An Open-Publishing Response to the COVID-19 Infodemic.

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript's figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.

The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.

An Open-Publishing Response to the COVID-19 Infodemic.

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript's figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.

Meta-analysis Comparing Outcomes of Two Different Negative Pressure Therapy Systems in Closed Incision Management.

BACKGROUND: Closed incision negative pressure therapy (ciNPT) is an emerging approach to managing closed incisions of patients at risk of postoperative complications. There are primarily 2 different commercially available ciNPT systems. Both systems consist of a single-use, battery-powered device and foam- or gauze-based peel-and-place dressing designed for closed incisions. These systems vary in design, and there are no data comparing outcomes between the 2 systems. METHODS: We performed 2 separate meta-analyses to compare surgical site infection (SSI) rates postuse of (1) ciNPT with foam dressing (FOAM) versus conventional dressings and (2) ciNPT with multilayer absorbent dressing (MLA) versus conventional dressings. RESULTS: Seven articles and 2 abstracts met inclusion criteria in the FOAM group (n = 489) versus the control group (n = 489) in meta-analysis 1; 7 articles and 1 abstract met inclusion criteria in the MLA group (n = 532) versus the control group (n = 540) in meta-analysis 2. Meta-analysis 1 showed that patients in the control group were 3.17 times more likely to develop an SSI compared with patients in the FOAM group [weighted mean odds ratios of FOAM group versus control group was 3.17 (P < 0.0001) with the 95% confidence intervals of 2.17-4.65]. Meta-analysis 2 showed no significant difference in SSI rates between patients in the MLA group and patients in the control group [weighted mean odds ratios of MLA group versus control group was 1.70 (P = 0.08) with the 95% confidence intervals of 0.94-3.08]. CONCLUSIONS: Comparing outcomes of two different ciNPT systems with a common comparator (conventional dressings) may provide an interim basis for comparing ciNPT systems until further comparative evidence is available. More comparative research is required to determine outcomes in clinical practice.

Secondary consent to biospecimen use in a prostate cancer biorepository.

BACKGROUND: Biorepository research has substantial societal benefits. This is one of the few studies to focus on male willingness to allow future research use of biospecimens. METHODS: This study analyzed the future research consent questions from a prostate cancer biorepository study (N = 1931). The consent form asked two questions regarding use of samples in future studies (1) without and (2) with protected health information (PHI). Yes to both questions of use of samples was categorized as Yes-Always; Yes to without and No to with PHI was categorized as Yes-Conditional; No to without PHI was categorized as Never. We analyzed this outcome to determine significant predictors for consent to Yes-Always vs. Yes-Conditional. RESULTS: 99.33 % consented to future use of samples; 88.19 % consented to future use without PHI, and among those men 10.2 % consented to future use with PHI. Comparing Yes Always and Yes Conditional responses, bivariate analyses showed that race, family history, stage of cancer, and grade of cancer (Gleason), were significant at the α = 0.05 level. Using stepwise multivariable logistic regression, we found that African-American men were significantly more likely to respond Yes Always when compared to White men (p < 0.001). Those with a family history of prostate cancer were significantly more likely to respond Yes Always (p = 0.002). CONCLUSIONS: There is general willingness to consent to future use of specimens without PHI among men.

Mouse low-grade gliomas contain cancer stem cells with unique molecular and functional properties.

The availability of adult malignant glioma stem cells (GSCs) has provided unprecedented opportunities to identify the mechanisms underlying treatment resistance. Unfortunately, there is a lack of comparable reagents for the study of pediatric low-grade glioma (LGG). Leveraging a neurofibromatosis 1 (Nf1) genetically engineered mouse LGG model, we report the isolation of CD133(+) multi-potent low-grade glioma stem cells (LG-GSCs), which generate glioma-like lesions histologically similar to the parent tumor following injection into immunocompetent hosts. In addition, we demonstrate that these LG-GSCs harbor selective resistance to currently employed conventional and biologically targeted anti-cancer agents, which reflect the acquisition of new targetable signaling pathway abnormalities. Using transcriptomic analysis to identify additional molecular properties, we discovered that mouse and human LG-GSCs harbor high levels of Abcg1 expression critical for protecting against ER-stress-induced mouse LG-GSC apoptosis. Collectively, these findings establish that LGG cancer stem cells have unique molecular and functional properties relevant to brain cancer treatment.

Effects of racial and ethnic group and health literacy on responses to genomic risk information in a medically underserved population.

OBJECTIVE: Few studies have examined how individuals respond to genomic risk information for common, chronic diseases. This randomized study examined differences in responses by type of genomic information (genetic test/family history) and disease condition (diabetes/heart disease), and by race/ethnicity in a medically underserved population. METHODS: 1,057 English-speaking adults completed a survey containing 1 of 4 vignettes (2-by-2 randomized design). Differences in dependent variables (i.e., interest in receiving genomic assessment, discussing with doctor or family, changing health habits) by experimental condition and race/ethnicity were examined using chi-squared tests and multivariable regression analysis. RESULTS: No significant differences were found in dependent variables by type of genomic information or disease condition. In multivariable models, Hispanics were more interested in receiving a genomic assessment than Whites (OR = 1.93; p < .0001); respondents with marginal (OR = 1.54; p = .005) or limited (OR = 1.85; p = .009) health literacy had greater interest than those with adequate health literacy. Blacks (OR = 1.78; p = .001) and Hispanics (OR = 1.85; p = .001) had greater interest in discussing information with family than Whites. Non-Hispanic Blacks (OR = 1.45; p = .04) had greater interest in discussing genomic information with a doctor than Whites. Blacks (ß = -0.41; p < .001) and Hispanics (ß = -0.25; p = .033) intended to change fewer health habits than Whites; health literacy was negatively associated with number of health habits participants intended to change. CONCLUSIONS: Findings suggest that race/ethnicity may affect responses to genomic risk information. Additional research could examine how cognitive representations of this information differ across racial/ethnic groups. Health literacy is also critical to consider in developing approaches to communicating genomic information.

Screening for colorectal cancer: using data to set prevention priorities.

INTRODUCTION: Adherence to colorectal cancer screening recommendations is known to vary by state, but less information is available about within-state variability. In the current study, we assess county-level screening rates for Missouri, with the goal of better targeting public health efforts to increase screening. METHODS: Prevalence of colorectal cancer screening among Missouri adults between the ages of 50 and 74 was obtained from 2008 and 2010 Behavioral Risk Factor Surveillance System data. We used multilevel logistic regression to generate county-specific estimates. After excluding 77 counties with fewer than 30 respondents, information was available about 3,739 individuals in 37 counties, representing 78.5 % of the state population. RESULTS: Across counties, the prevalence of being up-to-date with recommended colorectal cancer screening ranged from 25 to 70 %. CONCLUSION: State-level information about colorectal cancer screening masks substantial within-state variability. Assessing and monitoring county-level disparities in screening can guide public health efforts to increase screening and reduce colorectal cancer mortality. More complete population survey data will make such analysis possible.