bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Antimicrobial Residues in Tissues of Broilers Sold at a Local Market in Enugu State, Nigeria Using the European Four Plate Test
Authors: Onwumere-Idolor O. S. , Ogugua A. J. , Ezenduka E. V. , Nwanta J. A. , Anaga A. 
Published: September 2021

ABSTRACTBackgroundConsumption of animal tissues treated with antimicrobial agents may be deleterious if they contain violative levels of the residues. This study determined antimicrobial residues prevalence in broilers sold at Ikpa market, Nsukka, Nigeria.MethodsTissues from muscle, liver and kidney of 60 commercial broilers (180 samples) were tested for antimicrobial residues using the conventional Four Plate Test.ResultPrevalence of 80.0% (48/60) and 51.7% (93/180) was recorded in the birds and samples {muscle 40.0%(24/60); liver 55.0%(33/60) and kidney 60.0%(36/60)} respectively. There was no significant association between residue occurrence and tissue type (χ2 (2) = 5.206; p = 0.074). Possible antimicrobial classes detected were: macrolid (50.0%) at pH 8.0 with Micrococcus luteus; β-lactams and tetracyclines (64.4%) with Bacillus subtillis at pH 6.0; sulphonamides (53.3%) at pH 7.2 with Bacillus subtillis, and aminoglycosides (46.8%) at pH 8.0 with Bacillus subtillis. Twenty-four tissue samples were positive at all four pH levels indicating use of more than one class of antimicrobials during each treatment.ConclusionAntimicrobial residues were detected in commercial broilers (muscles, liver and kidney) sampled at Ikpa Market, Nsukka. This is of public health importance given that antimicrobial residues are not monitored in poultry consumed in Nigeria.
Identifying At-Risk Communities and Key Vulnerability Indicators in the COVID-19 Pandemic
Authors: Thais Savannah , Leibowitz Shaine , Gutierrez Alejandra Rios , Passarelli Alexandra , Santo Stephanie , Shipp Nora 
Published: September 2021

AbstractThroughout the COVID-19 pandemic, certain communities have been disproportionately exposed to detrimental health outcomes and socioeconomic injuries. Quantifying community needs is crucial for identifying testing and service deserts, effectively allocating resources, and informing funding and decision making. We have constructed research-driven metrics measuring the public health and economic impacts of COVID-19 on vulnerable populations. In this work we further examine and validate these indices by training supervised models to predict proxy outcomes and analyzing the feature importances to identify gaps in our original metric design. The indices analyzed in this work are unique among COVID-19 risk assessments due to their robust integration of disparate data sources. Together, they enable more effective responses to COVID-19 driven health inequities.
A condensate dynamic instability orchestrates oocyte actomyosin cortex activation
Authors: Yan Victoria Tianjing , Narayanan Arjun , Jülicher Frank , Grill Stephan W. 
Published: September 2021

AbstractA key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition. We here report on the discovery that inC. elegansoocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP, and ARP2/3 that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow, and then switch to disassembly before dissolving completely. We find that in contrast to condensate growth via diffusion, the growth dynamics of cortical condensates are chemically driven. Remarkably, the associated chemical reactions obey mass action kinetics despite governing both composition and size. We suggest that the resultant condensate dynamic instability suppresses coarsening of the active micro-emulsion, ensures reaction kinetics that are independent of condensate size, and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.
The origin and evolution of pollen transport in bees (Hymenoptera: Anthophila)
Authors: Portman Zachary M. 
Published: September 2021

