bluuebunny/crossref_metadata_2025_split huggingface dataset:
Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study
Authors: Mahil SK , Yates M , Yiu ZZN , Langan SM , Tsakok T , Dand N , Mason KJ , McAteer H , Meynell F , Coker B , Vincent A , Urmston D , Vesty A , Kelly J , Lancelot C , Moorhead L , Bachelez H , Capon F , Contreras CR , De La Cruz C , Meglio P Di , Gisondi P , Jullien D , Lambert J , Naldi L , Norton S , Puig L , Spuls P , Torres T , Warren RB , Waweru H , Weinman J , Brown MA , Galloway JB , Griffiths CM , Barker JN , Smith CH 
Published: May 2021

AbstractBackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.MethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.Results4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.ConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.
Covid-19 and the South Asian Countries: factors ruling the pandemic
Authors: Biswas Tannishtha , Mondal Madhura , Bhattacharya Srijan , Sarkar Moitrayee , Dhara Bikram , Mitra Arup Kumar , Chandra Ayan 
Published: May 2021

AbstractThe novel corona virus causing Covid-19 was first detected in the city of Wuhan, China in December, 2019. In matter of months Covid-19 was declared a pandemic by the World Health Organization. The focus of this research includes the probable factors that might have played an important role in the spread of this infection causing a global threat. In this study we dealt with the South Asian countries namely Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan. Data on the demography of the countries, the climatic and geographical conditions, the socio-economic statuses, GDP being in the forefront, was collected and compared with Covid-19 related data such as total number of positive, recovered and death cases, etc. to determine if there was any significant correlation. The wide range of correlations observed can curve the path for the future research to understand the factors behind the spread of the communicable disease, analyzing the dynamics of the future biological threats to mankind and design the precautionary or preventive methods accordingly.
SARS-CoV-2 infection and reinfection in a seroepidemiological workplace cohort in the United States
Authors: Finch Emilie , Lowe Rachel , Fischinger Stephanie , de St Aubin Michael , Siddiqui Sameed M. , Dayal Diana , Loesche Michael A. , Rhee Justin , Berger Samuel , Hu Yiyuan , Gluck Matthew J. , Mormann Benjamin , Hasdianda Mohammad A. , Musk Elon R. , Alter Galit , Menon Anil S. , Nilles Eric J. , Kucharski Adam J. 
Published: May 2021

AbstractIdentifying the extent of SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4411 US employees in four states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an adjusted odds ratio of 0.09 (95% CI: 0.005 – 0.48) for reinfection, implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 91% reduced odds of a subsequent PCR positive test. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a sixth month time period. We also highlight two major sources of bias and uncertainty to be considered when estimating reinfection risk, confounders and the choice of baseline time point, and show how to account for both in our analysis.
Asynchronous glutamate exocytosis is enhanced in low release probability synapses and is widely dispersed across the active zone
Authors: Mendonça Philipe R. F. , Tagliatti Erica , Langley Helen , Kotzadimitriou Dimitrios , Zamora-Chimal Criseida G. , Timofeeva Yulia , Volynski Kirill E. 
Published: May 2021

AbstractThe balance between fast synchronous and delayed asynchronous release of neurotransmitters has a major role in defining computational properties of neuronal synapses and regulation of neuronal network activity. However, how it is tuned at the single synapse level remains poorly understood. Here, using the fluorescent glutamate sensor SF-iGluSnFR, we image quantal vesicular release in tens to hundreds of individual synaptic outputs (presynaptic boutons) from single pyramidal cells in culture with 4 millisecond temporal resolution, and localise vesicular release sites with ~ 75 nm spatial resolution. We find that the ratio between synchronous and asynchronous synaptic vesicle exocytosis varies extensively among presynaptic boutons supplied by the same axon, and that asynchronous release fraction is elevated in parallel with short-term facilitation at synapses with low release probability. We further demonstrate that asynchronous exocytosis sites are more widely distributed within the presynaptic release area than synchronous sites. These findings are consistent with a model in which functional presynaptic properties are regulated via a synapsespecific adjustment of the coupling distance between presynaptic Ca2+channels and releaseready synaptic vesicles. Together our results reveal a universal relationship between the two major functional properties of synapses – the timing and the overall probability of neurotransmitter release.
Imaging Nanoscale Nuclear Structures with Expansion Microscopy
Authors: Faulkner Emma L. , Pike Jeremy A. , Densham Ruth M. , Garlick Evelyn , Thomas Steven G. , Neely Robert K. , Morris Joanna R. 
Published: May 2021

AbstractCommonly applied super-resolution light microscopies have provided insight into subcellular processes at the nanoscale. However, imaging depth, speed, throughput and cost remain significant challenges, reducing the numbers of three-dimensional, nanoscale processes that can be investigated and the number of laboratories able to undertake such analysis. Expansion microscopy solves many of these limitations but its application to imaging nuclear processes has been constrained by concerns of unequal nuclear expansion.Here we demonstrate the conditions for isotropic expansion of the nucleus. Using DNA damage response proteins, BRCA1, 53BP1 and RAD51 as exemplars we quantitatively describe the three-dimensional nanoscale organisation of over 50,000 DNA damage response structures. We demonstrate the ability to assess chromatin regulated events and show the simultaneous assessment of four elements. This study thus provides the means by which expansion microscopy can contribute to the investigation of nanoscale nuclear processes.
A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors
Authors: Riva Claudia , Hajduskova Martina , Gally Christelle , Ahier Arnaud , Jarriault Sophie 
Published: May 2021

