bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does sports participation increase risk in patients with long QT syndrome? Results from a large French cohort
Authors: Davydoff Caroline , Andorin Antoine , Minois Damien , Arnaud Marine , Minier Mathilde , Sacher Frédéric , Martins Raphael , Clementy Nicolas , Gourraud Jean Baptiste , Probst Vincent 
Published: March 2022

Abstract

Aims
Sports practice, especially in competition, is usually restrained in patients diagnosed with long QT syndrome (LQTS). Although data are scarce, a low incidence of cardiac arrhythmic events (CAEs) during sports practice is reported. We aim to evaluate the incidence of CAE during sports practice in LQTS patients.

Methods and results
All consecutive patients above 18 years of age diagnosed with LQTS and prospectively followed at the referral centre for inherited arrhythmia syndrome received a survey to retrospectively assess their sports practice prior to and after the diagnosis of LQTS. Two hundred and forty-six patients were included (57% females). The median age was 43 years, and the median QTc was 457 ms (428; 482). Patients reported a total of 4092 years [1376 (34%) after diagnosis] of sports practice: 2905 (77%) [1138 (39%) after diagnosis] years of leisure practice and 1187 (23%) [238 (20%) after diagnosis] years of competitive practice. One hundred and eighty (73%) patients practiced sport prior to the diagnosis of LQTS and 170 (69%) after. Prior to the diagnosis, four (2%) patients presented a CAE during leisure sports practice and one during competition. After diagnosis, only one patient presented a CAE, appropriately treated by an implantable cardioverter defibrillator discharge, in the context of beta-blocker non-compliance. The CAE event rate was 0.0007 events/year in the 1376 years of total sports practice after the diagnosis of LQTS.

Conclusion
After the diagnosis of LQTS, the occurrence of CAE is very low during sports practice, even in competitive practice. There was no CAE in patients properly treated with beta-blocker therapy with good compliance.
Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols
Authors: Rigou Sofia , Christo-Foroux Eugène , Santini Sébastien , Goncharov Artemiy , Strauss Jens , Grosse Guido , Fedorov Alexander N , Labadie Karine , Abergel Chantal , Claverie Jean-Michel 
Published: March 2022

AbstractIn the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 1011 total bp) were assembled (525 313 contigs &gt; 5 kb), their encoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.
Hnrnpul1 controls transcription, splicing, and modulates skeletal and limb development in vivo
Authors: Blackwell Danielle L , Fraser Sherri D , Caluseriu Oana , Vivori Claudia , Tyndall Amanda V , Lamont Ryan E , Parboosingh Jillian S , Innes A Micheil , Bernier François P , Childs Sarah J 
Published: March 2022

AbstractMutations in RNA-binding proteins can lead to pleiotropic phenotypes including craniofacial, skeletal, limb, and neurological symptoms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are involved in nucleic acid binding, transcription, and splicing through direct binding to DNA and RNA, or through interaction with other proteins in the spliceosome. We show a developmental role for Hnrnpul1 in zebrafish, resulting in reduced body and fin growth and missing bones. Defects in craniofacial tendon growth and adult-onset caudal scoliosis are also seen. We demonstrate a role for Hnrnpul1 in alternative splicing and transcriptional regulation using RNA-sequencing, particularly of genes involved in translation, ubiquitination, and DNA damage. Given its cross-species conservation and role in splicing, it would not be surprising if it had a role in human development. Whole-exome sequencing detected a homozygous frameshift variant in HNRNPUL1 in 2 siblings with congenital limb malformations, which is a candidate gene for their limb malformations. Zebrafish Hnrnpul1 mutants suggest an important developmental role of hnRNPUL1 and provide motivation for exploring the potential conservation of ancient regulatory circuits involving hnRNPUL1 in human development.
Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators
Authors: Paula Débora Pires , Barros Suellen Karina Albertoni , Pitta Rafael Major , Barreto Marliton Rocha , Togawa Roberto Coiti , Andow David A 
Published: March 2022

Abstract

Background
A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro).

Results
In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43–71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46–273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding.

