bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tobacco Smoking and Risk of SARS-CoV-2 Infection and Disease Severity Among Adults in an Integrated Healthcare System in California
Authors: Young-Wolff Kelly C , Slama Natalie , Alexeeff Stacey E , Sakoda Lori C , Fogelberg Renee , Myers Laura C , Campbell Cynthia I , Adams Alyce S , Prochaska Judith J 
Published: April 2022

Abstract

Introduction
The relationship between tobacco smoking status and SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19) severity is highly debated. We conducted a retrospective cohort study of &gt;2.4 million adults in a large healthcare system to evaluate whether smoking is associated with SARS-CoV-2 infection and disease severity.

Aims and Methods
This retrospective cohort study of 2,427,293 adults in KPNC from March 5, 2020 (baseline) to December 31, 2020 (pre-vaccine) included smoking status (current, former, never), socio-demographics, and comorbidities from the electronic health record. SARS-CoV-2 infection (identified by a positive PCR test) and COVID-19 severity (hospitalization, ICU admission or death ≤ 30 days of COVID-19 diagnosis) were estimated in time-to-event analyses using Cox proportional hazard regression models adjusting for covariates. Secondary analyses examined COVID-19 severity among patients with COVID-19 using logistic regression.

Results
During the study, 44,270 patients had SARS-CoV-2 infection. Current smoking was associated with lower adjusted rates of SARS-CoV-2 infection (aHR = 0.64 95% CI: 0.61–0.67), COVID-19-related hospitalization (aHR = 0.48 95% CI: 0.40–0.58), ICU admission (aHR = 0.62 95% CI: 0.42–0.87), and death (aHR = 0.52 95% CI: 0.27–0.89) than never-smoking. Former smoking was associated with a lower adjusted rate of SARS-CoV-2 infection (aHR = 0.96 95% CI: 0.94–0.99) and higher adjusted rates of hospitalization (aHR = 1.10 95% CI: 1.03–1.08) and death (aHR = 1.32 95% CI: 1.11–1.56) than never-smoking. Logistic regression analyses among patients with COVID-19 found lower odds of hospitalization for current versus never-smoking and higher odds of hospitalization and death for former versus never-smoking.

Conclusions
In the largest US study to date on smoking and COVID-19, current and former smoking showed lower risk of SARS-CoV-2 infection than never-smoking, while a history of smoking was associated with higher risk of severe COVID-19.

Implications
In this cohort study of 2.4 million adults, adjusting for socio-demographics and medical comorbidities, current tobacco smoking was associated with a lower risk of both SARS-CoV-2 infection and severe COVID-19 illness compared to never-smoking. A history of smoking was associated with a slightly lower risk of SARS-CoV-2 infection and a modestly higher risk of severe COVID-19 illness compared to never-smoking. The lower observed COVID-19 risk for current versus never-smoking deserves further investigation. Results support prioritizing individuals with smoking-related comorbidities for vaccine outreach and treatments as they become available.
Time to Blood Culture Positivity: An Independent Predictor of Mortality in Streptococcus Pyogenes Bacteremia
Authors: Bläckberg Anna , Svedevall Stina , Lundberg Katrina , Nilson Bo , Kahn Fredrik , Rasmussen Magnus 
Published: April 2022

Abstract

Background
Streptococcus pyogenes bacteremia is a severe condition with high mortality. Time to blood culture positivity (TTP) is known to predict the outcome in bacteremia with other pathogens. This study aimed to determine the association between TTP and outcome in S pyogenes bacteremia.

Methods
This retrospective observational cohort study comprised adults with S pyogenes bacteremia, identified through the laboratory database between 2015 and 2018, in the Region of Skåne, Sweden. Correlations between TTP and outcomes were investigated. Primary outcome was death within 30 days, and secondary outcomes were presence of sepsis or disease deterioration within the first 48 hours.

Results
A total of 347 episodes of S pyogenes bacteremia were identified, of which 61 were excluded, resulting in 286 included episodes. Median TTP was 10.4 (interquartile range, 8.4–11.4) hours. Thirty-day mortality was 10%. Median TTP was shorter in patients who died within 30 days compared to survivors (8.6 vs 10.4 hours; P &lt; .001). In a multivariable logistic regression, shorter TTP was associated with 30-day mortality when adjusting for age, Charlson Comorbidity Index, and focus of infection (odds ratio, 3.7 [95% confidence interval, 1.2–11.3]; P = .02). There was no statistically significant difference in TTP between patients with sepsis within 48 hours and those who did not have sepsis. Additionally, there was no statistically significant difference in TTP between patients with disease deterioration compared to those who did not deteriorate.

