Copy and Pasting vs. Customization: Using Qualitative Analysis of NIH Grantees’ Data Management Plans to Shape Future DMP Support

In 2019, our school began requiring all of its NIH grantees to submit data management plans designed to prepare researchers for future requirements, such as the NIH Final Policy on Data Management and Sharing. In 2020-2021, the second year of this mandate, we achieved near 100% compliance with 600+ project-level DMP submitted. This presentation discusses analyzing the free text responses for the 2020-2021 set of DMPs. These responses describe practices related to data collection procedures, QA/QC procedures, data retention periods, data sharing, and access permissions when team members leave. Additionally, we asked respondents to identify relevant funder data management or sharing requirements, citations for data reuse, and applicable standards for data and metadata so that we could gauge awareness of these topics. Our analytical process involves iteratively creating a codebook based on a randomly selected subset of DMP responses. Once the codebook has been developed, we will independently code a second subset of DMP responses to establish inter-rater reliability, then code the entire data set of DMP responses. We will summarize these results using descriptive statistics and visualizations of the themes identified. We will also explain how we plan to use these findings to create guidance for future support and development of DMPs for NIH grantees. Of particular interest will be any evidence for substantive customization of DMPs when the research warrants the sharing of data, versus evidence of “box ticking” behaviors and other priorities that take precedence over sharing. By identifying existing practices, this analysis may also help us surface successful data management and sharing strategies that can be propagated across communities of practice

Patterns of Information Behavior and Prostate Cancer Knowledge Among African-American Men

The purposes of this study are to explore cancer information acquisition patterns among African-American men and to evaluate relationships between information acquisition patterns and prostate cancer prevention and control knowledge. A random sample of 268 men participated in a statewide interviewer-administered, telephone survey. Men classified as non-seekers, non-medical source seekers, and medical source seekers of prostate cancer information differed on household income, level of education, and beliefs about personal risk for developing prostate cancer. Results from multiple regression analysis indicated that age, education, and information-seeking status were associated with overall levels of prostate cancer knowledge. Results from logistic regression analyses indicated that men who included physicians as one of many information resources (medical source seekers) had superior knowledge over non-seekers and non-medical source seekers on 33% of individual knowledge details. The findings emphasize the need to connect lower-income and lower-educated African-American men to physicians as a source of prostate cancer control information

Characterization of a Netrin-4 Like Protein in \u3cem\u3eTetrahymena thermophila\u3c/em\u3e

The netrin family of proteins has homeostatic roles in vertebrate development and angiogenesis, and pathophysiological roles in the progression and metastasis of cancer. We have previously characterized a netrin-1-like protein in Tetrahymena thermophila, and have shown that vertebrate netrin-1, netrin-3, and netrin-4 all serve as chemorepellents in this organism. We are currently using Western blotting and immunofluorescence to further characterize the netrin-like proteins in Tetrahymena. Western blotting with our anti-netrin-4 antibody shows a band that is clearly visible in whole cell extract, but shows little reactivity with secreted protein, indicating that most of our netrin-4-like protein remains within the cell. Western blotting of whole cell extract with anti-netrin-1, netrin-3, and netrin-4 antibodies shows a clear band measuring 50 kD that stains with all three antibodies. Some lower molecular weight bands are also evident in all three blots, possibly due to proteolytic activity. Immunolocalization with an anti-netrin-4 antibody shows some colocalization with netrin-1, netrin-3, and ER Tracker™. Our anti-netrin-4 antibody localizes to the oral groove, basal bodies, and nuclei of cells, indicating a possible structural role for the netrin-4-like protein in this organism. Further research will involve determining the primary amino acid sequence of the 50 kD protein and comparing it with the Tetrahymena thermophila proteome database to help ascertain the physiological role of this protein

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.

The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in the large intestine are important to human health. The responses of three common gut bacteria species, and one opportunistic pathogen, to 117 commonly consumed foods, chemical additives, and plant extracts were tested. Many compounds, including Stevia rebaudiana and bee propolis extracts, exhibited species-specific growth inhibition by prophage induction. Overall, these results show that various foods may change the abundances of gut bacteria by modulating temperate phage and suggests a novel path for landscaping the human gut microbiome

