bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood variation implicates respiratory limits on elevational ranges of Andean birds
Authors: Linck Ethan B. , Williamson Jessie L. , Bautista Emil , Beckman Elizabeth J. , Benham Phred M. , DuBay Shane G. , Flores L. Monica , Gadek Chauncey R. , Johnson Andrew B. , Jones Matthew R. , Núñez-Zapata Jano , Quiñonez Alessandra , Schmitt C. Jonathan , Susanibar Dora , Jorge Tiravanti C. , Verde-Guerra Karen , Wright Natalie A. , Valqui Thomas , Storz Jay F. , Witt Christopher C. 
Published: October 2021

AbstractThe extent to which species ranges reflect intrinsic physiological tolerances is a major, unsolved question in evolutionary ecology. To date, consensus has been hindered by the limited tractability of experimental approaches across most of the tree of life. Here, we apply a macrophysiological approach to understand how hematological traits related to oxygen transport shape elevational ranges in a tropical biodiversity hotspot. Along Andean elevational gradients, we measured traits that affect blood oxygen-carrying capacity—total and cellular hemoglobin concentration and hematocrit—for 2,355 individuals of 136 bird species. We used these data to evaluate the influence of hematological traits on elevational ranges. First, we asked whether hematological plasticity is predictive of elevational range breadth. Second, we asked whether variance in hematological traits changed as a function of distance from the midpoint of the elevational range. We found that the correlation between hematological plasticity and elevational range breadth was slightly positive, consistent with a facilitative role for plasticity in elevational range expansion. We further found reduced local variation in hematological traits near elevational range limits and at high elevations, patterns consistent with intensified natural selection, reduced effective population size, or compensatory changes in other cardiohematological traits with increasing distance from species-specific optima for oxygen availability. Our findings suggest that constraints on hematological plasticity and local genetic adaptation to oxygen availability promote the evolution of the narrow elevational ranges that underpin tropical montane biodiversity.
Time-series Multi-spectral Imaging in Soybean for Improving Biomass and Genomic Prediction Accuracy
Authors: Sakurai Kengo , Toda Yusuke , Kajiya-Kanegae Hiromi , Ohmori Yoshihiro , Yamasaki Yuji , Takahashi Hirokazu , Takanashi Hideki , Tsuda Mai , Tsujimoto Hisashi , Kaga Akito , Nakazono Mikio , Fujiwara Toru , Iwata Hiroyoshi 
Published: October 2021

AbstractMulti-spectral (MS) imaging enables the measurement of characteristics important for increasing the prediction accuracy of genotypic and phenotypic values for yield-related traits. In this study, we evaluated the potential application of temporal MS imaging for the prediction of above-ground biomass (AGB) and determined which developmental stages should be used for accurate prediction in soybean. Field experiments with 198 accessions of soybean were conducted with four different irrigation levels. Five vegetation indices (VIs) were calculated using MS images from soybean canopies from early to late growth stages. To predict the genotypic values of AGB, VIs at the different growth stages were used as secondary traits in a multi-trait genomic prediction. The accuracy of the prediction model increased starting at an early stage of growth (31 days after sowing). To predict phenotypic values of AGB, we employed multi-kernel genomic prediction. Consequently, the prediction accuracy of phenotypic values reached a maximum at a relatively early growth stage (38 days after sowing). Hence, the optimal timing for MS imaging may depend on the irrigation levels.
Evaluating metagenomic assembly approaches for biome-specific gene catalogues
Authors: Delgado Luis Fernando , Andersson Anders F. 
Published: October 2021