Conclusions
Knowledge on TTP might be a tool to determine the prognosis of a given patient with S pyogenes bacteremia.
An overview of international genetic evaluations of show jumping in sport horses
Authors: Doyle Jennifer L , Carroll Christopher J , Corbally Alison F , Fahey Alan G 
Published: April 2022

Abstract
The breeding of sport horses to compete in the Olympic disciplines of show jumping, eventing, and dressage is fast becoming a global industry with the increased use of reproductive technologies, including artificial insemination and embryo transfer. Reproductive technologies have facilitated the dissemination of genetics from elite horses across multiple countries and breeds as breeders are no longer limited by location. Due to this increased level of crossbreeding, there is an increased need for estimated breeding values (EBVs) for sport horse performance that can be compared across breeds and countries. However, the implementation of across-breed or across-country genetic evaluations has been limited by the differences in each studbook’s individual breeding programs and genetic evaluations. Consequently, the aim of this review was to compare the genetic evaluations for show jumping of sport horse studbooks worldwide. The top sport horse studbooks in the world according to the World Breeding Federation for Sport Horses Studbook Rankings 2019 were contacted by email to request information on their current breeding programs and genetic evaluations. Twenty-six of the 51 studbooks contacted replied to this request but only 18 of these studbooks conducted their own genetic evaluations or were part of a larger genetic evaluation in their country of origin. The other eight studbooks were not involved in genetic evaluations at present but expressed an interest in the implementation of such in the future. Overall, many differences were identified among the genetic evaluations of each studbook or each country. The definition of show jumping performance differed within each evaluation and the methods and models utilized also differed. Despite some stallions and mares being registered in multiple studbooks or having progeny in multiple studbooks, these differences make comparison of EBVs across studbooks difficult. Further transparency and collaboration of sport horse studbooks with organizations such as Interstallion, will be essential to facilitate any future implementation of international genetic evaluations for show jumping performance.
Feedlot pens with greenhouse roofs improve beef cattle performance in temperate weather
Authors: Hidalgo Jorge , García Muñiz José G , Cesarani Alberto , Larios Neon , Atzori Alberto S , Sánchez Fernando , Espino Marco , Gorocica Milton , Salcedo Roberto , Gonzalez John 
Published: April 2022

Abstract
Muddy pens can negatively affect welfare and performance of feedlot beef cattle. In some regions with temperate weather, plastic greenhouse covers, above the entire pens are used to fatten cattle in a clean and dry environment. The objective of this research was to investigate effects of greenhouse roofed pens on beef cattle feedlot performance in temperate weather. Data were collected from a feedlot located in Central Mexico between 2016 and 2019. The study included 1,062 closeouts of pens with 68,305 crossbred bulls fed in pens with or without a greenhouse roof. Feeding ranged from 82 to 210 d, depending on the initial weight of cattle, which ranged from 255 to 511 kg. For each pen, average daily dry matter intake (DMI; kg of DMI·animal−1·d−1), average daily gain (ADG, kg·animal−1·d−1), and feed efficiency (G:F, ADG/DMI) were measured. Factorial analyses were performed to test the interaction and main effects of initial weight grouping (light, medium, and heavy), roof, and season as fixed effects, and year as a random effect. None of the three-way interactions were significant (P &gt; 0.51). There was no initial weight grouping × roof interactions for DMI and ADG (P &gt; 0.31). There was (P = 0.03) an initial weight grouping × roof interaction for G:F, as pens of all initial weight groups had greater (P &lt; 0.01) G:F in pens with greenhouse roof than its counterpart in pens without greenhouse roof, but the advantage was greater for pens with light cattle (0.178 vs. 0.166; P &lt; 0.01). There was no initial weight grouping × season interactions for all variables (P &gt; 0.39). There was no roof × season interaction for DMI (P = 0.47), but there were interactions for ADG and G:F (P &lt; 0.01). The ADG was not different (P &gt; 0.13) during summer and autumn based on the roofing system, but pens with greenhouse roofs had greater ADG during spring (1.70 vs. 1.61) and winter (1.68 vs. 1.64; P ≤ 0.01). The G:F was greater (P &lt; 0.01) in all seasons for pens with a greenhouse roof, with the most prominent advantage during spring (0.173 vs. 0.160). There were main effects for cattle initial weight grouping and roof for all variables (P &lt; 0.01). Season affected DMI and G:F (P &lt; 0.01). Pens with greenhouse roofs had decreased DMI (9.70 vs. 9.86), greater ADG (1.67 vs. 1.63), and increased G:F (0.173 vs. 0.166) compared to pens without greenhouse roofs (P &lt; 0.01). Pens with greenhouse roofs in feedlots located in temperate regions positively affect beef cattle performance.
Demonstration of antibodies against SARS-CoV-2, neutralizing or binding, in seroconversion panels after mRNA-1273, BNT-162b2 and Ad26.COV2.S vaccine administration
Authors: Belda Francisco , Mora Oscar , Lopez-Martinez Monica , Torres Nerea , Vivanco Ana , Marfil Silvia , Pradenas Edwards , Massanella Marta , Blanco Julià , Christie Rebecca , Crowley Michael 
Published: April 2022

