time to market, or increased software quality and customer satisfaction. New theoretical models and empirical research are needed to understand the effects of distribution on evolving requirements.

The project will (1) conduct field studies and ethnography, (2) analyze work procedures via grounded theory and comparative methods, (3) construct tools for data analysis, model building, and model analysis, and (4) analyze models via simulations and goal analyses. It will apply a distributed requirements framework consisting of four forms of distribution (social, spatial, structural, and temporal) and four requirements tasks (discovery, specification, negotiation, monitoring) in conjunction with the theory of distributed cognition to analyze requirements knowledge evolution in software projects. Additionally, it will design new tools that help acquire, model, and analyze distributed requirements workflows.

The research aims to develop critical insights on emerging realities in large-scale design projects, which represent one of the drivers for economic growth and new forms of industrial organization. Yet, many software organizations are constrained by methodological and tool factors that do not recognize the increased challenges for requirements engineering. This research highlights the ways in which designers learn to manage the diversity of inputs and constraints, and seeks to understand processes that enhance software-based open innovation in the future.

The distinction between computing and communication has blurred with the improvements in semiconductor technology as well as the speed and reliability of computer networks. At a macroscopic level, individuals increasingly rely upon smart phones, cloud computing, and similar infrastructure that combines computing systems with networking to accomplish their daily tasks. Advantages are realized from the seamless interconnection of computing systems and the network. Many end-users even consider the client device, the server, and the network as one unit that is used for productivity and/or entertainment. At the microscopic level, similar efficiencies present themselves when computing and networking blend. In an ideal case, the linkage between the two areas should not require the use of special-purpose software, because installing software on a network node to enable this blending can potentially cause the node to be unstable, more complex, and introduce security flaws. However, there is a significant challenge in linking the two domains without the use of additional software. This research focuses on understanding and characterizing the connection between the computing node and the network.

Since the internal components of a node are shared resources between all processes, including those that require network-based I/O, it is possible to infer the load on the internal components by observing variations in delay between successive network packets that are generated by the node. This inference materializes as a "delay signature," and can be used to blend the areas of architecture and networking. Specifically, this information can be used to develop algorithms for network security and management. For example, by simply probing a node and collecting its responses, it can be determined that the internal components (e.g., microprocessor) are heavily utilized. If the node is expected to be idle, this could be an indication that the node has been compromised and is running unauthorized software. This information can also be used for job scheduling in cluster grids. By monitoring Message Passing Interface (MPI) messages between grid nodes, the loads on the nodes can be determined without querying nodes directly. As a result, resource discovery messages are not needed. Another use of this information can be to predict system degradation and failure. As a node's resources become exhausted, the node generates a unique traffic pattern. This pattern is emitted prior to node failure and can be used to signal a switch to a secondary server.

This project uses a holistic approach that combines computer architecture and computer networking to investigate and characterize how the microarchitecture affects the network packet generation process. The delay signature provides information that can be attributed to the internal state and settings of the microarchitecture. Architectural settings, such as processor affinity, multi-threading, and power-saving modes, affect the delay signature. The PIs use a hardware testbed and a system simulator to characterize the basic mechanisms within the microprocessor that are manifested in the observable delay signature.

The investigators incorporate team-based laboratory projects within their computer architecture and computer networking courses to demonstrate the relationship between the two domains and to promote integrated learning by students in both areas. Potential applications of the delay signature include providing security for networked nodes by monitoring unauthorized utilization and increasing resiliency of a computing system by detecting patterns that predict a node failure.

The distinction between computing and communication has blurred with the improvements in semiconductor technology as well as the speed and reliability of computer networks. At a macroscopic level, individuals increasingly rely upon smart phones, cloud computing, and similar infrastructure that combines computing systems with networking to accomplish their daily tasks. Many end-users even consider the client device, the server, and the network as one blended unit that is used for productivity and/or entertainment. At the microscopic level, the linkage between the two areas ideally should not require the use of special-purpose software, because installing software on a network node to enable this blending can potentially cause the node to be unstable or more complex, and potentially introduce security flaws. However, linking the two domains without the use of additional software remains a significant challenge. This research focuses on understanding and characterizing the connection between the computing node and the network to meet that challenge. For example, by simply probing a node's network traffic and collecting its responses, it can be determined that the internal components (e.g., microprocessor) are heavily utilized. If the node is expected to be idle, then this indicator could signal that the node has been compromised and is running unauthorized software.
 
This project uses a holistic approach that combines computer architecture and computer networking to investigate and characterize how the microarchitecture affects the network packet generation process. Since the internal components of a node are shared resources among all processes, including those that require network-based I/O, it is possible to infer the load on the internal components by observing variations in delay between successive network packets that are generated by the node. This inference materializes as a "delay signature," and can be used to blend the areas of architecture and networking. The delay signature provides information that can be attributed to the internal state and settings of the microarchitecture. Architectural settings, such as processor affinity, multi-threading, and power-saving modes, affect the delay signature. The PIs use a hardware testbed and a system simulator to characterize and model the basic system components that can have a significant (direct or indirect) impact on packet generation. The project culminates with the creation of a general-purpose engine that automates the detection of utilization signatures and uses those signatures to predict node utilization remotely. The PIs incorporate team-based laboratory projects within their computer architecture and computer networking courses to demonstrate the relationship between the two domains and to promote integrated learning by students in both areas. Further, the investigators employ an outreach plan with complementary components to: (1) encourage students to enter the science and engineering fields and (2) mentor potential faculty members to serve as educators and role models. Potential applications of the delay signature include: (1) providing security for networked nodes by monitoring unauthorized utilization and (2) providing efficient scheduling in cluster grids.

