bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 vaccine equity and the right to health for displaced Venezuelans in Latin America
Authors: Hill David C. , Andrade-Romo Zafiro , Solari Karla , Adams Ellithia , Forman Lisa , Grace Daniel , Silva-Santisteban Alfonso , Perez-Brumer Amaya 
Published: October 2022

AbstractGiven the magnitude of Venezuelan displacement in Latin America, there is a need to assess how migrants were, and will continue to be, addressed in COVID-19 vaccination policies. To explore migration status as a dimension of vaccine equity in Latin America and in relation to international human rights, we assessed national vaccination plans, peer-reviewed, and gray literature published between January 2020 and June 2021. Three key rights-related concerns were found to restrict the health rights of migrants in the region: 1) lack of prioritization of migrants in vaccine distribution; 2) onerous documentation requirements to be eligible for COVID-19 vaccination; and (3) how pervasive anti-migrant discrimination limited equitable health care access. While international human rights law prohibits against discrimination based on migration status, few countries analyzed realized their obligations to provide equal access to COVID-19 vaccines to non-citizens, including displaced Venezuelans. Especially for migrants and displaced people, effective and sustainable vaccination strategies for COVID-19 and future pandemics in Latin America must be guided not only by epidemiological risk but also seek to align with human rights obligations. To achieve this, States must also take special measures to facilitate vaccine access for communities facing systemic discrimination, exclusion, and marginalization.
A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic datasets
Authors: Vlasschaert Caitlyn , Mack Taralynn , Heimlich J. Brett , Niroula Abhishek , Uddin Mesbah , Weinstock Joshua , Sharber Brian , Silver Alexander J. , Xu Yaomin , Savona Michael , Gibson Christopher , Lanktree Matthew B. , Rauh Michael J. , Ebert Benjamin L. , Natarajan Pradeep , Jaiswal Siddhartha , Bick Alexander G. 
Published: October 2022

AbstractClonal hematopoiesis of indeterminate potential (CHIP) is a common form of age-related somatic mosaicism that is associated with significant morbidity and mortality. CHIP mutations can be identified in peripheral blood samples sequenced using approaches that cover the whole genome, whole exome or targeted genetic regions; however, differentiating true CHIP mutations from sequencing artifacts and germline variants is a considerable bioinformatic challenge. We present a stepwise method that combines filtering based on sequencing metrics, variant annotation, and novel population-based associations to increase the accuracy of CHIP calls. We apply this approach to ascertain CHIP in ∼550,000 individuals in the UK Biobank complete whole exome cohort and the All of Us Research Program initial whole genome release cohort. CHIP ascertainment on this scale unmasks recurrent artifactual variants and highlights the importance of specialized filtering approaches for several genes includingTET2andASXL1. We show how small changes in filtering parameters can considerably increase CHIP misclassification and reduce the effect size of epidemiological associations. Our high-fidelity call set refines prior population-based associations of CHIP with incident outcomes. For example, the annualized incidence of myeloid malignancy in individuals with small CHIP clones is 0.03%/year, which increases to 0.5%/year amongst individuals with very large CHIP clones. We also find a significantly lower prevalence of CHIP in individuals of self-reported Latino or Hispanic ethnicity in All of Us, highlighting the importance of including diverse populations. The standardization of CHIP calling will increase the fidelity of CHIP epidemiological work and is required for clinical CHIP diagnostic assays.
Spatial interactions between parrotfishes and implications for species coexistence
Authors: Manning J.C. , McCoy S.J. , Benhamou S. 
Published: October 2022