AbstractSeroconversion panels were collected before and after vaccination with three COVID-19 vaccines: two mRNA vaccines (mRNA-1273 and BNT-162b2) and one adenovirus vector vaccine (Ad26.COV2.S). The panels were tested for antibody activity by chemiluminescent immunoassay, ELISA and one was tested in a pseudovirus neutralization assay. Participants positive for anti-SARS-CoV-2 antibodies before vaccination (18.6%) had a higher response to the first vaccine dose than participants who tested negative. For two-dose vaccines, older participants showed a lower response to the first dose than younger participants. All participants showed positive antibody responses after the second vaccine. For the adenovirus vector vaccine, two participants did not generate antibody responses two weeks and two months after vaccination. Three participants were negative at two weeks but positive at two months. Pseudovirus neutralization showed good correlation with antibody activity (correlation coefficient =0.78, p<0.0001). Antibody responses in participants over 45 years old tended to be less robust.
Prediction of serious complications in patients with cancer and pulmonary thromboembolism: validation of the EPIPHANY Index in a prospective cohort of patients from the PERSEO Study
Authors: Sánchez-Cánovas Manuel , Jimenez-Fonseca Paula , Garay David Fernández , Solís Mónica Cejuela , Elía Diego Casado , Salvans Eva Coma , de la Haba Vacas Irma , Sánchez David Gómez , Montés Ana Fernández , Giménez Roberto Morales , de Tejada Mercedes Biosca Gómez , Arrula Virginia Arrazubi , López Silvia Sequero , Candelera Remedios Otero , Cendra Cristina Sánchez , de la Peña Marina Justo , Muñoz Diana Moreno , Sarmiento Mayra Orillo , de Castro Eva Martínez , Escobar Ignacio García , Vidal Alejandro Bernal , Moran Laura Ortega , Muñoz Martín Andrés J. , Bayona Rodrigo Sánchez , Martínez Ortiz María José , de la Peña Francisco Ayala , Vicente Vicente , Carmona-Bayonas Alberto 
Published: April 2022

ABSTRACTIntroductionThere is currently no validated score capable of classifying cancer-associated pulmonary embolism (PE) in its full spectrum of severity. This study has validated the EPIHANY Index, a new tool to predict serious complications in cancer patients with suspected or unsuspected PE.MethodThe PERSEO Study prospectively recruited individuals with PE and cancer from 22 Spanish hospitals. The estimation of the relative frequency θ of complications based on the EPIPHANY Index categories was made using the Bayesian alternative for the binomial test.ResultsNine hundred patients diagnosed with PE between 2017/2020 were recruited. The rate of serious complications at 15 days was 11.8%, 95% highest density interval [HDI], 9.8-14.1%. Of the EPIPHANY low-risk patients, 2.4% (95% HDI, 0.8-4.6%) had serious complications, as did 5.5% (95% HDI, 2.9-8.7%) of the moderate-risk participants and 21.0% (95% HDI, 17.0-24.0%) of those with high-risk episodes. The EPIPHANY Index correlated with overall survival. Both the EPIPHANY Index and the Hestia criteria exhibited greater negative predictive value and a lower negative likelihood ratio than the remaining models. The incidence of bleeding at 6 months was 6.2% (95% HDI, 2.9-9.5%) in low/moderate-risk vs 12.7% (95% HDI, 10.1-15.4%) in high-risk (p-value=0.037) episodes. Of the outpatients, complications at 15 days were recorded in 2.1% (95% HDI, 0.7-4.0%) of the cases with EPIPHANY low/intermediate-risk vs 5.3% (95% HDI, 1.7-11.8%) in high-risk cases.ConclusionWe have validated the EPIPHANY Index in patients with incidental or symptomatic cancer-related PE. This model can contribute to standardize decision-making in a scenario lacking quality evidence.SummaryWe have validated the EPIPHANY Index in patients with acute, incidental, or symptomatic cancer-related PE. This predictive model of complications can contribute to standardize decision-making in a scenario lacking quality evidence.
Motor signatures in digitized cognitive and memory tests enhances characterization of Parkinson’s disease
Authors: Ryu Jihye , Torres Elizabeth B 
Published: April 2022

