bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exercise‐induced histone H3 trimethylation at lysine 27 facilitates the adaptation of skeletal muscle to exercise in mice
Authors: Shimizu Junya , Kawano Fuminori 
Published: June 2022

AbstractHistone H3 trimethylation at lysine 27 (H3K27me3) is known to act as a transcriptionally repressive histone modification via heterochromatin formation. In skeletal muscle, it was also reported that H3K27me3 was enriched at the sites transcriptionally activated by exercise, although the role of H3K27me3 in adaptation to exercise is unknown. In this study, using mouse tibialis anterior muscle, we initially determined the genome‐wide enrichment of RNA polymerase II and histone H3 trimethylation at lysine 4 (H3K4me3) and H3K27me3 using chromatin immunoprecipitation, followed by sequencing analysis. The loci that were transcriptionally upregulated by a single bout of running exercise were marked by both H3K27me3 and H3K4me3, which were also correlated with the distribution of RNA polymerase II. The genes that were not responsive to exercise exhibited high H3K4me3 occupancy, similar to the upregulated genes but with less H3K27me3. Next, we tested the effects of GSK343, a specific inhibitor of enhancer of zeste homologue 2 (EZH2). Unexpectedly, GSK343 administration enhanced the H3K27me3 occupancy at the target loci, leading to the upregulation of gene responses to acute exercise. Administration of GSK343 also facilitated the phenotypic transformation of type IIb to type IIa fibres and the upregulation of AMPK phosphorylation and levels of heat shock protein 70, pyruvate dehydrogenase kinase 4, peroxisome proliferator‐activated receptor γ coactivator‐1α and muscle RING finger 1. Furthermore, in contrast to the accelerated adaptation to exercise by GSK343, administration of the EZH1/2 dual inhibitor valemetostat prevented the changes in the aforementioned parameters after exercise training. These results indicate that exercise‐induced H3K27me3 plays a key role in inducing exercise‐related effects in the skeletal muscle.
imageKey points
Exercise mediates histone H3 trimethylation at lysine 27 (H3K27me3) at transcriptionally upregulated loci in skeletal muscle, but the role of H3K27me3 in the adaptation of skeletal muscle to exercise training is unclear.
Chromatin immunoprecipitation followed by sequencing analysis demonstrated that H3K27me3, in addition to H3K4me3 modifications, is the hallmark of sites showing higher responses to acute exercise.
GSK343, a selective inhibitor of the enhancer of zeste homologue 2 (EZH2), enhanced the gene responses to a single bout of exercise and accelerated the adaptive changes during exercise training in association with myonuclear H3K27me3 accumulation.
Administration of valemetostat, an EZH1/2 dual inhibitor, repressed myonuclear H3K27me3 accumulation during training and caused a failure of adaptive changes.
Exercise‐induced H3K27me3 might play a key role in inducing exercise‐related effects in skeletal muscle.
Global-Position Tracking Control for Three-Dimensional Bipedal Robots Via Virtual Constraint Design and Multiple Lyapunov Analysis
Authors: Gu Yan , Gao Yuan , Yao Bin , Lee C. S. George 
Published: June 2022

Abstract
A safety-critical measure of legged locomotion performance is a robot's ability to track its desired time-varying position trajectory in an environment, which is herein termed as “global-position tracking.” This paper introduces a nonlinear control approach that achieves asymptotic global-position tracking for three-dimensional (3D) bipedal robots. Designing a global-position tracking controller presents a challenging problem due to the complex hybrid robot model and the time-varying desired global-position trajectory. Toward tackling this problem, the first main contribution is the construction of impact invariance to ensure all desired trajectories respect the foot-landing impact dynamics, which is a necessary condition for realizing asymptotic tracking of hybrid walking systems. Thanks to their independence of the desired global position, these conditions can be exploited to decouple the higher-level planning of the global position and the lower-level planning of the remaining trajectories, thereby greatly alleviating the computational burden of motion planning. The second main contribution is the Lyapunov-based stability analysis of the hybrid closed-loop system, which produces sufficient conditions to guide the controller design for achieving asymptotic global-position tracking during fully actuated walking. Simulations and experiments on a 3D bipedal robot with twenty revolute joints confirm the validity of the proposed control approach in guaranteeing accurate tracking.
Prehospital ABC (Age, Bystander and Cardiogram) scoring system to predict neurological outcomes of cardiopulmonary arrest on arrival: post hoc analysis of a multicentre prospective observational study
Authors: Uehara Kazuyuki , Tagami Takashi , Hyodo Hideya , Ohara Toshihiko , Sakurai Atsushi , Kitamura Nobuya , Nakada Taka-aki , Takeda Munekazu , Yokota Hiroyuki , Yasutake Masahiro 
Published: June 2022

