bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of rapid antibody test and chest computed tomography results of COVID-19 patients: A retrospective study
Authors: Ozturk Ali , Bozok Taylan , Bozok Tugce Simsek 
Published: February 2021

AbstractBackgroundThe coronavirus disease 2019 (COVID-19) continues to spread around the world. Therefore, rapid, simpler, and more accurate diagnostic tests are urgently needed to diagnose the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. The purpose of this study was to evaluate the SARS-CoV-2 IgM/ IgG rapid antibody test results in symptomatic patients with COVID-19 and their chest computed tomography (CT) data.MethodsA total of 320 patients admitted to our hospital for different durations due to COVID-19 were included in the study. Serum samples were obtained within 0 to 7 days from COVID-19 patients confirmed by RT-PCR and chest CT scan. According to the SARS-CoV-2 RT-PCR results, the patients included in the study were divided into two groups: PCR positive group (n=46), and PCR negative group (n=274).ResultsOf the 320 COVID-19 serum samples, IgM, IgG, and IgM/IgG were detected in 9.4%, 3.1%, and 17.8% within one week respectively. IgG/IgM antibodies were not detected in 69.7% of the patients. In the study, it was determined that 249 (77.8%) of 320 patients had positive chest CT scans. Four (5.6%) of 100 patients with negative chest CT scan had IgM positive and 2 (2.8%) had both IgM/ IgG positive. IgM was detected in 23 (9.2%), IgG in 1 (0.4%) and IgM/IgG in 35 (14%) of chest CT scan positive patients. The rate of CT findings in patients with antibody positivity (n=97) was found to be significantly higher than those with antibody negativity.ConclusionsThe results of the present study show the accurate and equivalent performance of serological antibody assays and chest CT in detecting SARS-CoV-2 0 to 7 days from the onset of COVID19 symptoms. When the RT-PCR is not available, we believe that the combination of immunochromatographic test and chest CT scan can increase diagnostic sensitivity for COVID-19.
Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak
Authors: Masoli Jane A.H. , Jeffries Aaron , Temperton Ben , Auckland Cressida , Michelsen Michelle , Warwick-Dugdale Joanna , Manley Robyn , Farbos Audrey , Ellard Sian , Knight Beatrice , Bewshea Claire , Sambles Christine , Harrison James , Bunce Ben , Carr Alexis , Hattersley Andrew T. , Michell Stephen Ll. , Studholme David J. 
Published: February 2021

AbstractBackgroundWe have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK.MethodsFollowing multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests.ResultsThirty staff (25%) and 16 patients (62%) tested positive for COVID-19. Genomic sequencing data showed significant overlap of viral haplotypes in staff who had overlapping shift patterns. Patient haplotypes were more distinct from each other but had overlap with staff haplotypes.ConclusionsThis study includes clinical and genomic epidemiological detail that demonstrates the value of a combined approach. Viral genetic sequencing has identified that staff transmission of COVID-19 was important in this community hospital outbreak.Key pointsDetailed analysis of a large community hospital outbreak in older adults and staff with concurrent clinical and genomic data, including working patterns.Staff transmission was important in this community hospital outbreak.We found plausible associations between staff and patient cases.
Delivery of recombinant SARS-CoV-2 envelope protein into human cells
Authors: Hutchison James M. , Capone Ricardo , Luu Dustin D. , Hadziselimovic Arina , Van Horn Wade D. , Sanders Charles R. 
Published: February 2021

