bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social capital, urbanization level, and COVID-19 vaccination uptake in the United States: A national level analysis
Authors: Qiao Shan , Li Zhenlong , Zhang Jiajia , Sun Xiaowen , Garrett Camryn , Li Xiaoming 
Published: March 2022

AbstractVaccination remains the most promising mitigation strategy for the COVID-19 pandemic. However, existing literature shows significant disparities in vaccination uptake in the United States. Using publicly available national-level data, we aimed to explore if county-level social capital can further explain disparities in vaccination uptake rate adjusting for demographic and social determinants of health (SDOH) variables; and if association between social capital and vaccination uptake may vary by urbanization level. Bivariate analyses and hierarchical multivariable quasi-binomial regression analysis were conducted, then the regression analysis was stratified by urban-rural status. The current study suggests that social capital contributes significantly to the disparities of vaccination uptake in the US. The results of stratification analysis show common predictors of vaccine uptake but also suggest various patterns based on urbanization level regarding the associations of COVID-19 vaccination uptake with SDOH and social capital factors. The study provides a new perspective to address disparities in vaccination uptake through fostering social capital within communities, which may inform tailored public health intervention efforts in enhancing social capital and promoting vaccination uptake.
Patients at risk of pulmonary fibrosis Post Covid-19: Epidemiology, pulmonary sequelaes and humoral response
Authors: Porto Miriam Hernández , Delgado Teresa , Aguirre-Jaime Armando , Ramos María Jose , Campos Silvia , Acosta Orlando , Llanos Ana Belén , Lecuona María 
Published: March 2022

AbstractBackgroundThe COVID-19 pandemic is one of the greatest public health problems. Our aims were to describe epidemiological characteristics, know the amount of protective antibodies and their permanence after a COVID-19 primary infection in patients with risk of pulmonary fibrosis.MethodsDescriptive epidemiological and follow-up study of the humoral response in patients at risk of pulmonary fibrosis Post-Covid-19 hospitalized, between March and October 2020, and who were followed up for a one year after hospital discharge.Results72 patients participated in the study, 52 showed pre-existing chronic comorbidities. COVID-19 clinical severity was rated in 6% mild, 58% as moderate and 36% as severe. After a year of follow-up, the forty percent had pulmonary sequelae, the most frequent (20%) was mild pulmonary fibrosis. Any case of reinfection was detected. All patients presented RBD IgG antibodies and 88% presented IgA antibodies after 8-9 months. The amount of RBD IgG was similar at 4-5 and 8-9 months post-Covid. There was no difference when level of RBD IgG according to the severity of the COVID-19 (p=0.441, p=0.594).ConclusionsMild pulmonary fibrosis sequelae is exceptional but was detected in a high percentage. The amount of RBD IgG is maintained throughout the convalescent phase and seems to protect against new reinfections despite of emerging viral variants. However, seems not predict the developed or not of pulmonary fibrosis.
A new compartment model of COVID-19 transmission: The broken-link model
Authors: Ikeda Yoichi , Sasaki Kenji , Nakano Takashi 
Published: March 2022

AbstractWe propose a new compartment model of COVID-19 spread, the broken-link model, which includes the effect from unconnected infectious links of the transmission. The traditional SIR-type epidemic models are widely used to analyze the spread status, and the models show the exponential growth of the number of infected people. However, even in the early stage of the spread, it is proven by the actual data that the exponential growth did not occur all over the world. We consider this is caused by the suppression of secondary and higher transmissions of COVID-19. We find that the proposed broken-link model quantitatively describes the mechanism of this suppression and is consistent with the actual data.
Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
Authors: Edie Stewart M. , Collins Katie S. , Jablonski David 
Published: March 2022

1.AbstractComparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak.’ Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. As the choice of homologous points for alignment can affect shape differences among specimens, so can the choice of orientation axes. Analysis of forty-five possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment implies a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we recognize one alignment in particular as a continuation of the historical approaches to morphometrics of shell form: orientation via the hinge line. Beyond bivalves, this axis-based approach to aligning specimens facilitates the comparison of continuous differences in shape among many other phylogenetically broad and morphologically disparate samples.
The multi-level regulation of clownfish metamorphosis by thyroid hormones
Authors: Roux Natacha , Miura Saori , Dussene Mélanie , Tara Yuki , Lee Fiona , de Bernard Simon , Reynaud Mathieu , Salis Pauline , Barua Agneesh , Boulahtouf Abdelhay , Balaguer Patrick , Gauthier Karine , Lecchini David , Gibert Yann , Besseau Laurence , Laudet Vincent 
Published: March 2022