Conclusions
Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods
Authors: Kim Hui-su , Jeon Sungwon , Kim Yeonkyung , Kim Changjae , Bhak Jihun , Bhak Jong 
Published: March 2022

Abstract

Background
KOREF is the Korean reference genome, which was constructed with various sequencing technologies including long reads, short reads, and optical mapping methods. It is also the first East Asian multiomic reference genome accompanied by extensive clinical information, time-series and multiomic data, and parental sequencing data. However, it was still not a chromosome-scale reference. Here, we updated the previous KOREF assembly to a new chromosome-level haploid assembly of KOREF, KOREF_S1v2.1. Oxford Nanopore Technologies (ONT) PromethION, Pacific Biosciences HiFi-CCS, and Hi-C technology were used to build the most accurate East Asian reference assembled so far.

Results
We produced 705 Gb ONT reads and 114 Gb Pacific Biosciences HiFi reads, and corrected ONT reads by Pacific Biosciences reads. The corrected ultra-long reads reached higher accuracy of 1.4% base errors than the previous KOREF_S1v1.0, which was mainly built with short reads. KOREF has parental genome information, and we successfully phased it using a trio-binning method, acquiring a near-complete haploid-assembly. The final assembly resulted in total length of 2.9 Gb with an N50 of 150 Mb, and the longest scaffold covered 97.3% of GRCh38’s chromosome 2. In addition, the final assembly showed high base accuracy, with &lt;0.01% base errors.

Conclusions
KOREF_S1v2.1 is the first chromosome-scale haploid assembly of the Korean reference genome with high contiguity and accuracy. Our study provides useful resources of the Korean reference genome and demonstrates a new strategy of hybrid assembly that combines ONT's PromethION and PacBio's HiFi-CCS.
Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits
Authors: Tong Hao , Nankar Amol N , Liu Jintao , Todorova Velichka , Ganeva Daniela , Grozeva Stanislava , Tringovska Ivanka , Pasev Gancho , Radeva-Ivanova Vesela , Gechev Tsanko , Kostova Dimitrina , Nikoloski Zoran 
Published: March 2022

Abstract
Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.
Tooth count, untreated caries and mortality in US adults: a population-based cohort study
Authors: Liu Jie , Zong Xiaoyu , Vogtmann Emily , Cao Chao , James Aimee S , Chan Andrew T , Rimm Eric B , Hayes Richard B , Colditz Graham A , Michaud Dominique S , Joshipura Kaumudi J , Abnet Christian C , Cao Yin 
Published: March 2022

Abstract

Background
The link between oral diseases and mortality remains under-explored. We aimed to evaluate the associations between tooth count, untreated caries and risk of all-cause and cause-specific mortality.

Methods
Data on 24 029 adults from the National Health and Nutrition Examination Survey 1988–94/1999–2010, with mortality linkage to the National Death Index to 31 December 2015, were analysed. Baseline total number of permanent teeth and any untreated caries were assessed by trained dental professionals.

Results
During up to 27 years of follow-up, 5270 deaths occurred. Fewer permanent teeth were associated with higher all-cause mortality, including heart disease and cancer mortality (all P &lt;0.05 for trend) but not cerebrovascular disease mortality. For every 10 teeth missing, the multivariable-adjusted hazard ratios (HRs) were 1.13 (95% CI: 1.08 to 1.18) for all-cause, 1.16 (95% CI: 1.05, 1.29) for heart disease and 1.19 (95% CI: 1.09, 1.29) for cancer mortality. Untreated caries was associated with increased all-cause (HR: 1.26, 95% CI: 1.15, 1.39) and heart disease mortality (HR: 1.48, 95% CI: 1.17, 1.88) but not cerebrovascular disease/cancer mortality, after adjusting for tooth count, periodontitis and sociodemographic/lifestyle factors. Compared with those without untreated caries and with 25–28 teeth, individuals with untreated caries and 1–16 teeth had a 53% increased risk of all-cause mortality (HR: 1.53, 95% CI: 1.27, 1.85) and 96 % increased risk of heart disease mortality (HR: 1.96, 95% CI: 1.28, 3.01).