AbstractSARS-CoV-2 envelope protein (S2-E) is a conserved membrane protein that is essential to coronavirus assembly and budding. Here, we describe the recombinant expression and purification of S2-E into amphipol-class amphipathic polymer solutions. The physical properties of amphipols underpin their ability to solubilize and stabilize membrane proteins without disrupting membranes. Amphipol delivery of S2-E to pre-formed planar bilayers results in spontaneous membrane integration and formation of viroporin ion channels. Amphipol delivery of the S2-E protein to human cells results in membrane integration followed by retrograde trafficking to a location adjacent to the endoplasmic reticulum-to-Golgi intermediate compartment (ERGIC) and the Golgi, which are the sites of coronavirus replication. Delivery of S2-E to cells enables both chemical biological approaches for future studies of SARS-CoV-2 pathogenesis and development of “Trojan Horse” anti-viral therapies. This work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.
Adequate knowledge of COVID-19 impacts good practices amongst health profession students in the Philippines
Authors: Dalanon Junhel , Redoble Rhomeljustein , Belotindos Jo-Ann , Reyes Candy Delos , Fabillar Jaime , Armero Ma. Shiril , Locsin Rozzano , Suzuki Yoshitaka , Okura Kazuo , Matsuka Yoshizo 
Published: February 2021

AbstractBackgroundThe spread of the coronavirus disease 2019 (COVID-19) in the Philippines started with its first suspected case on January 22, 2020. The government reacted by imposing several measures including community quarantine, class suspensions, drug therapy and vaccine development, and travel restrictions. This online survey was done amongst Filipino health professions undergraduate students to uncover the relationship between their knowledge, attitude, and practice during this pandemic.MethodsCross-sectional data were obtained from an online survey done on students of medicine, dentistry, optometry, rehabilitative sciences, and pharmacy.ResultsAt a response rate of 100% (n=1257), the results show that healthcare profession students in the Philippines have good knowledge (87.6%) and practices (63.6%) regarding COVID-19, yet attitude (63.6%) was just passable. This study also shows that a strong correlation exists between knowledge and practice concerning the current pandemic, r(2) = 0.08, P = 0.004.ConclusionAdequate knowledge of COVID-19 impacts good practices of avoiding crowded places and misuse of steam inhalation amongst health profession students in the Philippines. Knowledge and practice pertaining to the current pandemic have been found to be good, but attitude remains low.
TGF-β signaling suppresses TCA cycle metabolism in renal cancer
Authors: Nam Hyeyoung , Kundu Anirban , Karki Suman , Brinkley Garrett , Chandrashekar Darshan S. , Kirkman Richard L. , Liu Juan , Liberti Maria V. , Locasale Jason W. , Mitchell Tanecia , Varambally Sooryanarayana , Sudarshan Sunil 
Published: February 2021

ABSTRACTThe Warburg effect is one of most-well studied metabolic phenomenon in cancer cells. For the most part, these studies have focused on enhanced rates of glycolysis observed in various models. The presumption has been that mitochondrial metabolism is suppressed. However, recent studies indicate that the extent of mitochondrial metabolism is far more heterogeneous in tumors than originally presumed. One tumor type with suppression of mitochondrial metabolism is renal cell carcinoma (RCC). Prior studies indicate that suppressed TCA cycle enzyme mRNA expression is associated with aggressive RCC. Yet, the mechanisms that regulate the TCA cycle in RCC remain uncharacterized. Here, we demonstrate that loss of TCA cycle enzyme expression is retained in RCC metastatic tissues. Moreover, proteomic analysis demonstrates that reduced TCA cycle enzyme expression is far more pronounced in RCC relative to other tumor types. Loss of TCA cycle enzyme expression is correlated with reduced expression of the transcription factor peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) which is also lost in RCC tissues. PGC-1α re-expression in RCC cells restores the expression of TCA cycle enzymesin vitroandin vivoand leads to enhanced glucose carbon incorporation into TCA cycle intermediates. Mechanistically, TGF-β signaling, in concert with histone deacetylase 7 (HDAC7), suppresses TCA cycle enzyme expression. In turn, pharmacologic inhibition of TGF-β restores expression of TCA cycle enzyme expression and suppresses tumor growth in an orthotopic model of RCC. Taken together, our findings reveal a novel role for the TGF-β /HDAC7 axis in global suppression of TCA cycle enzymes in RCC and provide novel insight into the molecular basis of altered mitochondrial metabolism in this malignancy.
Direct tissue sensing reprograms TLR4+Tfh-like cells inflammatory profile in the joints of rheumatoid arthritis patients
Authors: Amaral-Silva Daniela , Torrão Rita C. , Torres Rita , Falcão Sandra , Gonçalves Maria João , Araújo Maria Paula , Martins Maria José , Lopes Carina , Neto Agna , Marona José , Costa Tiago , Castelão Walter , Silva Ana Bento , Silva Inês , Lourenço Maria Helena , Mateus Margarida , Gonçalves Nuno Pina , Manica Santiago , Costa Manuela , Pimentel-Santos Fernando , Mourão Ana Filipa , Branco Jaime C. , Soares Helena 
Published: February 2021

