bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Procedure for Bacterial Expression and Purification of the Fragile X Protein Family
Authors: Edwards Madison , Xu Mingzhi , Joseph Simpson 
Published: June 2020

AbstractThe fragile X protein family consists of three RNA-binding proteins involved in translational regulation. Fragile X mental retardation protein (FMRP) is well-studied, as its loss leads to fragile X syndrome, a neurodevelopmental disorder which is the most prevalent form of inherited mental retardation and the primary monogenetic cause of autism. Fragile X related proteins 1 and 2 (FXR1P & FXR2P) are autosomal paralogs of FMRP that are involved in promoting muscle development and neural development, respectively. There is great interest in studying this family of proteins, yet researchers have faced much difficulty in expressing and purifying the full-length versions of these proteins in sufficient quantities. We have developed a simple, rapid, and inexpensive procedure that allows for the recombinant expression and purification of full-length human FMRP, FXR1P, and FXR2P fromEscherichia coliin high yields, free of protein and nucleic acid contamination. In order to assess the proteins’ function after purification, we confirmed their binding to pseudoknot and G-quadruplex forming RNAs.
A low-cost platform suitable for sequencing-based recovery of natural variation in understudied plants
Authors: Howard-Till Rachel , Osorio Claudia E. , Till Bradley J. 
Published: June 2020

AbstractGenetic characterization of wild and cultivated plants provides valuable knowledge for conservation and agriculture. DNA sequencing technologies are improving and costs are dropping. Yet, analysis of many species is hindered because they grow in regions that lack infrastructure for advanced molecular biology. We developed and adapted low-cost methods that address these issues. Tissue is collected and stored in silica-gel, avoiding the need for liquid nitrogen and freezers. We have optimized low-cost home-made DNA extraction to increase yields, reduce costs, and produce DNA suitable for next generation sequencing. We also describe how to build a gel documentation system for DNA quantification. As a proof of principle, we use these methods to evaluate wildBerberis darwinii, native to Southern Chile.Method summaryWe describe a suite of low-cost do-it-yourself methods for field collection of plant tissues, extraction of genomic DNA suitable for next generation sequencing, and home-made agarose gel documentation suitable for DNA quantification. These methods enable the collection and preparation of samples for genomic analysis in regions with limited infrastructure.
Rapid Single Cell Evaluation of Human Disease and Disorder Targets Using REVEAL: SingleCell™
Authors: Kumar Namit , Golhar Ryan , Sharma Kriti Sen , Holloway James L , Sarangi Srikant , Neuhaus Isaac , Walsh Alice M. , Pitluk Zachary W. 
Published: June 2020

AbstractSingle-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypothesis by querying extensive single-cell datasets.Large single-cell datasets like human cell atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics and vaccine targets; as the world struggles to cope with the on-going spread of COVID-19 infections.In this manuscript we describe, REVEAL: SingleCell which enables storage, retrieval and rapid query of single-cell datasets inclusive of millions of cells. The analytical database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypothesis. One such example includes identifying the most prevalent cell type annotation tag on returned cells.We used REVEAL: SingleCell to evaluate expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in <60 seconds. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic.
Substrate Transport and Specificity in a Phospholipid Flippase
Authors: Wang Yong , Lyons Joseph A , Timcenko Milena , Kümmerer Felix , de Groot Bert L. , Nissen Poul , Gapsys Vytautas , Lindorff-Larsen Kresten 
Published: June 2020

