bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inconsistent Global Kinetic Energy Spectra in Reanalyses and Models
Authors: Aaron Wang Jih-Wang , Sardeshmukh Prashant D. 
Published: May 2021

AbstractGlobal upper tropospheric kinetic energy (KE) spectra in several global atmospheric circulation datasets are examined. The datasets considered include the ERA-Interim, JRA-55, and ERA5 reanalyses and two versions of NOAA-GFS analyses at horizontal resolutions ranging from 0.7° to 0.12°. The mesoscale portions of the spectra are found to be highly inconsistent. This is shown to be mainly due to inconsistencies in the scale-dependent numerical damping and in the large contributions to the global mesoscale KE from the KE in convective regions and near orography.The spectra also generally have a steeper mesoscale slope than the -5/3 slope of the observational Nastrom-Gage spectrum pursued at many modeling centers. The sensitivity of the slope in global models to 1) stochastically perturbing diabatic tendencies and 2) decreasing the horizontal hyper-viscosity coefficient is explored in large ensembles of 10-day forecasts made with the NCEP-GFS (0.7° grid) model. Both changes lead to larger mesoscale KE and a flatter spectral slope. The effect is stronger in the modified hyper-viscosity experiment.These results show that (a) despite assimilating vastly more observations than used in the original Nastrom-Gage studies, current high-resolution global analyses still do not converge to a single “true” global mesoscale KE spectrum, and (b) model KE spectra can be made flatter not just by increasing model resolution but also by perturbing model physics and decreasing horizontal diffusion. Such sensitivities and lack of consensus on the spectral slope also raise the possibility that the true global mesoscale spectral slope may not be a precisely -5/3 slope.
The source of uncertainty in projecting the anomalous western North Pacific anticyclone during El Niño–decaying summers
Authors: Wu Mingna , Zhou Tianjun , Chen Xiaolong 
Published: May 2021

AbstractThe western North Pacific anomalous anticyclone (WNPAC) is a key bridge that links El Niño and East Asian climate variability. Future projections of ENSO-related WNPAC changes under global warming are highly uncertain across climate models. Based on a 40-member ensemble from the Community Earth System Model Large Ensemble (CESM-LE) project, we investigate the effects of internal variability on the El Niño-related WNPAC projection. Here, we first develop a decomposition method to separate the contributions of El Niño amplitude change and non-amplitude change from the leading uncertainty in the El Niño-related WNPAC projection. Based on the decomposition, approximately 23% of the uncertainty in the El Niño-related WNPAC projection is attributed to the El Niño amplitude change, while the remaining 77% is from the non-amplitude change, which is mainly related to the change in the El Niño decaying pace. A larger (smaller) El Niño amplitude can enhance (weaken) the WNPAC through a stronger (weaker) tropical Indian Ocean (TIO) capacitor effect. For non-amplitude change, a faster (slower) El Niño decaying pace can also enhance (weaken) the WNPAC through descending Rossby waves in response to cold sea surface temperature anomalies (SSTA) over the tropical central-eastern Pacific. The decomposition method can be generalized to investigate the sources of uncertainty related to El Niño properties in climate projections and to help improve the understanding of changes in the interannual variability of East Asian-western Pacific climate under global warming.
Extreme Fire Weather Associated with Nocturnal Drying in Elevated Coastal Terrain of California
Authors: Bagley Richard B. , Clements Craig B. 
Published: May 2021

AbstractThe second largest fire shelter deployment in U.S. history occurred in August 2003 during the Devil Fire, which was burning in a remote and rugged region of the San Francisco Bay Area, when relative humidity abruptly dropped in the middle of the night, causing rapid fire growth. Nocturnal drying events in the higher elevations along California’s central coast are a unique phenomenon that poses a great risk to wildland firefighters. Single-digit relative humidity with dewpoints below −25°C is not uncommon during summer nights in this region. To provide the fire management community with knowledge of these hazardous conditions, an event criterion was established to develop a climatology of nocturnal drying and to investigate the synoptic patterns associated with these events. A lower-tropospheric source region of dry air was found over the northeastern Pacific Ocean corresponding to an area of maximum low-level divergence and associated subsidence. This dry air forms above a marine inversion and advects inland overnight with the marine layer and immerses higher-elevation terrain with warm and dry air. An average of 15–20 nocturnal drying events per year occur in elevations greater than 700 m in the San Francisco Bay Area, and their characteristics are highly variable, making them a challenge to forecast.
A Nationwide Survey of COVID-19 Testing in LGBTQ+ Populations in the United States
Authors: Martino Richard J. , Krause Kristen D. , Griffin Marybec , LoSchiavo Caleb , Comer-Carruthers Camilla , Karr Anita G. , Bullock Allie F. , Halkitis Perry N. 
Published: May 2021