ABSTRACTFor many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene-calling on the assembled contigs. The assembly can be conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is likely preferable. Thus, both approaches have pros and cons and it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: 1) assembly on individual samples followed by clustering of the resulting genes, 2) co-assembly on all samples, and 3) mix-assembly, combining individual and co-assembly. The mix-assembly approach resulted in a more extensive non-redundant gene set than the other approaches, and with more genes predicted to be complete and that could be functionally annotated. The mix-assembly consists of 67 million genes (Baltic Sea gene set; BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (<95% amino acid identity) to the Tara Oceans gene dataset, and hence BAGS represents a valuable resource for brackish water research.IMPORTANCESeveral ecosystem types, such as soils and oceans, are studied through metagenomics. It allows the analysis of genetic material of the microbes within a sample without the need for cultivation. When performing the DNA sequencing with an instrument that generates short sequence reads, these reads need to be assembled in order to obtain more complete gene sequences. In this paper, we have evaluated three strategies for assembling metagenome sequences using a large metagenomic dataset from the Baltic Sea. The method that we call mix-assembly generated the greatest number of non-redundant genes and the largest fraction of genes that were predicted to be complete. The resulting gene catalogue will serve as an important resource for brackish water research. We believe this method to be efficient also for generating gene catalogs for other biomes.
Exhaled particles from nanometre to millimetre and their origin in the human respiratory tract
Authors: Bagheri Gholamhossein , Schlenczek Oliver , Turco Laura , Thiede Birte , Stieger Katja , Kosub Jana-Michelle , Pöhlker Mira L. , Pöhlker Christopher , Moláček Jan , Scheithauer Simone , Bodenschatz Eberhard 
Published: October 2021

AbstractDetailed knowledge of the properties of exhaled particles from the human respiratory tract for all genders and ages is essential to determine the modes of transmission of airborne diseases. This applies not only to the current COVID-19 pandemic, but also to many others, be it measles, seasonal influenza or tuberculosis. To date, there are no data on the individual-specific concentrations and sizes of exhaled particles over the entire size range from nanometre to millimetre. Here we present a comprehensive data set, measured by particle size spectrometry and in-line holography covering the entire size range from 132 healthy volunteers aged 5 to 80 years for a defined set of breathing and vocalisation activities. We find age to have a large effect on small particle concentrations (<5 µm), doubling in children during adolescence and in adults over a 30-year period. In contrast, gender, body mass index, smoking or exercise habits have no discernible influence. Particles >20 µm show on average no measurable dependence on the type of vocalisation with the exception of shouting. We show evidence that particles <5 µm mainly originate in the lower respiratory tract, 5-15 µm in the larynx/pharynx, and >15 µm in the oral cavity.
COVID-19 mortality in Italy varies by patient age, sex and pandemic wave
Authors: Minnai Francesca , De Bellis Gianluca , Dragani Tommaso A. , Colombo Francesca 
Published: October 2021

AbstractBackgroundSARS-CoV-2 has caused a worldwide epidemic of enormous proportions, which resulted in different mortality rates in different countries for unknown reasons.AimWe aimed to evaluate which independent parameters are associated with risk of mortality from COVID-19 in a series that includes all Italian cases, ie, more than 4 million individuals infected with the SARS-CoV-2 coronavirus.MethodsWe analyzed factors associated with mortality using data from the Italian national database of SARS-CoV-2-positive cases, including more than 4 million cases, >415 thousand hospitalized for coronavirus disease-19 (COVID-19) and >127 thousand deceased. For patients for whom age, sex and date of infection detection were available, we determined the impact of these variables on mortality 30 days after the date of diagnosis or hospitalization.ResultsMultivariable Cox analysis showed that each of the analyzed variables independently affected COVID-19 mortality. Specifically, in the overall series, age was the main risk factor for mortality, with HR >100 in the age groups older than 65 years compared with a reference group of 15-44 years. Male sex presented an excess risk of death (HR = 2.1; 95% CI, 2.0–2.1). Patients infected in the first pandemic wave (before 30 June 2020) had a greater risk of death than those infected later (HR = 2.7; 95% CI, 2.7–2.8).ConclusionsIn a series of all confirmed SARS-CoV-2-infected cases in an entire European nation, elderly age was by far the most significant risk factor for COVID-19 mortality, confirming that protecting the elderly should be a priority in pandemic management. Male sex and being infected during the first wave were additional risk factors associated with COVID-19 mortality.
COVID-19 Neutralizing Antibody Surveillance Testing for Fully Vaccinated Individuals During Delta Variant Spread
Authors: Pan Jing , Li Zhigang , Wang Lin , Szymanski Joshua , Romano Maria , Yin Dylan , Wang Allen , Small Thomas , Zou Zhiying , Li Jing , Witham Greg , Wang Li , Zhang Yubei , Qi Kai , Yin Ray 
Published: October 2021

