bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative delimitation of radiant belt toward lake of lake-terrestrial ecotone
Authors: Cai Tian-yi , Ye Chun , Li Chun-hua , Zhang Fan , Wei Wei-wei 
Published: April 2022

Abstract
Background
Lake-terrestrial ecotone is a transition zone between terrestrial and aquatic ecosystems. Linking land and lake, it is thus highly sensitive and vulnerable to disturbances. It includes three parts, namely, radiant belt toward land, shoreline zone and radiant belt toward lake. Extending from multi-year average low water level line to open water, radiant belt toward lake is a key part of lake-terrestrial ecotone. However, the delimitation method for radiant belt toward is unsolved, which is a big obstacle to protecting lake-terrestrial ecotone effectively. Wave is a major hydrodynamic factor in lakes, especially large shallow lakes. For linking landward and waterward directions, the boundary of radiant belt toward lake may be affected by waves. Hence, exampled as Lake Taihu, this research was carried out from wave perspective.

Results
In July 2021, a total of 12 species aquatic macrophyte were collected, including 3 species of floating-leaved and 9 submerged macrophyte within radiant belt toward lake of Lake Taihu. Aquatic macrophyte were incorporated into calibrated wave models driven by constant winds via MIKE21 SW. Wave height attenuation was successfully simulated, ranging − 0.19% ~ 8.89% under eastern-wind condition and − 0.08% ~ 23.37% under western-wind condition. In general, wave height gradually attenuates from shore to water. The abrupt change point in relative wave height was used as the boundary of the radiant belt toward lake. A total of 26 sampling lines from bank to water around the whole lake of Lake Taihu were set, ranging 701 ~ 2155 m. Based on the setups of sampling lines, the delimitation range of Lake Taihu is about 1 ~ 2 km.

Conclusions
A novel approach was developed for quantitative delimitation of radiant belt toward lake. Both wind forcing and aquatic vegetation has slight impact on results of delimitation, indicating the feasibility of this approach. It determines a theoretical boundary of lake-terrestrial ecotone, which is helpful to a more precise protection and restoration of large shallow lakes. Moreover, it could provide a potential method for quantitative delimitation for large shallow lakes with similar conditions.
COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data
Authors: Phelan Jody , Deelder Wouter , Ward Daniel , Campino Susana , Hibberd Martin L. , Clark Taane G. 
Published: April 2022

Abstract
Background
SARS-CoV-2 virus sequencing has been applied to track the COVID-19 pandemic spread and assist the development of PCR-based diagnostics, serological assays, and vaccines. With sequencing becoming routine globally, bioinformatic tools are needed to assist in the robust processing of resulting genomic data.

Results
We developed a web-based bioinformatic pipeline (“COVID-Profiler”) that inputs raw or assembled sequencing data, displays raw alignments for quality control, annotates mutations found and performs phylogenetic analysis. The pipeline software can be applied to other (re-) emerging pathogens.

Conclusions
The webserver is available at http://genomics.lshtm.ac.uk/. The source code is available at https://github.com/jodyphelan/covid-profiler.
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach
Authors: Yang Ming-Ren , Wu Yu-Wei 
Published: April 2022

Abstract
Background
Predicting which pathogens might exhibit antimicrobial resistance (AMR) based on genomics data is one of the promising ways to swiftly and precisely identify AMR pathogens. Currently, the most widely used genomics approach is through identifying known AMR genes from genomic information in order to predict whether a pathogen might be resistant to certain antibiotic drugs. The list of known AMR genes, however, is still far from comprehensive and may result in inaccurate AMR pathogen predictions. We thus felt the need to expand the AMR gene set and proposed a pan-genome-based feature selection method to identify potential gene sets for AMR prediction purposes.

Results
By building pan-genome datasets and extracting gene presence/absence patterns from four bacterial species, each with more than 2000 strains, we showed that machine learning models built from pan-genome data can be very promising for predicting AMR pathogens. The gene set selected by the eXtreme Gradient Boosting (XGBoost) feature selection approach further improved prediction outcomes, and an incremental approach selecting subsets of XGBoost-selected features brought the machine learning model performance to the next level. Investigating selected gene sets revealed that on average about 50% of genes had no known function and very few of them were known AMR genes, indicating the potential of the selected gene sets to expand resistance gene repertoires.

Conclusions
We demonstrated that a pan-genome-based feature selection approach is suitable for building machine learning models for predicting AMR pathogens. The extracted gene sets may provide future clues to expand our knowledge of known AMR genes and provide novel hypotheses for inferring bacterial AMR mechanisms.
Celastrol mitigates staphyloxanthin biosynthesis and biofilm formation in Staphylococcus aureus via targeting key regulators of virulence; in vitro and in vivo approach
Authors: Yehia Fatma Al-zahraa A. , Yousef Nehal , Askoura Momen 
Published: April 2022

Abstract
Background
Staphylococcus aureus is a leading cause of human infections. The spread of antibiotic-resistant staphylococci has driven the search for novel strategies to supersede antibiotics use. Thus, targeting bacterial virulence rather than viability could be a possible alternative.

Results
The influence of celastrol on staphyloxanthin (STX) biosynthesis, biofilm formation, antibiotic susceptibility and host pathogenesis in S. aureus has been investigated. Celastrol efficiently reduced STX biosynthesis in S. aureus. Liquid chromatography-mass spectrometry (LC–MS) and molecular docking revealed that celastrol inhibits STX biosynthesis through its effect on CrtM. Quantitative measurement of STX intermediates showed a significant pigment inhibition via interference of celastrol with CrtM and accumulation of its substrate, farnesyl diphosphate. Importantly, celastrol-treated S. aureus was more sensitive to environmental stresses and human blood killing than untreated bacteria. Similarly, inhibition of STX upon celastrol treatment rendered S. aureus more susceptible to membrane targeting antibiotics. In addition to its anti-pigment capability, celastrol exhibits significant anti-biofilm activity against S. aureus as indicated by crystal violet assay and microscopy. Celastrol-treated cells showed deficient exopolysaccharide production and cell hydrophobicity. Moreover, celastrol markedly synergized the action of conventional antibiotics against S. aureus and reduced bacterial pathogenesis in vivo using mice infection model. These findings were further validated using qRT-PCR, demonstrating that celastrol could alter the expression of STX biosynthesis genes as well as biofilm formation related genes and bacterial virulence.