AbstractHome range behavior mediates species interactions and distributions, and spatiotemporal segregation may facilitate coexistence of competing species. We investigated home range behavior and spatial interactions in four common parrotfishes on coral reefs in Bonaire, Caribbean Netherlands, to determine how spatial interactions mediate species interactions and contribute to their coexistence. We first computed home ranges for males and females of each species. We then quantified spatial overlap (i.e., static interaction) between the home ranges of neighboring male parrotfishes and their activity in shared areas to estimate interaction potential for pairs of individuals. Finally, we analyzed dynamic interactions in simultaneously tracked, spatially co-occurring interspecific pairs of parrotfishes to investigate how they interact in shared space. Generally, spatial overlap of home ranges was much lower for intraspecific pairs than for interspecific pairs, but the probability of finding males in areas shared with males of other species was species-dependent. Males in interspecific pairs moved mostly independently of each other in shared areas, but we did find some evidence of avoidance in interspecific pairs sharing the most space. We discuss our findings within the context of parrotfish social and foraging ecology to further elucidate the spatial ecology of these functionally important reef fishes.
Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy
Authors: Rothman Jason Seth , Borges-Merjane Carolina , Holderith Noemi , Jonas Peter , Silver R. Angus 
Published: October 2022

AbstractStereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution by Keiding et al. (1972) accounts for lost caps by quantifying the smallest detectable profiles in terms of their limiting section angle (ϕ). However, this simple solution has not been widely adopted nor validated. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by quantifying ϕ of synaptic vesicles using electron-tomography 3D reconstructions. This analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using Monte Carlo simulations revealed an upper limit to determining ϕ, our analysis shows that mean ϕ can be used to estimate the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in rodent cerebella, where high packing density can be problematic for design-based methods.
Quality indicators on medicines packaging as guide to routine quality assurance for procured generic medicines: A community pharmacy survey in Nigeria
Authors: Orubu Ebiowei S.F , Ukuta Elamene C.O. , Robert Faith O. 
Published: October 2022

AbstractIntroductionWhile medicines quality assurance is best performed by a Stringent Regulatory Authority (SRA), many countries still lack this capacity. In these contexts, brand manufacturers take additional steps to signal authenticity to their consumers through the use of overt authentication technologies on medicines packaging. The aim of this study was to use quality indicators on the secondary packaging of medicines to identify, and, thus, risk rank, therapeutic groups most prone to being substandard or falsified.MethodThis study profiled medicines in the inventory of a conveniently selected pharmacy in Nigeria by three common packaging quality indicators: (i) National Agency for Food and Drug Administration, NAFDAC, registration number, (ii) a mobile authentication service, MAS, number, and (iii) a hologram.ResultsThe inventory contained 66 medicines available as 380 oral, parenteral, or topical products. Of these, 92% had a NAFDAC number, 20% had a MAS number, and 10% bore a hologram – either exclusively, or simultaneously. Antimicrobials – mostly antibiotics and antimalarials – were the most common therapeutic group containing one or all three quality indications. Antibiotic medicines for children formulated as suspensions and drops had the most quality assurance indicators on their packaging.ConclusionThis result suggests that antimicrobials, especially those formulated for use in children, may be the medicine group at the greatest risk of being substandard or falsified (SF) in Nigeria.The implication of this finding is the need for healthcare facilities to implement strict medicines quality assurance procurement practices especially for antimicrobials. Continued vigilance by the public would also be necessary.
Mushrooms arising from the mole latrine reveal the life of talpid moles: proposals of ‘myco-talpology’ and ‘habitat-cleaning symbiosis’
Authors: Sagara Naohiko , Tuno Nobuko , Fukasawa Yu , Kawada Shin-ichiro , Kasuya Taiga 
Published: October 2022