AbstractThe ability to transport pollen from flowers back to the nest represents a key innovation in the evolution of bees from predatory wasp ancestors. Currently, the origin and evolution of pollen transport remains unsettled. Older hypotheses proposed that crop transport was the original mode of pollen transport, but more recent molecular phylogenies have cast doubt on that view. Instead, more recent hypotheses contend that external transport of dry pollen is ancestral in bees. Here, I propose a new hypothesis to explain the origin and subsequent evolution of pollen transport in bees. I propose that pollen transport arose from adult pollen-feeding behavior and that internal transport of pollen is ancestral in bees. This then led to the evolution of external moist transport, which first required a transition step whereby pollen is temporarily accumulated on the venter on a patch of specialized hairs. Finally, external glazed and dry transport evolved from external moist pollen transport, and the evolution of dry transport led to changes in the location of scopae from the original location on the hind tibia and basitarsus. I illustrate many of these hypothetical evolutionary steps using modern-day bee behavior as an example, with a particular focus on the beePerdita tortifoliae. Examination of the evolution of pollen transport of pollen wasps (subfamily Masarinae) reveals that they have undergone a parallel evolutionary change. Overall, I lay out a broad hypothetical framework to explain the origin and subsequent evolution of pollen transport in bees. This marks a return to the earlier hypothesis that crop transport is ancestral, and it also represents the first in-depth hypothesis to explain how external transport of moistened pollen could have evolved. The evolutionary history of bees has many implications for the biology of bees in the present day, and I lay out a number of predictions that could help confirm or refute my hypotheses.
Density-independent processes decouple component and ensemble density feedbacks
Authors: Bradshaw Corey J. A. , Herrando-Pérez Salvador 
Published: September 2021

AbstractAnalysis of long-term trends in abundance provide insights into population dynamics. Population growth rates are the emergent interplay of fertility, survival, and dispersal, but the density feedbacks on some vital rates (component) can be decoupled from density feedback on population growth rates (ensemble). However, the mechanisms responsible for this decoupling are poorly understood. We simulated component density feedbacks on survival in age-structured populations of long-living vertebrates and quantified how imposed nonstationarity (density-independent mortality and variation in carrying-capacity) modified the ensemble feedback signal estimated from logistic-growth models to the simulated abundance time series. The statistical detection of ensemble density feedback was largely unaffected by density-independent processes, but catastrophic and proportional mortality eroded the effect of density-dependent survival on ensemble-feedback strength more strongly than variation in carrying capacity. Thus, phenomenological models offer a robust approach to capture density feedbacks from nonstationary census data when density-independent mortality is low.
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers
Authors: Roy Raj S. , Quadir Farhan , Soltanikazemi Elham , Cheng Jianlin 
Published: September 2021

AbstractMotivationDeep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue-residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue-residue contacts in homodimers from residue-residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue-residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features.ResultsTested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset, and CASP14-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.15%, and 24.81% respectively, which is substantially better than two existing deep learning interchain contact prediction methods. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs reasonably well, even though its accuracy is lower than when true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers.AvailabilityThe source code of DRCon is available athttps://github.com/jianlin-cheng/DRCon.Contactchengji@missouri.edu
Facile synthesis of crosslinked Cu:ZnS-lignocellulose nanocomposite: a potent antifungal and antisporulant system against the tea pathogen Exobasidium vexans
Authors: Chaliha Chayanika , Baruah Julie , Kalita Eeshan 
Published: September 2021

AbstractThe objective of the present study was to synthesize Cu doped ZnS nanocore crosslinked with lignocellulose (represented as Cu:ZnS-lignocellulose nanocomposite) for antifungal action against the devastating tea blister blight pathogen Exobasidium vexans. The characteristic features of the nanocomposite were analyzed via different physicochemical techniques like FTIR, XRD, XPS, SEM, SEM-EDX, Elemental mapping, PCS, and UV-PL studies. The FTIR and XPS investigations revealed the crosslinking between lignocellulose and the Cu:ZnS. The presence of lignocellulose was seen to attribute a potent antifungal efficacy, also enhancing the stability of the resulting nanocomposite in aqueous suspensions. The antifungal efficacy confirmed through disk diffusion and broth dilution assays have a maximum zone of inhibition of 1.75 cm2 and a MIC50 of 0.05 mg/ml against E. vexans. Additionally, the antisporulant activity was evident as the basidiospores failed to germinate in presence of the Cu:ZnS-lignocellulose nanocomposites. This shows potential for stemming the rapid infectivity of E. vexans by achieving disease inhibition at the early stage. Finally, the comparison with two commonly used commercial fungicides (copper oxychloride and fluconazole) demonstrated >10-fold higher antifungal activity for Cu:ZnS-lignocellulose nanocomposites.
High Resolution Ancestry Deconvolution for Next Generation Genomic Data
Authors: Hilmarsson Helgi , Kumar Arvind S. , Rastogi Richa , Bustamante Carlos D. , Montserrat Daniel Mas , Ioannidis Alexander G. 
Published: September 2021

