bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of Rhizoctonia solani Anastomosis Group 4 Strain Rhs4ca, a Widespread Pathomycete in Field Crops
Authors: Zhang Zhengkun , Xia Xinyao , Du Qian , Xia Lei , Ma Xiaoyu , Li Qiyun , Liu Wende 
Published: March 2021

Rhizoctonia solani is an important soil-borne fungal pathogen that causes serious diseases on many agricultural crops and vegetables. Here, we report a complete genome assembly of R. solani AG4 (assembly: 45.47 Mb; contig N50: 1.56 Mb), using a combination of Illumina paired-end and PacBio long-read sequencing data. A total of 267 noncoding RNAs and 11,592 genes were predicted, including 109 genes associated with carbohydrate-active enzymes and 2,488 genes involved in host-pathogen interactions. The complete genome of R. solani AG4 represents a valuable base for studying interactions between host plants and pathogenic fungi and to search for potential antimicrobial targets. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Environmental hazards, social inequality, and fetal loss: Implications of live-birth bias for estimation of disparities in birth outcomes
Authors: Goin Dana E. , Casey Joan A. , Kioumourtzoglou Marianthi-Anna , Cushing Lara J. , Morello-Frosch Rachel 
Published: March 2021

Background:
Restricting to live births can induce bias in studies of pregnancy and developmental outcomes, but whether this live-birth bias results in underestimating disparities is unknown. Bias may arise from collider stratification due to an unmeasured common cause of fetal loss and the outcome of interest, or depletion of susceptibles, where exposure differentially causes fetal loss among those with underlying susceptibility.

Methods:
We conducted a simulation study to examine the magnitude of live-birth bias in a population parameterized to resemble one year of conceptions in California (N = 625,000). We simulated exposure to a non–time-varying environmental hazard, risk of spontaneous abortion, and time to live birth using 1000 Monte Carlo simulations. Our outcome of interest was preterm birth. We included a social vulnerability factor to represent social disadvantage, and estimated overall risk differences for exposure and preterm birth using linear probability models and stratified by the social vulnerability factor. We calculated how often confidence intervals included the true point estimate (CI coverage probabilities) to illustrate whether effect estimates differed qualitatively from the truth.

Results:
Depletion of susceptibles resulted in a larger magnitude of bias compared with collider stratification, with larger bias among the socially vulnerable group. Coverage probabilities were not adversely affected by bias due to collider stratification. Depletion of susceptibles reduced coverage, especially among the socially vulnerable (coverage among socially vulnerable = 46%, coverage among nonsocially vulnerable = 91% in the most extreme scenario).

Conclusions:
In simulations, hazardous environmental exposures induced live-birth bias and the bias was larger for socially vulnerable women.
Effect of Workstation Type on the Relationship Between Fatigue, Physical Activity, Stress, and Sleep
Authors: Goel Rahul , Pham Alan , Nguyen Hung , Lindberg Casey , Gilligan Brian , Mehl Matthias R. , Heerwagen Judith , Kampschroer Kevin , Sternberg Esther M. , Najafi Bijan 
Published: March 2021

Objective:
This study examined office workstation types’ impact on the relationship between fatigue and three health metrics: physical activity, stress, and sleep quality.

Methods:
Data from 225 office workers were collected for perceived fatigue, perceived sleep quality (Pittsburgh Sleep Quality Index [PSQI]), physiological stress response (standard deviation of heart rate variability [HRV]), and physical activity (total activity in minutes) during three consecutive workdays. Stress and physical activity were measured using chest-worn sensors. Workers were then categorized as tired or not-tired based on the median of the fatigue rating.

Results:
Among tired workers, open-bench seating workers had increased physical activity, improved sleep quality, and reduced stress compared with workers in private offices and cubicles.