DESCRIPTION (provided by applicant): Rheumatoid arthritis (RA) is an autoimmune synovitis that affects 0.5% of the world population, yet the key autoantigen targets remain unknown. Production of autoantibodies, such as the anti-citrullinated protein antibodies (ACPAs), is a hallmark of RA. However, which antigens the critical ACPAs and other RA- associated autoantibodies target remains largely unknown. Also unknown is how these ACPAs develop, how similar the ACPA repertoires are between different individuals with RA, and whether and how they contribute to the pathogenesis of RA. So far, the research field has lacked the means to comprehensively characterize the autoantibodies associated with a given disease and to then rationally winnow them to those that are important-that is, those that either drive the disease or serve as identifiers of the key antigens that trigger the pathogenic T-cell response. We have now developed antibody repertoire capture technology, a high- throughput method that allows us to do just that. Harnessing the power of next-generation sequencing, we have developed a novel method for barcoding all the cDNAs generated from individual antibody-expressing cells, thereby enabling high-throughput analysis of the paired heavy- and light-chain immunoglobulin genes expressed by single B cells, plasmablasts, or plasma cells. We hypothesize that we can elucidate the pathogenic autoantibody responses associated with RA by defining the antibody repertoire of plasmablasts and antigen-sorted memory B cells in the blood, and of plasmablasts and plasma cells in the synovium, of individuals with RA. We will then bioinformatically analyze the antibody sequences we obtain to generate evolutionary trees of the antibody repertoires and thereby identify and clone the affinity-matured antibodies that are likely the key autoantibodies. We will identify the antigens targeted by these recombinant, affinity-matured autoantibodies, investigate how their specific sequences develop, dissect their binding and immunostimulatory properties, and assess their pathogenicity. Success of this proposal would shed light on the development of the autoantibody response and identify the key autoantigens targeted in RA, findings that could lead to the development of new diagnostics and therapies for RA.

This engineering education research project seeks to understand the degree to which intersectionality within the engineering academic profession has been addressed in minority mentoring initiatives for African American engineering doctoral students and postdoctoral researchers. Intersectionality is defined as the interplay of racial stereotypes, gender biases and other issues. A wide variety of mentoring programs in various formats have not been able to alter the slow progress of African Americans in engineering faculty ranks. This research will closely examine existing mentoring programs through a single focused lens of African American doctoral and postdoctoral scholars. The intent is to utilize focus groups, surveys and interviews to synthesize their experiences with mentoring programs. The PI will then design a holistic racial and gender attentive mentoring program that will be implemented on a national scale with approximately 120 participants. This effort will leverage a prior award to this PI focused on both identifying the barriers and opportunities facing African American engineering doctoral candidates aspiring to the professoriate, and the issues facing African American faculty at all ranks.

The broader significance and importance of this project is the potential for development of a successful, holistic mentoring model that can be more broadly adapted to other racial/gender groups. A successful mentoring model should increase the persistence of underrepresented groups in the engineering academic ranks. Increasing the numbers of faculty role models from diverse backgrounds will create a more inclusive educational environment that will encourage an increasing number of diverse students to pursue engineering studies.

This project overlaps with NSF's strategic goals of identifying, sharing and expanding best practices for broadening participation in the engineering workforce. NSF focuses on broadening participation of groups, institutions, and geographic regions underrepresented in STEM disciplines, working with academic and private sector partners to make certain that STEM education and workforce preparation, infrastructure, and research opportunities are broadly available to ensure that the technical workforce and scientists and engineers have the skills and opportunities needed to flourish in a global knowledge economy.

Computer science and engineering must diversity its workforce to meet the future demands for the technical professions. professional development for minority scholars to meet the anticipated needs in the technical workforce. Racial and ethnic minority groups, including African Americans, Hispanics, and Native Americans, remain substantially underrepresented in engineering and science, especially at the level of Ph.D. researchers and faculty. The Academic and Research Leadership Symposium (ARLS) is a symposium that is co-located with the Annual Convention of the National Society of Black Engineers (NSBE). The purpose of the ARLS is to develop minority engineers in academia, industry, and government laboratories, whose careers involve a strong focus on research, in order to prepare them for leadership and success in their chosen discipline. The ARLS has two threads: (1) a faculty development thread, and (2) a researcher development and networking thread. It provides an opportunity for seasoned researchers (university, corporate, government) to nurture connections with their peers, and be excited and inspired by the latest discoveries and technical advances across many disciplines of engineering and science. Opportunities for new collaborations and strategic career advancements are anticipated. The researcher development and networking thread consists of a networking reception with a keynote presentation by a high-profile researcher, a session on career development in an R&D centric environment (e.g., The Researcher Entrepreneur and Senior Leadership Strategies), and a poster session organized by members of the ARLS network for more in-depth technical discussions.