Conclusions
In nationally representative cohorts, fewer permanent teeth and untreated caries were associated with all-cause and heart disease mortality. Fewer teeth were also associated with higher cancer mortality.
Investigating the transparency of reporting in two-sample summary data Mendelian randomization studies using the MR-Base platform
Authors: Woolf Benjamin , Di Cara Nina , Moreno-Stokoe Christopher , Skrivankova Veronika , Drax Katie , Higgins Julian P T , Hemani Gibran , Munafò Marcus R , Davey Smith George , Yarmolinsky James , Richmond Rebecca C 
Published: March 2022

Abstract

Background
Two-sample Mendelian randomization (2SMR) is an increasingly popular epidemiological method that uses genetic variants as instruments for making causal inferences. Clear reporting of methods employed in such studies is important for evaluating their underlying quality. However, the quality of methodological reporting of 2SMR studies is currently unclear. We aimed to assess the reporting quality of studies that used MR-Base, one of the most popular platforms for implementing 2SMR analysis.

Methods
We created a bespoke reporting checklist to evaluate reporting quality of 2SMR studies. We then searched Web of Science Core Collection, PsycInfo, MEDLINE, EMBASE and Google Scholar citations of the MR-Base descriptor paper to identify published MR studies that used MR-Base for any component of the MR analysis. Study screening and data extraction were performed by at least two independent reviewers.

Results
In the primary analysis, 87 studies were included. Reporting quality was generally poor across studies, with a mean of 53% (SD = 14%) of items reported in each study. Many items required for evaluating the validity of key assumptions made in MR were poorly reported: only 44% of studies provided sufficient details for assessing if the genetic variant associates with the exposure (‘relevance’ assumption), 31% for assessing if there are any variant-outcome confounders (‘independence’ assumption), 89% for the assessing if the variant causes the outcome independently of the exposure (‘exclusion restriction’ assumption) and 32% for assumptions of falsification tests. We did not find evidence of a change in reporting quality over time or a difference in reporting quality between studies that used MR-Base and a random sample of MR studies that did not use this platform.

Conclusions
The quality of reporting of two-sample Mendelian randomization studies in our sample was generally poor. Journals and researchers should consider using the STROBE-MR guidelines to improve reporting quality.
Why Does the Omicron Variant Largely Spare Olfactory Function? Implications for the Pathogenesis of Anosmia in Coronavirus Disease 2019
Authors: Butowt Rafal , Bilińska Katarzyna , von Bartheld Christopher 
Published: March 2022

Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 causes much less olfactory dysfunction than the previous variants. There are several potential mechanisms for how omicron may change tissue tropism and spare olfactory function. The new mutations make omicron more hydrophobic and alkaline than previous variants, which may reduce penetration of the mucus layer. Overall, the new mutations minimally change receptor binding affinity, but entry efficiency into host cells is reduced in cells expressing transmembrane serine protease 2 (TMPRSS2). Because the support cells in the olfactory epithelium abundantly express TMPRSS2, these main target cells in the olfactory epithelium may become infected less by the new omicron variant.
3 Continuous Renal Replacement Therapy for the Treatment of Burn Shock: A Post Hoc Analysis
Authors: Basel Anthony P , Britton Garrett W , Evans Jordan , Dado David , Scott Laura L , Grantham Lonnie E , Cancio Leopoldo C , Chung Kevin K 
Published: March 2022

Abstract

Introduction
Burn shock is a consequence of burns that cover ≥20% TBSA and may be complicated by acute kidney injury, which is commonly treated with continuous renal replacement therapy (CRRT). However, early initiation of CRRT has not been clinically evaluated for the treatment of burn shock.

Methods
Data were obtained from the Renal Replacement Therapy in Severe Burns: A Multicenter Observational Study. In that study, baseline (t0) measurements were taken at the time of CRRT initiation and ~24 (t1) and ~48 (t2) hours thereafter. Patients were included in this analysis if they had ≥20% TBSA and began CRRT within 2 days of injury. Patients were categorized as Group A (began CRRT on same day as injury), Group B (began CRRT on day 1 postburn), and Group C (began CRRT on day 2 postburn). Outcomes measured at t0, t1, and t2 and hospital and ICU length of stay (LOS) were analyzed using generalized linear mixed models. Cox proportional hazards models were used to assess survival to hospital discharge (HD). All models were adjusted, e.g. for age, % full thickness, etc. Burn center was included as a random effect.

