I\u27m With Her. And Her. And Her.

This paper describes my experience at the Women\u27s March on Washington in 2017 and how it has given me a new perspective

Creating a data resource: What will it take to build a medical information commons?

National and international public-private partnerships, consortia, and government initiatives are underway to collect and share genomic, personal, and healthcare data on a massive scale. Ideally, these efforts will contribute to the creation of a medical information commons (MIC), a comprehensive data resource that is widely available for both research and clinical uses. Stakeholder participation is essential in clarifying goals, deepening understanding of areas of complexity, and addressing long-standing policy concerns such as privacy and security and data ownership. This article describes eight core principles proposed by a diverse group of expert stakeholders to guide the formation of a successful, sustainable MIC. These principles promote formation of an ethically sound, inclusive, participant-centric MIC and provide a framework for advancing the policy response to data-sharing opportunities and challenges

Chaco Canyon Dig Unearths Ethical Concerns

The field of paleogenomics (the study of ancient genomes) is rapidly advancing with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a recent article by Kennett et al. (2017), “Archaeogenomic evidence reveals prehistoric matrilineal dynasty,” that brings several ethical issues to light that should be addressed in paleogenomics research (Kennett et al. 2017). The study helps elucidate the matrilineal relationships in ancient Chacoan society through ancient DNA analysis. However, we, as Indigenous researchers and allies, raise ethical concerns with the study’s scientific conclusions that can be problematic for Native American communities: (1) the lack of tribal consultation, (2) the use of culturally-insensitive descriptions, and (3) the potential impact on marginalized groups. Further, we explore the limitations of the Native American Graves Protection and Repatriation Act (NAGPRA), which addresses repatriation but not research, as clear ethical guidelines have not been established for research involving Native American ancestors, especially those deemed “culturally unaffiliated”. As multiple studies of culturally unaffiliated remains have been initiated recently, it is imperative that researchers consider the ethical ramifications of paleogenomics research. Past research indiscretions have created a history of mistrust and exploitation in many Native American communities. To promote ethical engagement of Native American communities in research, we therefore suggest careful attention to the ethical considerations, strong tribal consultation requirements, and greater collaborations amongst museums, federal agencies, researchers, scientific journals, and granting agencies

Evaluation of transboundary environmental issues in Central Europe

Central Europe has experienced environmental degradation for hundreds of years. The proximity of countries, their shared resources, and transboundary movement of environmental pollution, create the potential for regional environmental strife. The goal of this project was to identify the sources and sinks of environmental pollution in Central Europe and evaluate the possible impact of transboundary movement of pollution on the countries of Central Europe. In meeting the objectives of identifying sources of contaminants, determining transboundary movement of contaminants, and assessing socio-economic implications, large quantities of disparate data were examined. To facilitate use of the data, the authors refined mapping procedures that enable processing information from virtually any map or spreadsheet data that can be geo-referenced. Because the procedure is freed from a priori constraints of scale that confound most Geographical Information Systems, they have the capacity to generate new projections and apply sophisticated statistical analyses to the data. The analysis indicates substantial environmental problems. While transboundary pollution issues may spawn conflict among the Central European countries and their neighbors, it appears that common environmental problems facing the entire region have had the effect of bringing the countries together, even though opportunities for deteriorating relationships may still arise

Implementation of Electronic Adherence Monitors and Associated Interventions for Routine HIV Antiretroviral Therapy in Uganda: Promising Findings

BackgroundHigh, sustained adherence is critical for achieving the individual and public health benefits of HIV antiretroviral therapy (ART). Electronic monitors provide detailed adherence information and can enable real-time interventions; however, their use to date has largely been confined to research. This pilot study (NCT03825952) sought to understand feasibility and acceptability a relatively low-cost version of this technology and associated interventions for routine ART delivery in sub-Saharan Africa.MethodsWe provided two ART clinics in rural, southwestern Uganda with electronic adherence monitors for data-informed counseling as well as optional SMS messages to clients and/or social supporters (daily or triggered by missed or delayed doses) and/or an alarm. Clinic and ART client experiences were observed for 3 months per client, including time and motion studies. Qualitative interviews among clients, clinicians, and healthcare administrators were informed by the Consolidated Framework for Implementation Research.ResultsFifty-one ART clients were enrolled; 57% were male and the median age was 34 years. Choice of associated intervention varied among participants. The median number of visits during follow-up was two per client. Counselors reviewed the adherence data with 90% of clients at least once; 67% reviewed data at all visits. Average adherence was 94%; four clients had adherence gaps >1 week. Acceptability was high; all but one client found the monitor "very useful” and all found SMS “very useful.” Clinic visits among clients with the intervention lasted 4 min longer on average than those in standard care. The monitors and daily SMS generally functioned well, although excess SMS were triggered, primarily due to cellular network delays. Overall, participants felt the technology improved adherence, clinic experiences, and clinician-client relationships. Few worried about stigma and privacy. Cost was a concern for implementation, particularly at scale.ConclusionWe successfully implemented a relatively low-cost electronic ART adherence monitor and associated interventions for routine care in rural Uganda. Feasibility and acceptability were generally high, and individuals were identified who could benefit from adherence support. Future work should involve longitudinal follow-up of diverse populations, clinical outcomes, and detailed cost-effectiveness analysis to help drive policy decisions around the uptake of this technology for routine clinical care.Clinical Trial Registrationidentifier: NCT03825952