AbstractMost marine organisms have a biphasic life cycle during which a pelagic larva is transformed into a radically different juvenile. In vertebrates the role of thyroid hormones (TH) in triggering this transition is well known, but how the morphological and physiological changes are integrated in a coherent way with the ecological transition remains poorly explored. To gain insight into this question, we performed an integrative analysis of metamorphosis of a marine teleost, the clownfish Amphiprion ocellaris. We reveal how TH coordinate a change in color vision as well as a major metabolic shift in energy production, hence highlighting its central integrative role in regulating this transformation. By manipulating the activity of LXR, a major regulator of metabolism, we also reveal a tight link between metabolic changes and metamorphosis progression. Strikingly, we observed that these regulations are at play in the wild revealing how hormones coordinate energy needs with available resources during life cycle.
Tumor purity adjusted beta values improve biological interpretability of high-dimensional DNA methylation data
Authors: Johan Staaf , Mattias Aine 
Published: March 2022

AbstractA common issue affecting DNA methylation analysis in tumor tissue is the presence of a substantial amount of non-tumor methylation signal derived from the surrounding microenvironment. Although approaches for quantifying and correcting for the infiltration component have been proposed previously, we believe these have not fully addressed the issue in a comprehensive and universally applicable way. We present a multi-population framework for adjusting DNA methylation beta values on the Illumina 450/850K platform using generic purity estimates to account for non-tumor signal. Our approach also provides an indirect estimate of the aggregate methylation state of the surrounding normal tissue. Using whole exome sequencing derived purity estimates and Illumina 450K methylation array data generated by The Cancer Genome Atlas project (TCGA), we provide a demonstration of this framework in breast cancer illustrating the effect of beta correction on the aggregate methylation beta value distribution, clustering accuracy, and global methylation profiles.
GWAS and meta-analysis identifies multiple new genetic mechanisms underlying severe Covid-19
Authors: Pairo-Castineira Erola , Rawlik Konrad , Klaric Lucija , Kousathanas Athanasios , Richmond Anne , Millar Jonathan , Russell Clark D , Malinauskas Tomas , Thwaites Ryan , Stuckey Alex , Odhams Christopher A , Walker Susan , Griffiths Fiona , Oosthuyzen Wilna , Morrice Kirstie , Keating Sean , Nichol Alistair , Semple Malcolm G , Knight Julian , Shankar-Hari Manu , Summers Charlotte , Hinds Charles , Horby Peter , Ling Lowell , McAuley Danny , Montgomery Hugh , Openshaw Peter J.M. , Walsh Timothy , Tenesa Albert ,   GenOMICC Investigators,   SCOURGE Consortium,   ISARIC4C Investigators,   23andMe, Scott Richard H , Caulfield Mark J , Moutsianas Loukas , Ponting Chris P , Wilson James F , Vitart Veronique , Pereira Alexandre C , Luchessi Andre , Parra Esteban , Cruz-Guerrero Raquel , Carracedo Angel , Fawkes Angie , Murphy Lee , Rowan Kathy , Law Andy , Hendry Sara Clohisey , Baillie J. Kenneth 
Published: March 2022

AbstractPulmonary inflammation drives critical illness in Covid-19, 1;2 creating a clinically homogeneous extreme phenotype, which we have previously shown to be highly efficient for discovery of genetic associations. 3;4 Despite the advanced stage of illness, we have found that immunomodulatory therapies have strong beneficial effects in this group. 1;5 Further genetic discoveries may identify additional therapeutic targets to modulate severe disease. 6 In this new data release from the GenOMICC (Genetics Of Mortality in Critical Care) study we include new microarray genotyping data from additional critically-ill cases in the UK and Brazil, together with cohorts of severe Covid-19 from the ISARIC4C 7 and SCOURGE 8 studies, and meta-analysis with previously-reported data. We find an additional 14 new genetic associations. Many are in potentially druggable targets, in inflammatory signalling (JAK1, PDE4A), monocyte-macrophage differentiation (CSF2), immunometabolism (SLC2A5, AK5), and host factors required for viral entry and replication (TMPRSS2, RAB2A). As with our previous work, these results provide tractable therapeutic targets for modulation of harmful host-mediated inflammation in Covid-19.
SARS-CoV-2 Spike evolution influences GBP and IFITM sensitivity
Authors: Mesner Dejan , Reuschl Ann-Kathrin , Whelan Matthew V.X , Bronzovich Taylor , Haider Tafhima , Thorne Lucy G. , Towers Greg J. , Jolly Clare 
Published: March 2022

