Differentiation of Andean and Mesoamerican accessions in a proposed core collection of grain amaranths

Grain amaranths are made up of three New World species of pseudo-cereals with C4 photosynthesis from the dicotyledonous family Amaranthaceae and the genus Amaranthus. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of Amaranthus, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species Amaranthus caudatus and Amaranthus quitensis shared fewer alleles with Mesoamerican species Amaranthus cruentus and Amaranthus hypochondriacus, compared to each group individually. Amaranthus hybridus was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression

Dynamics of superconducting nanowires shunted with an external resistor

We present the first study of superconducting nanowires shunted with an external resistor, geared towards understanding and controlling coherence and dissipation in nanowires. The dynamics is probed by measuring the evolution of the V-I characteristics and the distributions of switching and retrapping currents upon varying the shunt resistor and temperature. Theoretical analysis of the experiments indicates that as the value of the shunt resistance is decreased, the dynamics turns more coherent presumably due to stabilization of phase-slip centers in the wire and furthermore the switching current approaches the Bardeen's prediction for equilibrium depairing current. By a detailed comparison between theory and experimental, we make headway into identifying regimes in which the quasi-one-dimensional wire can effectively be described by a zero-dimensional circuit model analogous to the RCSJ (resistively and capacitively shunted Josephson junction) model of Stewart and McCumber. Besides its fundamental significance, our study has implications for a range of promising technological applications.Comment: 15 pages, 14 figure

Standardization of electroencephalography for multi-site, multi-platform and multi-investigator studies: Insights from the canadian biomarker integration network in depression

Subsequent to global initiatives in mapping the human brain and investigations of neurobiological markers for brain disorders, the number of multi-site studies involving the collection and sharing of large volumes of brain data, including electroencephalography (EEG), has been increasing. Among the complexities of conducting multi-site studies and increasing the shelf life of biological data beyond the original study are timely standardization and documentation of relevant study parameters. We presentthe insights gained and guidelines established within the EEG working group of the Canadian Biomarker Integration Network in Depression (CAN-BIND). CAN-BIND is a multi-site, multi-investigator, and multiproject network supported by the Ontario Brain Institute with access to Brain-CODE, an informatics platform that hosts a multitude of biological data across a growing list of brain pathologies. We describe our approaches and insights on documenting and standardizing parameters across the study design, data collection, monitoring, analysis, integration, knowledge-translation, and data archiving phases of CAN-BIND projects. We introduce a custom-built EEG toolbox to track data preprocessing with open-access for the scientific community. We also evaluate the impact of variation in equipment setup on the accuracy of acquired data. Collectively, this work is intended to inspire establishing comprehensive and standardized guidelines for multi-site studies

Glacier retreat creating new Pacific salmon habitat in western North America

Glacier retreat poses risks and benefits for species of cultural and economic importance. One example is Pacific salmon (Oncorhynchus spp.), supporting subsistence harvests, and commercial and recreational fisheries worth billions of dollars annually. Although decreases in summer streamflow and warming freshwater is reducing salmon habitat quality in parts of their range, glacier retreat is creating new streams and lakes that salmon can colonize. However, potential gains in future salmon habitat associated with glacier loss have yet to be quantified across the range of Pacific salmon. Here we project future gains in Pacific salmon freshwater habitat by linking a model of glacier mass change for 315 glaciers, forced by five different Global Climate Models, with a simple model of salmon stream habitat potential throughout the Pacific Mountain ranges of western North America. We project that by the year 2100 glacier retreat will create 6,146 (±1,619) km of new streams accessible for colonization by Pacific salmon, of which 1,930 (±569) km have the potential to be used for spawning and juvenile rearing, representing 0 to 27% gains within the 18 sub-regions we studied. These findings can inform proactive management and conservation of Pacific salmon in this era of rapid climate change.Ye

A nearly continuous measure of birth weight for gestational age using a United States national reference