Convocation

Program listing performers and works performe

Mitigating the noise of DESI mocks using analytic control variates

In order to address fundamental questions related to the expansion history of the Universe and its primordial nature with the next generation of galaxy experiments, we need to model reliably large-scale structure observables such as the correlation function and the power spectrum. Cosmological $N$-body simulations provide a reference through which we can test our models, but their output suffers from sample variance on large scales. Fortunately, this is the regime where accurate analytic approximations exist. To reduce the variance, which is key to making optimal use of these simulations, we can leverage the accuracy and precision of such analytic descriptions using Control Variates (CV). We apply two control variate formulations to mock catalogs generated in anticipation of upcoming data from the Dark Energy Spectroscopic Instrument (DESI) to test the robustness of its analysis pipeline. Our CV-reduced measurements, of the power spectrum and correlation function, both pre- and post-reconstruction, offer a factor of 5-10 improvement in the measurement error compared with the raw measurements from the DESI mock catalogs. We explore the relevant properties of the galaxy samples that dictate this reduction and comment on the improvements we find on some of the derived quantities relevant to Baryon Acoustic Oscillation (BAO) analysis. We also provide an optimized package for computing the power spectra and other two-point statistics of an arbitrary galaxy catalog as well as a pipeline for obtaining CV-reduced measurements on any of the AbacusSummit cubic box outputs. We make our scripts, notebooks, and benchmark tests against existing software publicly available and report a speed improvement of a factor of $\sim$10 for a grid size of $N_{\rm mesh} = 256^3$ compared with $\texttt{nbodykit}$.Comment: 15 pages, 9 figures, public package (for power spectrum and control variates estimation

History and classification of Aigai virus (formerly Crimean-Congo haemorrhagic fever virus genotype VI)

Crimean-Congo haemorrhagic fever virus (CCHFV) is the medically most important member of the rapidly expanding bunyaviral family Nairoviridae. Traditionally, CCHFV isolates have been assigned to six distinct genotypes. Here, the International Committee on Taxonomy of Viruses (ICTV) Nairoviridae Study Group outlines the reasons for the recent decision to re-classify genogroup VI (aka Europe-2 or AP-92-like) as a distinct virus, Aigai virus (AIGV)

Nucleoside Analogue Reverse Transcriptase Inhibitors Differentially Inhibit Human LINE-1 Retrotransposition

Intact LINE-1 elements are the only retrotransposons encoded by the human genome known to be capable of autonomous replication. Numerous cases of genetic disease have been traced to gene disruptions caused by LINE-1 retrotransposition events in germ-line cells. In addition, genomic instability resulting from LINE-1 retrotransposition in somatic cells has been proposed as a contributing factor to oncogenesis and to cancer progression. LINE-1 element activity may also play a role in normal physiology. LINE-1 retrotransposition reporter assay, we evaluated the abilities of several antiretroviral compounds to inhibit LINE-1 retrotransposition. The nucleoside analogue reverse transcriptase inhibitors (nRTIs): stavudine, zidovudine, tenofovir disoproxil fumarate, and lamivudine all inhibited LINE-1 retrotransposition with varying degrees of potencies, while the non-nucleoside HIV-1 reverse transcriptase inhibitor nevirapine showed no effect.Our data demonstrates the ability for nRTIs to suppress LINE-1 retrotransposition. This is immediately applicable to studies aimed at examining potential roles for LINE-1 retrotransposition in physiological processes. In addition, our data raises novel safety considerations for nRTIs based on their potential to disrupt physiological processes involving LINE-1 retrotransposition