ABSTRACTAs genome-wide association studies and genetic risk prediction models are extended to globally diverse and admixed cohorts, ancestry deconvolution has become an increasingly important tool. Also known as local ancestry inference (LAI), this technique identifies the ancestry of each region of an individual’s genome, thus permitting downstream analyses to account for genetic effects that vary between ancestries. Since existing LAI methods were developed before the rise of massive, whole genome biobanks, they are computationally burdened by these large next generation datasets. Current LAI algorithms also fail to harness the potential of whole genome sequences, falling well short of the accuracy that such high variant densities can enable. Here we introduce Gnomix, a set of algorithms that address each of these points, achieving higher accuracy and swifter computational performance than any existing LAI method, while also enabling portable models that are particularly useful when training data are not shareable due to privacy or other restrictions. We demonstrate Gnomix (and its swift phase correction counterpart Gnofix) on worldwide whole-genome data from both humans and canids and utilize its high resolution accuracy to identify the location of ancient New World haplotypes in the Xoloitzcuintle, dating back over 100 generations. Code is available at https://github.com/AI-sandbox/gnomix.
A bipartite chromatophore targeting peptide and N-terminal processing of proteins in the Paulinella chromatophore
Authors: Oberleitner Linda , Perrar Andreas , Macorano Luis , Huesgen Pitter F. , Nowack Eva C. M. 
Published: September 2021

AbstractThe cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles - termed chromatophores - that evolved from a cyanobacterium ∼100 million years ago, independently from plastids in plants and algae. Despite its more recent origin, at least one third of the chromatophore proteome consists of nucleus-encoded proteins that are imported by an unknown mechanism across the chromatophore double envelope membranes. Chromatophore-targeted proteins fall into two classes. Proteins exceeding 250 amino acids carry a conserved N-terminal sequence extension, termed the ‘chromatophore transit peptide’ (crTP), that is presumably involved in guiding these proteins into the chromatophore. Short imported proteins do not carry discernable targeting signals. To explore whether the import of protein is accompanied by their N-terminal processing, here we used a mass spectrometry-based approach to determine protein N-termini in Paulinella chromatophora and identified N-termini of 208 chromatophore-localized proteins. Our study revealed extensive N-terminal modifications by acetylation and proteolytic processing in both, the nucleus and chromatophore-encoded fraction of the chromatophore proteome. Mature N-termini of 37 crTP-carrying proteins were identified, of which 30 were cleaved in a common processing region. Our results imply that the crTP mediates trafficking through the Golgi, is bipartite and surprisingly only the N-terminal third (‘part 1’) becomes cleaved upon import, whereas the rest (‘part 2’) remains at the mature proteins. In contrast, short imported proteins remain largely unprocessed. Finally, this work sheds light on N-terminal processing of proteins encoded in an evolutionary-early-stage photosynthetic organelle and suggests host-derived post-translationally acting factors involved in dynamic regulation of the chromatophore-encoded chromatophore proteome.One sentence summaryProteins targeted to the evolutionary-early-stage photosynthetic organelle of Paulinella carry a bipartite N-terminal targeting sequence that is only partially removed upon protein import.
Field clinical performance of SARS-CoV-2 point-of-care diagnostic tests: a living systematic review of trials up to 17th of August, 2021
Authors: Hawthorne Gabriel , Harvey Adam 
Published: September 2021