A diverse engineering university faculty and workforce are necessary to achieve and maintain a country that is prosperous, secure, and attentive to the technological and social well-being of all individuals. Thus, this research study investigates one of the challenges to a diverse engineering faculty and workforce by exploring the causes behind why African Americans remain one of the most underrepresented racial groups in engineering faculty positions, remaining steady at 2.5% for the past five years, despite intervention programs that aim to broaden the participation of minorities in engineering. This three-year study explores the barriers and opportunities facing a cohort of (1) African American engineering PhD students/candidates/postdocs pursuing engineering faculty careers and (2) current and former African American engineering faculty members. The proposed study examines factors that impact the production of African American PhDs in engineering, as well as those factors that affect the pathway to tenured faculty positions in engineering. This research includes an assessment of the current engineering faculty climate through surveying and interviewing African Americans in engineering, from PhD candidates and postdoctoral students through full professors, including a subset of former African American engineering faculty. This study analyzes the faculty-engineering climate by including the implementation of a national survey for Black PhD engineering students, Black engineering faculty, and a subset of former Black engineering faculty. The PIs will also interview a subset of each of these groups. The methodological and analytical structure of this study is guided by the literature on racial/gender stereotypes and Social Cognitive Career Theory. The intellectual merit of this work should lead to a better understanding of the career trajectories African American PhDs in engineering and the technical, societal, and cultural influences that impact their career decision making. Although this study focuses on African American faculty, overall faculty diversity creates a more effective learning environment. Schools with greater racial diversity tend to have better retention, satisfaction, and intellectual development. The broader impact of this study has the potential to change the model of how engineering candidates of color are mentored and primed for engineering faculty positions.

The IEEE International Symposium on Hardware-Oriented Security and Trust (HOST) brings together an interdisciplinary group of researchers and practitioners in hardware security. The program features technical papers, panels and invited talks, and discussion sessions. The seventh HOST will be held in fall 2015 in the Washington, DC, area. The funds support travel grants for students to attend the conference. HOST is the top conference devoted to hardware security. By increasing student participation at the HOST conference, it may encourage more students to get involved in hardware security research and pursue further graduate education and careers in this area.

The Principal Project will characterize B cell responses in patients with autoimmune disease by using a DNA-barcoding technology recently developed in the Robinson lab, termed 'antibody repertoire capture' (ARC). The approach couples DNA barcoding with next-generation sequencing to enable large-scale characterization of the paired heavy-chain (HC) and light-chain (LC) immunoglobulin genes expressed by single plasmablasts or antigen-specific B cells. Although methods exist for profiling antibodies, none are able to comprehensively characterize the, antibodies involved in an active immune response and to then bioinformatically identify those most likely to be functional i.e., those that either drive the disease or serve as identifiers of the key antigens that trigger pathogenic autoimmune responses. The scale of the sequencing datasets generated by ARC enables bioinformatic generation of phylogenetic trees of the antibody repertoire. These phylogenetic trees guide identification of clonal families of affinity-matured antibodies and thereby rational selection of key antibodies, which can then be expressed for direct analysis of their binding and functional properties. We propose to use ARC to sequence and comprehensively dissect the autoantibody responses in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), and, leveraging resources from the other ACE Projects and Cores, to test the overarching hypothesis that monoclonal autoantibodies contribute to the pathogenesis of RA and SLE by forming proinflammatory immune complexes (ICs) that dual-stimulate immune cells (by simultaneously engaging a pattern recognition receptor and either the B-cell or the Fc receptor). For instance, we hypothesize that RA-associated anti-citrullinated proteins antibodies (ACPAs) form ICs that dual-stimulate macrophages to produce TNF, and B cells to produce ACPAs; and that SLE-associated anti-nuclear antibodies (ANAs) bind nuclear antigens and thereby form ICs that dual-stimulate dendritic cells to produce IFN, and B cells to produce ANAs. In Aim 1, we will use ARC to sequence the antibody repertoires in patients with RA or SLE and identify antibody profiles that are associated with specific clinical subtypes or response to therapy. In Aim 2, we will clone and express rationally selected, affinity-matured antibodies from individuals with RA or SLE, and elucidate their autoantigen targets. In Aim 3, will characterize key RA and SLE recombinant antibodies identified in Aim 2 and uncover mechanisnis by which they contribute to autoimmune inflammation. Success would provide insights into the role of autoantibodies and the mechanisms by which they contribute to the pathogenesis of RA and SLE, and could lead to development of novel diagnostic tests and therapeutic approaches.