Objectives Lesbian, gay, bisexual, transgender, or queer and questioning (LGBTQ+) people and populations face myriad health disparities that are likely to be evident during the COVID-19 pandemic. The objectives of our study were to describe patterns of COVID-19 testing among LGBTQ+ people and to differentiate rates of COVID-19 testing and test results by sociodemographic characteristics. Methods Participants residing in the United States and US territories (N = 1090) aged ≥18 completed an internet-based survey from May through July 2020 that assessed COVID-19 testing and test results and sociodemographic characteristics, including sexual orientation and gender identity (SOGI). We analyzed data on receipt and results of polymerase chain reaction (PCR) and antibody testing for SARS-CoV-2 and symptoms of COVID-19 in relation to sociodemographic characteristics. Results Of the 1090 participants, 182 (16.7%) received a PCR test; of these, 16 (8.8%) had a positive test result. Of the 124 (11.4%) who received an antibody test, 45 (36.3%) had antibodies. Rates of PCR testing were higher among participants who were non–US-born (25.4%) versus US-born (16.3%) and employed full-time or part-time (18.5%) versus unemployed (10.8%). Antibody testing rates were higher among gay cisgender men (17.2%) versus other SOGI groups, non–US-born (25.4%) versus US-born participants, employed (12.6%) versus unemployed participants, and participants residing in the Northeast (20.0%) versus other regions. Among SOGI groups with sufficient cell sizes (n > 10), positive PCR results were highest among cisgender gay men (16.1%). Conclusions The differential patterns of testing and positivity, particularly among gay men in our sample, confirm the need to create COVID-19 public health messaging and programming that attend to the LGBTQ+ population.
Sedentary Behaviour Among Male Adolescents in Sagamu, Southwest Nigeria
Authors: Odusoga Oluwatosin B. , Sholeye Oluwafolahan O. 
Published: May 2021

Background Sedentary behaviour (SB) is a leading risk factor for development of non-communicable diseases (NCDs) and associated morbidity worldwide. Several studies have reported a high prevalence of sedentary behaviour among adolescents in developing countries with a male preponderance. The Nigerian male adolescent is similarly faced with lifestyle challenges as his counterparts in other countries. Aim This study determined the pattern, knowledge and factors associated with sedentary behaviour among male adolescents in Sagamu, Nigeria. Method A cross-sectional study was carried out among 330 in-school male adolescents in Sagamu, selected via multi-stage sampling technique. Data were collected using a semi-structured, self-administered questionnaire and analyzed using IBM SPSS version 20. Relevant descriptive and inferential statistics were calculated, with p < .05. Participation was fully voluntary and strict confidentiality was ensured. Result The mean age of respondents was 15.9 ± 1.4 years; 86.9% of respondents were aged 15-19years. About 94.8% of sedentary respondents had poor knowledge. Over 90% of respondents were sedentary. Screen-based behaviour (79%) contributed more to respondents’ pattern of SB while using a tablet or a smart phone (23.6%) singularly contributed the largest to sedentariness. SB was associated with motorized transport ( p = .038), smoking ( p ≤ .001) and central obesity status ( p = .040) but not with socio-demographic characteristics and alcohol intake. Conclusion Knowledge of SB was poor among respondents. The prevalence of sedentary behaviour was high and associated with central obesity, smoking and motorized transport. School-based interventions including health education, should be initiated to reduce the risk of developing NCDs.
Cardiovascular Health in Individuals with Exceptional Longevity Residing in Arkansas
Authors: Mize Brandi M. , Duke Brandon , Pangle Amanda K. , Wei Jeanne Y. , Azhar Gohar 
Published: May 2021