AbstractMyco-talpology is the science of moles and mushrooms based on our discovery in 1976 that underground nests of talpid moles can be located by the aboveground fruiting of the agaricsHebeloma danicumorHebeloma sagarae, a Japanese sibling species of EuropeanHebeloma radicosum. Hyphae of these mushrooms specifically colonise mole latrines near nests, forming ectomycorrhizas with the roots of their host trees. By this process, the hyphae and roots absorb, transform, and translocate the nutrients from mole excretions, cleaning the mole’s habitat. The mushrooms fruit on the ground with thick root-like tissue stretching up from the ectomycorrhizas. The presence of the fruit bodies serves as the only indicator for underground mole nests, enabling us to provide novel insights into mole ecology. We excavated 74H. sagaraeorH. danicumsites in Japan and 13H. radicosumsites in Europe and identified the nesting species. These investigations provided new perspectives on latrine making, nest structure, breeding and nestlings, the neighbouring presence of different Talpini species, and long-term nesting at the same site with inhabitant changes. Moreover, they suggested that a tripartite habitat-cleaning symbiosis among moles, mushrooms, and mushroom-host trees in the latrine must have existed for a long time in Japanese and European forests. While moles are traditionally considered inhabitants of open areas, their special relationship with mushrooms and trees suggests they may originally be forest inhabitants.
KBeagle: An Adaptive Strategy and Tool for Improvement of Imputation Accuracy and Computing Efficiency
Authors: Qin Jie , Liu Xinrui , Liu Yaxin , Peng Wei , Kangzhu Yixi , Zhong Jincheng , Wang Jiabo 
Published: October 2022

AbstractWith the development of molecular biology and genetics, deep sequencing technology has become the main way to discover genetic variation and reveal the molecular structure of genome. Due to the complexity of the whole genome segment structure, a large number of missing genotypes have appeared after sequencing, and these missing genotypes can be imputed by genotype imputation method. With the in-depth study of genotype imputation methods, computational intensive and computationally efficient imputation software come into being. Beagle software, as an efficient imputation software, is widely used because of its advantages of low memory consumption, fast running speed and relatively high imputation accuracy. K-Means clustering can divide individuals with similar population structure into a class, so that individuals in the same class can share longer haplotype fragments. Therefore, combining K-Means clustering algorithm with Beagle software can improve the interpolation accuracy. The Beagle and KBeagle method was used to compare the imputation efficiency. The KBeagle method presents a higher imputation matching rate and a shorter computing time. In the genome selection and heritability estimated section, the genotype dataset after imputed, unimputed, and with real genotype show similar prediction accuracy. However the estimated heritability using genotype dataset after imputed is closer to the estimation by the dataset with real genotype. We generated a compounds and efficient imputation method, which presents valuable resource for improvement of imputation accuracy and computing time. We envisage the application of KBeagle will be focus on the livestock sequencing study under strong genetic structure.
Genotypic Characterization of Urinary Tract Infections causing bacteria isolates among Adults at Kiambu Level 5 Hospital, Kenya: Selected Extended Spectrum β-Lactamase genes and Biofilm Formation
Authors: Wanja Fredrick Kimunya , Omwenga Eric Omori , Ngugi Caroline Wangare , Maina John Ndemi , Kiiru John Ndemi 
Published: October 2022

AbstractThe menace of antimicrobial resistance to public health is constantly arising globally. Many pathogenic bacteria use mechanisms such as mutations and biofilm formation, which significantly reduces efficacy of antimicrobial agents. In this cross-sectional study, we aimed at determining the prevalence of selected extended spectrum β-lactamase (ESβLs) genes and analyse the possible biofilm formation abilities of the isolated bacteria causing urinary tract infection among adult patients seeking medicare at Kiambu Level 5 hospital, Kenya. The double-disk synergy test was used for phenotypic identification of ESβLs producing isolates, while microtiter plate assays with some modifications were used to test biofilm formation analysis. A total of 10 isolates were bioassayed for ESβL genes presence out of 57 bacteria isolates obtained from urine samples. From this study, theblaTEMgenes were found to be the most prevalent ESβLs genes (100%), followed byblaOXAandblaSHVgenes at 40% and 30% respectively. In addition, the co-carriage ofblaTEMandblaSHVwas revealed at 50% lower than that ofblaTEM+ blaOXAgenes at 66.7% among the studyE. coliisolates. Biofilm formation finding disclosed that most of the isolates form biofilms 36 (63.2%), with Gram-negatives being the most biofilm formers 25 (69.4%) compared to the Gram-positive 11 (30.6%).E. coli15(41.7 %),Klebsiella sp. 7(19.4%) andS. aureus7(19.4%) were the most common biofilm formers. Further analysis showed no significant difference in biofilm formation among all tested isolates with a p-value of more than 0.05. However, overall Gram-positive isolates had a significant P-value of 0.056. Although biofilm formation’s impact on urinary tract infections is not fully recognized, the carriage of ESβLs resistance genes and the biofilm formation ability negatively impact effectiveness of UTI treatment. Therefore, we advocate for surveillance studies to map ESβLs distribution and biofilm formation genes among UTI etiological agents to halt UTI treatment failure.
A Systematic Review on Medical Oxygen Ecosystem: Current State and Recent Advancements
Authors: Haque Ehtashamul , Tarek Saber Al , Sarker Farhana , Haque Md. Atiqul , Mamun Khondaker A. 
Published: October 2022