AbstractCD4+T cells mediate rheumatoid arthritis (RA) pathogenesis through both antibody-dependent and independent mechanisms. It remains unclear how synovial microenvironment impinges on CD4+T cells pathogenic functions. Here, we identified a TLR4+follicular helper T (Tfh) cell-like population present in the blood and expanded in synovial fluid. Mechanistically, we unveiled that homotypic T-T cell interactions through non-cognate HLA-DR:TCR contacts regulate TLR4 expression on T cells. TLR4+T cells possess a two-pronged pathogenic activity. Upon TCR and ICOS engagement, TLR4+T cells produce IL-21, a cytokine known to sponsor antibody production. However, direct TLR4+engagement on T cells, by endogenous ligands in the arthritic joint, reprograms them towards an IL-17 inflammatory profile compatible with tissue damage program. Blocking TLR4 signaling with a specific inhibitor impaired IL-17 production in response to synovial fluid recognition. Ex vivo, synovial fluid TLR4+T cells produced IL-17, but not IL-21. TLR4+T cells appear to uniquely reconcile an ability to promote systemic antibody production with a local synovial driven tissue damage program. TLR4+T cells could constitute an attractive cellular target and predictive biomarker for erosive arthritis.
Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe
Authors: Rohrlach Adam B. , Papac Luka , Childebayeva Ainash , Rivollat Maïté , Villalba-Mouco Vanessa , Neumann Gunnar U. , Penske Sandra , Skourtanioti Eirini , van de Loosdrecht Marieke , Akar Murat , Boyadzhiev Kamen , Boyadzhiev Yavor , Deguilloux Marie-France , Dobeš Miroslav , Erdal Yilmaz S. , Ernée Michal , Frangipane Marcella , Furmanek Miroslaw , Friederich Susanne , Ghesquière Emmanuel , Hałuszko Agata , Hansen Svend , Küßner Mario , Mannino Marcello , Özbal Rana , Reinhold Sabine , Rottier Stéphane , Salazar-García Domingo Carlos , Soler Diaz Jorge , Stockhammer Philipp W. , de Togores Muñoz Consuelo Roca , Aslihan Yener K , Posth Cosimo , Krause Johannes , Herbig Alexander , Haak Wolfgang 
Published: February 2021

AbstractUniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective.Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture arrays such as the 1240K, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield.Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the “mappable” regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240K capture, YMCA significantly improves the coverage and number of sites hit on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants.To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
Selective MAP1LC3C (LC3C) autophagy requires noncanonical initiation regulators and the paralog-specific C-terminal peptide
Authors: Bischoff Megan E. , Zang Yuanwei , Chou Johnson , Price Adam D. , Ehmer Birgit , Talbot Nicholas J. , Newbold Michael J. , Paul Anurag , Guan Jun-Lin , Plas David R. , Meller Jarek , Czyzyk-Krzeska Maria F. 
Published: February 2021

AbstractLC3s are canonical proteins necessary for the formation of autophagosomes. We have previously established that two paralogs, LC3B and LC3C, have opposite activities in renal cancer, with LC3B playing oncogenic role and LC3C tumor suppressing role. LC3C is an evolutionary late gene, present only in higher primates and humans. Its most distinct feature is a C-terminal 20 amino acid peptide cleaved in the process of glycine 126 lipidation. Here we investigated mechanisms of LC3C selective autophagy. LC3C autophagy requires noncanonical upstream regulatory complexes that include ULK3, UVRAG, RUBCN, PIK3C2A, and a member of ESCRT, TSG101. We established that Postdivision Midbody Rings (PDMBs) implicated in cancer stem cell regulation are direct targets of LC3C autophagy. LC3C C-terminal peptide is necessary and sufficient to mediate LC3C-dependent selective degradation of PDMBs. This work establishes a new noncanonical human-specific selective autophagic program relevant to cancer stem cells.
The effect of hydrophobic gases on the nervous system of Daphnia magna
Authors: Robledo-Sánchez K. Carlo Martín , Ruiz-Suárez J. C. 
Published: February 2021