AbstractSARS-CoV-2 spike requires proteolytic processing for viral entry. The presence of a polybasic furin-cleavage site (FCS) in spike, and evolution towards an optimised FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Here we show that interferon-inducible antiviral restriction factors Guanylate binding proteins (GBP) 2 and 5 interfere with furin-mediated cleavage of SARS-CoV-2 spike and inhibit the infectivity of early-lineage Wuhan-Hu-1, while VOCs Alpha and Delta have evolved to escape restriction. Strikingly, we find Omicron is unique amongst VOCs, being restricted by GBP2/5, and also IFITM1, 2 and 3. Replacing the spike S2 domain in Omicron with Delta shows S2 is the determinant of entry route and IFITM sensitivity. We conclude that VOC evolution under different selective pressures has influenced sensitivity to spike-targeting restriction factors, with Omicron selecting spike changes that not only mediate antibody escape, and altered tropism, but also sensitivity to innate immunity.
Species-specific cutaneous protein signatures upon incision injury and correlation with distinct pain-related phenotypes in humans
Authors: Segelcke Daniel , van der Burgt Max , Kappert Christin , Schmidt-Garcia Daniela , Sondermann Julia R. , Bigalke Stephan , Pradier Bruno , Gomez-Varela David , Zahn Peter K. , Schmidt Manuela , Pogatzki-Zahn Esther M. 
Published: March 2022

AbstractPain after surgery is common, and its management remains a clinical challenge. Severe acute and prolonged post-surgical pain impairs immediate recovery and leads to long-term consequences like chronic pain, opioid dependency, and reduced quality of life. Althought rodent pain incision models exist, translation to patients is still hampered. To bridge this gap, we combined sensory phenotyping with quantitative proteomics and protein networks in humans and mice after skin incision representing an established model for surgical pain. Initially, we revealed, for the first time, similarities and differences of protein-protein interaction (PPI) networks across both species. Next, we comprehensively phenotyped humans for pain-related symptoms and observed phenotypes with incision-induced proteome changes. Remarkably, post-incision PPI-networks differed between volunteers with small incision-related hyperalgesic areas (“Low responder”) versus those with large areas (“High responder”). The latter exhibited a pronounced proteolytic environment associated with persistent inflammation, while an anti-inflammatory protein signature was observed in Low responders. Taken together, we provide unprecedented insights into peripheral processes relevant for developing hyperalgesia and pain after incision. This knowledge will immensely facilitate bidirectional translational pain studies and guide future research on the pathophysiology of pain after surgery and the discovery of novel targets for its treatment and prevention.
Fish microbiomes 101: disentangling the rules governing marine fish mucosal microbiomes across 101 species
Authors: Minich Jeremiah , Härer Andreas , Vechinski Joseph , Frable Benjamin W , Skelton Zachary , Kunselman Emily , Shane Mike , Perry Daniela , Gonzalez Antonio , McDonald Daniel , Knight Rob , Michael Todd P. , Allen Eric E 
Published: March 2022

AbstractFish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence the fish microbiome. The microbiota from 101 species of Southern California marine fishes, spanning 22 orders, 55 families, and 83 genera representing ~25% of local marine fish diversity, was analyzed to identify patterns that explain microbial diversity patterns in a geographical subset of marine fish biodiversity. We compared fish microbiomes (gill, skin, midgut, and hindgut) using alpha, beta, and gamma diversity along with establishing a novel method to estimate microbial biomass (Qiime2 plugin katharoseq). For oceanic fishes from the neritic zone, host size and distance from shore were negatively associated with microbial biomass densities and diversity in the gills. Body site was the strongest driver for beta diversity with strong evidence of phylosymbiosis observed across the gill, skin, and hindgut, but not midgut. The majority of microbes from all fish body sites were of unknown origin but overall sea water generally contributes more microbes to fish mucus compared to marine sediment. In a meta-analysis of vertebrate hindguts (569 species), mammals had the highest gamma diversity when controlling for host species number while fishes had the highest percent of unique microbial taxa (92%). In fishes, the midgut, gill, and skin contains the majority of microbial diversity which collectively can be 5.5 times higher than the hindgut. The composite dataset will be useful to vertebrate microbiome researchers and fish biologists interested in microbial ecology with applications in aquaculture and fisheries management.
Resource use differences of two coexisting chironomid species at localized scales
Authors: McCormick Amanda R. , Phillips Joseph S. , Botsch Jamieson C. , Ólafsson Jón S. , Ives Anthony R. 
Published: March 2022