AbstractBackgroundAlthough there is a growing interest in using wearable sensors to characterize movement disorders, there is a lack of methodology for developing clinically interpretable kinematics biomarkers. Such digital biomarkers would provide a more objective diagnosis, capturing finer degrees of motor deficits, while retaining the information of traditional clinical tests.ObjectivesWe aim at digitizing traditional tests of cognitive and memory performance to derive motor biometrics of pen-strokes and voice, thereby complementing clinical tests with objective criteria, while enhancing the overall motor characterization of Parkinson’s disease (PD).Methods35 participants including patients with PD, healthy young and age-matched controls performed a series of drawing and memory tasks, while their pen movement and voice were digitized. We examined the moment-to-moment variability of time-series reflecting the pen speed and voice amplitude.ResultsThe stochastic signatures of the fluctuations in pen drawing speed and voice amplitude of patients with PD show lower noise-to-signal ratio compared to those derived from the younger and age-matched neurotypical controls. It appears that contact motions of the pen strokes on the tablet evokes sensory feedback for more immediate and predictable control in PD, compared to controls, while voice amplitude loses its neurotypical richness.ConclusionsWe offer new standardized data types and analytics to help advance our understanding of hidden motor aspects of cognitive and memory clinical assays commonly used in Parkinson’s disease.
Detection of a BA.1/BA.2 recombinant in travelers arriving in Hong Kong, February 2022
Authors: Gu Haogao , Ng Daisy YM , Liu Gigi YZ , Cheng Samuel SM , Krishnan Pavithra , Chang Lydia DJ , Cheuk Sammi SY , Hui Mani MY , Lam Tommy TY , Peiris Malik , Poon Leo 
Published: April 2022

AbstractWe studied SARS-CoV-2 genomes from travelers arriving in Hong Kong from November-2021 to February-2022. Apart from detecting Omicron (BA.1, BA1.1. and BA.2) and Delta variants, we detected a BA.1/BA.2 recombinant in two epidemiologically linked cases. This recombinant has a breakpoint near the 5’ end of Spike gene (nucleotide position 20055-21618).
Socioeconomic inequality in the double burden of child malnutrition in the Eastern and Southern African Region
Authors: Caleyachetty Rishi , Kumar Niraj , Bekele Hana , Manaseki-Holland Semira 
Published: April 2022

AbstractSocioeconomic inequalities in the double burden of child malnutrition threatens global nutrition targets 2025, especially in Eastern and Southern Africa. We aimed to quantify these inequalities from nationally representative household surveys in 13 Eastern and Southern African countries between 2000 and 2018. 13 of the latest Demographic and Health Surveys including 72,231 children under five year olds were studied. Prevalence of stunting, wasting and overweight (including obesity) were disagregated by wealth quintiles, maternal education categories and urban-rural residence for visual inspection of inequalities, and the slope index of inequality (SII) and the relative index of inequality (RII) were estimated for each country. Country-specific estimates were pooled using random-effects meta-analyses. Regional stunting and wasting prevalence was higher among children living in the poorest households, with mother’s with the lowest educational level and in rural areas. In contrast, regional overweight (including obesity) prevalence was higher among children living in the richest households, with mother’s with the highest educational level and urban areas. Tackling social inequalities in the distribution of the double burden of malnutrition among children in the Eastern and Southern African region will require strategies that address the reasons socially disadvantaged children become more exposed to stunting or wasting.
Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles
Authors: Olm Matthew R. , Dahan Dylan , Carter Matthew M. , Merrill Bryan D. , Yu Brian , Jain Sunit , Meng Xian Dong , Tripathi Surya , Wastyk Hannah , Neff Norma , Holmes Susan , Sonnenburg Erica D. , Jha Aashish R. , Sonnenburg Justin L. 
Published: April 2022