AbstractType 4 P-type ATPases are lipid flippases which help maintain asymmetric phospholipid distribution in eukaryotic membranes by driving unidirectional translocation of phospholipid substrates. Recent cryo-EM and crystal structures have provided a detailed view of flippases, and we here use molecular dynamics simulations to study the first steps of phospholipid transport and lipid substrate specificity. Our simulations and new cryo-EM structure shows phospholipid binding to a groove and subsequent movement towards the centre of the membrane, and reveal a preference for phosphatidylserine lipids. We find that only the lipid head group stays in the groove while the lipid tails remain in the membrane, thus visualizing how flippases have evolved to transport large substrates. The flippase also induces deformation and thinning of the outer leaflet facilitating lipid recruitment. Our simulations provide insight into substrate binding to flippases and suggest that multiple sites and steps in the functional cycle contribute to substrate selectivity.
Three LysM effectors ofZymoseptoria triticicollectively disarm chitin-triggered plant immunity
Authors: Tian Hui , MacKenzie Craig I. , Rodriguez-Moreno Luis , van den Berg Grardy C.M. , Chen Hongxin , Rudd Jason J. , Mesters Jeroen R. , Thomma Bart P.H.J. 
Published: June 2020

SUMMARYChitin is a major structural component of fungal cell walls and acts as a microbe-associated molecular pattern (MAMP) that, upon recognition by a plant host, triggers the activation of immune responses. In order to avoid the activation of these responses, the Septoria tritici blotch (STB) pathogen of wheat,Zymoseptoria tritici, secretes LysM effector proteins. Previously, the LysM effectors Mg1LysM and Mg3LysM were shown to protect fungal hyphae against host chitinases. Furthermore, Mg3LysM, but not Mg1LysM, was shown to suppress chitin-induced reactive oxygen species (ROS) production. Whereas initially a third LysM effector gene was disregarded as a presumed pseudogene, we now provide functional data to show that also this gene encodes a LysM effector, named Mgx1LysM, that is functional during wheat colonization. While Mg3LysM confers a major contribution toZ. triticivirulence, Mgx1LysM and Mg1LysM contribute toZ. triticivirulence with smaller effects. All three LysM effectors display partial functional redundancy. We furthermore demonstrate that Mgx1LysM binds chitin, suppresses the chitin-induced ROS burst and is able to protect fungal hyphae against chitinase hydrolysis. Finally, we demonstrate that Mgx1LysM is able to undergo chitin-induced polymerisation. Collectively, our data show thatZymoseptoria triticiutilizes three LysM effectors to disarm chitin-triggered wheat immunity.
Learning Mitigates Genetic Drift
Authors: Lenart Peter , Bienertová-Vašků Julie , Berec Luděk 
Published: June 2020

AbstractGenetic drift is a basic evolutionary principle describing random changes in allelic frequencies, with far-reaching consequences in various topics ranging from species conservation efforts to speciation. The conventional approach assumes that genetic drift has the same effect on all populations undergoing the same change in size, regardless of different behaviors and history of the populations. However, here we reason that processes leading to a systematic increase of individuals’ chances of survival, such as learning or immunological memory, can mitigate the effects of genetic drift even if the overall mortality rate in the population does not change. We further test this notion in an agent-based model monitoring allele frequencies in a population of prey, either able or not able to learn. Importantly, both these populations start with the same effective size and have the same and constant overall mortality rates. Our results demonstrate that even under these conditions, learning can mitigate drift if generations overlap. Furthermore, this effect holds regardless if the population is haploid or diploid or whether it reproduces sexually or asexually. Therefore, our findings demonstrate that learning is an overlooked factor affecting the effective population size. These findings may be of importance not only for basic evolutionary theory but also for other fields using the concept of genetic drift.
Modelling movement and landscape connectivity of New Zealand native birds in highly structured agroecosystem networks
Authors: Zhang Jingjing , Pannell Jennifer L. , Case Bradley S. , Hinchliffe Graham , Stanley Margaret C. , Buckley Hannah L. 
Published: June 2020