? DESCRIPTION (provided by applicant): The broad, long term objective of the Stanford Technology Accelerating Medicines Partnership (STAMP) Center is to serve as the leader within the RA/SLE AMP Network in the development and implementation of multiplexed mechanistic assays for AMP studies. Although we propose to focus on SLE, our methods will be used in pilot studies for RA and can be applied to any autoimmune disease. Investigators participating in this AMP proposal, and other collaborators at Stanford, have been leading innovators in the development of high-throughput genomics and proteomics technologies for studying cancer and autoimmunity. Project 1 (Steve Quake and Howard Chang) will perform transcript profiling using RNA-Seq of single cells isolated from tissue samples and blood, then separating into individual wells using Fluidigm-based microfluidics devices (C1) or FACS. The Chang lab will determine binding of transcription factors to open chromatin, repressing and/or activating transcriptional programs involving NFAT, NF¿B, RORs, IRFs, STATs, and other transcription factors. Project 2 (Garry Nolan) will employ CyTOF to study cells obtained from blood and tissue, characterizing cell surface molecules, signaling molecules, and phospho-specific epitopes in discrete cellular subsets. Upregulated transcripts from Project 1 will inform selection of CyTOF antibodies in an iterative process during the UH3 funding period. Project 3 (Bill Robinson, Mark Davis and PJ Utz) will use autoantibody profiling, FACS, repertoire-sequencing and yeast display to characterize antigen- specific B and T cells in blood and isolated from tissues. The Robinson and Davis labs will characterize the B and T cell receptor repertoire by sequencing heavy and light chain genes from FACS sorted plasmablasts, and FACS or tetramer sorted T cells, as well as cells isolated from tissue. Monoclonal antibodies will be cloned, expressed, and purified for antigen identification. Antigen targets will be discovered (Utz and Robinson) using protein arrays, which will serve as a core assay for all AMP Network Centers. Pilot projects are also proposed including plasma virome sequencing and two projects to develop and implement multiplexed ion beam imaging (MIBI). Finally, to insure availability of blood, kidney, skin, and synovium for our studies, subjects will be recruited from Stanford and the Bay Area (SLE); UCLA and Cedars- Sinai (SLE); and UCSD (RA), as well as from other AMP Centers. Integration of all assays at one AMP Center will facilitate discovery of pathways, molecules, and new drug targets.

Influenza viruses are major respiratory tract pathogens that present significant risks to individuals of all ages, particularly during pandemics. These risks would be greatly amplified should the lethal avian influenza strains, such as H5N1 and H7N9, become capable of human-to-human transmission, or if a new recombinant strain were engineered as a bioterror agent. Although vaccination can prevent influenza-associated morbidity and mortality, it does not do so in some people, even in healthy adults. This proposal seeks to leverage technological advances in the Robinson and Blish laboratories to build on findings from prior CCHI studies at Stanford that highlighted environmental exposures and the diversity and maturity of the lymphocyte repertoire as critical factors influencing vaccine responses. We hypothesize that prior environmental exposures influence the maturity and diversity of the immune repertoire and responses to different vaccines and play a greater role than genetics in generating effective vaccine-induced immunity against influenza. To investigate this hypothesis, we will use technologies recently developed in the Robinson and Blish laboratories to comprehensively define the phenotypic and functional repertoires of B cells, T cells and NK cells responding to influenza vaccination. We will couple our unique ability to measure the diversity, clonality, and functions of T, B, and NK cell populations at the single-cell level with the resources, expertise, and emerging technologies provided by the other U19 Projects and Cores (e.g., blood samples and clinical data from an extensive twin cohort assembled by the Clinical Core; CyTOF provided by the HIMC and developed by Project 4). In Aim 1, we will evaluate B cell, T cell and NK cell responses to influenza vaccination in monozygotic and dizygotic twins to determine the role of genetics and environment in the response to vaccination, comparing concordance in monozygotic twin pairs to that in dizygotic twin pairs. In Aim 2, we will determine how the vaccination method influences lymphocyte diversity and maturity, by comparing the B, T, and NK cell repertoire and responsiveness between monozygotic twin pairs receiving intranasally administered live attenuated vaccine (LAIV) and those receiving parenterally administered inactivated flu vaccine (TIV). In Aim 3, we will perform an integrated analysis of the datasets from this and other U19 Projects and Cores to determine the optimal levels of immune diversity and maturity that predict effective vaccination. Thus, by dissecting an extensive twin cohort with state-of-the-art tools, we propose to deliver a singularly detailed, integrated picture of the mechanisms governing human immune responses to influenza vaccination.

DESCRIPTION (provided by applicant): Antibodies against tumor-related antigens are produced in humans with a variety of cancers. Although several methods exist for profiling antibodies, none are able to comprehensively characterize the antibodies produced in an immune response and to then rationally identify those likely to be functional-i.e., those that are key to the containment or pathogenesis of cancer. To address this challenge, we are developing technology that uses DNA barcoding for the large-scale sequencing of paired heavy- (HC) and light-chain (LC) antibody genes from individual B cells. This technology enables sequencing of the paired HC+LC antibody genes from hundreds to thousands of individual B cells in each experiment, thereby yielding antibody sequence datasets that enable bioinformatic generation of phylogenetic trees representing the antibody repertoire, as well as rational selection of key antibodies for recombinant expression, characterization of their antigen targets, and use as diagnostics or therapeutics. In cancer, we hypothesize that in-depth characterization of the antibody repertoire produced by circulating plasmablasts will uncover functional anti-tumor antibody responses. We detected high levels of plasmablasts (activated B cells) in the blood of individuals with metastatic lung adenocarcinoma whose cancer had not progressed several years after therapy. We applied our antibody repertoire capture (ARC) technology to plasmablasts isolated from a lung adenocarcinoma patient, and used bioinformatics to generate an phylogenetic tree of the antibody response and to select antibodies from large clonal families for recombinant expression. We identified three recombinant antibodies that bound in immunohistochemical analyses to >80% of lung adenocarcinomas derived from other patients. This application comprises four aims: In Aim 1, we will (i) develop a microfluidic front end that increases the throughput and depth of sequencing of ARC by an order of magnitude, and (ii) technically validate ARC for sequencing anti- cancer antibody responses. In Aim 2, we will use ARC to profile and compare the antibody responses in non- progressors and progressors with lung adenocarcinoma. In Aim 3, we will clone and express rationally selected, affinity-matured antibodies of plasmablasts from individuals with lung adenocarcinoma and identify their tumor antigen targets. In Aim 4, we will evaluate the potential of select anti-tumor antibodies and tumor antigens to serve as diagnostic/prognostic biomarkers or therapeutics for lung adenocarcinoma. Success of the proposed studies would transform cancer research by technically refining and validating ARC technology as a tool for the analysis of anti-cancer antibody responses-one that would advance our understanding of anti-cancer antibody responses and facilitate development of antibody-based diagnostics and therapeutics.