Conclusions:
Office workstation types influence physical activity and levels of stress during work hours, which in turn affect sleep quality.
A Novel Fast CT Perfusion Core-Penumbra Mismatch Score
Authors: Pozzi-Mucelli Roberta A. , Furlanis Giovanni , Caruso Paola , Lugnan Carlo , Zdjelar Adrian , Degrassi Ferruccio , Bottaro Lorella , Ukmar Maja , Naccarato Marcello , Manganotti Paolo , Cova Maria A. 
Published: March 2021

Background:
Advanced neuroimaging can identify patients who can most benefit from reperfusion treatment, discriminating between ischemic core and penumbra area in a quick and accurate manner. Despite core-penumbra mismatch being an independent prognostic factor, computed tomography perfusion (CTP) assessment is still debated in hyperacute decision-making. The authors aimed to study a novel CTP mismatch score in emergency settings and to investigate its relation with clinical outcome in acute ischemic stroke patients treated with intravenous thrombolysis (IVT).

Methods:
Neuroimaging and clinical data of 226 consecutive acute ischemic stroke patients were analyzed. The study population was divided into 5 different CTP scores: (0) without perfusion deficit, (1) only penumbra, (2) penumbra > core, (3) core ≥ penumbra, (4) only core. For differences in outcome between treated and nontreated patients, and among CTP core-penumbra groups to be assessed, the authors have evaluated the outcome in terms of National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS) at discharge and symptomatic intracerebral hemorrhage.

Results:
A decrease in NIHSS was statistically greater in IVT-treated patients compared to nontreated patients showing only penumbra (ΔNIHSS%: 80.0% vs. 50.0%; P=0.0023) or no perfusion deficit (ΔNIHSS%: 89.4% vs. 61.5%; P=0.027) on CTP maps. The same trend was found in other groups without significant difference. A significant correlation was found in IVT patients between core/penumbra score and outcome in terms of ΔNIHSS (Kendall τ=−0.19; P=0.004).

Conclusions:
The authors proposed a novel immediate CTP assessment to score perfusion mismatch in emergency settings to guide clinicians’ decision-making for aggressive treatment and to prevent stroke-related disability.
Scaling and responses of extreme hourly precipitation in three climate experiments with a convection-permitting model
Authors: Lenderink Geert , de Vries Hylke , Fowler Hayley J. , Barbero Renaud , van Ulft Bert , van Meijgaard Erik 
Published: March 2021

It is widely recognized that future rainfall extremes will intensify. This expectation is tied to the Clausius-Clapeyron (CC) relation, stating that the maximum water vapour content in the atmosphere increases by 6–7% per degree warming. Scaling rates for the dependency of hourly precipitation extremes on near-surface (dew point) temperature derived from day-to-day variability have been found to exceed this relation (super-CC). However, both the applicability of this approach in a long-term climate change context, and the physical realism of super-CC rates have been questioned. Here, we analyse three different climate change experiments with a convection-permitting model over Western Europe: simple uniform-warming, 11-year pseudo-global warming and 11-year global climate model driven. The uniform-warming experiment results in consistent increases to the intensity of hourly rainfall extremes of approximately 11% per degree for moderate to high extremes. The other two, more realistic, experiments show smaller increases—usually at or below the CC rate—for moderate extremes, mostly resulting from significant decreases to rainfall occurrence. However, changes to the most extreme events are broadly consistent with 1.5–2 times the CC rate (10–14% per degree), as predicted from the present-day scaling rate for the highest percentiles. This result has important implications for climate adaptation.This article is part of a discussion meeting issue ‘Intensification of short-duration rainfall extremes and implications for flash flood risks’.
Sensitivity of organized convective storms to model grid spacing in current and future climates
Authors: Prein A. F. , Rasmussen R. M. , Wang D. , Giangrande S. E. 
Published: March 2021