AbstractUnderstanding how spatial heterogeneity affects movement and dispersal is critical for maintaining functional connectivity in agroecosystems. Least-cost path models are popular conservation tools to quantify the cost of a species dispersing though the landscapes. However, the variability of species in life history traits and landscape configurations can affect their space-use patterns and should be considered in agroecosystem management aiming to improve functional biodiversity. In this study, we modelled the connectivity properties of native species on a real agroecosystem landscape dominated by sheep and beef farming in north Canterbury, New Zealand, where the recovery of native bird population is desired. We chose two species to act as case studies that were contrasting in their mobility: New Zealand pigeon/kererū (Hemiphaga novaeseelandiae; highly mobile) and southern brown kiwi/tokoeka (Apteryx australis; flightless). Networks of the least-cost paths of kererū and tokoeka were constructed based on their habitat preferences and movement capacities, and we compared and contrasted the connectivity properties and network topographies of their networks. We then compared the network metrics of western side (higher density of forest) with the eastern side (dominated by grazed grassland) of the study area where the vegetation composition was vastly different for both species. The results shown three variables were the most important contributors to the structure of the dispersal networks: the nature of the matrix, spatial structure of vegetation patches, and the gap-crossing ability of the study species. Tokoeka were able to utilise smaller habitat patches as stepping-stones for dispersal, while kererū can select more preferred habitat patches due to their high movement capacity. In contrast to the eastern side, we observed the western/forested side to have more, and stronger, links among habitat patches for both species, due to the presence of several large patches of native forest. Our work suggested that one size does not fit all, rather, conservation strategies that account for species’ life histories and movement traits are required to identify and preserve a connected ecological network.
Comparison of 12 molecular detection assays for SARS-CoV-2
Authors: Matsumura Yasufumi , Shimizu Tsunehiro , Noguchi Taro , Nakano Satoshi , Yamamoto Masaki , Nagao Miki 
Published: June 2020

AbstractMolecular testing for SARS-CoV-2 is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. All the assays showed a specificity of 100% (95% confidence interval, 95.8 to 100). The N2 assay kit of the US Centers for Disease Control and Prevention (CDC) and the N2 assay of the Japanese National Institute of Infectious Disease (NIID) were the most sensitive assays with 100% sensitivity (95% confidence interval, 94.7 to 100), followed by the CDC N1 kit, E assay by Corman, and NIID N2 assay multiplex with internal control reactions. These assays are reliable as first-line molecular assays in laboratories when combined with appropriate internal control reactions.
COVID-19 Antibody in Thai Community Hospitals
Authors: Nopsopon Tanawin , Pongpirul Krit , Chotirosniramit Korn , Hiransuthikul Narin 
Published: June 2020

AbstractBackgroundCOVID-19 seroprevalence data has been scarce, especially in less developed countries with a relatively low infection rate.MethodsA locally developed rapid IgM/IgG test kit was used for screening hospital staff and patients who required procedural treatment or surgery in 52 hospitals in Thailand from April 8 to June 26, 2020. A total of 857 participants were tested—675 were hospital staff and 182 were pre-procedural patients. (Thai Clinical Trials Registry: TCTR20200426002)ResultsOverall, 5.5% of the participants (47 of 857) had positive immunoglobulin M (IgM), 0.2% (2 of 857) had positive immunoglobulin G (IgG) and IgM. Hospitals located in the Central part of Thailand had the highest IgM seroprevalence (11.9%). Preprocedural patients had a higher rate of positive IgM than the hospital staff (12.1% vs. 3.7%). Participants with present upper respiratory tract symptoms had a higher rate of positive IgM than those without (9.6% vs. 4.5%). Three quarters (80.5%, 690 of 857) of the participants were asymptomatic, of which, 31 had positive IgM (4.5%) which consisted of 20 of 566 healthcare workers (3.5%) and 11 of 124 preprocedural patients (8.9%).ConclusionsCOVID-19 antibody test could detect a substantial number of potential silent spreaders in Thai community hospitals. Antibody testing should be encouraged for mass screening, especially in asymptomatic individuals.
Contact Tracing Evaluation for COVID-19 Transmission during the Reopening Phase in a Rural College Town
Authors: Moon Sifat Afroj , Scoglio Caterina 
Published: June 2020