AbstractThe abundances of competing species may show positive correlations in time and space if they rely on a shared resource. Such positive correlations might obscure resource partitioning that facilitates coexistence of competitors and affects their abundances, spatial distributions, and population dynamics. Here, we examine the potential for resource partitioning between two ecologically similar midge species (Diptera: Chironomidae) in Lake Mývatn, Iceland.Tanytarsus gracilentusandChironomus islandicuslarvae coexist at high abundances in benthic habitats, and they have been previously described as feeding upon diatoms and detritus. Furthermore, both species show large, roughly synchronized population fluctuations, implying potential reliance on a shared fluctuating resource and posing the question of how these species coexist at high abundances. We first considered spatial partitioning of larvae; across multiple sites, abundances of both species were positively correlated. Thus, spatial partitioning across different sites in the lake did not appear to be strong. We then inferred differences in dietary resource use with stable carbon isotopes.T. gracilentuslarvae had higher δ13C values thanC. islandicus(mean difference = 5.39 ± 1.84‰), suggesting interspecific differences in resource use. Differences in resource selectivity, tube-building behavior, and feeding styles may facilitate resource partitioning between these two species. Relative to surface sediments,T. gracilentushad higher δ13C values (1.84 ± 0.96‰), suggesting that they selectively graze on13C-enriched resources such as productive algae from the surface of their tubes. In contrast,C. islandicushad lower δ13C values than surface sediments (−2.87 ± 1.95‰), suggesting reliance on isotopically depleted resources, which may include detrital organic matter and associated microbes that larvae selectively consume from the sediment surface or within their tube walls. Overall, our study illustrates that coexisting and ecologically similar species may show positive correlations in space and time while using different resources at fine spatial scales.
Morphofunctional changes at the active zone during synaptic vesicle exocytosis
Authors: Radecke Julika , Seeger Raphaela , Kádková Anna , Laugks Ulrike , Khosrozadeh Amin , Goldie Kenneth N. , Lučić Vladan , Sørensen Jakob B. , Zuber Benoît 
Published: March 2022

AbstractThe fusion of synaptic vesicles (SVs) with the plasma membrane (PM) proceeds through intermediate steps that remain poorly resolved. Additionally, the effect of persistent high or low exocytosis activity on intermediate steps remains unknown. Through time-resolved cryo-electron tomography, we ordered events into a sequence. Following stimulation, proximal tethered SVs rapidly form additional tethers with the PM. Simultaneously, fusion initiation occurs by membrane curvature (‘buckling’) of the SV and PM. It is followed by the formation of a fusion pore, and the collapse of SV membrane. At this time, membrane-proximal, but not membrane-distal, vesicles lose their interconnections, allowing them to move towards the PM. Two mutations of SNAP-25 that arrests or disinhibit spontaneous release, respectively, both caused a loss of interconnectors, while the disinhibiting mutant also caused a loss of membrane proximal multiple-tethered SVs. Overall, tether formation and connector dissolution is triggered by stimulation and respond to the spontaneous fusion rate. These morphological observations likely correspond to the transition of SVs from one functional pool to another.
Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments
Authors: Sugiyama Yuki , Uno Kohei , Matsui Yusuke 
Published: March 2022

AbstractTwo-dimensional video-based pose estimation is a technique that can estimate human skeletal coordinates from video data alone. It is also being applied to gait analysis and, particularly, due to its simplicity of measurement, it has the potential to be applied to the gait analysis of large populations. In contrast, it is considered difficult to completely homogenize the environment and settings during the measurement of large populations. Therefore, it is necessary to appropriately deal with technical errors that are not related to the biological factors of interest. In this study, by analyzing a large cohort database, we have identified four major types of anomalies that occur during gait analysis using OpenPose in uncontrolled environments: anatomical, biomechanical, and physical anomalies and errors due to estimation. We have also developed a workflow for identifying and correcting those anomalies and confirmed that the workflow is reproducible through simulation experiments. Our results will help obtain a comprehensive understanding of the anomalies to be addressed in a pre-processing for 2D video-based gait analysis of large populations.Author summaryGait is one of the important biomarkers of health conditions. With developing mobile health technologies, it is becoming easier to measure our health. However, to realize preventive medicine, establishing evidence is a critical issue, and we need to collect data from a large population. Two-dimensional video-based pose estimation can be a solution for the gait analysis of such a population. However, the technical accuracy and limitations of this analysis have not yet been sufficiently discussed. In this study, by analyzing the largest database currently available, we systematically identified four types of technical anomalies that occur during gait measurement: anatomical, biomechanical, and physical anomalies and errors dues to estimation. We have also shown how to deal with these issues and made solutions available as software so that researchers can reproduce them. In the future, increasing number of studies will use 2D video-based pose estimation to research health-related gait among large populations. We believe that our work will provide a guideline for researchers and clinicians involved in these studies to discuss design and algorithms.