BackgroundThere is currently limited evidence to guide prehospital identification of patients with cardiopulmonary arrest on arrival (CPAOA) to hospital who have potentially favourable neurological function. This study aimed to develop a simple scoring system that can be determined at the contact point with emergency medical services to predict neurological outcomes.MethodsWe analysed data from patients with CPAOA using a regional Japanese database (SOS-KANTO), from January 2012 to March 2013. Patients were randomly assigned into derivation and validation cohorts. Favourable neurological outcomes were defined as cerebral performance category 1 or 2. We developed a new scoring system using logistic regression analysis with the following predictors: age, no-flow time, initial cardiac rhythm and arrest place. The model was internally validated by assessing discrimination and calibration.ResultsAmong 4907 patients in the derivation cohort and 4908 patients in the validation cohort, the probabilities of favourable outcome were 0.9% and 0.8%, respectively. In the derivation cohort, age ≤70 years (OR 5.11; 95% CI 2.35 to 11.14), no-flow time ≤5 min (OR 4.06; 95% CI 2.06 to 8.01) and ventricular tachycardia or fibrillation as initial cardiac rhythm (OR 6.66; 95% CI 3.45 to 12.88) were identified as predictors of favourable outcome. The ABC score consisting of Age, information from Bystander and Cardiogram was created. The areas under the receiver operating characteristic curves of this score were 0.863 in the derivation and 0.885 in the validation cohorts. Positive likelihood ratios were 6.15 and 6.39 in patients with scores >2 points and were 11.06 and 17.75 in those with 3 points.ConclusionThe ABC score showed good accuracy for predicting favourable neurological outcomes in patients with CPAOA. This simple scoring system could potentially be used to select patients for extracorporeal cardiopulmonary resuscitation and minimise low-flow time.
Changes in patterns of youth multiple tobacco and/or e-cigarette product use in the US between 2014 and 2020: a multiple-group latent class analysis
Authors: Sun Tianze , Lim Carmen C W , Rutherford Brienna N , Johnson Benjamin , Connor Jason , Gartner Coral E , Hall Wayne D , Leung Janni , Chan Gary 
Published: June 2022

BackgroundMultiple tobacco and e-cigarette product (MTEP) use, the concurrent use of two or more different types of tobacco and/or e-cigarettes products, is common among young people in the US. Changes in patterns of MTEP use among US youth between 2014 and 2020 were identified and the determinants of MTEP use were examined.MethodsFour years of repeated cross-sectional data from the US National Youth Tobacco Survey of middle and high school students from grade 6 to 12 (Ntotal=77 402). Multigroup latent class analysis (LCA) was applied to the data series to allow for simultaneous identification of MTEP use patterns between 2014 and 2020. Logistic regression was used to predict class membership on demographic and tobacco-related variables.FindingsOver the 7-year period, LCA identified three patterns: minimal/non-users (MNU: ~89.8%), mostly occasional e-cigarette and cigarette users (MOEC: ~9%) and polytobacco users (POLY: ~1.2%). From 2014 to 2020, MNU increased from 86.4% to 92% (p<0.05), while MOEC and POLY decreased from 11.2% to 7.9% and from 2.4% to 0.1%, respectively. The probability of regular e-cigarette use increased from 0 to 2.3% among MNU, 6% to 31.9% among MOEC and 29.6% to 67.6% among POLY (p<0.05). In binomial logistic regression, being male, in high school, non-heterosexual, living with someone who uses tobacco at home, having cognitive difficulties, having lower perceptions of tobacco’s danger and exposure to tobacco marketing were associated with greater odds of MOEC and POLY than MNU.ConclusionsThere was an increase in regular e-cigarette use in all three classes, but a corresponding decrease in the proportion of MTEP use. Public health interventions to discourage uptake of e-cigarettes, such as tighter restrictions on marketing to minors, are warranted and there is a need to consider disparities in the determinants of MTEP use.
Better recognition of limnic materials at the great group and subgroup levels of the Organic Order of the Canadian System of Soil Classification
Authors: Saurette Daniel D. , Deragon Raphaël 
Published: June 2022

