Illinois Waterfowl Surveys and Investigations W-43-R-62 Annual Progress Report Period: 1 July 2014 – 30 June 2015

This study addresses the following objectives: 1)Inventory abundance and distribution of waterfowl and other waterbirds (a minimum of 10 species and guilds) during autumn migration at a minimum of 40 sites along the Illinois and central Mississippi rivers; 2) Investigate the ecology of canvasback and lesser scaup during spring migration in the central Illinois River valley (IRV) and Pool 19 of the Mississippi River; 3) Estimate waterfowl and other waterbird population sizes (a minimum of 10 species and guilds) during autumn migration using an aerial quadrat survey in the IRV for comparison with aerial inventories (Objective 1); 4) Determine breeding bird use of a minimum of 10 moist-soil wetlands managed for waterfowl during summer in central Illinois; 5) Investigate the breeding ecology of sandhill cranes during spring and summer in northeastern Illinois; 6) Distribute our findings to site managers and biologists, make recommendations for future management, and draw conclusions relevant to regional conservation planning during the project period as appropriate and requested.Illinois Department of Natural Resources, Division of Wildlife & U.S. Fish and Wildlife Service Contract Number: RC09-13FWUIUCunpublishednot peer reviewedOpe

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA

HIV-infected individuals are living longer on antiretro-viral therapy, but many patients display signs that in some ways resemble premature aging. To investigate and quantify the impact of chronic HIV infection on aging, we report a global analysis of the whole-blood DNA methylomes of 137 HIV+ individuals under sustained therapy along with 44 matched HIV- individuals. First,we develop and validate epigenetic models of aging that are independent of blood cell composition. Using these models, we find that both chronic and recent HIV infection lead to an average aging advancement of 4.9 years, increasing expected mortality risk by 19%. In addition, sustained infection results in global deregulation of the methylome across \u3e80,000 CpGs and specific hypomethylation of the region encoding the human leukocyte antigen locus (HLA).We find that decreased HLA methylation is predictive of lower CD4/CD8T cell ratio, linking molecular aging, epigenetic regulation, and disease progression

Identifying disability level in multiple sclerosis patients in a U.S.-based health plan claims database.

AIMS: In clinical trials, disability progression in multiple sclerosis (MS) is measured by the Kurtzke expanded disability status scale (EDSS), which is not captured in routine clinical care in the U.S. This study developed a claims-based disability score (CDS) based on the EDSS for assigning MS disability level in a U.S. claims database. METHODS: This retrospective cohort study of patients with MS in the U.S., utilized adjudicated health plan claims data linked to electronic medical records (EMRs) data. Patients were identified between 1 January 2012 and 31 December 2016 and indexed on the first date of MS diagnosis. The CDS was developed to assign disability level at baseline using claims and ambulatory EMR records observed over the 1-year baseline period. All-cause healthcare costs were assessed by baseline disability level to validate the CDS. RESULTS: In total, 45,687 patients were identified in claims (full sample) and 1,599 linked to EMR (core sample). Over half of patients in both samples were classified with mild disability at baseline. Adjusted healthcare costs in patients with moderate and severe disability were 15% (p CONCLUSIONS: The CDS is the first claims-based measure of MS disability utilizing data from EMR. This novel measure advances the opportunity to examine outcomes by disability accumulation in the absence of standard markers of disease progression. Although formal validation of the CDS was not possible due to lack of available EDSS in the EMR, the economic burden results align with prior publications and show that healthcare costs increase with increasing disability. Future validation studies of the CDS are warranted

Work and Welfare in the American States: Analyzing the Effects of the JOBS Program

This research seeks to determine whether the Job Opportunities and Basic Skills GOBS) program (established under the 1988 Family Support Act) was successful in reducing the number of welfare recipients among U.S. states for the period 1984 to 1996. Within the context of two theoretical perspectives-developmental and rational choice-we assess the impact of JOBS on AFDC participation rates using a pooled time-series design. At best, JOBS had a minimal effect. We estimate that states with higher proportions of their AFDC populations enrolled in JOBS programs had only slightly lower rates of participation in AFDC. Other forces were far more influential in reducing welfare participation. In particular, states with higher per capita income, lower female unemployment rates, lower poverty rates, and higher wages for low-paying jobs had the lowest welfare recipiency The AFDC participation rates of neighboring states had a significant effect, as well. The analysis showed that more generous AFDC benefits exerted strong upward pressure on a state's welfare rolls.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress

SummaryWe screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O’nyong’nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern

Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.</p

Inheritance of DNA methylation differences in the mangrove Rhizophora mangle

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.Peer reviewe

Achieving a quantum smart workforce

Interest in building dedicated Quantum Information Science and Engineering (QISE) education programs has greatly expanded in recent years. These programs are inherently convergent, complex, often resource intensive and likely require collaboration with a broad variety of stakeholders. In order to address this combination of challenges, we have captured ideas from many members in the community. This manuscript not only addresses policy makers and funding agencies (both public and private and from the regional to the international level) but also contains needs identified by industry leaders and discusses the difficulties inherent in creating an inclusive QISE curriculum. We report on the status of eighteen post-secondary education programs in QISE and provide guidance for building new programs. Lastly, we encourage the development of a comprehensive strategic plan for quantum education and workforce development as a means to make the most of the ongoing substantial investments being made in QISE.Comment: 18 pages, 2 figures, 1 tabl

The higher education impact agenda, scientific realism and policy change: the case of electoral integrity in Britain

Pressures have increasingly been put upon social scientists to prove their economic, cultural and social value through ‘impact agendas’ in higher education. There has been little conceptual and empirical discussion of the challenges involved in achieving impact and the dangers of evaluating it, however. This article argues that a critical realist approach to social science can help to identify some of these key challenges and the institutional incompatibilities between impact regimes and university research in free societies. These incompatibilities are brought out through an autobiographical ‘insider-account’ of trying to achieve impact in the field of electoral integrity in Britain. The article argues that there is a more complex relationship between research and the real world which means that the nature of knowledge might change as it becomes known by reflexive agents. Secondly, the researchers are joined into social relations with a variety of actors, including those who might be the object of study in their research. Researchers are often weakly positioned in these relations. Some forms of impact, such as achieving policy change, are therefore exceptionally difficult as they are dependent on other actors. Strategies for trying to achieve impact are drawn out such as collaborating with civil society groups and parliamentarians to lobby for policy change