Vanderbilt University, Fisk University, and Wake Forest University will collaborate to develop, study and refine a model to recruit, retain and advance historically underrepresented minority (URM) women from doctoral degree attainment to postdoctoral fellowship to tenured track positions in STEM. This alliance was created in response to the NSF's Alliances for Graduate Education and the Professoriate (AGEP) program solicitation (NSF 16-552) The AGEP program seeks to advance knowledge about models to improve pathways to the professoriate and success of URM graduate students, postdoctoral fellows and faculty in specific STEM disciplines and/or STEM education research fields. AGEP Transformation Alliances develop, replicate or reproduce; implement and study, via integrated educational and social science research, models to transform the dissertator phase of doctoral education, postdoctoral training and/or faculty advancement, and the transitions within and across the pathway levels, of URMs in STEM and/or STEM education research careers.

As our nation is confronted with a STEM achievement gap between URM and non-URM undergraduate and graduate students, our universities and colleges struggle to recruit, retain and promote URM STEM faculty who serve as role models and academic leaders for URM students to learn from, to work with and to emulate. Recent NSF reports indicate that URM STEM associate and full professors occupy 8% of these senior faculty positions at all 4-year colleges and universities and about 6% of these positions at the nation's most research-intensive institutions. URM women hold smaller shares of these academic STEM positions and an increase in their representation is essential since female URM undergraduate students, enrolled in STEM majors, outnumber their male peers. The current AGEP project has potential to advance a model to improve the representation of URM women in STEM faculty positions, eventually providing URM STEM role models to a STEM undergraduate and graduate students at postsecondary academic institutions.

The project includes activities to transition postdoctoral fellows into faculty positions, or a postdoc-to-faculty bridge program, to provide junior faculty with mentoring and to assist junior faculty in developing strong scholarly identities. The integrated research will include cross-sectional surveys, three-year longitudinal surveys and small-group interviews to gain a better understanding of the processes facilitating the choices women and URMs make in their STEM careers. Variables to study include gender and race differences, social relationship influences, the academic-professional culture and the institutional context. Vanderbilt and Fisk Universities will institutionalize the key model interventions, stage the model components for implementation at Wake Forest University, and disseminate the model to the network of 40 institutions represented in the Collaborative to Advance Equity through Research. The National Academy of Science's Ford Foundation Diversity Fellows program will work with the alliance to identify and recruit promising postdoctoral associates for project participation. The Anna Julia Cooper Center at Wake Forest will conduct scale up and dissemination activities for the alliance. Formative and summative evaluation work will be performed by an external evaluation team, via a subaward from Vanderbilt to the Institute for Broadening Participation. An external advisory board will provide advice to the project team through annual consultation.

Across the nation, there is a dearth of underrepresented faculty in engineering and computing, and many explanations have been presented to explain the shortages in popular and scientific literature. Over the years, a plethora of strategies, initiatives, and programs have been created to address the broadening participation challenges in the engineering professoriate, but minimum visible gains have been achieved. This project is closely aligned with a long-standing interest of the National Science Foundation to increase the number of underrepresented faculty in the engineering and computing professoriate. By executing this project, the investigators expect that there will be an increase the number of Black engineering and social scientist faculty who are trained to serve as coaches and mentors for scholars from underrepresented groups at the crucial, pre-faculty career stage; increase in the number of diverse doctoral and postdoctoral scholars who become employed as engineering and computing faculty; and improvement of the success rate of Black engineering and computing faculty through the tenure process. As way of increasing the number of underrepresented groups who enter the engineering professoriate, the project's plan comprised the following:

(1) Developing effective materials for coaching-based mentorship of future engineering faculty.
(2) Recruiting and training current tenured faculty in engineering and social science to serve as coaches
(3) Implementing the coaching-based mentorship.
(4) Implementing a plan to sustain the coaching-based mentorship beyond the project funding.
(5) Implementing a plan to sustain the coaching-based mentorship beyond the project funding.
(6) Coordinating and assessing the coaching-based mentorship.