Results
More than half of the 48 patients included were treated at just 2 burn centers. Timing of CRRT initiation varied by center, with all patients at one center starting CRRT on either the day of injury or the day after injury. Nearly 96% of patients had AKI at CRRT start and, of those, 22 were at stage 1 or 2. Patients generally had severe burns; Group A had more inhalation injuries and higher %TBSA, % full thickness, and Baux scores than Groups B and C. Shock index (SI) was persistently elevated across all 3 time points and did not vary by timing of CRRT initiation (p=0.37). Vasopressor dependency index (VDI) was also not associated with timing of CRRT initiation (p &gt;0.99), although mean VDI for Groups B and C declined over time. For all 3 groups, fluid balance decreased from t0, but there were no differences among the groups (all p &gt;0.30). Survival to HD was better for patients with lower TBSA (i.e. 20-49%) compared to those with TBSA ≥50% (hazard ratio=0.37; 95% CI=0.15-0.91). In contrast, timing of CRRT initiation was not associated with survival (p=0.73). Among patients that survived to HD, the mean hospital LOS was shorter for Groups A (13 days; p=0.01) and B (39 days; p=0.03) compared to Group C (131 days). Mean ICU LOS was also shorter for Groups A (13 days; p=0.01) and B (52 days; p=0.03) than for Group C (168 days).

Conclusions
In this analysis, earlier initiation of CRRT did not improve survival to hospital discharge. Nonetheless, starting patients on CRRT early may be advantageous for reducing ICU and hospital LOS for those patients that do survive.
8 Less Is More: Reconsidering Hourly Urine Output Goals in Burn Resuscitation
Authors: Nosanov Lauren B , Harris Kathryn E , Libraro Kaitlyn M , Lorico Jeremiah P , Heffernan Jamie M , Chang Philip H , Houng Abraham , Gallagher Jim 
Published: March 2022

Abstract

Introduction
Significant morbidity and mortality is seen with high volume burn resuscitations. Surpassing the Ivy Index, defined as 250 milliliters/kilogram (ml/kg), has been correlated with increased incidence of complications such as abdominal compartment syndrome. Cognizance of factors contributing to over-resuscitation can help optimize fluid administration strategies to minimize associated morbidity.

Methods
A single-center Quality Improvement review was performed of all adult (age ≧ 18 years) burn-injured patients presenting to a major metropolitan burn center with burns ≧ 20% total body surface area (TBSA) between 12/2020-8/2021. Those not surviving the first 24 hours were excluded. Patient demographics and injury characteristics were collected, and resuscitation volumes and timing were recorded prospectively. Patients were categorized by whether their initial 24-hour intake exceeded their Ivy Index, and groups were compared to assess factors associated with over-resuscitation.

Results
During the study period 11 patients met inclusion criteria, and one early mortality was excluded. Patients were predominantly male (70.0%), with mean age 49.9±17.4 years. Burns were primarily due to flame injury, with mean TBSA 41.4±18.6%. Patients required resuscitation volumes of 5.9±1.7 ml/kg/TBSA%, with half surpassing their Ivy Index in the first 24 hours. These patients had larger burns (55.1±17.0% v. 27.7±5.1%) with a significantly higher third degree component (41.4±15.8% v. 15.4±15.2%, p = 0.029). None had diagnosed inhalation injury, and none required abdominal decompression for resuscitation-related compartment syndrome. Observed mortality rate was 30.0%. Patients resuscitating beyond their Ivy Index had significantly higher hourly urine output rates (0.96 v. 0.52 ml/kg, p = 0.024), and hourly urine output was significantly higher among non-survivors as compared to survivors (1.10 v. 0.60 ml/kg, p = 0.033).

Conclusions
Patients with severe burn injury are at high risk for over-resuscitation and associated complications. While traditional teaching instructs a goal of hourly urine output of 0.5-1.0 ml/kg, our study shows that patients resuscitated on the higher end of this range were significantly more likely to surpass their Ivy Index and less likely to survive.