BACKGROUND: Fully understanding the determinants and sequelae of fetal growth requires a continuous measure of birth weight adjusted for gestational age. Published United States reference data, however, provide estimates only of the median and lowest and highest 5(th )and 10(th )percentiles for birth weight at each gestational age. The purpose of our analysis was to create more continuous reference measures of birth weight for gestational age for use in epidemiologic analyses. METHODS: We used data from the most recent nationwide United States Natality datasets to generate multiple reference percentiles of birth weight at each completed week of gestation from 22 through 44 weeks. Gestational age was determined from last menstrual period. We analyzed data from 6,690,717 singleton infants with recorded birth weight and sex born to United States resident mothers in 1999 and 2000. RESULTS: Birth weight rose with greater gestational age, with increasing slopes during the third trimester and a leveling off beyond 40 weeks. Boys had higher birth weights than girls, later born children higher weights than firstborns, and infants born to non-Hispanic white mothers higher birth weights than those born to non-Hispanic black mothers. These results correspond well with previously published estimates reporting limited percentiles. CONCLUSIONS: Our method provides comprehensive reference values of birth weight at 22 through 44 completed weeks of gestation, derived from broadly based nationwide data. Other approaches require assumptions of normality or of a functional relationship between gestational age and birth weight, which may not be appropriate. These data should prove useful for researchers investigating the predictors and outcomes of altered fetal growth

Localized Populations of CD8low/− MHC Class I Tetramer+ SIV-Specific T Cells in Lymphoid Follicles and Genital Epithelium

CD8 T cells play an important role in controlling viral infections. We investigated the in situ localization of simian immunodeficiency virus (SIV)-specific T cells in lymph and genital tissues from SIV-infected macaques using MHC-class I tetramers. The majority of tetramer-binding cells localized in T cell zones and were CD8+. Curiously, small subpopulations of tetramer-binding cells that had little to no surface CD8 were detected in situ both early and late post-infection, and in both vaginally and rectally inoculated macaques. These tetramer+CD8low/− cells were more often localized in apparent B cell follicles relative to T cell zones and more often found near or within the genital epithelium than the submucosa. Cells analyzed by flow cytometry showed similar populations of cells. Further immunohistological characterization revealed small populations of tetramer+CD20− cells inside B cell follicles and that tetramer+ cells did not stain with γδ-TCR nor CD4 antibodies. Negative control tetramer staining indicated that tetramer+CD8low/− cells were not likely NK cells non-specifically binding to MHC tetramers. These findings have important implications for SIV-specific and other antigen-specific T cell function in these specific tissue locations, and suggest a model in which antigen-specific CD8+ T cells down modulate CD8 upon entering B cell follicles or the epithelial layer of tissues, or alternatively a model in which only antigen-specific CD8 T cells that down-modulate CD8 can enter B cell follicles or the epithelium

Factors Associated With Death in Critically Ill Patients With Coronavirus Disease 2019 in the US

