bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-Based Detection of Whole-Genome Duplications in a Phylogeny
Authors: Zwaenepoel Arthur , Van de Peer Yves 
Published: April 2020

AbstractAncient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the “background” gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set of a priori selected WGD hypotheses and cannot be used to discover WGDs in a phylogeny. In this study, we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth–death model that includes WGD in a flexible hierarchical Bayesian approach and use reversible-jump Markov chain Monte Carlo to perform Bayesian inference of branch-specific duplication, loss, and WGD retention rates across the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants, and discuss the statistical intricacies of model-based WGD inference.
CoCoCoNet: conserved and comparative co-expression across a diverse set of species
Authors: Lee John , Shah Manthan , Ballouz Sara , Crow Megan , Gillis Jesse 
Published: April 2020

AbstractCo-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.
Extraforaminal Thoracic and Lumbar Spinal Nerve Ultrasound-Guided Percutaneous Peripheral Nerve Stimulation
Authors: Gargya Akshat , Singh Harmandeep , Lin Tiffany , Gulati Amitabh 
Published: April 2020

Abstract

Objective
Peripheral nerve stimulation provides targeted stimulation and pain relief within a specific nerve distribution. This technical case report provides a method to perform selective nerve root stimulation of thoracic and lumbar spinal nerves using ultrasonography.

Methods
Ultrasound-guided peripheral nerve stimulation of thoracic and lumbar spinal nerves allows better visualization of soft tissue anatomy and planning of needle trajectory.

Conclusions
Ultrasound-guided peripheral nerve stimulation procedures may provide a safer method for neurostimulation lead placement when compared with fluoroscopic-guided techniques.
On Grounds, Anchors, and Diseases: A Reply to Glackin
Authors: Miller Tate Alex James , Davies Thomas 
Published: April 2020

Abstract
Shane Glackin's 2019 Philosophical Quarterly article aims to (a) offer a framework for understanding the philosophical debate about the nature of disease and (b) utilise this framework to reply to several standard objections to normativist (particularly social constructivist) theories of disease. Specifically, Glackin claims his model avoids three central challenges to normativism, which we term the ‘Flippancy Problem’ (which charges that normativism implies diseases can be cured by adjusting our attitudes towards them), ‘Repugnancy Problem’ (which charges that normativism implies we must endorse repugnant historical views regarding ‘conditions’ like Drapetomania as ‘genuine diseases in their day’), and the ‘Explanatory Problem’ (which charges that normativism cannot explain why diseases warrant certain kinds of medical intervention without lapsing into vicious circularity). Although we find Glackin's framework helpful in clarifying the terrain of the debate, we argue these three challenges continue to afflict his preferred construal of the normativist/social constructivist position.
Mortality, causes of death and influence of medication use in patients with systemic lupus erythematosus vs matched controls
Authors: Bultink Irene E M , de Vries Frank , van Vollenhoven Ronald F , Lalmohamed Arief 
Published: April 2020

Abstract

Objectives
We wanted to estimate the magnitude of the risk from all-cause, cause-specific and sex-specific mortality in patients with SLE and relative risks compared with matched controls and to evaluate the influence of exposure to medication on risk of mortality in SLE.

Methods
We conducted a population-based cohort study using the Clinical Practice Research Datalink, Hospital Episode Statistics and national death certificates (from 1987 to 2012). Each SLE patient (n = 4343) was matched with up to six controls (n = 21 780) by age and sex. Cox proportional hazards models were used to estimate overall and cause-specific mortality rate ratios.

Results
Patients with SLE had a 1.8-fold increased mortality rate for all-cause mortality compared with age- and sex-matched subjects [adjusted hazard ratio (HR) = 1.80, 95% CI: 1.57, 2.08]. The HR was highest in patients aged 18–39 years (adjusted HR = 4.87, 95% CI: 1.93, 12.3). Mortality rates were not significantly different between male and female patients. Cumulative glucocorticoid use raised the mortality rate, whereas the HR was reduced by 45% with cumulative low-dose HCQ use. Patients with SLE had increased cause-specific mortality rates for cardiovascular disease, infections, non-infectious respiratory disease and for death attributable to accidents or suicide, whereas the mortality rate for cancer was reduced in comparison to controls.