AbstractBackgroundMedical oxygen is an essential component of modern healthcare, with a wide variety of applications ranging from supplemental use in surgery and trauma patients to the primary medication in oxygen therapy. This is the most effective treatment for any respiratory illness. Despite the importance of oxygen for public health and its demand as a life-saving drug, research on the subject is limited, with the majority of studies conducted following the outbreak of the COVID-19 pandemic. Due to the lack of empirical studies, we aimed to compile the recent research efforts with the current state of the field through a systematic review.MethodsWe have performed a systematic review targeting the medical oxygen ecosystem, following the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P). For the study, we have limited our scope to healthcare facilities and domiciliary applications of medical oxygen. We considered the articles published in the last twenty years, starting from the SARS outbreak in November 2002 to 15thMay 2022.ResultsOur systematic search resulted in forty-one preliminary articles, with three more articles appended for a complete outlook on the topic. Based on the selected articles, the current state of the topic was presented through detailed discussion and analysis.ConclusionWe have presented an in-depth discussion of the research works found through the systematic search while extrapolating to provide insights on the current subject scenario. We have highlighted the areas with inadequate contemporary studies and presented some research gaps in the field.
Impact of vaccination on the presence and severity of symptoms of hospitalised patients with an infection by the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1)
Authors: Beraud Guillaume , Bouetard Laura , Civljak Rok , Michon Jocelyn , Tulek Necla , Lejeune Sophie , Millot Romain , Garchet-Beaudron Aurélie , Lefebvre Maeva , Velikov Petar , Festou Benjamin , Abgrall Sophie , Lizatovic Ivan Kresimir , Baldolli Aurélie , Esmer Huseyin , Blanchi Sophie , Froidevaux Gabrielle , Kapincheva Nikol , Faucher Jean-François , Duvnjak Mario , Afşar Elçin , Švitek Luka , Yarimoglu Saliha , Yarimoglu Rafet , Janssen Cécile , Epaulard Olivier 
Published: October 2022

AbstractObjectivesThe emergence of SARS-CoV-2 variants raised questions over the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalised patients.MethodsWe conducted an international, multicentric, retrospective study in 14 centres (Bulgaria, Croatia, France, Turkey). We collected data on patients hospitalised ≥24 hours between 01/12/2021 and 03/03/2022, with PCR-confirmed infection at a time of exclusive Omicron circulation, with hospitalisation related or not to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least 2 injections of either mRNA and/or ChAdOx1-S, or 1 injection of Ad26.CoV2-S vaccines.ResultsAmong the 1215 patients (median [IQR] age 73.0 [57.0; 84.0]; 51.3% males), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28-day mortality (RR=0.50 [0.32-0.77]), ICU admission (R=0.40 [0.26-0.62], and oxygen requirement (RR=0.34 [0.25-0.46]), independently of age and comorbidities. When co-analysing these Omicron patients with 948 Delta patients from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (RR=0.53 [0.37-0.76]), ICU admission (R=0.19 [0.12-0.28], and oxygen requirements (RR=0.50 [0.38-0.67]), independently of age, comorbidities and vaccination status.ConclusionsmRNA- and adenovirus-based vaccines have remained effective on severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independently of vaccination and patient characteristics.
Faecal cytokine levels of preterm infants coupled with microbiome profiles represent a potential non-invasive method to predict severity of necrotizing enterocolitis
Authors: Zenner Christian , Chalklen Lisa , Adjei Helena , Dalby Matthew J. , Mitra Suparna , Cornwell Emma , Shaw Alex , Sim Kathleen , Kroll J. Simon , Hall Lindsay J. 
Published: October 2022