Cardiovascular disease is a common comorbidity associated with an aging population. However, there is a unique group of individuals whose age-defying qualities are still being investigated. This retrospective chart review analyzed various cardiac and metabolic health parameters to characterize the prevalence of heart failure and metabolic derangements in individuals aged 90 years old or older in central Arkansas. Only 236 of the 291 patients in our study cohort had blood pressures recorded. Of these, 50% had systolic blood pressures ≥140 mmHg. Additionally, 77% had pulse pressures ≥50 mmHg. Of the 96 patients with BNP data, 44% had values ≥300 pg/mL. There was a slight positive correlation between aging and HDL cholesterol, while there was a negative correlation between aging and both total cholesterol and LDL cholesterol. A majority of our patients had both elevated systolic blood pressures and elevated pulse pressures. A majority also had high BNP values, indicative of some degree of heart failure. Additionally, atrial fibrillation was a common arrhythmia identified on EKG. However, these oldest of the old patients had fewer documented metabolic derangements. These findings lay important groundwork for further investigation into lifestyle and genetic components that allow them to live exceptionally long with such comorbidities.
Biomechanical Evaluation of a New Fixation Method for Stabilization of Sagittal Split Ramus Osteotomy After Mandibular Advancement
Authors: Kuik Karel , Ho Jean Pierre T. F. , Klop Cornelis , de Ruiter Maurits H. T. , Kleverlaan Cornelis J. , de Lange Jan , Hoekema Aarnoud 
Published: May 2021

Study Design: Biomechanical in vitro study. Mandibular advancement after sagittal split ramus osteotomy (SSRO) is a common procedure in orthognathic surgery. Several fixation methods are used for stabilization of SSRO. Objective: The aim of this study was to compare a new fixation method (gridplate) with more contemporary applied methods of fixation. Material and Methods: In this study, 50 polyurethane hemimandibles with a prefabricated SSRO were used as specimens. All hemimandibles were advanced by 8 mm and divided into 5 groups with different fixation methods: (A) one 4-hole miniplate with 4 monocortical screws; (B) two 4-hole miniplates with 8 monocortical screws; (C) one 4-hole miniplate with 4 monocortical screws and 1 bicortical screw in the retromolar area (hybrid method); (D) 3 bicortical screws in an inverted-L pattern; and (E) one 8-hole gridplate with 8 monocortical screws. Loads in newtons were recorded at displacements of the mandibular incisive edge at 1 mm, 3 mm and 5 mm. Results: Fixation with 3 bicortical screws and the gridplate presented the most stability, followed by two 4-hole miniplates. Fixation with the hybrid method or the single miniplate showed the least stability. Conclusion: According to the results of this study, the 8-hole gridplate design appears a sufficient fixation method regarding stabilization of SSRO with larger mandibular advancement.
Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database
Authors: Srivastava Kshitij , Fratzscher Anne-Sophie , Lan Bo , Flegel Willy Albert 
Published: May 2021

Abstract
Background
Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available.

Study design and methods
Phased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm.

Results
We confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing.

Conclusions
Tracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene.
Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite
Authors: Cassan Océane , Lèbre Sophie , Martin Antoine 
Published: May 2021

AbstractBackgroundHigh-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience. Although existing solutions usually provide adequate procedures for normalization, exploration or differential expression, more advanced features, such as gene clustering or regulatory network inference, often miss or do not reflect current state of the art methodologies.ResultsWe developed here a user interface called DIANE (Dashboard for the Inference and Analysis of Networks from Expression data) designed to harness the potential of multi-factorial expression datasets from any organisms through a precise set of methods. DIANE interactive workflow provides normalization, dimensionality reduction, differential expression and ontology enrichment. Gene clustering can be performed and explored via configurable Mixture Models, and Random Forests are used to infer gene regulatory networks. DIANE also includes a novel procedure to assess the statistical significance of regulator-target influence measures based on permutations for Random Forest importance metrics. All along the pipeline, session reports and results can be downloaded to ensure clear and reproducible analyses.ConclusionsWe demonstrate the value and the benefits of DIANE using a recently published data set describing the transcriptional response of Arabidopsis thaliana under the combination of temperature, drought and salinity perturbations. We show that DIANE can intuitively carry out informative exploration and statistical procedures with RNA-Seq data, perform model based gene expression profiles clustering and go further into gene network reconstruction, providing relevant candidate genes or signalling pathways to explore. DIANE is available as a web service (https://diane.bpmp.inrae.fr), or can be installed and locally launched as a complete R package.
Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads
Authors: Commichaux Seth , Javkar Kiran , Ramachandran Padmini , Nagarajan Niranjan , Bertrand Denis , Chen Yi , Reed Elizabeth , Gonzalez-Escalona Narjol , Strain Errol , Rand Hugh , Pop Mihai , Ottesen Andrea 
Published: May 2021