AbstractWe recently performed 568 rapid neutralizing antibody (NAb) tests on 164 fully vaccinated individuals who received either Moderna or Pfizer COVID-19 vaccine regimens over 7 weeks. The NAb levels against the wild type (WA1/2020), Delta, and Kappa variants were measured and compared. Depending on each individual’s medical condition and vaccination status, the NAb levels for most of the fully vaccinated people decreased within 2-6 months, while a small number of individuals either generated non-detectable amount of NAbs after full vaccination (e.g., immunocompromised), or had high NAb levels lasting beyond 6 months. Since the NAb levels vary significantly among different individuals and decrease over time, the deployment of a low-cost rapid test to monitor NAb levels against both the wild type and emerging variants among fully vaccinated individuals can play a very crucial role to control the current pandemic. Our study provides an example of using such a rapid NAb test to fill this currently unmet medical need.
Forgoing healthcare during the COVID-19 pandemic in Geneva, Switzerland – a cross-sectional population-based study
Authors: Menon Lakshmi Krishna , Richard Viviane , de Mestral Carlos , Baysson Helene , Wisniak Ania , Guessous Idris , Stringhini Silvia ,   for the Specchio-COVID19 Study Group
Published: October 2021

AbstractBackgroundHealth systems around the world continue to navigate through operational challenges surfaced by the COVID-19 pandemic; these have implications for access to healthcare. In this study, we estimate the prevalence and reasons for forgoing healthcare during the pandemic in Geneva, Switzerland; a country with a universal and mandatory private health insurance coverage.MethodsParticipants from a randomly selected population-based sample of the adult population living in the Canton of Geneva completed an online socio-demographic and lifestyle questionnaire between November 2020 and January 2021. The prevalence and reasons for forgoing healthcare since the beginning of the COVID-19 pandemic were examined descriptively, and logistic regression models were used to assess determinants for forgoing healthcare.ResultsThe study included 5,397 participants, among which 8.0% reported having forgone healthcare since the beginning of the COVID-19 pandemic; participants with a disadvantaged financial situation (OR=2.04; 95% CI: 1.56-2.65), and those reporting an average (OR=2.55; 95% CI: 1.94-3.32) or poor health (OR=4.40; 95% CI: 2.40-7.68) were more likely to forgo healthcare. The most common reasons to forgo healthcare were appointment cancellations by healthcare providers (53.9%), fear of infection (35.3%), and personal organizational issues (11.1%).ConclusionOur paper highlights the effects of the COVID-19 pandemic on access to healthcare and identifies population sub-groups at-risk for forgoing healthcare. These results necessitate public health efforts to ensure equitable and accessible healthcare as the COVID-19 pandemic continues.Highlights8% of the Geneva, Switzerland, adults renounced healthcare in the COVID-19 pandemicMain forgoing healthcare reasons are appointment cancellation and fear of infectionUnderprivileged participants with poor health are more likely to forgo healthcare
Initial SARS-CoV-2 viral load is associated with disease severity: a retrospective cohort study
Authors: Souverein Dennis , van Stralen Karlijn , van Lelyveld Steven , van Gemeren Claudia , Haverkort Milly , Snijders Dominic , Soetekouw Robin , Kapteijns Erik , de Jong Evelien , Hermanides Gonneke , Aronson Sem , Wagemakers Alex , Euser Sjoerd 
Published: October 2021

