bluuebunny/crossref_metadata_2025_split huggingface dataset:
Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report
Authors: Hernandez Matthew M. , Gonzalez-Reiche Ana S. , Alshammary Hala , Fabre Shelcie , Khan Zenab , van De Guchte Adriana , Obla Ajay , Ellis Ethan , Sullivan Mitchell J. , Tan Jessica , Alburquerque Bremy , Soto Juan , Wang Ching-Yi , Sridhar Shwetha Hara , Wang Ying-Chih , Smith Melissa , Sebra Robert , Paniz-Mondolfi Alberto E. , Gitman Melissa R. , Nowak Michael D. , Cordon-Cardo Carlos , Luksza Marta , Krammer Florian , van Bakel Harm , Simon Viviana , Sordillo Emilia Mia 
Published: February 2021

ABSTRACTNew York City (NYC) emerged as a coronavirus disease 2019 (COVID-19) epicenter in March 2020, but there is limited information regarding potentially unrecognized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first reported case. We utilized a sample pooling strategy to screen for SARS-CoV-2 RNA in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across our NYC health system who were evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We obtained complete SARS-CoV-2 genome sequences from samples collected between late February and early March. Additionally, we detected SARS-CoV-2 RNA in pooled specimens collected in the week ending 25 January 2020, indicating that SARS-CoV-2 caused sporadic infections in NYC a full month before the first officially documented case.ONE SENTENCE SUMMARYMolecular surveillance demonstrates that SARS-CoV-2 caused influenza-like illness in NYC before the first reported case.
Categorizing ultra-processed food intake in large-scale cohort studies: evidence from the Nurses’ Health Studies, the Health Professionals Follow-up Study, and the Growing Up Today Study
Authors: Khandpur Neha , Rossato Sinara , Drouin-Chartier Jean-Philippe , Du Mengxi , Martinez Euridice , Sampson Laura , Monteiro Carlos , Zhang Fang Fang , Willett Walter , Fung Teresa T. , Sun Qi 
Published: February 2021

AbstractObjectiveThere is limited description and documentation of the methods used for the categorization of dietary intake according to the NOVA classification, in large-scale cohort studies. This manuscript details the strategy employed for categorizing the food intake, assessed using food frequency questionnaires (FFQs), of participants in the Nurses’ Health Studies (NHS) I and II, the Health Professionals Follow-up Study (HPFS), and the Growing Up Today Studies (GUTS) I and II into the four NOVA groups to identify the ultra-processed portion of their diets.MethodsA four-stage approach was employed: (1) compilation of all food items from the FFQs used at different waves of data collection; (2) assignment of food items to a NOVA group by three researchers working independently; (3) checking for consensus in categorization and shortlisting food items for which there was disagreement; (4) discussions with experts and use of additional resources (research dieticians, cohort-specific documents, online grocery store scans) to guide the final categorization of the short-listed items.ResultsAt stage 1, 205 and 315 food items were compiled from the adult and GUTS FFQ food lists, respectively. Over 70% of food items from all cohorts were assigned to a NOVA group after stage 2 and the remainder were shortlisted for further discussion (stage 3). Two rounds of reviews at stage 4 helped with the categorization of 96.5% of items from the adult cohorts and 90.7% items from the youth cohort. The remaining products were assigned to a non-ultra-processed food group and ear-marked for sensitivity analyses. Of all items in the food lists, 36.1% in the adult cohorts and 43.5% in the GUTS cohorts were identified as ultra-processed.ConclusionAn iterative, conservative approach was used to categorize food items from the NHS, HPFS and GUTS FFQ food lists according to their grade of processing. The approach relied on discussions with experts and was informed by insights from the research dieticians, information provided by cohort-specific documents, and scans of online supermarkets. Future work is needed to validate this approach.
Emerging SARS-CoV-2 Lineages in Middle Eastern Jordan with Increasing Mutations Near Antibody Recognition Sites
Authors: Hajjo Rima , Sabbah Dima A. , Bardaweel Sanaa K. 
Published: February 2021

AbstractThe genomic analysis of the 556 viral sequences from Jordan uncovered three dominant genetic SARS-CoV-2 lineages that are currently circulating in Jordan: B.1.1.312 (76%), B.1.36.10 (11%), and B.1.1.7 (6%), replacing the genetic strains that were dominant before sustained community transmission in Jordan. This raises speculations about these new genetic lineages and their relationship to the severity of disease symptoms in Jordan.
A new variant of ASIC2 mediates sodium retention in nephrotic syndrome
Authors: Fila Marc , Sassi Ali , Brideau Gaëlle , Cheval Lydie , Morla Luciana , Houillier Pascal , Walter Christine , Gennaoui Michel , Collignon L Laure , Keck Mathilde , Planelles Gabrielle , Bakouh Naziha , Peuchmaur Michel , Deschênes Georges , Anegon Ignacio , Remy Séverine , Vogt Bruno , Crambert Gilles , Doucet Alain 
Published: February 2021