SUMMARYTransdifferentiation, or direct cell reprogramming, is the direct conversion of one fully differentiated cell type into another. Whether core mechanisms are shared between different transdifferentiation events, which can occur naturally in presence or in absence of cell division, is unclear. Our lab has previously characterized the Y-to-PDA natural transdifferentiation inCaenorhabditis elegans, which occurs without cell division and requires orthologs of vertebrates’ reprogramming factors. In this study, focusing on another transdifferentiation process, the K rectal cell-to-DVB GABAergic neuron, we report that the Y-to-PDA reprogramming factor SEM-4/SALL, SOX-2, CEH-6/POU are required for K-to-DVB transdifferentiation to allow the erasure of the rectal identity. In addition, cell division is necessary but not sufficient for this transdifferentiation event while the Wnt signaling plays distinct functions during the process including the selection of the daughter cell with a different fate, loss of the rectal identity and imposition of the specific neuronal subtype identity. We provide evidence that both the Wnt signaling and Y-to-PDA reprogramming factor SEM-4/SALL, SOX-2, CEH-6/POU act in parallel for the rectal identity erasure. Our results further support a model where antagonistic activities of SOX-2 and POP-1 and decreasing SOX-2 levels over time provide a timer for the acquisition of the final identity. In addition, the different levels of SOX-2 provide a mechanism for the integration of Wnt opposite dedifferentiation and re-differentiation functions during K-to-DVB transdifferentiation.
RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks
Authors: Markin Alexey , Wagle Sanket , Anderson Tavis K. , Eulenstein Oliver 
Published: May 2021

AbstractMotivationA phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g., hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method calledRF-Netfor accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens.ResultsHere we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, calledFast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. Additionally, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical influenza A virus evolutionary analyses.AvailabilityRF-Net 2is available athttps://github.com/flu-crew/rf-net-2.
Population analysis ofVibrio choleraein aquatic reservoirs reveals a novel sister species(Vibrio paracholeraesp. nov.) with a history of association with human infections
Authors: Islam Mohammad Tarequl , Nasreen Tania , Kirchberger Paul , Liang Kevin Y. H. , Orata Fabini , Johura Fatema-Tuz , Im Monica S. , Tarr Cheryl L. , Alam Munirul , Boucher Yann F. 
Published: May 2021

AbstractMost efforts to understand the biology ofVibrio choleraehave focused on a single group, the pandemic-generating lineage harbouring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in theV. choleraepopulations inhabiting in regions with varying history of cholera cases and how that might influence the abundance of pandemic strains, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka (cholera endemic) located in the Ganges delta, and of Falmouth (no known history of cholera), a small coastal town on the US East Coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny ofV. choleraespecies, sufficiently differentiated genetically and phenotypically to form a novel species. Strains from this species have been anecdotally isolated from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhoea. In 1935 Gardner and Venkatraman unofficially referred to a member of this group asVibrio paracholerae. In recognition of this earlier designation, we propose the nameVibrio paracholerae, sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species.ImportanceCholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution and environmental adaptation of the causative agentVibrio choleraeand tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics ofVibrio choleraein an inland locality which is known as endemic for cholera and compared with that of a cholera free coastal location. We found the consistent presence of the pandemic generatingV. choleraein cholera-endemic Dhaka and an exclusive presence of a lineage phylogenetically distinct from otherV. cholerae. Our study suggests that this lineage represents a novel species having pathogenic potential and a human link to its environmental abundance. The possible association with human population, co-existence and interaction with toxigenicV. choleraein the natural environment make this potential human pathogen an important subject for future studies.
Evaluation of wound healing effects of ginsenoside Rg1 and red ginseng extract in STZ-induced diabetic wound model: an in vivo pilot study
Authors: Lim Ji Yun , Suk Choi Young , Lee Hye Rim , Min An Hye , Lee Young Koo 
Published: May 2021