ABSTRACTBackgroundWe aimed to assess the association between initial SARS-CoV-2 viral load and the subsequent hospital and intensive care unit (ICU) admission and overall survival.MethodsAll persons with a positive SARS-CoV-2 RT-PCR result from a combined nasopharyngeal (NP) and oropharyngeal (OP) swab (first samples from unique persons only) that was collected between March 17, 2020, and March 31, 2021, in Public Health testing facilities in the region Kennemerland, province of North Holland, the Netherlands were included. Data on hospital (and ICU) admission were collected from the two large teaching hospitals in the region Kennemerland.ResultsIn total, 20,207 SARS-CoV-2 positive persons were included in this study, of whom 310 (1.5%) were hospitalized in a regional hospital within 30 days of their positive SARS-CoV-2 RT-PCR test. When persons were categorized in three SARS-CoV-2 viral load groups, the high viral load group (Cp < 25) was associated with an increased risk of hospitalization as compared to the low viral load group (Cp > 30) (ORadjusted [95%CI]: 1.57 [1.11-2.26], p-value=0.012), adjusted for age and sex. The same association was seen for ICU admission (ORadjusted [95%CI]: 7.06 [2.15-43.57], p-value=0.007). For a subset of 243 of the 310 hospitalized patients, the association of initial SARS-CoV-2 Cp-value with in-hospital mortality was analyzed. The initial SARS-CoV-2 Cp-value of the 17 patients who deceased in the hospital was significantly lower (indicating a higher viral load) compared to the 226 survivors: median Cp-value [IQR]: 22.7 [3.4] vs. 25.0 [5.2], OR[95%CI]: 0.81 [0.68-0.94], p-value = 0.010.ConclusionsOur data show that higher initial SARS-CoV-2 viral load is associated with an increased risk of hospital admission, ICU admission, and in-hospital mortality. We believe that our findings emphasize the added value of reporting SARS-CoV-2 viral load based on Cp-values to identify persons who are at the highest risk of adverse outcomes such as hospital or ICU admission and who therefore may benefit from more intensive monitoring.
ContaTester: Fast cross-contamination estimation and identification for large human sequencing cohorts
Authors: Delafoy Damien , Mercier Jonathan , Larsonneur Elise , Wiart Nicolas , Sandron Florian , Mejean Thomas , Meslage Stéphane , Daian Delphine , Olaso Robert , Boland Anne , Deleuze Jean-François , Meyer Vincent 
Published: October 2021

AbstractBackgroundInterest in genomic medicine for human health studies and clinical applications is rapidly increasing. Clinical applications require contamination-free samples to avoid misleading results and provide a sound basis for diagnosis.ResultsHere we present ContaTester, a tool which requires only allele balance information gathered from a VCF file to detect cross-contamination in germline human DNA samples. Based on a regression model of allele balance distribution, ContaTester allows fast checking of contamination levels for single samples or large cohorts (less than two minutes per sample). We demonstrate the efficiency of ContaTester using experimental validations: ContaTester shows similar results to methods requiring alignment data but with a significantly reduced storage footprint and less computation time. Additionally, for contamination levels above 5%, ContaTester can identify contaminants across a cohort, providing important clues for troubleshooting and quality assessment.ConclusionsContaTester estimates contamination levels from VCF files generated from whole genome sequencing normal sample and provides reliable contaminant identification for cohorts or experimental batches.
Capillary stall quantification from optical coherence tomography angiogram maximum intensity projections
Authors: Fruekilde Signe K. , Jiménez Eugenio G. , Drasbek Kim R. , Bailey Christopher J. 
Published: October 2021