In the Canadian System of Soil Classification (CSSC), soils of the Organic order are classified at the great group level primarily based on the dominant organic material in the middle tier. The system recognizes four types of organic horizons: fibric (Of), mesic (Om), humic (Oh), and coprogenous earth (Oco), of which only the latter is not recognized at the great group level of the Organic order. Furthermore, at the subgroup level, Limnic subgroups cannot have terric or hydric layers. This is problematic in soils where the middle tier is dominated by limnic materials, and those which have dominantly limnic materials and have a terric layer. We describe 29 soil profiles in Ontario and Quebec, which are either poorly captured in the CSSC or that cannot be classified into the Organic order based on their diagnostic criteria. Based on an analysis of soil survey information in five provinces across Canada, we estimate 32 057 ha of organic soils which potentially contain limnic deposits. In key vegetable-producing areas of Quebec, large organic deposits in agricultural production are subject to peat subsidence and erosion, resulting in shallower depths to underlying coprogenous earth, which is not a suitable medium for crop production. This can potentially have negative effects on crops when mixed with humic materials in the plow layer. Due to these taxonomic and agronomic considerations, we propose the addition of a new great group, Limnisol, and suggest further integration of limnic materials at the subgroup level for the Humisol, Mesisol, and Fibrisol great groups.
Ultracold neutron storage and transport at the PSI UCN source
Authors: Bison G. , Daum M. , Kirch K. , Lauss B. , Ries D. , Schmidt-Wellenburg P. , Zsigmond G. 
Published: June 2022

AbstractEfficient neutron transport is a key ingredient to the performance of ultracold neutron (UCN) sources, important to meeting the challenges placed by high precision fundamental physics experiments. At the Paul Scherrer Institute’s UCN source we have been continuously improving our understanding of the UCN source parameters by performing a series of studies to characterize neutron production and moderation, and UCN production, extraction, and transport efficiency to the beamport. The present study on the absolute UCN transport efficiency completes our previous publications. We report on complementary measurements, namely one on the height-dependent UCN density and a second on the transmission of a calibrated quantity of UCN over a$$\sim 16$$∼16 m long UCN guide section connecting one beamport via the source storage vessel to another beamport. These allow us quantifying and optimizing the performance of the guide system based on extensive Monte Carlo simulations.
Permafrost geomorphology
Authors: Burn Christopher R. , Lewkowicz Antoni G. 
Published: June 2022

Abstract
Permafrost geomorphology came of age in 1965–2000, evolving from a field-based subdiscipline largely based on qualitative observation to one of detailed process measurement, field experimentation, and analytical modelling. In this, the development of permafrost geomorphology exemplified the change in geomorphology as a whole. Fundamental advances were made in understanding the development of ice wedges and ice-wedge polygons and the genesis and growth of closed-system pingos, especially by J. Ross Mackay working in the continuous permafrost terrain of the western Canadian Arctic coastlands. Mackay also investigated moisture movement in relation to the ground thermal regime, which led to seminal insights regarding ground freezing, frost heave, near-surface ground ice development, and hummocky micro-relief. Others used these ideas to examine frost shattering of rocks and the development of sorted circles, as most well known from Svalbard. In the second half of the period, measurements of permafrost creep and deformation of hillslopes and rock glaciers were presented, complementing antecedent measurements of solifluction in the active layer. Significant investigations of thermokarst development foreshadowed the preoccupation with permafrost thaw that now gathers so much attention.
The “Inside” Story on Tumor-Expressed PD-L1
Authors: Hanks Brent A. 
Published: June 2022