Mesoscale convective systems (MCSs) are complexes of thunderstorms that become organized and cover hundreds of kilometres over several hours. MCSs are prolific rain producers in the tropics and mid-latitudes and are the major cause of warm-season flooding. Traditionally, climate models have difficulties in simulating MCSs partly due to the misrepresentation of complex process interactions that operate across a large range of scales. Significant improvements in simulating MCSs have been found in kilometre-scale models that explicitly simulate deep convection. However, these models operate in the grey zone of turbulent motion and have known deficiencies in simulating small-scale processes (e.g. entrainment, vertical mass transport). Here, we perform mid-latitude idealized ensemble MCS simulations under current and future climate conditions in three atmospheric regimes: hydrostatic (12 km horizontal grid spacing; Δx), non-hydrostatic (Δx = 4, 2 and 1 km) and large eddy scale (Δx = 500 m and 250 m). Our results show a dramatic improvement in simulating MCS precipitation, movement, cold pools, and cloud properties when transitioning from 12 km to 4 km Δx. Decreasing Δxbeyond 4 km results in modest improvements except for up- and downdraft sizes, average vertical mass fluxes, and cloud top height and temperature, which continue to change. Most important for climate modelling is that Δx = 4 km simulations reliably capture most MCS climate change signals compared to those of the Δx = 250 m runs. Significantly different climate change signals are found in Δx = 12 km runs that overestimate extreme precipitation changes by up to 100%.This article is part of a discussion meeting issue ‘Intensification of short-duration rainfall extremes and implications for flash flood risks’.
Challenges and outlook for convection-permitting climate modelling
Authors: Kendon E. J. , Prein A. F. , Senior C. A. , Stirling A. 
Published: March 2021

Climate projections at very high resolution (kilometre-scale grid spacing) are becoming affordable. These ‘convection-permitting’ models (CPMs), commonly used for weather forecasting, better represent land-surface characteristics and small-scale processes in the atmosphere such as convection. They provide a step change in our understanding of future changes at local scales and for extreme weather events. For short-duration precipitation extremes, this includes capturing local storm feedbacks, which may modify future increases. Despite the major advance CPMs offer, there are still key challenges and outstanding science issues. Heavy rainfall tends to be too intense; there are challenges in representing land-surface processes; sub-kilometre scale processes still need to be parametrized, with existing parametrization schemes often requiring development for use in CPMs; CPMs rely on the quality of lateral boundary forcing and typically do not include ocean-coupling; large CPM ensembles that comprehensively sample future uncertainties are costly. Significant progress is expected over the next few years: scale-aware schemes may improve the representation of unresolved convective updrafts; work is underway to improve the modelling of complex land-surface fluxes; CPM ensemble experiments are underway and methods to synthesize this information with larger coarser-resolution model ensembles will lead to local-scale predictions with more comprehensive uncertainty context for user application. Large-domain (continental or tropics-wide) CPM climate simulations, potentially with additional earth-system processes such as ocean and wave coupling and terrestrial hydrology, are an exciting prospect, allowing not just improved representation of local processes but also of remote teleconnections.This article is part of a discussion meeting issue ‘Intensification of short-duration rainfall extremes and implications for flash flood risks’.
Incorporating climate change in flood estimation guidance
Authors: Wasko Conrad , Westra Seth , Nathan Rory , Orr Harriet G. , Villarini Gabriele , Villalobos Herrera Roberto , Fowler Hayley J. 
Published: March 2021

Research into potential implications of climate change on flood hazard has made significant progress over the past decade, yet efforts to translate this research into practical guidance for flood estimation remain in their infancy. In this commentary, we address the question: how best can practical flood guidance be modified to incorporate the additional uncertainty due to climate change? We begin by summarizing the physical causes of changes in flooding and then discuss common methods of design flood estimation in the context of uncertainty. We find that although climate science operates across aleatory, epistemic and deep uncertainty, engineering practitioners generally only address aleatory uncertainty associated with natural variability through standards-based approaches. A review of existing literature and flood guidance reveals that although research efforts in hydrology do not always reflect the methods used in flood estimation, significant progress has been made with many jurisdictions around the world now incorporating climate change in their flood guidance. We conclude that the deep uncertainty that climate change brings signals a need to shift towards more flexible design and planning approaches, and future research effort should focus on providing information that supports the range of flood estimation methods used in practice.This article is part of a discussion meeting issue ‘Intensification of short-duration rainfall extremes and implications for flash flood risks'.
Managing the effects of extreme sub-daily rainfall and flash floods—a practitioner's perspective
Authors: Dale Murray 
Published: March 2021