Conclusion
British patients with SLE had a 1.8-fold increased mortality rate compared with the general population. Glucocorticoid use and being diagnosed at a younger age were associated with an increased risk of mortality. HCQ use significantly reduced the mortality rate, but this association was found only in the lowest cumulative dosage exposure group.
Impact of storage conditions and premix type on phytase stability
Authors: Saensukjaroenphon Marut , Evans Caitlin E , Paulk Chad B , Gebhardt Jordan T , Woodworth Jason C , Stark Charles R , Bergstrom Jon R , Jones Cassandra K 
Published: April 2020

AbstractPotential use of medium-chain fatty acids (MCFA), increased temperatures and exposure time may be implemented to mitigate biological hazards in premixes and feed ingredients. However, there are no data on how these strategies influence phytase stability. For Exp. 1, there were no four- and three-way interactions among premix type (PT), oil type (OT), storage condition (SC), and storage time (ST) for phytase stability (P &gt; 0.111). There were two-way interactions for PT × SC (P &lt; 0.001) and SC × ST (P &lt; 0.001). The OT did not affect phytase stability when premixes-containing phytase were added as either mineral oil (MO) or MCFA (P = 0.382). For Exp. 2, there was no interaction between PT and OT (P = 0.121). There were also no differences for phytase stability between vitamin premix (VP)- and vitamin trace mineral (VTM) premix-containing phytase were heated at 60 °C (P = 0.141) and between premixes-containing phytase were mixed with 1% MO added and 1% MCFA (P = 0.957). Therefore, the phytase was stable when mixed with both VP and VTM premix and stored at 22 °C with 28.4% relative humidity (RH). The phytase stability was dramatically decreased when the phytase was mixed with premixes and stored at 39.5 °C with 78.8% RH. Also, MCFA did not influence phytase degradation during storage up to 90 d and in the heat pulse process. The phytase activity was decreased by 20% after the premixes containing the phytase was heated at 60 °C for approximately 9.5 h. If both MCFA and heat pulse treatment have similar efficiency at neutralizing or reducing the target pathogen, the process of chemical treatment could become a more practical practice.
MawuAP1 promotes flowering and fruit development in the basal angiosperm Magnolia wufengensis (Magnoliaceae)
Authors: Li Cunjie , Chen Liyuan , Fan Xiaoning , Qi Wenjuan , Ma Jiang , Tian Tian , Zhou Tao , Ma Luyi , Chen Faju 
Published: April 2020

AbstractThe APETALA1/SQUAMOSA (AP1/SQUA)-like genes of flowering plants play crucial roles in the development processes of floral meristems, sepals, petals and fruits. Although many of the AP1/SQUA-like genes have been characterized in angiosperms, few have been identified in basal angiosperm taxa. Therefore, the functional evolution of the AP1/SQUA subfamily is still unclear. We characterized an AP1 homolog, MawuAP1, from Magnolia wufengensis that is an ornamental woody plant belonging to the basal angiosperms. Gene sequence and phylogenetic analyses suggested that MawuAP1 was clustered with the FUL-like homologous genes of basal angiosperms and had FUL motif and paleoAP1 motif domain, but it did not have the euAP1 motif domain of core eudicots. Expression pattern analysis showed that MawuAP1 was highly expressed in vegetative and floral organs, particularly in the early stage of flower bud development and pre-anthesis. Protein–protein interaction pattern analysis revealed that MawuAP1 has interaction with an A-class gene (MawuAP1), C-class gene (MawuAG-1) and E-class gene (MawuAGL9) of the MADS-box family genes. Ectopic expression in Arabidopsis thaliana indicated that MawuAP1 could significantly promote flowering and fruit development, but it could not restore the sepal and petal formation of ap1 mutants. These results demonstrated that there are functional differences in the specification of sepal and petal floral organs and development of fruits among the AP1/SQUA-like genes, and functional conservation in the regulation of floral meristem. These findings provide strong evidence for the important functions of MawuAP1 in floral meristem determination, promoting flowering and fruit development, and further highlight the importance of AP1/SQUA subfamily in biological evolution and diversity.
Performance of Fabrics for Home-Made Masks Against the Spread of Respiratory Infections Through Droplets: A Quantitative Mechanistic Study
Authors: Aydin Onur , Emon Bashar , Cheng Shyuan , Hong Liu , Chamorro Leonardo P. , Saif M. Taher A. 
Published: April 2020