AbstractRed ginseng is an immune-enhancing compound that exhibits anti-inflammatory action. The ginsenoside Rg1, an ingredient of red ginseng, has been shown to play an important role in tumor suppression, wound healing, and angiogenesis. This study evaluated the effects of red ginseng extract and Rg1 in a diabetic wound model. Diabetes was induced with streptozotocin (STZ) in 8-week-old male Institute of Cancer Research (ICR) mice weighing 30–35 g. A full-thickness skin defect was treated by applying a dressing every 3 days. The mice were divided into three groups. Group 1 was administered an extract of red ginseng (10 mg/kg/d,n= 27, oral) and group 2 was administered Rg1 (10 mg/kg/d,n= 27, oral). Group 3 was a control group treated with phosphate-buffered saline (0.3 mL/kg/d,n= 27, oral). Red ginseng extract and Rg1 were orally administered to mice daily for 10 days following injury in groups 1 and 2, respectively. Both increased mRNA and protein levels of vascular endothelial growth factor (VEGF) and transforming growth factor (TGF)-β1 compared to controls. In addition, the wounds of animals in the Rg1 group were significantly smaller between days 7 and 10 (p< 0.05). VEGF and TGF-β1 were not expressed in diabetic mice in the control group. Both red ginseng extract and Rg1 promoted the production of VEGF and TGF-β1, which are important in wound healing. Our results for Rg1 suggest its potential to promote diabetic wound healing by stimulating the production or activity of VEGF and TGF-β1 factors involved in the wound healing process.
Influence of GdVO4:Eu3+nanocrystals on growth, germination, root cell viability and oxidative stress of wheat (Triticum aestivumL.) seedlings
Authors: Ekner-Grzyb Anna , Chmielowska-Bąk Jagna , Szczeszak Agata 
Published: May 2021

AbstractIncreasing application of lanthanide-doped nanocrystals (LDNCs) entails a risk of a harmful impact on the natural environment. Therefore, in the presented study the influence of gadolinium orthovanadates doped with Eu3+nanocrystals on wheat (Triticum aestivumL.), chosen as a model plant species, was investigated. The seeds were grown in Petri dishes filled with colloids of LDNCs at the concentrations of: 0, 10, 50 and 100 µg/ml. The plants’ growth endpoints (number of roots, roots length, roots mass, hypocotyl length and hypocotyl mass) and germination rate were found to be not significantly changed after the exposure to GdVO4:Eu3+nanocrystals at all used concentrations. The presence of LDNCs also had no effect on oxidative stress intensity determined on the basis of the amount of lipid peroxidation product (thiobarbituric acid reactive substances; TBARS) of the roots. Similarly, TTC (tetrazolium chloride) assay did not show any differences in cells’ viability. However, root cells of the treated seedlings contained less amount of Evans Blue (EB) when compared to the control.
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction
Authors: Deutekom Eva S. , van Dam Teunis J.P. , Snel Berend 
Published: May 2021

AbstractPhylogenetic profiling in eukaryotes is of continued interest to study and predict the functional relationships between proteins. This interest is likely driven by the increased number of available diverse genomes and computational methods to infer orthologies. The evaluation of phylogenetic profiles has mainly focussed on reference genome selection in prokaryotes. However, it has been proven to be challenging to obtain high prediction accuracies in eukaryotes. As part of our recent comparison of orthology inference methods for eukaryotic genomes, we observed a surprisingly high performance for predicting interacting orthologous groups. This high performance, in turn, prompted the question of what factors influence the success of phylogenetic profiling when applied to eukaryotic genomes.Here we analyse the effect of species, orthologous group and interactome selection on protein interaction prediction using phylogenetic profiles. We select species based on the diversity and quality of the genomes and compare this supervised selection with randomly generated genome subsets. We also analyse the effect on the performance of orthologous groups defined to be in the last eukaryotic common ancestor of eukaryotes to that of orthologous groups that are not. Finally, we consider the effects of reference interactome set filtering and reference interactome species.In agreement with other studies, we find an effect of genome selection based on quality, less of an effect based on genome diversity, but a more notable effect based on the amount of information contained within the genomes. Most importantly, we find it is not merely selecting the correct genomes that is important for high prediction performance. Other choices in meta parameters such as orthologous group selection, the reference species of the interaction set, and the quality of the interaction set have a much larger impact on the performance when predicting protein interactions using phylogenetic profiles. These findings shed light on the differences in reported performance amongst phylogenetic profiles approaches, and reveal on a more fundamental level for which types of protein interactions this method has most promise when applied to eukaryotes.
1H,13C and15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution
Authors: Agback Tatiana , Dominguez Francisco , Frolov Ilya , Frolova Elena I. , Agback Peter 
Published: May 2021

AbstractStructural characterization of the SARS-CoV-2 full length nsp1 protein will be an essential tool for developing new target-directed antiviral drugs against SARS-CoV-2 and for further understanding of intra- and intermolecular interactions of this protein. As a first step in the NMR studies of the protein, we report the1H,13C and15N resonance backbone assignment as well as the Cβ of the apo form of the full-lengthSARS-CoV-2 nsp1 including folded domain together with the flaking N- and C-terminal intrinsically disordered fragments. The 19.8 kD protein was characterized by high-resolution NMR. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. According to the obtained assignment, the secondary structure of the folded domain in solution was almost identical to its previously published X-ray structure, but some discrepancies have been detected. In the solution SARS-CoV-2 nsp1 exhibited disordered, flexible N- and C-termini with different dynamic characteristics. The short peptide in the beginning of the disordered C-terminal domain adopted two different conformations distinguishable on the NMR time scale. We propose that the disordered and folded nsp1 domains are not fully independent units but are rather involved in intramolecular interactions. Studies of the structure and dynamics of the SARS-CoV-2 mutant in solution are on-going and will provide important insights into the molecular mechanisms underlying these interactions.