Humanity’s diverse predatory niche and its ecological consequences

Although humans have long been predators with enduring nutritive and cultural relationships with their prey, seldom have conservation ecologists considered the divergent predatory behavior of contemporary, industrialized humans. Recognizing that the number, strength and diversity of predator-prey relationships can profoundly influence biodiversity, here we analyze humanity’s modern day predatory interactions with vertebrates and estimate their ecological consequences. Analysing IUCN ‘use and trade’ data for ~47,000 species, we show that fishers, hunters and other animal collectors prey on more than a third (~15,000 species) of Earth’s vertebrates. Assessed over equivalent ranges, humans exploit up to 300 times more species than comparable non-human predators. Exploitation for the pet trade, medicine, and other uses now affects almost as many species as those targeted for food consumption, and almost 40% of exploited species are threatened by human use. Trait space analyses show that birds and mammals threatened by exploitation occupy a disproportionally large and unique region of ecological trait space, now at risk of loss. These patterns suggest far more species are subject to human-imposed ecological (e.g., landscapes of fear) and evolutionary (e.g., harvest selection) processes than previously considered. Moreover, continued overexploitation will likely bear profound consequences for biodiversity and ecosystem function

Presidential Commission on the Supreme Court of the United States Final Report

On April 9, 2021, President Joseph R. Biden, Jr. issued Executive Order 14023 establishing this Commission, to consist of “individuals having experience with and knowledge of the Federal judiciary and the Supreme Court of the United States.” The Order charged the Commission with producing a report for the President that addresses three sets of questions. First, the Report should include “[a]n account of the contemporary commentary and debate about the role and operation of the Supreme Court in our constitutional system and about the functioning of the constitutional process by which the President nominates and, by and with the advice and consent of the Senate, appoints Justices to the Supreme Court.” Second, the Report should consider the “historical background of other periods in the Nation’s history when the Supreme Court’s role and the nominations and advice-and-consent process were subject to critical assessment and prompted proposals for reform.” Third, the Report should provide an analysis of the principal arguments for and against particular proposals to reform the Supreme Court, “including an appraisal of [their] merits and legality,” and should be informed by “a broad spectrum of ideas.” The Report begins by explaining the genesis of today’s Court reform debate, including by identifying developments that gave rise to President Biden’s decision to issue the April 2021 Executive Order, particularly the debates surrounding the most recent nominations. This Introduction emphasizes that the Court’s composition and jurisprudence long have been subjects of public controversy and debate in the nation’s civic life: The Court serves as a crucial guardian of the rule of law and also plays a central role in major social and political conflicts. Its decisions have profound effects on the life of the nation. Though conflict surrounding the processes by which the President nominates and the Senate confirms Justices is not new, it has become more intensely partisan in recent years. The Introduction also articulates three common and interrelated ideas frequently invoked in reform debates and throughout the Chapters of the Report: the importance of protecting or enhancing the Court’s legitimacy; the role of judicial independence in our system of government; and the value of democracy and its relationship to the Supreme Court’s decisionmaking. These important ideas can mean different things to different people. The Introduction discusses the range of meanings ascribed to these terms, with the aim of clarifying how they are deployed in arguments for and against reform

Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel

To date, most BC GWASs have been performed Background Polygenic risk score (PRS), calculated in individuals of European (EUR) ancestry, and based on genome-wide association studies (GWASs), the generalisation of EUR-based PRS to other can improve breast cancer (BC) risk assessment. populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. Methods We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. Results In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). Conclusions Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.</p

Between Antagonism and Eros: The Feud as Couple Form and Netflix’s GLOW

A feud is an antagonism that is continuous and extended; “a state of prolonged mutual hostility” (OED). Historically, feuds take place between families or communities, or result from failed couples. Considered as a couple form in its own right, however, the feud is associated with aesthetic forms often coded as camp, queer, or feminized. In such popular, serialized forms, the feud must be open ended and of unforeseen futurity, for resolution brings an end to the feud as such and dissolves the couple. Thus, feuds reject normative modes of coupling (such as the nuclear family) that center harmonious or happy feelings. The article begins with the political economy of the feud through an examination of the pre-modern form of the blood feud and continues with its late-modern presence in popular culture. We rehearse the idea of the feud as it emerges from anthropology and philosophy, especially as it impacts notions of debt and alternative economies, before thinking through the contemporary “coupling” of the feud in popular culture, fandom, and, via the performance form of professional wrestling and Netflix’s GLOW

Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance for all participants. Methods CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes (path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with polypectomy when polyps were identified. Comparison was made with a retrospective cohort reported by the International Mismatch Repair Consortium (IMRC). This comprised confirmed and inferred path_MMR carriers who were first- or second-degree relatives of Lynch syndrome probands. Results In the PLSD, 8,153 subjects had follow-up colonoscopy surveillance for a total of 67,604 years and 578 carriers had CRC diagnosed. Average cumulative incidences of CRC in path_MLH1 carriers at 70 years of age were 52% in males and 41% in females; for path_MSH2 50% and 39%; for path_MSH6 13% and 17% and for path_PMS2 11% and 8%. In contrast, in the IMRC cohort, corresponding cumulative incidences were 40% and 27%; 34% and 23%; 16% and 8% and 7% and 6%. Comparing just the European carriers in the two series gave similar findings. Numbers in the PLSD series did not allow comparisons of carriers from other continents separately. Cumulative incidences at 25 years were < 1% in all retrospective groups. Conclusions Prospectively observed CRC incidences (PLSD) in path_MLH1 and path_MSH2 carriers undergoing colonoscopy surveillance and polypectomy were higher than in the retrospective (IMRC) series, and were not reduced in path_MSH6 carriers. These findings were the opposite to those expected. CRC point incidence before 50 years of age was reduced in path_PMS2 carriers subjected to colonoscopy, but not significantly so

Prevalence and attributable health burden of chronic respiratory diseases, 1990–2017: A systematic analysis for the global burden of disease study 2017

© 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license Background: Previous attempts to characterise the burden of chronic respiratory diseases have focused only on specific disease conditions, such as chronic obstructive pulmonary disease (COPD) or asthma. In this study, we aimed to characterise the burden of chronic respiratory diseases globally, providing a comprehensive and up-to-date analysis on geographical and time trends from 1990 to 2017. Methods: Using data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017, we estimated the prevalence, morbidity, and mortality attributable to chronic respiratory diseases through an analysis of deaths, disability-adjusted life-years (DALYs), and years of life lost (YLL) by GBD super-region, from 1990 to 2017, stratified by age and sex. Specific diseases analysed included asthma, COPD, interstitial lung disease and pulmonary sarcoidosis, pneumoconiosis, and other chronic respiratory diseases. We also assessed the contribution of risk factors (smoking, second-hand smoke, ambient particulate matter and ozone pollution, household air pollution from solid fuels, and occupational risks) to chronic respiratory disease-attributable DALYs. Findings: In 2017, 544·9 million people (95% uncertainty interval [UI] 506·9–584·8) worldwide had a chronic respiratory disease, representing an increase of 39·8% compared with 1990. Chronic respiratory disease prevalence showed wide variability across GBD super-regions, with the highest prevalence among both males and females in high-income regions, and the lowest prevalence in sub-Saharan Africa and south Asia. The age-sex-specific prevalence of each chronic respiratory disease in 2017 was also highly variable geographically. Chronic respiratory diseases were the third leading cause of death in 2017 (7·0% [95% UI 6·8–7·2] of all deaths), behind cardiovascular diseases and neoplasms. Deaths due to chronic respiratory diseases numbered 3 914 196 (95% UI 3 790 578–4 044 819) in 2017, an increase of 18·0% since 1990, while total DALYs increased by 13·3%. However, when accounting for ageing and population growth, declines were observed in age-standardised prevalence (14·3% decrease), age-standardised death rates (42·6%), and age-standardised DALY rates (38·2%). In males and females, most chronic respiratory disease-attributable deaths and DALYs were due to COPD. In regional analyses, mortality rates from chronic respiratory diseases were greatest in south Asia and lowest in sub-Saharan Africa, also across both sexes. Notably, although absolute prevalence was lower in south Asia than in most other super-regions, YLLs due to chronic respiratory diseases across the subcontinent were the highest in the world. Death rates due to interstitial lung disease and pulmonary sarcoidosis were greater than those due to pneumoconiosis in all super-regions. Smoking was the leading risk factor for chronic respiratory disease-related disability across all regions for men. Among women, household air pollution from solid fuels was the predominant risk factor for chronic respiratory diseases in south Asia and sub-Saharan Africa, while ambient particulate matter represented the leading risk factor in southeast Asia, east Asia, and Oceania, and in the Middle East and north Africa super-region. Interpretation: Our study shows that chronic respiratory diseases remain a leading cause of death and disability worldwide, with growth in absolute numbers but sharp declines in several age-standardised estimators since 1990. Premature mortality from chronic respiratory diseases seems to be highest in regions with less-resourced health systems on a per-capita basis. Funding: Bill & Melinda Gates Foundation