AbstractRespiratory infections may spread through droplets and aerosols released by infected individuals coughing, sneezing, or speaking. In the case of Coronavirus Disease 2019 (COVID-19), spread can occur from symptomatic, pre-symptomatic, and asymptomatic persons. Given the limited supply of professional face masks and respirators, the U.S. Centers for Disease Control and Prevention (CDC) has recommended home-made cloth face coverings for use by the general public in areas of significant community-based transmission. There is, however, little information on the effectiveness of cloth face coverings in reducing droplet dissemination. Here, we ascertained the performance of 11 household fabrics at blocking high-velocity droplets, using a commercial medical mask as a benchmark. We also assessed their breathability (air permeability), texture, fiber composition, and water absorption properties. We found that droplet blocking efficiency anti-correlates with breathability; less breathable fabrics being more effective in blocking. However, materials with high breathability are desirable for comfort and to reduce airflow through gaps between the mask and face. Our measurements indicate that 2 or 3 layers of highly permeable fabric, such as T-shirt cloth, may block droplets with an efficacy similar to that of medical masks, while still maintaining comparable breathability. Overall, our study suggests that cloth face coverings, especially with multiple layers, may help reduce droplet transmission of respiratory infections. Furthermore, face coverings made from biodegradable fabrics such as cotton allow washing and reusing, and can help reduce the adverse environmental effects of widespread use of commercial disposable and non-biodegradable facemasks.
Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays
Authors: Crawford Katharine H.D. , Eguia Rachel , Dingens Adam S. , Loes Andrea N. , Malone Keara D. , Wolf Caitlin R. , Chu Helen Y. , Tortorici M. Alejandra , Veesler David , Murphy Michael , Pettie Deleah , King Neil P. , Balazs Alejandro B. , Bloom Jesse D. 
Published: April 2020

AbstractSARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.
Association of mitochondrial DNA copy number with cardiometabolic diseases in a large cross-sectional study of multiple ancestries
Authors: Liu Xue , Longchamps Ryan J. , Wiggins Kerri , Raffield Laura M. , Bielak Lawrence F. , Zhao Wei , Pitsillides Achilleas , Blackwell Thomas , Yao Jie , Guo Xiuqing , Kurniansyah Nuzulul , Thyagarajan Bharat , Pankratz Nathan , Rich Stephen S. , Taylor Kent D. , Peyser Patricia A. , Heckbert Susan R. , Seshadri Sudha , Cupples L Adrienne , Boerwinkle Eric , Grove Megan L. , Larson Nicholas , Smith Jennifer A. , Vasan Ramachandran S , Sofer Tamar , Fitzpatrick Annette L , Fornage Myriam , Ding Jun , Correa Adolfo , Abecasis Goncalo , Psaty Bruce M. , Wilson James G. , Levy Daniel , Rotter Jerome I. , Bis Joshua C. , Satizabal Claudia L , Arking Dan E. , Liu Chunyu 
Published: April 2020

AbstractAimsWe tested the hypothesis that mitochondrial DNA copy number (CN) is associated with cardiometabolic disease (CMD) traits.Methods and resultsWe determined the cross-sectional association of mtDNA CN measured in whole blood with several CMD traits in 65,996 individuals (mean age 60, 54% women, and 79% European descent). Cohort- and ancestry/ethnicity-specific association analysis was performed adjusting for trait- and cohort-specific covariates. Age was slightly positively associated with age (0.03 s.d. / 10 years (95% CI=0.01, 0.05)) before 65 years, while every 10 years older age was associated with 0.14 s.d. lower level of mtDNA CN after 65 years (95% CI= -0.18, -0.10). In meta-analysis without adjustment for white blood cell (WBC) and differential count in participants of European descent (N=52,491), low mtDNA CN was associated with increased odds of obesity (OR with 95% CI=1.13 (1.11, 1.16), P=3.3e-30) and hypertension (OR=1.05 (1.03, 1.08), P=4.0e-07). Further adjusting for WBC and differential count in the same participants of European descent (N=44,035), associations became non-significant (P>0.05) for hypertension, attenuated for obesity (ORwithout cell count=1.15 (1.12, 1.18) versus ORcell count=1.06 (1.03, 1.08)) but strengthened for hyperlipidemia (ORwithout cell counts=1.03 (1.00, 1.06) versus ORcell counts=1.06 (1.03, 1.09)). The magnitude and directionality of most associations were consistent between participants of European descent and other ethnicity/ancestry origins.ConclusionLow levels of mtDNA CN in peripheral blood were associated with an increased risk of CMD diseases.
A phased approach to unlocking during the COVID-19 pandemic – Lessons from trend analysis
Authors: Stedman Mike , Davies Mark , Lunt Mark , Verma Arpana , Anderson Simon G. , Heald Adrian H 
Published: April 2020