Abstract
While the extracellular domain of PD-L1 is well-recognized for playing a critical role in immune evasion by suppressing CD8+ T-cell activity through direct PD-1 interactions, a series of studies has evolved highlighting important functional roles for the PD-L1 cytoplasmic domain in supporting various aspects of tumorigenesis. Kornepati and colleagues contribute to our overall understanding of PD-L1 in tumor biology by describing a link between tumor PD-L1 expression and DNA repair. These studies demonstrate that PD-L1 promotes breast cancer type 1 (BRCA1)–mediated homologous recombination while inhibiting cytosolic DNA sensing, thus suppressing tumor immunogenicity. Notably, these effects could not be reversed with anti-PD-L1 antibodies utilized in the clinic, suggesting that pharmacologic agents promoting PD-L1 degradation may be a more effective treatment strategy for select tumors. Studies that are improving our understanding of the pathways driven by PD-L1 cytoplasmic signaling are providing increased insight into the design of next generation combinatorial immunotherapy strategies.
See related article by Kornepati et al., p. 2156
Fronteiras Religiosas em movimento no Cone-Sul
Authors: Oro Ari Pedro 
Published: June 2022

A characteristic of modernity is the transnationalization of goods and of culture, including religion. This text shows how this occurs in the Cone-Sul involving Afro-Brazilian Religions and Brazilian Neo-Pentecostal churches which spread out from Rio Grande do Sul accross national borders to neighboring countries in the La Plata region. After a consideration of the empirical data available about the expansion of these two religious groups to Argentina and Uruguay, we will review explanations furnished by researchers on this theme.
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs
Authors: Zhong Shanliang , Feng Jifeng 
Published: June 2022

Abstract
Background
Some circular RNAs (circRNAs) can be translated into functional peptides by small open reading frames (ORFs) in a cap-independent manner. Internal ribosomal entry site (IRES) and N6-methyladenosine (m6A) were reported to drive translation of circRNAs. Experimental methods confirming the presence of IRES and m6A site are time consuming and labor intensive. Lacking computational tools to predict ORFs, IRESs and m6A sites for circRNAs makes it harder.

Results
In this report, we present circPrimer 2.0, a Java based software for annotating circRNAs and predicting ORFs, IRESs, and m6A sites of circRNAs. circPrimer 2.0 has a graphical and a command-line interface that enables the tool to be embed into an analysis pipeline.

Conclusions
circprimer 2.0 is an easy-to-use software for annotating circRNAs and predicting translation potential of circRNAs, and freely available at www.bio-inf.cn.
phyloMDA: an R package for phylogeny-aware microbiome data analysis
Authors: Liu Tiantian , Zhou Chao , Wang Huimin , Zhao Hongyu , Wang Tao 
Published: June 2022

Abstract
Background
Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how shared evolutionary history affects the different patterns in host-associated microbial communities.

Results
In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data analysis. It includes the Dirichlet-tree multinomial model for multivariate abundance data, tree-guided empirical Bayes estimation of microbial compositions, and tree-based multiscale regression methods with relative abundances as predictors.

Conclusion
phyloMDA is a versatile and user-friendly tool to analyze microbiome data while incorporating the phylogenetic information and addressing some of the challenges posed by the data.
Whole-genome-sequence-based characterization of an NDM-5-producing uropathogenic Escherichia coli EC1390
Authors: Thuy Tran Thi Dieu , Lu Hsu-Feng , Kuo Pei-Yun , Lin Wei-Hung , Lin Tzu-Ping , Lee Yi-Tzu , Duong Tran Thi Thuy , Wang Ming-Cheng , Lee Yi-Hong , Wen Li-Li , Chen Yu-Chen , Kao Cheng-Yen 
Published: June 2022

Abstract
Background
Urinary tract infection (UTI) is one of the most common outpatient bacterial infections. In this study, we isolated and characterized an extensively-drug resistant (XDR) NDM-5-producing Escherichia coli EC1390 from a UTI patient by using whole-genome sequencing (WGS) in combination with phenotypic assays.