Abstract
Background
Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantially reduce the amount of culturing needed before a high quality genome can be recovered. Highly accurate short read data is analyzed for single nucleotide polymorphisms and multi-locus sequence types to differentiate strains but cannot span many genomic repeats, resulting in highly fragmented assemblies. Long reads can span repeats, resulting in much more contiguous assemblies, but have lower accuracy than short reads.

Results
We evaluated the accuracy of Listeria monocytogenes assemblies from enrichments (quasimetagenomes) of naturally-contaminated ice cream using long read (Oxford Nanopore) and short read (Illumina) sequencing data. Accuracy of ten assembly approaches, over a range of sequencing depths, was evaluated by comparing sequence similarity of genes in assemblies to a complete reference genome. Long read assemblies reconstructed a circularized genome as well as a 71 kbp plasmid after 24 h of enrichment; however, high error rates prevented high fidelity gene assembly, even at 150X depth of coverage. Short read assemblies accurately reconstructed the core genes after 28 h of enrichment but produced highly fragmented genomes. Hybrid approaches demonstrated promising results but had biases based upon the initial assembly strategy. Short read assemblies scaffolded with long reads accurately assembled the core genes after just 24 h of enrichment, but were highly fragmented. Long read assemblies polished with short reads reconstructed a circularized genome and plasmid and assembled all the genes after 24 h enrichment but with less fidelity for the core genes than the short read assemblies.

Conclusion
The integration of long and short read sequencing of quasimetagenomes expedited the reconstruction of a high quality pathogen genome compared to either platform alone. A new and more complete level of information about genome structure, gene order and mobile elements can be added to the public health response by incorporating long read analyses with the standard short read WGS outbreak response.
In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process
Authors: Ranade Sonali Sachin , Egertsdotter Ulrika 
Published: May 2021

AbstractBackgroundSomatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation.ResultsCurrent work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g.BBM,LEC1,LEC1-LIKE, LEC2andFUSCA3, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes fromArabidopsis thalianawere used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genusPicea(Picea abies) andPinus(Pinus taeda), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences ofArabidopsis thalianaproteins and phylogenetic analysis (Phylogeny.fr).ConclusionsThis in silico analysis suggests absence ofLEC2inPicea abiesandPinus taeda, the conifer species whose genomes have been sequenced. Based on available sequence data to date,LEC2was also not detected in the other conifer species included in the study.LEC2is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack ofLEC2are discussed.
Pulmonary embolism originating from germ cell tumor causes severe left ventricular dysfunction in a healthy young adult with full recovery: a case report
Authors: Elenizi Khaled , Alharthi Rasha , Galinier Michel 
Published: May 2021

Abstract
Background
Cancer associated thrombosis is recognized. However, pulmonary embolism (PE) from testicular cancer is rarely reported. Right ventricular (RV) function and PE are closely related. The RV cannot cope with a sudden increase in afterload because of PE and this causes dysfunction, but isolated left ventricular dysfunction in this context is not reported in the literature.

Case presentation
We report an unusual association of pulmonary embolism and testicular germ cell tumor complicating severe left heart failure and full recovery at three months follow up in a 33-year-old patient with no prior medical history. The diagnosis was made after comprehensive history taking and physical examination with the help of different imaging modalities. Full recovery was achieved after optimal medical therapy.

Conclusion
This case raises our awareness of unusual clinical presentation as we report associated left-sided severe heart failure in cancer-related pulmonary embolism. Pulmonary embolism in healthy young adults warrant in-depth causative exploration.