ObjectivesNecrotizing enterocolitis (NEC) is a life-threatening disease, and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell’s staging is routinely used to guide diagnosis, but early diagnostic signs are non-specific, potentially leading to unobserved disease progression, which is problematic given the often rapid deterioration observed in NEC infants. New techniques, using biomarkers as diagnostic tool to improve diagnosis of NEC, are emerging. Here we investigated faecal cytokine levels, coupled with gut microbiota profiles, as a non-invasive method to discover specific NEC-associated signatures that can be applied as potential diagnostic markers.Study designPremature babies born below 32 weeks of gestation were admitted to the 2-site neonatal intensive care unit (NICU) of Imperial College hospitals (St. Mary’s or Queen Charlotte’s & Chelsea) between January 2011 and December 2012. All but two babies received a first course of antibiotics from birth onwards. Faecal samples from diapers were collected consecutively during the NICU stay.ResultsEvaluation of microbiota profiles between the study groups revealed only minor differences. However, at later time points, significant changes in microbiota structure were observed for Firmicutes, withEnterococcusbeing the least abundant in Bell stage 2/3 NEC. Faecal cytokine levels were similar to those found in previous studies evaluating systemic cytokine concentrations in NEC settings, but measurement in faeces represents a non-invasive method to evaluate the early onset of the disease. For IL-1α, IL-5 and IL-10, a significantly rising gradient of levels were observed from healthy to NEC1 to NEC2/3.ConclusionsDifferences in certain faecal cytokine profiles in patients with NEC indicate their potential use as diagnostic biomarkers to facilitate earlier diagnosis. Additionally, associations between microbial and cytokine profiles, contribute to improving knowledge about NEC pathogenesis.
Epidemiological surveillance of respiratory pathogens in wastewater in Belgium
Authors: Rector Annabel , Bloemen Mandy , Thijssen Marijn , Pussig Bram , Beuselinck Kurt , Van Ranst Marc , Wollants Elke 
Published: October 2022

ABSTRACTBackgroundDetailed information on the circulation of respiratory viruses in the community is crucial to gain better understanding of the burden of respiratory infections on society.MethodsBy using an in-house respiratory panel for simultaneous detection of 29 respiratory pathogens (22 viruses and 7 bacteria/fungi), we explored the possibility to use wastewater sampling to monitor the circulation of respiratory pathogens at population level.ResultsWe were able to detect all respiratory viruses included in the panel (influenza A, respiratory syncytial virus (RSV), human metapneumovirus (HMPV), parainfluenza viruses (PIV) 1-4, adenovirus (Adv), human bocavirus (HBoV), enterovirus/rhinovirus (EV/RV), enterovirus D68 (EV-D68), parechovirus (HPeV), human coronaviruses (HCoV)-NL63, -229E, -OC43, -HKU-1 and -SARS, cytomegalovirus (CMV) and herpes simplex virus (HSV)-1 and -2), except for influenza B and HCoV MERS which were not circulating in Belgium during the two year study period. An upsurge of EV-D68 infections in Europe in September 2021 was clearly reflected in the wastewater samples. For the viruses where epidemiological data on virus circulation in Belgium were available, these matched the wastewater data. The wastewater pretreatment that was used, optimized for viral enrichment, was as such not suited for the surveillance of bacteria and fungi.ConclusionsCommunity circulation levels of respiratory viruses were well reflected in wastewater samples, indicating that wastewater-based epidemiology can be a valuable tool in the epidemiology and management of respiratory infections.