Methods
Antimicrobial susceptibility to 23 drugs was determined by disk diffusion method. The genome sequence of EC1390 was determined by Nanopore MinION MK1C platform. Conjugation assays were performed to test the transferability of EC1390 plasmids to E. coli recipient C600. Phenotypic assays, including growth curve, biofilm formation, iron acquisition ability, and cell adhesion, were performed to characterize the function of EC1390 plasmids.

Results
Our results showed that EC1390 was only susceptible to tigecycline and colistin, and thus was classified as XDR E. coli. A de novo genome assembly was generated using Nanopore 73,050 reads with an N50 value of 20,936 bp and an N90 value of 7,624 bp. WGS analysis showed that EC1390 belonged to the O101-H10 serotype and phylogenetic group A E. coli. Moreover, EC1390 contained 2 conjugative plasmids with a replicon IncFIA (pEC1390-1 with 156,286 bp) and IncFII (pEC1390-2 with 71,840 bp), respectively. No significant difference was observed in the bacterial growth rate in LB broth and iron acquisition ability between C600, C600 containing pEC1390-1, C600 containing pEC1390-2, and C600 containing pEC1390-1 and pEC1390-2. However, the bacterial growth rate in nutrition-limited M9 broth was increased in C600 containing pEC1390-2, and the cell adhesion ability was increased in C600 containing both pEC1390-1 and pEC1390-2. Moreover, these plasmids modulated the biofilm formation under different conditions.

Conclusions
In summary, we characterized the genome of XDR-E. coli EC1390 and identified two plasmids contributing to the antimicrobial resistance, growth of bacteria in a nutrition-limited medium, biofilm formation, and cell adhesion.
Plant organ- and growth stage-diversity of endophytic bacteria with potential as biofertilisers isolated from wheat (Triticum aestivum L.)
Authors: Pang Fahu , Tao Aili , Ayra-Pardo Camilo , Wang Tan , Yu Ziwei , Huang Siliang 
Published: June 2022

Abstract
Background
Chemical fertilisers are extensively used for crop production, which may cause soil deterioration and water pollution. Endophytic bacteria with plant-growth-promoting (PGP) activities may provide a solution to sustainably improve crop yields, including in-demand staples such as wheat. However, the diversity of the PGP endophytic bacteria in wheat across plant organs and growth stages has not been thoroughly characterised.

Results
Here, we report the isolation of endophytic bacteria from root, stem, leaf and seed of three winter wheat varieties at tillering, jointing, heading and seed-filling growth stages that were identified via 16S rRNA gene sequence analysis. Strains were screened for indole-3-acetic acid (IAA) production, potassium and phosphate solubilisation and the ability to grow on a nitrogen-free medium. Strain's capacity to stimulate various plant growth parameters, such as dry root weight, dry above-ground parts weight and plant height, was evaluated in pot trials. A total of 127 strains were randomly selected from 610 isolated endophytic bacterial cultures, representing ten genera and 22 taxa. Some taxa were organ-specific; others were growth-stage-specific. Bacillus aryabhattai, B. stratosphericus, Leclercia adecarboxylata and Pseudomonas oryzihabitans were detected as wheat endophytes for the first time. The IAA production, inorganic phosphorous solubilisation, organic phosphorus solubilisation, potassium solubilisation and growth on N-free medium were detected in 45%, 29%, 37%, 2.4% and 37.8% of the 127 strains, respectively. In pot trials, each strain showed variable effects on inoculated wheat plants regarding the evaluated growth parameters.

Conclusions
Wheat endophytic bacteria showed organ- and growth-stage diversity, which may reflect their adaptations to different plant tissues and seasonal variations, and differed in their PGP abilities. Bacillus was the most predominant bacterial taxa isolated from winter wheat plants. Our study confirmed wheat root as the best reservoir for screening endophytic bacteria with potential as biofertilisers.