AbstractIdiopathic nephrotic syndrome (INS) is characterized by proteinuria and renal Na retention leading to oedema. This Na retention is usually attributed to epithelial sodium channel (ENaC) activation following plasma aldosterone increase. However, most nephrotic patients show normal aldosterone levels. Using a corticosteroid-clamped rat model of INS (CC-PAN), we showed that the observed electrogenic and amiloride-sensitive Na retention could not be attributed to ENaC. We, then, identified a truncated variant of acid sensing ion channel 2b (ASIC2b) that induced sustained acid-stimulated sodium currents when co-expressed with ASIC2a. Interestingly, CC-PAN nephrotic ASIC2b-null rats did not develop sodium retention. We finally showed that expression of the truncated ASIC2b in kidney was dependent on the presence of albumin in the tubule lumen and activation of ERK in renal cells. Finally, the presence of ASIC2 mRNA was also detected in kidney biopsies from patients with INS but in any of the patients with other renal diseases. We have, therefore, identified a novel variant of ASIC2b responsible for the renal Na retention in the pathological context of INS.
Accommodating site variation in neuroimaging data using normative and hierarchical Bayesian models
Authors: Bayer Johanna M. M. , Dinga Richard , Kia Seyed Mostafa , Kottaram Akhil R. , Wolfers Thomas , Lv Jinglei , Zalesky Andrew , Schmaal Lianne , Marquand Andre 
Published: February 2021

AbstractThe potential of normative modeling to make individualized predictions from neuroimaging data has enabled inferences that go beyond the case-control approach. However, site effects are often confounded with variables of interest in a complex manner and can bias estimates of normative models, which has impeded the application of normative models to large multi-site neuroimaging data sets. In this study, we suggest accommodating for these site effects by including them as random effects in a hierarchical Bayesian model. We compared the performance of a linear and a non-linear hierarchical Bayesian model in modeling the effect of age on cortical thickness. We used data of 570 healthy individuals from the ABIDE (autism brain imaging data exchange) data set in our experiments. In addition, we used data from individuals with autism to test whether our models are able to retain clinically useful information while removing site effects. We compared the proposed single stage hierarchical Bayesian method to several harmonization techniques commonly used to deal with additive and multiplicative site effects using a two stage regression, including regressing out site and harmonizing for site with ComBat, both with and without explicitly preserving variance related to age and sex as biological variation of interest. In addition, we made predictions from raw data, in which site has not been accommodated for. The proposed hierarchical Bayesian method showed the best predictive performance according to multiple metrics. Beyond that, the resulting z-scores showed little to no residual site effects, yet still retained clinically useful information. In contrast, performance was particularly poor for the regression model and the ComBat model in which age and sex were not explicitly modeled. In all two stage harmonization models, predictions were poorly scaled, suffering from a loss of more than 90 % of the original variance. Our results show the value of hierarchical Bayesian regression methods for accommodating site variation in neuroimaging data, which provides an alternative to harmonization techniques. While the approach we propose may have broad utility, our approach is particularly well suited to normative modelling where the primary interest is in accurate modelling of inter-subject variation and statistical quantification of deviations from a reference model.1HighlightsDevelopment and presentation of normative modeling approach based on hierarchical Bayesian modeling that can be applied to large multi-site neuroimaging data sets.Comparison of performance of Hierarchical Bayesian model including site as predictor to several common ways to harmonize for multi-site effects.Presentation of normative modeling as site correction tool.
Shadow ORFs illuminated: long overlapping genes inPseudomonas aeruginosaare translated and under purifying selection
Authors: Kreitmeier Michaela , Ardern Zachary , Abele Miriam , Ludwig Christina , Scherer Siegfried , Neuhaus Klaus 
Published: February 2021

AbstractThe existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the medically important Gram-negative bacteriumPseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing data. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically highly restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes.
Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle,Leptinotarsa decemlineata
Authors: Pélissié Benjamin , Chen Yolanda H. , Cohen Zachary P. , Crossley Michael S. , Hawthorne David J. , Izzo Victor , Schoville Sean D. 
Published: February 2021

AbstractBackgroundInsecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices. An improved understanding of the evolutionary mechanisms that allow pests to rapidly adapt to novel control tactics will help prevent economically damaging outbreaks. The Colorado potato beetle (CPB),Leptinotarsa decemlineata,is a global super-pest that rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation.ResultsPopulation genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit only modest reductions in nucleotide diversity, relative to non-pest ancestral populations, and show evidence of recent demographic expansion. Genome scans of selection provide clear signatures of repeated adaptation across different CPB populations, with especially strong evidence that insecticide resistance involves selection of different genes in different populations. Similarly, analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns.ConclusionCPB evolves insecticide resistance repeatedly across agricultural regions, and oftentimes at the same loci, supporting a prominent role of polygenic evolution from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. An important future goal will be to understand how polygenic resistance phenotypes spread among local pest populations, in order to refine integrated pest management practices to maintain the efficacy and sustainability of novel control techniques.
Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum inC. elegans
Authors: Rajaei Moein , Shekhar Saxena Ayush , Johnson Lindsay M. , Snyder Michael C. , Crombie Timothy A. , Tanny Robyn E. , Andersen Erik C. , Joyner-Matos Joanna , Baer Charles F. 
Published: February 2021

AbstractImportant clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the lab as in nature. The ratio of transitions to transversions (Ts/Tv) is consistently lower inC. elegansmutation accumulation (MA) experiments than in nature, which has been argued to be in part due to increased oxidative stress in the lab environment. Using whole-genome sequence data from a set ofC. elegansMA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased endogenous oxidative stress, we find that the base-substitution spectrum is similar betweenmev-1lines, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). By contrast, the rate of short insertions is greater in themev-1lines, consistent with studies in other organisms in which environmental stress led to an increase in the rate of insertion-deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are qualitatively different from those of non-mononucleotide sequence, both for indels and base-substitutions, and whereas the non-mononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different. The discrepancy in mutational spectra between lab MA experiments and natural variation is likely due to a consistent (but unknown) effect of the lab environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.
Testing potential mechanisms of conspecific sperm precedence inDrosophila pseudoobscura
Authors: Peckenpaugh Brooke , Castillo Dean M. , Moyle Leonie C. 
Published: February 2021

AbstractDrosophila pseudoobscurafemales that co-occur with sister speciesD. persimilisshow elevated fertilization by conspecific sperm when they mate with both a heterospecific and a conspecific male. This phenomenon, known as conspecific sperm precedence (CSP), has evolved as a mechanism to avoid maladaptive hybridization withD. persimilis. In this study, we assessed pericopulatory (during mating) and postcopulatory (after mating) traits in crosses with sympatric or allopatricD. pseudoobscurafemales and conspecific or heterospecific males to evaluate potential mechanisms of CSP in this system. We observed shorter copulation duration in crosses with sympatric females, but found no difference in quantity of sperm transferred or female reproductive tract toxicity between sympatry and allopatry. Our data also support the hypothesis that parasperm, a short, sterile sperm morph, can protect fertile eusperm from theD. pseudoobscurafemale reproductive tract, though it is unclear how this might affect patterns of sperm use in sympatry vs. allopatry. Overall, these results suggest that copulation duration could potentially contribute to the elevated CSP observed in sympatry.
Correcting excess mortality for pandemic-associated population decreases
Authors: Faust Jeremy Samuel , Du Chengan , Li Shu-Xia , Lin Zhenqiu , Krumholz Harlan M. 
Published: February 2021

AbstractObjectivesWe identify a correction for excess mortality that takes the sudden unexpected changes in the size of the United States population into account.DesignThis is a weekly cross-sectional analysis of all-cause mortality since week 5, 2020. We describe and apply a simple correction that takes population changes into account in order to provide corrected weekly estimates of expected deaths for 2020 and 2021.SettingThe United States.ParticipantsAll United States residents.InterventionsThe covid-19 pandemic.Main outcome measuresExpected and excess mortality for the United States during the covid-19 period.ResultsAs of week 53, 2020 (ending January 2, 2021), approximately >10,200 more excess deaths have occurred in the United States than could be detected if expected deaths projections were not amended to reflect population decreases during 2020. The figure is projected to rise to >12,600 (>600 weekly) by week 5, 2021. Assuming recent excess mortality and pandemic-associated visa reductions continue until the earliest time herd immunity could be approached resulting from a combination of infections and vaccinations (week 17, 2021), if point estimates of expected deaths are not corrected, expected deaths will be overestimated (and therefore potential excess mortality underestimated) by ∼43,000 during 2021, or >53,300 since the outbreak of the pandemic measurement period (beginning week 5, 2020). By late December 2021, weekly expected death differences are projected to approach 1,000 per week.ConclusionsCurrent models measuring excess mortality should be revised immediately so that public health officials do not lose the ability to detect ongoing excess mortality as the population changes continue to compound, lowering the number of weekly expected deaths. A similar approach should be used in the middle and late phases of all future pandemics.
How has the COVID-19 pandemic impacted on smoking and nicotine dependence among people with severe mental ill health? Analysis of linked data from a UK Closing the Gap Cohort
Authors: Peckham Emily , Allgar Victoria , Crosland Suzanne , Heron Paul , Johnston Gordon , Newbronner Elizabeth , Ratschen Elena , Spanakis Panagiotis , Wadman Ruth , Walker Lauren , Gilbody Simon 
Published: February 2021