Importance: The US is currently an epicenter of the coronavirus disease 2019 (COVID-19) pandemic, yet few national data are available on patient characteristics, treatment, and outcomes of critical illness from COVID-19. Objectives: To assess factors associated with death and to examine interhospital variation in treatment and outcomes for patients with COVID-19. Design, Setting, and Participants: This multicenter cohort study assessed 2215 adults with laboratory-confirmed COVID-19 who were admitted to intensive care units (ICUs) at 65 hospitals across the US from March 4 to April 4, 2020. Exposures: Patient-level data, including demographics, comorbidities, and organ dysfunction, and hospital characteristics, including number of ICU beds. Main Outcomes and Measures: The primary outcome was 28-day in-hospital mortality. Multilevel logistic regression was used to evaluate factors associated with death and to examine interhospital variation in treatment and outcomes. Results: A total of 2215 patients (mean [SD] age, 60.5 [14.5] years; 1436 [64.8%] male; 1738 [78.5%] with at least 1 chronic comorbidity) were included in the study. At 28 days after ICU admission, 784 patients (35.4%) had died, 824 (37.2%) were discharged, and 607 (27.4%) remained hospitalized. At the end of study follow-up (median, 16 days; interquartile range, 8-28 days), 875 patients (39.5%) had died, 1203 (54.3%) were discharged, and 137 (6.2%) remained hospitalized. Factors independently associated with death included older age (≥80 vs <40 years of age: odds ratio [OR], 11.15; 95% CI, 6.19-20.06), male sex (OR, 1.50; 95% CI, 1.19-1.90), higher body mass index (≥40 vs <25: OR, 1.51; 95% CI, 1.01-2.25), coronary artery disease (OR, 1.47; 95% CI, 1.07-2.02), active cancer (OR, 2.15; 95% CI, 1.35-3.43), and the presence of hypoxemia (Pao2:Fio2<100 vs ≥300 mm Hg: OR, 2.94; 95% CI, 2.11-4.08), liver dysfunction (liver Sequential Organ Failure Assessment score of 2 vs 0: OR, 2.61; 95% CI, 1.30–5.25), and kidney dysfunction (renal Sequential Organ Failure Assessment score of 4 vs 0: OR, 2.43; 95% CI, 1.46–4.05) at ICU admission. Patients admitted to hospitals with fewer ICU beds had a higher risk of death (<50 vs ≥100 ICU beds: OR, 3.28; 95% CI, 2.16-4.99). Hospitals varied considerably in the risk-adjusted proportion of patients who died (range, 6.6%-80.8%) and in the percentage of patients who received hydroxychloroquine, tocilizumab, and other treatments and supportive therapies. Conclusions and Relevance: This study identified demographic, clinical, and hospital-level risk factors that may be associated with death in critically ill patients with COVID-19 and can facilitate the identification of medications and supportive therapies to improve outcomes.Dr. Gupta reported receiving grants from the National Institutes of Health (NIH) and is a scientific coordinator for GlaxoSmithKline’s ASCEND (Anemia Studies in Chronic Kidney Disease: Erythropoiesis via a Novel Prolyl Hydroxylase Inhibitor Daprodustat) trial. Dr. Chan reported receiving grants from the Renal Research Institute outside the submitted work. Dr. Mathews reported receiving grants from the NIH/National Heart, Lung, and Blood Institute (NHLBI) during the conduct of the study and serves on the steering committee for the BREATHE trial (Breathing Retraining for Asthma–Trial of Home Exercises), funded by Roivant/Kinevant Sciences. Dr. Melamed reported receiving honoraria from the American Board of Internal Medicine and Icon Medical Consulting. Dr. Reiser reported receiving personal fees from Biomarin, TRISAQ, Thermo BCT, Astellas, Massachusetts General Hospital, Genentech, UptoDate, Merck, Inceptionsci, GLG, and Clearview and grants from the NIH and Nephcure outside the submitted work. Dr. Srivastava reported receiving personal fees from Horizon Pharma PLC, AstraZeneca, and CVS Caremark outside the submitted work. Dr. Vijayan reported receiving personal fees from NxStage, Boeringer Ingelheim, and Sanofi outside the submitted work. Dr. Velez reported receiving personal fees from Mallinckrodt Pharmaceuticals, Retrophin, and Otsuka Pharmaceuticals outside the submitted work. Dr. Shaefi reported receiving grants from the NIH/National Institute on Aging and NIH/National Institute of General Medical Sciences outside the submitted work. Dr. Admon reported receiving grants from the NIH/NHLBI during the conduct of the study. Dr. Donnelly reported receiving grants from the NIH/NHLBI during the conduct of the study and personal fees from the American College of Emergency Physicians/Annals of Emergency Medicine outside the submitted work. Dr. Hernán reported receiving grants from the NIH during the conduct of the study. Dr. Semler reported receiving grants from the NIH/NHLBI during the conduct of the study. No other disclosures were reported

An Image-Free Opto-Mechanical System for Creating Virtual Environments and Imaging Neuronal Activity in Freely Moving Caenorhabditis elegans

Non-invasive recording in untethered animals is arguably the ultimate step in the analysis of neuronal function, but such recordings remain elusive. To address this problem, we devised a system that tracks neuron-sized fluorescent targets in real time. The system can be used to create virtual environments by optogenetic activation of sensory neurons, or to image activity in identified neurons at high magnification. By recording activity in neurons of freely moving C. elegans, we tested the long-standing hypothesis that forward and reverse locomotion are generated by distinct neuronal circuits. Surprisingly, we found motor neurons that are active during both types of locomotion, suggesting a new model of locomotion control in C. elegans. These results emphasize the importance of recording neuronal activity in freely moving animals and significantly expand the potential of imaging techniques by providing a mean to stabilize fluorescent targets