AbstractOptical coherence tomography (OCT) is applicable to the study of cerebral microvasculaturein vivo. Optimised acquisition schemes enable the generation of three-dimensional OCT angiograms,i.e., volumetric images of red blood cell flux in capillary networks, currently at a repetition rate of up to 1/10 seconds. This makes testable a new class of hypotheses that strive to bridge the gap between microscopic phenomena occurring at the spatial scale of neurons, and less invasive but crude techniques to measure macroscopic blood flow dynamics. Here we present a method for quantifying the occurrence of transient capillary stalls in OCT angiograms,i.e., events during which blood flow through a capillary branch is temporarily occluded. By making the assumption that information on such events is present predominantly in the imaging plane, we implemented a pipeline that automatically segments a network of interconnected capillaries from the maximum intensity projections (MIP) of a series of 3D angiograms. We then developed tools enabling rapid manual assessment of the binary flow status (open/stalled) of hundreds of capillary segments based on the intensity profile of each segment across time. The entire pipeline is optimized to run on a standard laptop computer, requiring no high-performance, low-availability resources, despite very large data volumes. To further reduce the threshold of adoption, and ultimately to support the development of reproducible research methods in the young field, we provide the documented code for scrutiny and re-use under a permissive open-source license.
Context-dependent selectivity to natural scenes in the retina
Authors: Goldin Matías A. , Lefebvre Baptiste , Virgili Samuele , Ecker Alexander , Mora Thierry , Ferrari Ulisse , Marre Olivier 
Published: October 2021

AbstractRetina ganglion cells extract specific features from natural scenes and send this information to the brain. In particular, they respond to local light increase (ON responses), and/or decrease (OFF). However, it is unclear if this ON-OFF selectivity, characterized with synthetic stimuli, is maintained when they are stimulated with natural scenes. Here we recorded the responses of ganglion cells of mice and axolotls to stimuli composed of natural images slightly perturbed by patterns of random noise to determine their selectivity during natural stimulation. The ON-OFF selectivity strongly depended on the natural image. A single ganglion cell can signal luminance increase for one natural image, and luminance decrease for another. Modeling and experiments showed that this was due to the non-linear combination of different pathways of the retinal circuit. Despite the versatility of the ON-OFF selectivity, a systematic analysis demonstrated that contrast was reliably encoded in these responses. Our perturbative approach thus uncovers the selectivity of retinal ganglion cells to more complex features than initially thought during natural scene stimulation.
Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors
Authors: Angkeow Julia W. , Monaco Daniel R. , Chen Athena , Venkataraman Thiagarajan , Jayaraman Sahana , Valencia Cristian , Sie Brandon M. , Liechti Thomas , Farhadi Payam Noroozi , Funez-dePagnier Gabriela , Sherman-Baust Cheryl A. , Wong May Q. , Sears Cynthia L. , Simner Patricia J. , Round June L. , Duggal Priya , Laserson Uri , Steiner Theodore S. , Sen Ranjan , Lloyd Thomas E. , Roederer Mario , Mammen Andrew L. , Longman Randy S. , Rider Lisa G. , Larman H. Benjamin 
Published: October 2021

AbstractMicrobial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via programmable Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, costeffective approach for multiplexed detection of exposure and response to thousands of microbial protein products. Here we designed and constructed a library of 95,601 56 amino acid peptide tiles spanning a subset of environmental proteins more likely to be associated with immune responses: those with “toxin” or “virulence factor” keyword annotations. PhIP-Seq was used to profile the circulating antibodies of ~1,000 individuals against this “ToxScan” library of 14,430 toxins and virulence factors from 1,312 genera of organisms. In addition to a detailed analysis of six commonly encountered human commensals and pathogens, we study the age-dependent stability of the ToxScan profile and use a genome-wide association study (GWAS) to find that the MHC-II locus modulates the selection of bacterial epitopes. We detect previously described anti-flagellin antibody responses in a Crohn’s disease cohort and identify a novel association between anti-flagellin antibodies and juvenile dermatomyositis (JDM). PhIP-Seq with the ToxScan library provides a new window into exposure and immune responses to environmental protein toxins and virulence factors, which can be used to study human health and disease at cohort scale.