Extreme sub-daily rainfall affects flooding in the UK and urban pollution management. Water utilities in the UK need to understand the characteristics of this rainfall, and how it may change in the future in order to plan for and manage these impacts. There is also significant interest from infrastructure owners and urban authorities exposed to flood risk from short-period, intense rainfall events. This paper describes how UK flood risk guidance incorporates allowances for climate change and how recent research using convection-permitting climate models is helping to inform this guidance. The guidance documents are used by engineers and scientists in the modelling of sewer networks, smaller river catchments and urban drainage areas and provide values to ‘uplift' rainfall event data used as model inputs to reflect climate change model projections. With an increasing focus on continuous simulation modelling using time series rainfall, research into adjusting time series data to reflect future rainfall characteristics in convection-permitting climate models is discussed. Other knowledge gaps for practitioners discussed are the potential changing shape (profile) of future rainfall events and future changes in antecedent wetness conditions. The author explains the challenge of developing simple and effective guidance for practitioners from the complex scientific output.
This article is part of a discussion meeting issue ‘Intensification of short-duration rainfall extremes and implications for flash flood risks’.
Trade-offs between individual and ensemble forecasts of an emerging infectious disease
Authors: Oidtman Rachel J. , Omodei Elisa , Kraemer Moritz U. G. , Castañeda-Orjuela Carlos A. , Cruz-Rivera Erica , Misnaza-Castrillón Sandra , Cifuentes Myriam Patricia , Rincon Luz Emilse , Cañon Viviana , de Alarcon Pedro , España Guido , Huber John H. , Hill Sarah C. , Barker Christopher M. , Johansson Michael A. , Manore Carrie A. , Reiner Robert C. , Rodriguez-Barraquer Isabel , Siraj Amir S. , Frias-Martinez Enrique , García-Herranz Manuel , Perkins T. Alex 
Published: March 2021

AbstractWhen new pathogens emerge, numerous questions arise about their future spread, some of which can be addressed with probabilistic forecasts. The many uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among model structures and assumptions, however. To assess the potential for uncertainties about emerging pathogens to affect forecasts of their spread, we evaluated the performance of a suite of 16 forecasting models in the context of the 2015-2016 Zika epidemic in Colombia. Each model featured a different combination of assumptions about the role of human mobility in driving transmission, spatiotemporal variation in transmission potential, and the number of times the virus was introduced. All models used the same core transmission model and the same iterative data assimilation algorithm to generate forecasts. By assessing forecast performance through time using logarithmic scoring with ensemble weighting, we found that which model assumptions had the most ensemble weight changed through time. In particular, spatially coupled models had higher ensemble weights in the early and late phases of the epidemic, whereas non-spatial models had higher ensemble weights at the peak of the epidemic. We compared forecast performance of the equally weighted ensemble model to each individual model and identified a trade-off whereby certain individual models outperformed the ensemble model early in the epidemic but the ensemble model outperformed all individual models on average. On balance, our results suggest that suites of models that span uncertainty across alternative assumptions are necessary to obtain robust forecasts in the context of emerging infectious diseases.
Seroepidemiology of SARS-CoV-2 infections in an urban Nicaraguan population
Authors: González Fredman , Vielot Nadja A. , Sciaudone Michael , Toval-Ruíz Christian , Premkumar Lakshmanane , Gutierrez Lester , Cuadra Edwing Centeno , Blandón Patricia , Silva Aravinda M. de , Rubinstein Rebecca , Bowman Natalie , Becker-Dreps Sylvia , Bucardo Filemon 
Published: March 2021