Guided by the theoretical and scientific literature on Communities of Practice (CoP) and Social Cognitive Career Theory (SCCT), the investigators outlined a comprehensive project to develop and implement a coaching-based mentoring program to enhance approaches to diversify the engineering and computing professoriate and to develop methods to teach and train tenured engineering and social science faculty effective mentoring skills. For this project, the investigators plan to extend this mentoring intervention to 40 underrepresented doctoral and postdoctoral scholars in engineering and computing, with a particular focus on those who are interested in pursuing faculty positions. Additionally, the plan includes the services of an external evaluator, who will execute multi-level, multi-phased, mixed methods data collections from all the key project stakeholders (e.g., coaches, mentees, postdoctoral manager, graduate students, and the investigators. This project is timely and likely to help improve engineering success outcomes in the professoriate and doctoral programs.

Reliability analysis of integrated circuits (ICs) has become a greater concern in the development of computing systems. Technology scaling offers more transistors to enable system-on-a-chip (SoC) integration, but it also means more transistors that can be affected by radiation-induced faults. Designers must consider how those faults impact the entire computing system by including levels of abstraction in both hardware and software. Reliability cannot be addressed by considering the device, circuit, architecture, or application layer individually. Cross-layered modeling and simulation enables a better understanding of the complex interactions among particle physics, fabrication technology, processor architecture, and the software stack in order to develop reliable computing systems. With the increase in cost and time of the system design process, pre-fabrication modeling of radiation effects has become a critical field of research. By understanding these processes, designers can meet traditional constraints of performance and power, while addressing concerns for the soft error rate (SER). Potential application domains include, but are not limited to, automotive embedded systems, high-performance computing, and spaceborne environments.
 
This project creates a research infrastructure that links soft error simulations at the device, circuit, architecture, and application levels. This infrastructure provides a testbed for characterizing the resilience of algorithms for computer and computational sciences. It also contains testbeds for evaluating the reliability of the architecture and the design of computing systems. By providing up-to-date models of the effects of single events on current and future technologies, it facilitates the development of computing models and technologies based on emerging scientific ideas from the research community. The infrastructure will be accessible to a larger research community through web-based content (e.g., online tutorials and webinars) and interactive workshops at conferences and symposia. This project broadens the participation of groups traditionally underrepresented in the areas of science, technology, engineering, and mathematics (STEM) through outreach to encourage students to enter the science and engineering fields. The STEM Scholars Program at North Carolina A&T provides a computing skills workshop to African-American high school students.

? DESCRIPTION (provided by applicant): This renewal proposal for the Adult and Pediatric Rheumatology Training Program focuses on providing exceptional basic, translational and clinical research training to MD/MD PhD trainees interested in research careers studying autoimmunity and rheumatic diseases. A Selection Committee selects 5 of the most qualified candidates from the high quality pool of rheumatology and immunology fellows, as well as MD/MD PhD or PhD fellows from other departments who have strong commitments to these research areas. Physician fellows are eligible at the end of their clinical training and must commit to 2 years of training with >80% protected research time. Fellows can select training in either Basic and Translational Research (Track 1) or Clinical Investigation (Track 2).Training in each track will be comprised of a hypothesis-driven research project, required and recommended course work specific to the research track, and skill development (eg., grant and manuscript preparation) required for a successful independent research career. Trainees in Clinical Investigation (Track 2) are eligible for obtaining a Master of Science (MS) in epidemiology or health policy. These fellows should commit to 3 years of training to insure adequate time to complete. Other trainees in Track 2 have selected course work from the MS curriculum. In addition to course work, all trainees in both Tracks, required to attend weekly lectures in rheumatic diseases, journal clubs, immunology and rheumatology yearly retreats, semiannual T32 fellow specific retreats, and Responsible Conduct of Research courses. Multiple other offerings are specific to each Track such as Advanced Immunology Seminars or the Intensive Course in Clinical Research, and trainees are encouraged to cross-over when interested. These various courses, conferences and venues will provide opportunities for interactions between the rheumatology and immunology T32 trainees and the many other immunology fellows, faculty and students involved in the broad base of research at Stanford. Faculty mentors are selected carefully for their research expertise and mentoring competencies. Rigorous evaluation of the program identifies opportunities for improvement and progress toward goals. We will leverage Stanford's rich research and training culture to provide the environment to train the next generation of academic independent investigators in rheumatology and Immunology.

? DESCRIPTION (provided by applicant): The broad, long term objective of the Stanford Technology Accelerating Medicines Partnership (STAMP) Center is to serve as the leader within the RA/SLE AMP Network in the development and implementation of multiplexed mechanistic assays for AMP studies. Although we propose to focus on SLE, our methods will be used in pilot studies for RA and can be applied to any autoimmune disease. Investigators participating in this AMP proposal, and other collaborators at Stanford, have been leading innovators in the development of high-throughput genomics and proteomics technologies for studying cancer and autoimmunity. Project 1 (Steve Quake and Howard Chang) will perform transcript profiling using RNA-Seq of single cells isolated from tissue samples and blood, then separating into individual wells using Fluidigm-based microfluidics devices (C1) or FACS. The Chang lab will determine binding of transcription factors to open chromatin, repressing and/or activating transcriptional programs involving NFAT, NF¿B, RORs, IRFs, STATs, and other transcription factors. Project 2 (Garry Nolan) will employ CyTOF to study cells obtained from blood and tissue, characterizing cell surface molecules, signaling molecules, and phospho-specific epitopes in discrete cellular subsets. Upregulated transcripts from Project 1 will inform selection of CyTOF antibodies in an iterative process during the UH3 funding period. Project 3 (Bill Robinson, Mark Davis and PJ Utz) will use autoantibody profiling, FACS, repertoire-sequencing and yeast display to characterize antigen- specific B and T cells in blood and isolated from tissues. The Robinson and Davis labs will characterize the B and T cell receptor repertoire by sequencing heavy and light chain genes from FACS sorted plasmablasts, and FACS or tetramer sorted T cells, as well as cells isolated from tissue. Monoclonal antibodies will be cloned, expressed, and purified for antigen identification. Antigen targets will be discovered (Utz and Robinson) using protein arrays, which will serve as a core assay for all AMP Network Centers. Pilot projects are also proposed including plasma virome sequencing and two projects to develop and implement multiplexed ion beam imaging (MIBI). Finally, to insure availability of blood, kidney, skin, and synovium for our studies, subjects will be recruited from Stanford and the Bay Area (SLE); UCLA and Cedars- Sinai (SLE); and UCSD (RA), as well as from other AMP Centers. Integration of all assays at one AMP Center will facilitate discovery of pathways, molecules, and new drug targets.

