High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies

Processes of subjectivization and inclusive language

En este trabajo, sin afán alguno de establecer juicios que autoricen o nieguen la pertinencia de los usos del lenguaje inclusivo, proponemos un análisis lingüístico-discursivo de las resoluciones emitidas por cuatro universidades argentinas que han aceptado el uso del lenguaje inclusivo en alguna de sus formas y en distintos tipos de producciones académicas escritas y orales.Nuestro objetivo es mostrar que el sentido de los discursos no es de naturaleza veritativa ni depende de las elecciones voluntarias e intencionales de los sujetos; antes bien, los efectos desentido se construyen dialógica y argumentativamente. A la luz del enfoque dialógico de la argumentación y la polifonía, proponemos así que las mencionadas resoluciones exponen sistemáticamente una imagen de la enunciación como causada por (semi)marcos de discurso dialógicos que deben recuperarse y que remiten a prácticas discursivas que toman el uso mismo del lenguaje como objeto y su correlato en las prácticas sociales. Al mismo tiempo, mostramos cómo en esas respuestas dialógicas, quedan materializados posicionamientos subjetivos críticos que aunque diversos, devuelven a los sujetos la ilusión de ser dueños de su decir.In this paper, without wanting to deny the use of inclusive language’s relevance, we propose a linguistic-discursive analysis of the resolutions issued by four Argentine universities that have accepted inclusive language in some of its forms and different types of written and oral academic productions. We aim to show that the discourse’s meaning is not of a veritative nature or de-pends on the subjects’ voluntary and intentional choices. Rather, the effects of meaning construct dialogically and argumenta-tively. In light of the dialogical approach to argumentation and polyphony, we propose that the resolutions mentioned above systematically expose an enunciation image caused by (semi-)dialogical discourse. Frameworks that must be recovered and refer to discursive practices that take the very use of language as an object and its correlation in social practices. At the same time, we show how in these dialogical responses, critical subjective positions remain materialized that, although diverse, give the subjects the illusion of being masters of their saying.Fil: Garcia Negroni, Maria Marta. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de San Andrés; ArgentinaFil: Hall, Beatriz. Universidad Nacional de Lomas de Zamora. Facultad de Ciencias Sociales; Argentina. Universidad de Buenos Aires; Argentin

Resources, key traits and the size of fungal epidemics in Daphnia populations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111939/1/jane12363.pd

Evaluation of Interdisciplinary Terrorism Preparedness Programs: A Pilot Focus Group Study

This is the publisher's version, also available electronically from http://www.ingentaconnect.comMany terrorism preparedness trainings occur throughout the United States, yet few qualitatively examine trainees' needs and interests, reactions to training, or suggestions for training improvement. Eleven posttraining focus groups were conducted with 31 training participants at six sites. Participants were stratified by health profession discipline, and discipline-specific moderators conducted each session to better understand and probe for feedback. One additional moderator attended all sessions to increase consistency in methods across sessions. Focus group participants assessed changes in their perceptions, knowledge, and beliefs about terrorism preparedness. Participants reported perceiving terrorism as a potential threat but less likely than natural disasters. All-hazards crossover training for responding to terrorism and natural disasters was requested. The training was viewed positively, including the enrollment process, training content, and reference materials. Participants reported increased confidence in abilities to recognize a terrorist event. Participants stated they would like the training repeated annually with more first responders in attendance. Participants from rural areas had unique training needs based on limited resources and multiple roles of staff. While most participants wanted a longer, multispecialty conference with in-depth, discipline-specific breakout sessions, physicians requested shorter, separate training. Multispecialty training methods were successful and appreciated. This pilot study may serve as a template for qualitative evaluation of terrorism preparedness conferences for health professionals

Temperature Drives Epidemics in a Zooplankton-Fungus Disease System: A Trait-Driven Approach Points to Transmission via Host Foraging

Climatic warming will likely have idiosyncratic impacts on infectious diseases, causing some to increase while others decrease or shift geographically. A mechanistic framework could better predict these different temperature-disease outcomes. However, such a framework remains challenging to develop, due to the nonlinear and (sometimes) opposing thermal responses of different host and parasite traits and due to the difficulty of validating model predictions with observations and experiments. We address these challenges in a zooplanktonfungus (Daphnia dentifera–Metschnikowia bicuspidata) system. We test the hypothesis that warmer temperatures promote disease spread and produce larger epidemics. In lakes, epidemics that start earlier and warmer in autumn grow much larger. In a mesocosm experiment, warmer temperatures produced larger epidemics. A mechanistic model parameterized with trait assays revealed that this pattern arose primarily from the temperature dependence of transmission rate (b), governed by the increasing foraging (and, hence, parasite exposure) rate of hosts ( f ). In the trait assays, parasite production seemed sufficiently responsive to shape epidemics as well; however, this trait proved too thermally insensitive in the mesocosm experiment and lake survey to matter much. Thus, in warmer environments, increased foraging of hosts raised transmission rate, yielding bigger epidemics through a potentially general, exposure-based mechanism for ectotherms. This mechanistic approach highlights how a trait-based framework will enhance predictive insight into responses of infectious disease to a warmer world

Habitat, predators, and hosts regulate disease in Daphnia through direct and indirect pathways