SummarySmoking rates are higher for people who use mental health services which contributes substantially to health inequalities. Smoking can lead to worse COVID-19 outcomes, yet it remains unclear whether smoking has changed for people who use mental health services. We examined smoking patterns in a large clinical cohort of people with SMI before and during the pandemic. We found high levels of nicotine dependence and heavier patterns of smoking. Whilst some people had reported quitting, it is likely that smoking inequalities have become further entrenched. Mental health services should seek to mitigate this modifiable risk and source of poor health.
A Bayesian hierarchical model with integrated covariate selection and misclassification matrices to estimate neonatal and child causes of death
Authors: Mulick Amy R. , Oza Shefali , Prieto-Merino David , Villavicencio Francisco , Cousens Simon , Perin Jamie 
Published: February 2021

SummaryReducing neonatal and child mortality is a global priority. In countries without comprehensive vital registration data to inform policy and planning, statistical modelling is used to estimate the distribution of key causes of death. This modelling presents challenges given that the input data are few, noisy, often not nationally representative of the country from which they are derived, and often do not report separately on all of the key causes. As more nationally representative data come to be available, it becomes possible to produce country estimates that go beyond fixed-effects models with national-level covariates by incorporating country-specific random effects. However, the existing frequentist multinomial model is limited by convergence problems when adding random effects, and had not incorporated a covariate selection procedure simultaneously over all causes. We report here on the translation of a fixed effects, frequentist model into a Bayesian framework to address these problems, incorporating a misclassification matrix with the potential to correct for mis-reported as well as unreported causes. We apply the new method and compare the model parameters and predicted distributions of eight key causes of death with those based on the previous, frequentist model.
Mosquitoes (Diptera: Culicidae) of Ecuador: A revised checklist, new records and species of medical importance
Authors: Ponce Patricio , Cevallos Varsovia , Carrazco-Montalvo Andrés 
Published: February 2021

AbstractEcuador is one of the countries with the highest biodiversity in the world, this can also be seen in the Culicidae family. However, there are a limited number of studies on this group. This work provides a baseline reference for this insect group and information about numerous potential and vector disease species. Species names and records were extracted from the National Mosquito Reference Collection at INSPI-Quito, published literature and web databases. The specimens at the INSPI collection were identified using morphological keys and, in a few cases, using molecular markers in the genus Anopheles. An updated list includes the subfamilies Culicinae and Anophelinae, eight tribes, 22 genera and 200 species. We present 18 species cataloged as new records for Ecuador represented in two subfamilies, 6 tribes and 9 genera. Taxonomic notes, geographical distribution and medical importance data for the species involved are provided. The updated list of Mosquitoes (Diptera: Culicidae) is a guide for researchers and health personnel when studying biodiversity, fauna, insect vectors and strategies to prevent the spread of vector diseases.
Glycan-Based Shaping Of The Microbiota During Primate Evolution
Authors: Singh Sumnima , Bastos-Amador Patricia , Thompson Jessica A. , Truglio Mauro , Yilmaz Bahtiyar , Cardoso Silvia , Sobral Daniel , Soares Miguel P. 
Published: February 2021

AbstractGenes encoding certain glycosyltransferases are thought to be under relatively high selection pressure, due to the involvement of the glycans that they synthesize in host-microbe interactions. Here we used a mouse model to investigate whether the loss of α-1,3-galactosyltransferase (GGTA1) function and Galα1-3Galβ1-4GlcNAcβ1-R (αGal) expression during primate evolution might have affected host-microbiota interactions. We found thatGgta1deletion in mice shaped the composition of the gut microbiota in relation to the bacterial species present. This occurred via an immunoglobulin (Ig)-dependent mechanism, associated with IgA targeting of αGal-expressing bacteria. Systemic infection by the Ig-shaped microbiota elicited a less severe form of sepsis than infection with the non-Ig-shaped microbiota. This suggests that in the absence of host αGal, the microbiota is shaped towards lower pathogenicity, likely providing a fitness gain to the host. We infer that high selection pressure exerted by bacterial sepsis may have contributed to increase frequency ofGGTA1loss-of-function mutations in ancestral primates that gave rise to humans.