Contact tracing can play a vital role in controlling human-to-human transmission of a highly contagious disease such as COVID-19. To investigate the benefits and costs of contact tracing, we develop an individual-based contact-network model and a susceptible-exposed-infected-confirmed (SEIC) epidemic model for the stochastic simulations of COVID-19 transmission. We estimate the unknown parameters (reproductive ratio R0 and confirmed rate δ2) by using observed confirmed case data. After a two month-lockdown, states in the USA have started the reopening process. We investigate for four different reopening situations: under “stay-at-home” order or no reopening, 25 % reopening, 50 % reopening, and 75 % reopening. We model contact tracing in a two-layer network by modifying the basic SEIC epidemic model. The two-layer network is composed by the contact network in the first layer and the tracing network in the second layer. Since the full contact list of an infected individual patient can be hard to obtain, then we consider different fractions of contacts from 60% to 5%. The goal of this paper is to assess the effectiveness of contact tracing to control the COVID-19 spreading during the initial phase of the reopening process of a rural college town.In this research, we assess the benefits and cost of contact tracing as a key mitigation strategy to control the spreading of COVID-19. In terms of benefits, our simulation results show that increasing the fraction of traced contacts decreases the size of the epidemic. For example, tracing 20% of the contacts is enough for all four reopening scenarios to reduce the epidemic size by half. Considering the act of quarantining susceptible households as the contact tracing cost, we have observed an interesting phenomenon. When we increase the fraction of traced contacts from 5% to 20%, the number of quarantined susceptible people increases because each individual confirmed case is mentioning more contacts. However, when we increase the fraction of traced contacts from 20% to 60%, the number of quarantined susceptible people decreases because the increment of the mentioned contacts is balanced by a reduced number of confirmed cases. The outcomes of this research are valuable in the reopening process of the USA. Furthermore, the framework is generic enough to use any locations and for other diseases as well.
COVID-19-associated ARDS treated with DEXamethasone (CoDEX): Study design and rationale for a randomized trial
Authors: Tomazini Bruno M. , Maia Israel S. , Bueno Flavia R. , Silva Maria Vitoria A.O. , Baldassare Franca Pellison , Costa Eduardo Leite V. , Moura Ricardo A.B. , Honorato Michele , Costa André N. , Cavalcanti Alexandre B. , Rosa Regis , Avezum Álvaro , Veiga Viviane C. , Lopes Renato D. , Damiani Lucas P. , Machado Flávia R. , Berwanger Otavio , Azevedo Luciano C.P. ,   for the COALITION COVID-19 Brazil III Investigators
Published: June 2020

ABSTRACTOBJECTIVESThe infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) spreads worldwide and is considered a pandemic. The most common manifestation of SARS-CoV2 infection (Coronavirus disease 2019 - COVID-19) is viral pneumonia with varying degrees of respiratory compromise and up to 40% of hospitalized patients might develop Acute Respiratory Distress Syndrome (ARDS). Several clinical trials evaluated the role of corticosteroids in non-COVID-19 ARDS with conflicting results. We designed a trial to evaluate the effectiveness of early intravenous dexamethasone administration on the number of days alive and free of mechanical ventilation within 28 days after randomization in adult patients with moderate or severe ARDS due to confirmed or probable COVID-19.METHODSThis is a pragmatic, prospective, randomized, stratified, multicenter, open-label, controlled trial including 350 patients with early-onset (less than 48h before randomization) moderate or severe ARDS, defined by the Berlin criteria, due to COVID-19. Eligible patients will be randomly allocated to either standard treatment plus dexamethasone (intervention group) or standard treatment without dexamethasone (control group). Patients in the intervention group will receive dexamethasone 20mg IV once daily for 5 days, followed by dexamethasone 10mg IV once daily for additional 5 days or until Intensive Care Unit (ICU) discharge, whichever occurs first. The primary outcome is ventilator-free days within 28 days after randomization, defined as days alive and free from invasive mechanical ventilation. Secondary outcomes are all-cause mortality rates at day 28, evaluation of the clinical status at day 15 assessed with a 6-level ordinal scale, mechanical ventilation duration from randomization to day 28, Sequential Organ Failure Assessment (SOFA) Score evaluation at 48h, 72h and 7 days and ICU-free days within 28.ETHICS AND DISSEMINATIONThis trial was approved by the Brazilian National Committee of Ethics in Research (Comissão Nacional de Ética em Pesquisa - CONEP) and National Health Surveillance Agency (ANVISA). An independent data monitoring committee will perform interim analyses and evaluate adverse events throughout the trial. Results will be submitted for publication after enrolment and follow-up are complete.ClinicalTrials.gov identifierNCT04327401
A cross-sectional study of immune seroconversion to SARS-CoV-2 in front-line maternity health professionals
Authors: Bampoe Sohail , Lucas Dominique Nuala , Neall Georgina , Sceales Penny , Aggarwal Reena , Caulfield Kim , Siassakos Dimitrios , Odor Peter Mark 
Published: June 2020