Community ecology can link habitat to disease via interactions among habitat, focal hosts, other hosts, their parasites, and predators. However, complicated food web interactions (i.e., trophic interactions among predators and their impacts on host density and diversity) often obscure the important pathways regulating disease. Here, we disentangle community drivers in a case study of planktonic disease, using a two‐step approach. In step one, we tested univariate field patterns linking community interactions directly to two disease metrics. Density of focal hosts (Daphnia dentifera) was related to density but not prevalence of fungal (Metschnikowia bicuspidata) infections. Both disease metrics appeared to be driven by selective predators that cull infected hosts (fish, e.g., Lepomis macrochirus), sloppy predators that spread parasites while feeding (midges, Chaoborus punctipennis), and spore predators that reduce contact between focal hosts and parasites (other zooplankton, especially small‐bodied Ceriodaphnia sp.). Host diversity also negatively correlated with disease, suggesting a dilution effect. However, several of these univariate patterns were initially misleading, due to confounding ecological links among habitat, predators, host density, and host diversity. In step two, path models uncovered and explained these misleading patterns, and grounded them in habitat structure (refuge size). First, rather than directly reducing infection prevalence, fish predation drove disease indirectly through changes in density of midges and frequency of small spore predators (which became more frequent in lakes with small refuges). Second, small spore predators drove the two disease metrics through fundamentally different pathways: they directly reduced infection prevalence, but indirectly reduced density of infected hosts by lowering density of focal hosts (likely via competition). Third, the univariate diversity–disease pattern (signaling a dilution effect) merely reflected the confounding direct effects of these small spore predators. Diversity per se had no effect on disease, after accounting for the links between small spore predators, diversity, and infection prevalence. In turn, these small spore predators were regulated by both size‐selective fish predation and refuge size. Thus, path models not only explain each of these surprising results, but also trace their origins back to habitat structure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134436/1/ecm1222_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134436/2/ecm1222-sup-0001-AppendixS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134436/3/ecm1222.pd

Sudden Infant Death Syndrome (SIDS) and the routine otoacoustic emission infant hearing screening test: an epidemiological retrospective case-control study

Objectives To investigate whether decreased otoacoustic emission (OAE) signal recordings in the right ear are associated with an increased risk of sudden infant death syndrome (SIDS) and to monitor any temporal changes in risk factors. Design Retrospective case-control study. Setting Telephone interviews with families recruited in England between July 2016 and October 2017 who experienced the unexpected death of a child <4 years old since 2008 and control families recruited from maternity wards in Bristol and Birmingham. Participants We recruited 91 (89%) of the 102 bereaved families who made initial contact, 64 deaths were under 1 year (sudden unexpected death in infancy) of which 60 remained unexplained (SIDS). Of the 220 control families, 194 (88%) follow-up interviews were conducted. We had analysable hearing data for 24 SIDS infants (40%) and 98 controls (51%). Results OAE signals were marginally increased rather than decreased among SIDS infants for the right ear, especially at lower frequencies, but not significantly so. The strongest predictors of SIDS were bed-sharing in hazardous (infant sleeping next to a carer who smoked, drank alcohol or slept on a sofa) circumstances (35% vs 3% controls, p<0.0001), infants found prone (33% vs 3% controls, p<0.0001) and infants whose health in the final week was â € not good' (53% vs 9% controls, p<0.0001). The prevalence of maternal smoking during pregnancy among both SIDS mothers (20%) and controls (10%) was much lower than previous studies. Conclusions Hearing data were difficult to obtain; larger numbers would be needed to determine if asymmetrical differences between the right and left ear were a marker for SIDS. A national prospective registry for monitoring and a renewed campaign to a new generation of parents needs to be considered underlining the initial message to place infants on their backs for sleep and the more recent message to avoid bed-sharing in hazardous circumstances

Ocean and atmosphere teleconnections modulate east tropical Pacific productivity at late to middle Pleistocene terminations

The modern Eastern Equatorial Pacific (EEP) is a key oceanographic region for regulating the Earth's climate system, accounting for between 5–10% of global marine production whilst also representing a major source of carbon dioxide efflux to the atmosphere. Changes in ocean dynamics linked to the nutrient supply from the Southern Ocean have been suggested to have played a dominant role in regulating EEP productivity over glacial–interglacial timescales of the past 500 ka. Yet, the full extent of the climate and oceanic teleconnections and the mechanisms promoting the observed increase of productivity occurring at glacial terminations remain poorly understood. Here we present multi-proxy, micropaleontological, geochemical and sedimentological records from the easternmost EEP to infer changes in atmospheric patterns and oceanic processes potentially influencing regional primary productivity over glacial–interglacial cycles of the mid-late Pleistocene (∼0–650 ka). These proxy data support a leading role for the north–south migration of the Intertropical Convergence Zone (ITCZ) in shaping past productivity variability in the EEP. Productivity increases during glacial periods and notably peaks at major and “extra” glacial terminations (those occurring 1–2 precession cycles after some major terminations) coincident with the inferred southernmost position of the ITCZ. The comparison of our reconstructions with proxy records of climate variability suggests the intensification of related extratropical atmospheric and oceanic teleconnections during deglaciation events. These processes may have re-activated the supply of southern sourced nutrients to the EEP, potentially contributing to enhanced productivity in the EEP and thus counterbalancing the oceanic carbon dioxide outgassing at glacial terminations