AbstractHundreds of hydrophobic substances: alkanes, alcohols, benzodiacepines, barbiturates, ethers and even gases, can induce General Anaesthesia (GA) in mammal animals. Moreover, it has been suggested that the primary site of action of such agents is on the spinal cord. Here, we investigate a scenario that is in double measure important to understand the mechanisms behind GA: its induction under water in invertebrate animals. We evaluate the capacity of xenon, nitrous oxide and krypton to suppress harmful sensations, provoked by intense light, in the crustacean D. magna. Due to the hydrophobic characteristics of those gases, we designed a special chamber to force them to dissolve in water at pressures up to to 50 atmospheres, whereas at the same time measure in real time the motility of the animals. Surprisingly, the aquatic animals are immobilized with xenon and nitrous oxide. Under this condition, they don’t respond to a noxious stimulus. Our results are crucial to understand the action of inert gases in GA and the role of the spinal cord.
Drivers of inter-population variation in the gut microbiomes of sister species ofPhanaeusdung beetles
Authors: Winfrey Claire C. , Sheldon Kimberly S. 
Published: February 2021

ABSTRACTThe microbiome plays key roles in host physiology and ecology, but how the microbiome varies among populations of hosts is not well understood. However, different abiotic and biotic selection pressures across a species’ range likely lead to variation in the microbiome. In addition, symbiotic microbiota may differ more between closely-related species in sympatry than in allopatry if selection favors the reduction of interspecific competition. We investigated variation in the maternally-transmitted, beneficial gut microbiomes ofPhanaeus vindexandP. difformis, sister species of dung beetle that compete for the same resources in sympatry and occur across diverse climatic conditions. We sampled and sequenced bacterial/archaeal 16S rDNA from guts ofP. difformisandP. vindexcollected across 17 sympatric and allopatric sites. Gut microbial communities were best predicted by temperature and precipitation, cattle present at sites, and spatial relationships among sites. Contrary to our hypotheses, we did not find that the gut microbial communities ofP. vindexandP. difformisdiffered more in sympatry than in allopatry, nor thatP. vindex, the more broadly distributed of the two species, exhibited greater microbiome turnover among populations. However, the gut microbiome ofP. vindexshifted more between sympatric and allopatric populations than did that ofP. difformis, suggesting character displacement. While more research is needed, it is possible that differences in gut microbial communities allowP. vindexandP. difformisto partition their niches in sympatry. Our work argues for further exploration of the gut microbiome’s potential role in niche partitioning and local adaptation.
Dispersal syndromes affect ecosystem functioning in ciliate microcosms
Authors: Raffard Allan , Campana Julie , Legrand Delphine , Schtickzelle Nicolas , Jacob Staffan 
Published: February 2021

AbstractDispersal is a key process mediating ecological and evolutionary dynamics. Its effects on metapopulations dynamics, population genetics or species range distribution can depend on phenotypic differences between dispersing and non-dispersing individuals (i.e., dispersal syndromes). However, scaling up to the importance of dispersal syndromes for meta-ecosystems have rarely been considered, despite intraspecific phenotypic variability is now recognised as an important factor mediating ecosystem functioning. In this study, we characterised the intraspecific variability of dispersal syndromes in twenty isolated genotypes of the ciliateTetrahymena thermophilato test their consequences for biomass productivity in communities composed of fiveTetrahymenaspecies. To do so, dispersers and residents of each genotype were introduced, each separately, in ciliate communities composed of four other competing species of the genusTetrahymenato investigate the effects of dispersal syndromes. We found that introducing dispersers led to a lower biomass compared to introducing residents. This effect was highly consistent across the twentyT. thermophilagenotypes despite their marked differences of dispersal syndromes. Finally, we found a strong genotypic effect on biomass production, confirming that intraspecific variability in general affected ecosystem functions in our system. Our study shows that intraspecific variability and the existence of dispersal syndromes can impact the functioning of spatially structured ecosystems in a consistent and therefore predictable way.
The biosynthesis of phospholipids is linked to the cell cycle in a model eukaryote
Authors: Vítová Milada , Lanta Vojtěch , Čížková Mária , Jakubec Martin , Rise Frode , Halskau Øyvind , Bišová Kateřina , Furse Samuel 
Published: February 2021