AbstractPoint-of-care assays offer a decentralized and fast solution to the diagnosis of SARS-CoV-2, providing benefits for patients, healthcare workers and healthcare facilities. This technology has the potential to prevent outbreaks, enable fast adoption of potentially life-saving measures and improve hospital workflow. While reviews regarding the laboratory performance of those assays exist, a review focused on the real-life clinical performance and true point-of-care feasibility of those platforms is missing. Therefore, the objective of this study is to help clinicians, healthcare providers and organizations to understand the real-life performance of point-of-care assays, aiding in their implementation in decentralised, true point-of-care facilities, or inside hospitals. 1246 studies were screened in 3 databases and 87 studies were included, evaluating 27 antigen tests and 11 nucleic-acid amplification platforms deemed feasible for true point-of-care placement. We excluded studies that used processed samples, pre-selected populations, archived samples and laboratory-only evaluations and strongly favored prospective trial designs. We also investigated package inserts, instructions for use, comments on published studies and manufacturer’s websites in order to assess feasibility of point-of-care placement and additional information of relevance to the end-user. Apart from performance in the form of sensitivity and specificity, we present information on time to results, hands-on time, kit storage, machine operating conditions and regulatory status. To the best of our knowledge, this is the first review to systematically compare point-of-care test performance in real-life clinical practice. We found the performance of tests in clinical practice to be markedly different from the manufacturers reported performance and laboratory- only evaluations in the majority of scenarios. Our findings may help in the decision-making process related to SARS-CoV-2 test in real-life clinical settings.Rationale for the reviewA review focused on the real-life clinical performance and point-of-care feasibility of SARS-CoV-2 diagnostic platforms is missing, impairing the ability of individuals, healthcare providers and test providers to make informed decisions.Objective(s) or question(s) the review addressesThe objective of this study is to help clinicians, healthcare providers and organizations to understand the real-life performance of point-of-care assays, aiding in their implementation in decentralised, true point-of-care facilities or in complex healthcare environments.
Long Term Accuracy of SARS-CoV-2 Interferon-γ Release Assay and its Application in Household Investigation
Authors: Murugesan Kanagavel , Jagannathan Prasanna , Altamirano Jonathan , Maldonado Yvonne A , Bonilla Hector F. , Jacobson Karen B. , Parsonnet Julie , Andrews Jason R. , Shi Run-Zhang , Boyd Scott , Pinsky Benjamin A. , Singh Upinder , Banaei Niaz 
Published: September 2021

AbstractBackgroundAn immunodiagnostic assay that sensitively detects a cell-mediated immune response to SARS-CoV-2 is needed for epidemiological investigation and for clinical assessment of T cell-mediated immune response to vaccines, particularly in the context of emerging variants that might escape antibody responses.MethodsThe performance of a whole blood interferon-gamma (IFN-γ) release assay (IGRA) for the detection of SARS-CoV-2 antigen-specific CD4 and CD8 T cells was evaluated in COVID-19 convalescents tested serially up to 10 months post-infection and in healthy blood donors. SARS-CoV-2 IGRA was applied in contacts of households with index cases. Freshly collected blood in the lithium heparin tube was left unstimulated, stimulated with a SARS-CoV-2 peptide pool, and stimulated with mitogen.ResultsThe overall sensitivity and specificity of IGRA were 84.5% (153/181; 95% confidence interval [CI] 79.0-89.0) and 86.6% (123/142; 95% CI;80.0-91.2), respectively. The sensitivity declined from 100% (16/16; 95% CI 80.6-100) at 0.5-month post-infection to 79.5% (31/39; 95% CI 64.4-89.2) at 10 months post-infection (P<0.01). The IFN-γ response remained relatively robust at 10 months post-infection (3.8 vs. 1.3 IU/mL, respectively). In 14 households, IGRA showed a positivity rate of 100% (12/12) and 65.2% (15/23), and IgG of 50.0% (6/12) and 43.5% (10/23) in index cases and contacts, respectively, exhibiting a difference of +50% (95% CI +25.4-+74.6) and +21.7% (95% CI, +9.23-+42.3), respectively. Either IGRA or IgG was positive in 100% (12/12) of index cases and 73.9% (17/23) of contacts.ConclusionsThe SARS-CoV-2 IGRA is a useful clinical diagnostic tool for assessing cell-mediated immune response to SARS-CoV-2.Key pointsSARS-CoV-2 immunodiagnostics are needed to identify infected individuals in order to understand the transmission dynamics of emerging variants and to assess vaccine response. Interferon-gamma release assay maintains sensitivity 10 months post-infection in convalescents and detects more household contacts than IgG.
Health-care workers in gastrointestinal endoscopy are at higher risk for SARS-CoV-2 infection compared to other aerosol-generating disciplines
Authors: Römmele Christoph , Ebigbo Alanna , Kahn Maria , Zellmer Stephan , Muzalyova Anna , Hammel Gertrud , Bartenschlager Christina , Beyer Albert , Rosendahl Jonas , Schlittenbauer Tilo , Zenk Johannes , Al-Nawas Bilal , Frankenberger Roland , Hoffmann Jürgen , Arens Christoph , Lammert Frank , Traidl-Hoffmann Claudia , Messmann Helmut 
Published: September 2021