Physical science and engineering remain the least diverse of all STEM fields---with regard to women, underrepresented minorities, and persons with disabilities---across all levels of STEM education and training. SCI-STEPS is an NSF INCLUDES Design and Development Launch Pilot that will address this persistent challenge by developing a complete end-to-end pipeline (or system of pathways) from the beginning of college to the PhD, and then into the workforce. Many isolated efforts to broaden participation have shown promise, but they have not produced big enough impact. SCI-STEPS represents a concerted set of coordinated interventions---consciously facilitated, systemically linked, and purposefully disseminated. SCI-STEPS represents a broad regional network among major research universities, Historically Black Colleges and Universities, comprehensive universities, community colleges, national labs, and major scientific organizations. The goal of the network is to ensure that underrepresented individuals in the physical sciences and engineering can get from their starting point in STEM higher education---freshmen at 2-year or 4-year college---through the higher education pathways leading to an appropriate terminal degree and employment in the STEM workforce.

Women, underrepresented minorities, and persons with disabilities collectively represent the majority of college-age individuals entering higher education with an expressed interest in physical science and engineering. A growing body of research indicates that academic and social integration may be even more influential than academic abilities for retention of students. Thus, interventions aimed at stemming the losses of these individuals must ultimately be aimed at changing the system---including unwelcoming institutional climates, racial/ethnic/gender stereotyping, a lack of mentors with whom to identify, and evaluation methods that emphasize conformity over individual capabilities---rather than changing the individual. The SCI-STEPS pilot focuses effort on institutional readiness for implementation of best practice interventions at four key junctures: (i) college freshman to sophomore; (ii) undergraduate to graduate; (iii) PhD to postdoc; and (iv) postdoc to workforce.The pilot will proceed in three steps: (1) a planning phase, (2) development of an initial end-to-end pathways model with four Juncture Transition teams, and (3) scale-up of the SCI-STEPS "network of networks" with all initial partners. By addressing these objectives through a collective impact framework and embedded research, this pilot will demonstrate how best-practice interventions at each pathway juncture can be dovetailed and scaled up across a broad range of institutional types and across a large but distinct geographical area. Addressing these objectives will thus also serve to advance Broadening Participation efforts at a national scale, by suggesting the forms of institutional partnerships and best-practices that may inform other alliances in other STEM disciplines and/or different regional areas.

Despite well-funded efforts to diversify engineering in the United States, Americans who identify as Black, Latinx, and Indigenous (Native American, Alaskan, or Hawaiian) remain underrepresented and marginalized throughout engineering academic training and employment. Previous research has identified that underrepresented PhD-degreed engineers of color are less likely to be employed in engineering jobs compared to their overrepresented counterparts. However, there is much less certainty on the reasons behind this disparity. Moreover, the employment paths of White women in science, technology, engineering, and math (STEM) employment have been extensively explored along with the career trajectories of graduate students of color in STEM, but there has been very little attention to engineers of color with PhDs post-graduation. The focus of this research is to understand the employment paths for two populations: underrepresented engineers of color who have successfully navigated the challenges of obtaining an engineering PhD, along with Asian engineering PhD holders who are well-represented in the field. This research will investigate two critical factors that can help explain disparities for underrepresented engineers of color: (1) their experiences of racialization, and (2) their interest in using engineering as a mechanism to decrease social inequities. This research will address the gap in understanding the factors that drive these disparities in engineering employment outcomes across racial groups and how to decrease them, thereby aiding engineering education and industry communities in becoming and remaining more diverse, innovative, and affirming.

The researchers will answer these questions through a mixed-methods design, including a longitudinal survey component and qualitative in-depth interviews. Survey respondents will be engineers of color who are working in industry and the academic workforce within a decade of graduating with their PhD. Participants will be recruited through the professional networking site LinkedIn as well as professional organizations for engineers of color. In the first phase, survey data and analysis, using structural equation modeling, will determine how respondents' experiences of racial inequity and bias at work and their motivations and efforts to address social inequities through engineering vis-a-vis their employers, predict their employment outcomes (e.g., commitment, intentions to quit) by increasing their "job embeddedness." The analyses will test this model across different race groups. Collecting follow-up employment data one year later will provide a measure of actual persistence. Survey findings will inform the content of the qualitative interview protocol. Interview participants will be people of color with an engineering PhD who are not directly using their engineering skillset because they either switched from an engineering job into a non-engineering job or transitioned into a leadership or administrative position. These findings will help to identify why engineers of color with advanced doctoral training are either: (a) dissatisfied and pushed away from this workforce or (b) persist in their work to transition into different roles that allow them to diversify the field. Insights from this research will inform workplace training webinars promoting diversity and inclusion in engineering workplaces in both industry and academia.

