Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Taxonomy based on science is necessary for global conservation

Peer reviewe

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Modeling Vegetative Buffer Performance Considering Topographic Data Accuracy

Riparian buffers are a promising tool in efforts to reduce sediment contribution to streams. Models that predict the capacity of buffers to trap sediment have recently been developed. A number of parameters that are required to conduct such modeling efforts are derived from the topography of the site. In this study, three topographic data sources were used to generate the model input for an agricultural field with a riparian buffer. The runoff and sediment transport in the system was then simulated for three years. As a result, the area that contributed runoff and sediment to the buffer was substantially different for each of the topographic data sources. In addition, the predicted runoff and sediment loss from the field was different for each case. Finally, the predicted sediment delivered to the stream was substantially affected by the accuracy of the topographic data source

Sea-level-induced seismicity and submarine landslide occurrence

The temporal coincidence between rapid late Pleistocene sealevel rise and large-scale slope failures is widely documented. Nevertheless, the physical mechanisms that link these phenomena are poorly understood, particularly along nonglaciated margins. Here we investigate the causal relationships between rapid sea-level rise, flexural stress loading, and increased seismicity rates along passive margins. We find that Coulomb failure stress across fault systems of passive continental margins may have increased more than 1 MPa during rapid late Pleistocene-early Holocene sea-level rise, an amount sufficient to trigger fault reactivation and rupture. These results suggest that sea-level-modulated seismicity may have contributed to a number of poorly understood but widely observed phenomena, including (1) increased frequency of large-scale submarine landslides during rapid, late Pleistocene sea-level rise; (2) emplacement of coarse-grained mass transport deposits on deep-sea fans during the early stages of marine transgression; and (3) the unroofing and release of methane gas sequestered in continental slope sediments. © 2013 Geological Society of America

FLOW PATHWAYS AND SEDIMENT TRAPPING IN A FIELD-SCALE VEGETATIVE FILTER

Vegetative filters (VF) are a best management practice installed in many areas to control sediment movement to water bodies. It is commonly assumed that runoff proceeds perpendicularly across a VF as sheet flow. However, there is little research information on natural pathways of water movement and performance of field-scale VF. The objectives of this study were: (1) to quantify the performance of a VF where the flow path is not controlled by artificial borders and flow path lengths are field-scale, and (2) to develop methods to detect and quantify overland flow convergence and divergence in a VF. Our hypothesis is that flow converges and diverges in field-scale VF and that flow pathways that define flow convergence and divergence areas can be predicted using high-resolution topography (i.e., maps). Overland flow and sediment mass flow were monitored in two 13 × 15 m subareas of a 13 × 225 m grass buffer located in Polk County in east-central Nebraska. Monitoring included a high-resolution survey to 3 cm resolution, dye tracer studies to identify flow pathways, and measurement of maximum flow depths at 51 points in each subarea. Despite relatively planar topography (a result of grading for surface irrigation), there were converging and diverging areas of overland flow in the buffer subareas. Convergence ratios ranged from −1.55 to 0.34. Predicted flow pathways using the high-resolution topography (i.e., map) closely followed actual flow paths. Overland flow was not uniformly distributed, and flow depths were not uniform across the subareas. Despite converging and diverging flow, the field-scale VF trapped approximately 80% of the incoming sediment

Assessment of canyon wall failure process from multibeam bathymetry and Remotely Operated Vehicle (ROV) observations, U.S. Atlantic continental margin