AbstractWith the COVID-19 pandemic leading to radical political control of social behaviour, including restricted movement outsides homes. Can more detailed analysis of the published confirmed local case data from the pandemic in England using infection ratio and comparing local level data provide a deeper understanding of the wider community infection and inform the future unlocking process.The historic daily published 78,842 confirmed cases in England up to 13/4/2020 in each of 149 Upper Tier Local Authority (UTLA) were converted to Average Daily Infection Rate (RADIR), an R-value - the number of further people infected by one infected person after their 5-day incubation and during their 5-day infectious phase, and the associated Rate of Change of Infection Rate (ΔIR) also calculated. Results compared to look for significant variances between regions. Stepwise regression was carried out to see what local factors could be linked to the difference in local infection rates.The peak of COVID-19 infection has passed. The current RADIR is now below 1. The rate of decline is such that within 14 days it may be below 0.5. There are significant variations in the current RADIR and ΔIR between the UTLAs, suggesting that the disease locally may be at different stages.Regression analysis across UTLAs found that the only factor that could be related to the fall in RADIR was an increase in the number of confirmed infection/1,000 population. Extrapolation of these results showed that based on assuming a link to increased immunity, unreported community infection may be over 200 times higher than the reported confirmed cases providing evidence that by the end of the second week in April 26% of the population may already have had the disease and so now have increased immunity. Linking these increased estimated infected numbers to recorded deaths indicates a possible mortality rate of 0.14%.Analysis of the current reported local case data using the infectious ratio does provide greater insight into the current levels of community infection and can be used to make better-informed decisions about the future management of restricted social behaviour and movement
COVID-19 pandemic: examining the faces of spatial differences in the morbidity and mortality in sub-Saharan Africa, Europe and USA
Authors: Otitoloju Adebayo A. , Okafor Ifeoma P. , Fasona Mayowa , Bawa-Allah Kafilat A. , Isanbor Chukwuemeka , Chukwudozie Onyeka S. , Folarin Olawale S. , Adubi Taiwo O. , Sogbanmu Temitope O. , Ogbeibu Anthony E. 
Published: April 2020

AbstractBackgroundCOVID-19, the disease associated with the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently a global pandemic with several thousands of confirmed cases of infection and death. However, the death rate across affected countries shows variation deserving of critical evaluation.MethodsIn this study, we evaluated differentials in COVID-19 confirmed cases of infection and associated deaths of selected countries in Sub-Sahara Africa (Nigeria and Ghana), South Africa, Europe (Italy, Spain, Sweden and UK) and USA. Data acquired for various standard databases on mutational shift of the SARS-CoV-2 virus based on geographical location, BCG vaccination policy, malaria endemicity, climatic conditions (temperature), differential healthcare approaches were evaluated over a period of 45 days from the date of reporting the index case.ResultsThe number of confirmed cases of infection and associated deaths in Sub-Sahara Africa were found to be very low compared to the very high values in Europe and USA over the same period. Recovery rate from COVID-19 is not correlated with the mutational attributes of the virus with the sequenced strain from Nigeria having no significant difference (p>0.05) from other geographical regions. Significantly higher (p<0.05) infection rate and mortality from COVID-19 were observed in countries (Europe and USA) without a current universal BCG vaccination policy compared to those with one (Sub-Sahara African countries). Countries with high malaria burden had significantly lower (p<0.05) cases of COVID-19 than those with low malaria burden. A strong negative correlation (−0.595) between mean annual temperature and COVID-19 infection and death was observed with 14.8% variances between temperature and COVID-19 occurrence among the countries. A clear distinction was observed in the COVID-19 disease management between the developed countries (Europe and USA) and Sub-Sahara Africa.ConclusionsThe study established that the wide variation in the outcome of the COVID-19 disease burden in the selected countries are attributable largely to climatic condition (temperature) and differential healthcare approaches to management of the disease. We recommend consideration and mainstreaming of these findings for urgent intervention and management of COVID-19 across these continents.
Estimating the undetected infections in the Covid-19 outbreak by harnessing capture-recapture methods
Authors: Böhning Dankmar , Rocchetti Irene , Maruotti Antonello , Holling Heinz 
Published: April 2020

AbstractA major open question, affecting the policy makers decisions, is the estimation of the true size of COVID-19 infections. Most of them are undetected, because of a large number of asymptomatic cases. We provide an efficient, easy to compute and robust lower bound estimator for the number of undetected cases. A “modified” version of the Chao estimator is proposed, based on the cumulative time-series distribution of cases and deaths. Heterogeneity has been accounted for by assuming a geometrical distribution underlying the data generation process. An (approximated) analytical variance formula has been properly derived to compute reliable confidence intervals at 95%. An application to Austrian situation is provided and results from other European Countries are mentioned in the discussion.