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.

Bivalves, such as mussels, oysters, and clams, belong to the second most diverse animal phylum. They play a critical role in coastal ecosystems, help maintain water quality, and are widely used in aquaculture. Despite their importance, many developmental processes are not well understood in bivalves. Several genes have been identified to be correlated with male and female specification and development; however, their exact role is not yet known. The goal of this project is to characterize these genes in bivalve development and identify their roles in the process of differentiating male and female reproductive organs. Our methods involve documenting levels of in gene expression in different tissues and experimentally lowering their expression level to observe changes in development. This project will provide critical insight into the process of male and female specification and differentiation of reproductive organs. Our project will also help to increase opportunities for students that have obligations outside of the classroom that hinder their ability to pursue a STEM degrees. Research shows that online laboratory courses, especially those that include “Do it yourself” (DIY) kits and manuals, can be as effective as in person labs and decrease barriers for students that have difficulty devoting time to in person laboratory courses. This project aims to create a completely online DIY laboratory in marine biology and physiology that will act as a model for increasing accessibility to STEM labs and broaden participation.

Although some hypothetical models have been proposed for mechanisms underlying male and female specific gonadal development in mollusks, there have been very few experimental tests of gene function in this process. Using phylotranscriptomics, we have identified several putative gonadal development genes in bivalves, including a mollusk specific DMRT gene: DMRT1L. The primary objective of our proposed project is to characterize the role of putative gonadal development genes in a model, gonochoristic, adult bivalve, the blue mussel M. edulis through two specific aims: (1) Determine the temporal and tissue-specific expression patterns of male and female gonadal development genes using RT-qPCR and in situ hybridization in relation to gametogenesis. (2) Evaluate changes in gonadal development in males and females following knockdown of key gonadal development genes using RNAi (SoxH, DMRT1L, FoxL2, β-catenin). These genes have been studied in bivalves; however, this work has relied on correlations in gene expression between males and females and knowledge gained from distantly related species. The proposed work will verify the roles of these putative male and female developmental genes and will enable us to develop a transcript-based gonadal development pathway for bivalves. This proposed work will be transformative to understanding the relationships between male and female development pathways across distantly related metazoan species and how they evolved.

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.

Rheumatoid arthritis (RA) is an autoimmune synovitis that affects 0.5% of the world population. RA is characterized by intermittent flares of clinical arthritis that is thought to be mediated in part by anti- citrullinated protein autoimmune responses. The best established environmental risk factors for developing RA include cigarette smoking and periodontal disease, suggesting oral mucosa is a critical site for disease initiation. Nevertheless, the mechanisms by which these environmental exposures lead to RA development and progression remain poorly understood. We have established a clinical and technical protocol for repeated home finger stick blood collection in RA patients to allow for longitudinal RNA sequencing (RNAseq). Using this novel approach, we recently discovered bacteria characteristic of human oral mucosa in the blood of anti-CCP+ RA patients, followed by activation of a signature B cell immune response 3 weeks later, and then clinical flare of disease activity 2 weeks after that. We also investigated B cell responses to these pathogens. We demonstrated elevations in IgA blood plasmablasts both in pre-clinical RA as well as in established RA, with the continual re-activation of a distinct set of IgA/IgG plasmablast clonal families in established RA suggesting a persistent mucosally-driven germinal center reaction. We demonstrate that the recombinant Mabs encoded by the persistently reactivated IgA/G plamablast clonal families encode antibodies that react with both human citrullinated antigens and citrullinated isoforms of oral bacteria identified in the blood of patients antecedent to flares. We anticipate that RA plasmablast Mabs with distinct specificities, either alone or in immune complexes, mediate activation of distinct cellular responses that promote synovitis and tissue destruction in RA. This R01 proposal will test the hypothesis that mucosal breaks trigger plasmablast responses that encode anti-bacterial antibodies that cross-react with host citrullinated antigens. We further hypothesize that mucosal bacteria-induced ACPA activate cellular responses, including macrophage TNF production, NETosis and osteoclast activation, which promote synovitis and joint tissue destruction in RA. Aim 1 will identify the antibody repertoires responsive to pre-flare bacteremia in two independent cohorts of RA patients. Aim 2 will characterize RA plasmablast IgA/G Mabs and sera for reactivity to citrullinated isoforms of bacterial species derived from subgingival collections. Aim 3 will characterize periodontitis tissue for evidence of RA-related autoimmunity. Aim 4 will determine the mechanisms by which cross reactive Mabs, either alone or in immune complexes, mediate arthritis. Success of this proposal would demonstrate that citrullinated periodontal bacteria and mucosal breaks play a key role in mediating RA flare, findings that could lead to development of new diagnostic and therapeutic approaches.