AbstractInfant microbiome assembly is intensely studied in infants from industrialized nations, but little is known about this process in populations living non-industrialized lifestyles. In this study we deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with over twenty percent of genomes detected in the Hadza infant gut representing phylogenetically diverse novel species. Industrialized infants, even those who are breastfed, have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early-life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.Recognition of work on indigenous communitiesResearch involving indigenous communities is needed for a variety of reasons including to ensure that scientific discoveries and understanding appropriately represent all populations and do not only benefit those living in industrialized nations. Special considerations must be made to ensure that this research is conducted ethically and in a non-exploitative manner. In this study we performed deep metagenomic sequencing on fecal samples that were collected from Hadza hunter-gatherers in 2013/2014 and were analyzed in previous publications using different methods (1, 2). A material transfer agreement with the National Institute for Medical Research in Tanzania ensures that stool samples collected are used solely for academic purposes, permission for the study was obtained from the National Institute of Medical Research (MR/53i 100/83, NIMR/HQ/R.8a/Vol.IX/1542) and the Tanzania Commission for Science and Technology, and verbal consent was obtained from the Hadza after the study’s intent and scope was described with the help of a translator. The publications that first described these samples included several scientists and Tanzanian field-guides as co-authors for the critical roles they played in sample collection, but as no new samples were collected in this study, only scientists who contributed to the analyses described here were included as co-authors in this publication. It is currently not possible for us to travel to Tanzania and present our results to the Hadza people, however we intend to do so once the conditions of the COVID-19 pandemic allow it.
Unifying genetic association tests via regression: Prospective and retrospective, parametric and non-parametric, and genotype- and allele-based tests
Authors: Zhang Lin , Sun Lei 
Published: April 2022

AbstractGenetic association analysis, evaluating the relationship between genetic markers and complex and heritable traits, is the basis of genome-wide association studies. In response, many association tests have been developed, and they are generally classified as prospective vs. retrospective, parametric vs. non-parametric, and genotype- vs. allele-based association tests. While method classification is useful, it is confusing and challenging for practitioners to decide on the ‘optimal’ test to use for their data. Although there are known differences between some of the popular association tests, we provide new results that show the analytical connections between the different tests for both population- and family-based study designs.RésuméInsérer votre résumé ici. We will supply a French abstract for those authors who can’t prepare it themselves.
A dual mechanism of APC/C inhibition by MAP kinases
Authors: Sun Li , Bai Shuang , Chen Jia-li , Deng Da-jie , Luo Zhou-qing , Wang Yamei , Jin Quan-wen 
Published: April 2022

ABSTRACTMitotic anaphase onset is a key cellular process that is tightly regulated by multiple kinases. The involvement of mitogen-activated protein kinases (MAPKs) in this process has been established long ago in Xenopus egg extracts. However, despite its importance, it is still unclear which MAPK(s) is actually involved, this impedes the further understanding of the regulatory cascade. In this study, we first demonstrated that the involvement of MAPKs in mitotic anaphase onset regulation is evolutionarily conserved in the fission yeast (Schizosaccharomyces pombe). Then, we found that two of the three fission yeast MAPK signaling pathways act in concert to restrain anaphase-promoting complex/cyclosome (APC/C) activity upon activation of the spindle assembly checkpoint (SAC). The first pathway involves the phosphorylation of Mad2, a component of the core mitotic check complex (MCC), by MAPK Sty1, which enhances the tight binding of MCC to APC/C. The second pathway involves MAPK Pmk1 phosphorylation of Slp1Cdc20, the fission yeast homologue of Cdc20 and the co-activator of APC/C, which promotes the degradation of Slp1Cdc20. Both phosphorylation events are required to sustain mitotic arrest in response to spindle defects. These results clarified a detailed regulation cascade of the ubiquitous MAPK signaling in spindle checkpoint activation, APC/C inhibition and anaphase entry, which is vital for accurate chromosome segregation and cell viability.