ABSTRACTObjectiveHealthcare workers (HCW) are at high risk of SARS-CoV-2 infection due to exposure to potentially infectious material, especially during aerosol-generating procedures (AGP). We aimed to investigate the prevalence of infection among HCW in medical disciplines with AGP.DesignA nationwide questionnaire-based study in in- and outpatient settings was conducted between 12/16/2020 and 01/24/2021. Data on SARS-CoV-2 infections among HCW and potential risk factors were investigated.Results2,070 healthcare facilities with 25,113 employees were included in the study. Despite a higher rate of pre-interventional testing, clinics treated three times more confirmed SARS-CoV-2 cases than private practices (28.8% vs. 88.4%, p<0.001). Overall infection rate among HCW accounted for 4.7%. Multivariate analysis revealed that ZIP-regions having comparably higher incidences were significantly associated with increased risk of infection. Furthermore, clinical setting and the GIE specialty have more than double the risk of infection (OR 2.63; 95% CI 2.501-2.817, p<0.01 and OR 2.35; 95% CI 2.245-2.498, p<0.01). The number of procedures performed per day was also significantly associated with an increased risk of infection (OR 1.01; 95% CI 1.007-1.014), p<0.01). No treatment of confirmed SARS-CoV-2 cases was tending to lower the risk of infection (OR 0.72; 95% CI 0.507-1.025, p=0.068).ConclusionHCW in GIE seem to be at higher risk of infection than those in other AGP, especially in the clinical setting. Regions having comparably higher incidences as well as the number of procedures performed per day were also significantly associated with increased risk of infection.Significance of this studyWhat is already known on this subject?Health care workers, especially those exposed to aerosol generating procedures, are assumed to have an increased risk of SARS-CoV-2 infection. However, data confirming this are lacking, especially for the outpatient care setting.What are the new findings?Health care workers in gastrointestinal endoscopy have a higher risk of SARS-CoV-2-infection than in other AGPs. This risk is particularly higher-in clinical settings compared to private practices-in regions having comparably higher incidences-the more procedures are performed per dayHow might it impact on clinical practice in the foreseeable future?Our study suggests making additional efforts to protect HCW in the gastrointestinal work field.
Human Milk Antibodies Elicited by BNT162b2 Vaccination have reduced activity against SARS-CoV-2 Variants of Concern
Authors: Low Jia Ming , Gu Yue , Ng Melissa Shu Feng , Wang Liang Wei , Amin Zubair , Zhong Youjia , MacAry Paul A 
Published: September 2021

AbstractWe detected the presence of SARS-CoV-2 specific IgA against all major VOCs in milk out to 6 weeks after D2 of BNT162b2. These likely confer some protection to the breastfed infants, who are ineligible for vaccination and are at risk of severe COVID-19.However, we detected significantly reduced milk IgA binding to VOCs, including the globally dominant Delta variant, suggesting reduced protection for breastfeeding infants. Additionally, these antibodies were significantly reduced by as early as 4-6 weeks after D2.