Over the last few years, canyons along the northern U.S. Atlantic continental margin have been the focus of intensive research examining canyon evolution, submarine geohazards, benthic ecology and deep-sea coral habitat. New high-resolution multibeam bathymetry and Remotely Operated Vehicle (ROV) dives in the major shelf-breaching and minor slope canyons, provided the opportunity to investigate the size of, and processes responsible for, canyon wall failures. The canyons cut through thick Late Cretaceous to Recent mixed siliciclastic and carbonate-rich lithologies which impart a primary control on the style of failures observed. Broad-scale canyon morphology across much of the margin can be correlated to the exposed lithology. Near vertical walls, sedimented benches, talus slopes, and canyon floor debris aprons were present in most canyons. The extent of these features depends on canyon wall cohesion and level of internal fracturing, and resistance to biological and chemical erosion. Evidence of brittle failure over different spatial and temporal scales, physical abrasion by downslope moving flows, and bioerosion, in the form of burrows and surficial scrape marks provide insight into the modification processes active in these canyons. The presence of sessile fauna, including long-lived, slow growing corals and sponges, on canyon walls, especially those affected by failure provide a critical, but as yet, poorly understood chronological record of geologic processes within these systems

Perceptions of Hurricane Track Forecasts in the U.S.A

Hurricanes Isaac (2012), Harvey (2017), and Irma (2017) were storms with different geophysical characteristics and track forecast consistencies. Despite the differences, common themes emerged from the perception of track forecasts from evacuees for each storm. Surveys with a mixture of closed and open-ended responses were conducted during the evacuations of each storm while the storm characteristics and decision-making were fresh in the minds of evacuees. Track perception accuracy for each evacuee was quantified by taking the difference between three metrics: Perceived Track and Official Track (PT - OT); Perceived Track and Forecast Track (PT - FT); and Home Location and Perceived Track (HL - PT). Evacuees from Hurricanes Isaac and Harvey displayed a tendency to perceive hurricane tracks closer to their home locations than what was forecast to occur and what actually occurred. The large sample collected for Hurricane Irma provided a chance to statistically verify some of the hypotheses generated from Isaac and Harvey. Results from Hurricane Irma confirmed that evacuees expected a storm closer to their home locations after controlling for regional influences. Furthermore, participants with greater previous hurricane experience perceived a track closer to their home locations, and participants residing in zip codes corresponding with non-mandatory evacuation zones also perceived tracks closer to their home locations. These findings suggest that most evacuees from hurricanes in the USA appear to perceive storms closer to their home locations and overestimate wind speeds at their homes, thus overestimating the true danger from land-falling hurricanes in many storms

Bathymetric Terrain Model of the Atlantic Margin for Marine Geological Investigations Open-File Report 2012-1266

For more information on the USGS-the Federal source for science about the Earth, it&apos;s natural and living resources, natural hazards, and the environment-visit http://www.usgs.gov or call 1-888-ASK-USGS For an overview of USGS information products, including maps, imagery, and publications, visit http://www.usgs.gov/pubprod To order this and other USGS information products, visit http://store.usgs.gov Although these data have been processed successfully on a computer system at the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. The USGS or the U.S. Government shall not be held liable for improper or incorrect use of the data described and/or contained herein.ny use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted material contained within this report. iii Acknowledgements This report was prepared as part of a multiyear project funded by the NRC to study potential effects of tsunamis produced from marine landslides. We thank the Captain and crew of the NOAA Ship Okeanos Explorer for their recent mapping efforts along the Atlantic margin. William Danforth and Richard Signell of the USGS provided helpful comments. We thank VeeAnn Cross of the USGS for her comments on the metadata, Andrea Toran for her expertise in Web design, and Anna Glover for her editorial review of this report. Abstract Bathymetric terrain models of seafloor morphology are an important component of marine geological investigations. Advances in acquisition and processing technologies of bathymetric data have facilitated the creation of high-resolution bathymetric surfaces that approach the resolution of similar surfaces available for onshore investigations. These bathymetric terrain models provide a detailed representation of the Earth&apos;s subaqueous surface and, when combined with other geophysical and geological datasets, allow for interpretation of modern and ancient geological processes. The purpose of the bathymetric terrain model presented in this report is to provide a high-quality bathymetric surface of the Atlantic margin of the United States that can be used to augment current and future marine geological investigations. The input data for this bathymetric terrain model, covering almost 305,000 square kilometers, were acquired by several sources, including the U.S