SummaryCOVID-19, the respiratory disease caused by the SARS-CoV-2, is thought to cause a milder illness in pregnancy with a greater proportion of asymptomatic carriers. This has important implications for the risk of patient-to-staff, staff-to-staff and staff-to patient transmission among health professionals in maternity. The aim of this study was to investigate the prevalence of previously undiagnosed SARS-CoV-2 infection in health professionals from two tertiary-level maternity units in London, UK and to determine associations between HCW characteristics, reported symptoms and serological evidence of prior SARS-CoV-2 infection.200 anaesthetists, midwives and obstetricians with no previously confirmed diagnosis of COVID-19 were tested for immune seroconversion using laboratory IgG assays. Comprehensive symptom and medical histories were also collected. 5/40 (12.5%; 95% CI: 4.2-26.8) anaesthetists, 7/52 (13.5%; 95% CI: 5.6-25.8%) obstetricians and 17/108 (15.7%; 95% CI: 9.5-24.0%) midwives were seropositive, with an overall total of 29/200 (14.5%; 95% CI: 9.9-20.1%) of maternity healthcare workers testing positive for IgG antibodies against SARS-CoV-2. Of those who had seroconverted, 10/29 (35.5%) were completely asymptomatic. Fever or cough were only present in 6/29 (20.7%) and (10/29 (34.5%) respectively. Anosmia was the most common symptom occurring in 15/29 (51.7%) seropositive participants and was the only symptom that was predictive of positive seroconversion (OR 18; 95% CI 6 – 55). 58.6% of those who were seropositive had not self-isolated at any point and continued to provide patient care in the hospital setting.This study was the largest study of baseline immune seroconversion in maternity healthcare workers conducted to date and reveals that 1 in 6 were seropositive, of whom 1 in 3 were asymptomatic. This has significant implications for the risk of occupational transmission of SARS-CoV-2 for both staff and patients in maternity and regular testing of staff, including asymptomatic staff should be considered to reduce transmission risk.
A Systematic Review and Meta-analysis of D-Dimer Levels in Patients Hospitalized with Coronavirus Disease 2019 (COVID-19)
Authors: Bansal Agam , Singh Achintya D , Jain Vardhmaan , Aggarwal Manik , Gupta Samiksha , Padappayil Rana P , Gupta Mohak , Mian Agrima 
Published: June 2020

AbstractAimTo determine if the d-dimer levels are elevated in individuals with COVID 19 having worse clinical outcomes including all-cause mortality, ICU admission or ARDSMethodsWe conducted a systematic review and meta-analysis of published literature in Pubmed, Embase and Cochrane database through April 9, 2020 for studies evaluating the d-dimer levels in patients with and without a worse clinical outcome (all-cause mortality, ICU admission and ARDS). A total of 6 studies included in the meta-analysis.ResultsThe values of d-dimer were found to be significantly increased in patients with the composite clinical end point than in those without (SMD, 1.67 ug/ml (95% CI, 0.72-2.62 ug/ml). The SMD of the studies (Tang et al, Zhou et al, Chen et al), which used only mortality as an outcome measure was 2.5 ug/mL (95% CI, 0.62-4.41).ConclusionThe results of this concise meta-analysis suggest that d-dimer is significantly increased in patients having a worse clinical outcome (all-cause mortality, ICU admission or ARDS).