ABSTRACTIn a Nicaraguan population-based cohort, SARS-CoV-2 seroprevalence was 34%, with higher prevalence in children compared to adults. Having a seropositive household member was associated with a two-fold probability of individual seropositivity, suggesting a role for household transmission. Co-morbidities and preventive behaviors were not associated with SARS-CoV-2 seroprevalence.
SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients
Authors: Dimcheff Derek E. , Valesano Andrew L. , Rumfelt Kalee E. , Fitzsimmons William J. , Blair Christopher , Mirabelli Carmen , Petrie Joshua G. , Martin Emily T. , Bhambhani Chandan , Tewari Muneesh , Lauring Adam S. 
Published: March 2021

AbstractUnderstanding viral load in patients infected with SARS-CoV-2 is critical to epidemiology and infection control. Previous studies have demonstrated that SARS-CoV-2 RNA can be detected for many weeks after symptom onset. The clinical significance of this finding is unclear and, in most patients, likely does not represent active infection. There are, however, patients who shed infectious virus for weeks. Detection of subgenomic RNA transcripts expressed by SARS-CoV-2 has been proposed to represent productive infection and may be a tractable marker for monitoring infectivity. Here, we use RT-PCR to quantify total and subgenomic nucleocapsid (N) and envelope (E) transcripts in 190 SARS-CoV-2 positive samples collected on hospital admission. We relate these findings to duration of symptoms. We find that all transcripts decline at the same rate; however, subgenomic E becomes undetectable before other transcripts. In Kaplan-Meier analysis the median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic RNA compared to total RNA suggesting subgenomic transcript copy number is highly dependent on copy number of total transcripts. The mean difference between total N and subgenomic N is 16-fold (4.0 cycles) and the mean difference between total E and sub-genomic E is 137-fold (7.1 cycles). This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number. Although Subgenomic E is undetectable at a time that may more closely reflect the duration of infectivity, its utility in determining active infection may be no more useful than a copy number threshold determined for total transcripts.
Evaluation of a SARS-CoV-2 Vaccine NVX-CoV2373 in Younger and Older Adults
Authors: Formica Neil , Mallory Raburn , Albert Gary , Robinson Michelle , Plested Joyce S. , Cho Iksung , Robertson Andreana , Dubovsky Filip , Glenn Gregory M. ,   for the 2019nCoV-101 Study Group
Published: March 2021

ABSTRACTBackgroundNVX-CoV2373 is a recombinant severe acute respiratory coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins and Matrix-M1 adjuvant.MethodsThe phase 2 component of our randomized, placebo-controlled, phase 1-2 trial was designed to identify which dosing regimen of NVX-CoV2373 should move forward into late phase studies in younger (18-59 years) and older (60-84 years) participants and was based on immunogenicity and safety data through day 35 (14 days after the second dose). Participants were randomly assigned to receive either one or two intramuscular doses of 5-µg or 25-µg NVX-CoV2373 or placebo, 21 days apart. Primary endpoints were immunoglobulin G (IgG) anti-spike protein response, 7-day solicited reactogenicity, and unsolicited adverse events. A key secondary endpoint was wild-type virus neutralizing antibody response.ResultsAfter randomization, approximately 250 participants each were assigned to one of four vaccine groups or placebo. Of these, approximately 45% were older participants. Reactogenicity was predominantly mild to moderate in severity and of short duration (median <3 days) after first and second vaccination with NVX-CoV2373, with higher frequencies and intensity after second vaccination and with the higher dose, and occurred less frequently and was of lower intensity in older participants. The two-dose regimen of 5-µg NVX-CoV2373 induced robust geometric mean titer (GMT) IgG anti-spike protein (65,019 and 28,137 EU/mL) and wild-type virus neutralizing antibody (2201 and 981 titers) responses in younger and older participants, respectively, with seroconversion rates of 100% in both age groups. Neutralizing antibody responses exceeded those seen in convalescent sera for both age groups.ConclusionsThe study confirmed that the two-dose regimen of 5-µg NVX-CoV2373 is highly immunogenic and well tolerated in both younger and older participants.(Funded by the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number: NCT04368988).