AbstractThe structural challenges faced by eukaryotic cells through the cell cycle are key for understanding cell viability and proliferation. In this study, we tested the hypothesis that the biosynthesis of structural lipids is linked to the cell cycle. If true, this would suggest that the cell’s structure would form part the control of the cell cycle. Lipidomics (31P NMR and MS), proteomics (Western immunoblotting) and transcriptomics (RT-qPCR) techniques were used to profile the lipid fraction and characterise aspects of its metabolism at seven stages of the cell cycle of the model eukaryote,Desmodesmus quadricauda. We found considerable, transient increases in the abundance of phosphatidylethanolamine during the G1phase (+35%, ethanolamine phosphate cytidylyltransferase increased 2·5×) and phosphatidylglycerol over the G1/pre-replication phase boundary (+100%, phosphatidylglycerol synthase increased 22×). The relative abundance of phosphatidylcholine fell by ~35% during the G1.N-Methyl transferases for the conversion of phosphatidylethanolamine into phosphatidylcholine were not found in thede novotranscriptome profile, though a choline phosphate transferase was found, suggesting that the Kennedy pathway is the principal route for the synthesis of PC. The fatty acid profiles of the four most abundant lipids suggested that these lipids were not generally converted between one another. The relative abundance of both phosphatidylinositol and its synthase remained constant despite an eightfold increase in cell volume. We conclude that the biosynthesis of the three most abundant structural phospholipids is linked to the cell cycle inD. quadricauda.
Practices and trends in last-mile delivery of poultry vaccines in rural areas in developing countries: the case of Newcastle disease vaccine delivery in Bungoma County, Kenya
Authors: Chemuliti JK. , Ogolla KO. , Mbogoh SG. , Mochabo KM. , Kibore BK 
Published: February 2021

AbstractNewcastle disease (ND) is the single most important infection of village chicken in smallholder farming systems in developing countries. Vaccines for ND control are available but the delivery of safe and potent vaccines in resource-poor settings remains a big challenge due to difficulties in the maintenance of cold chain. This paper reports the results of a study that was carried out in Kenya to assess the storage and handling practices of Newcastle disease vaccines by agro-veterinary shops (agro-shops) during acquisition, storage, and sale to smallholders’ farmers. Data were collected from one hundred and thirty-two agro-shops using semi-structured questionnaires, observation sheets and actual purchase of vaccines over the counter. The results showed that the majority (82 percent) of the agro-shops had a domestic refrigerator that was connected to the electricity grid but many (61 percent) did not have power backup. Sixty percent of them only stocked thermolabile vaccines. Recurrent power outages (62 percent), high cost of electricity (62 percent), and long-distance to vaccine sources (33 percent) were the most common challenges in vaccine storage and sale. Some agro-shops switched refrigerators on and off while others removed vaccines from refrigerators for overnight stay in cool boxes to minimize electricity costs. In some cases, the sale of vaccines was restricted to market days and late afternoon when ambient temperatures were lower to minimize vaccines storage time and vaccine spoilage respectively. Thermostable vaccines were not stored as recommended by the manufacturer and few agro-shops (23 percent) sold reconstituted vaccines. Most shops adequately packaged thermolabile vaccines in improvised materials during sale. Overall, most of the ND vaccine handling and storage practices in the last mile appeared to aim at safeguarding the safety and potency of vaccines, but further research could elucidate the effects of these practices on the quality and potency of ND vaccines.