Conclusions
Celastrol is a novel anti-virulent agent against S. aureus suggesting, a prospective therapeutic role for celastrol as a multi-targeted anti-pathogenic agent.
Cryopreservation of vegetative cells and zygotes of the multicellular volvocine green alga Gonium pectorale
Authors: Nozaki Hisayoshi , Mori Fumi , Tanaka Yoko , Matsuzaki Ryo , Yamaguchi Haruyo , Kawachi Masanobu 
Published: April 2022

Abstract
Background
Colonial and multicellular volvocine green algae have been extensively studied recently in various fields of the biological sciences. However, only one species (Pandorina morum) has been cryopreserved in public culture collections.

Results
Here, we investigated conditions for cryopreservation of the multicellular volvocine alga Gonium pectorale using vegetative colonies or cells and zygotes. Rates of vegetative cell survival in a G. pectorale strain after two-step cooling and freezing in liquid nitrogen were compared between different concentrations (3% and 6%) of the cryoprotectant N,N-dimethylformamide (DMF) and two types of tubes (0.2-mL polymerase chain reaction tubes and 2-mL cryotubes) used for cryopreservation. Among the four conditions investigated, the highest rate of survival [2.7 ± 3.6% (0.54–10%) by the most probable number (MPN) method] was obtained when 2.0-mL cryotubes containing 1.0 mL of culture samples with 6% DMF were subjected to cryogenic treatment. Using these optimized cryopreservation conditions, survival rates after freezing in liquid nitrogen were examined for twelve other strains of G. pectorale and twelve strains of five other Gonium species. We obtained ≥ 0.1% MPN survival in nine of the twelve G. pectorale strains tested. However, < 0.1% MPN survival was detected in eleven of twelve strains of five other Gonium species. In total, ten cryopreserved strains of G. pectorale were newly established in the Microbial Culture Collection at the National Institute for Environmental Studies. Although the cryopreservation of zygotes of volvocine algae has not been previously reported, high rates (approximately 60%) of G. pectorale zygote germination were observed after thawing zygotes that had been cryopreserved with 5% or 10% methanol as the cryoprotectant during two-step cooling and freezing in liquid nitrogen.

Conclusions
The present study demonstrated that cryopreservation of G. pectorale is possible with 6% DMF as a cryoprotectant and 1.0-mL culture samples in 2.0-mL cryotubes subjected to two-step cooling in a programmable freezer.
Upregulation of GLRs expression by light in Arabidopsis leaves
Authors: Hebda Anna , Liszka Aleksandra , Lewandowska Aleksandra , Lyczakowski Jan J. , Gabryś Halina , Krzeszowiec Weronika 
Published: April 2022

AbstractBackgroundGlutamate receptor-like (GLR) channels are plant homologs of iGluRs, animal ionotropic glutamate receptors which participate in neurotransmission. GLRs mediate plant adaptive processes and photomorphogenesis. Despite their contribution to light-dependent processes, signaling mechanisms that modulateGLRresponse to light remain unknown. Here we show that leaf expression of 7 out of 20 ArabidopsisGLRsis significantly up-regulated by monochromatic irradiation.ResultsOur data indicates that both red and blue light stimulate the expression of selectedAtGLRs. Using a photosynthesis inhibitor and different irradiation regimes, we demonstrated that retrograde signaling from photosystem II is unlikely to be involved in light-dependentGLRup-regulation. Analysis of transcriptional patterns in mutants of key photoreceptors allowed us to observe that both phytochromes and cryptochromes are likely to be involved in the control of light-dependent up-regulation ofAtGLRexpression, with phytochromes playing a clearly dominating role in this process.ConclusionsIn mature Arabidopsis leaves, phytochromes, assisted by cryptochromes, mediate light-driven transcriptional up-regulation of several genes encoding GLR proteins. Since GLRs are known to be involved in a wide range of plant developmental processes our results provide mechanistic insight into how light may influence plant growth and development.
Transcriptome profiling of flower buds of male-sterile lines provides new insights into male sterility mechanism in alfalfa
Authors: Xu Bo , Wu Rina , Shi Fengling , Gao Cuiping , Wang Jia 
Published: April 2022

Abstract
Background
The use of heterosis to produce hybrid seeds is a challenge to breeding for improved crop yield. In previous studies, we isolated a male sterile alfalfa hybrid and successfully obtained a genetically stable alfalfa male sterile line through backcrossing, henceforth named MS-4. In this study, we used RNA-seq technology to analyze the transcriptome profiles of the male sterile line (MS-4) and the male fertile line (MF) of alfalfa to elucidate the mechanism of male sterility.

Results
We screened a total of 11,812 differentially expressed genes (DEGs) from both MS-4 and MF lines at three different stages of anther development. Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that these DEGs are mainly involved in processes such as energy metabolism, lipid and amino acid metabolism, carbohydrate metabolism, in addition to cell synthesis and aging. The results from protein–protein interaction (PPI) network analysis showed that the ribosomal protein (MS.Gene25178) was the core gene in the network. We also found that transcriptional regulation was an influential factor in the development of anthers.

Conclusions
Our findings provide new insights into understanding of the fertility changes in the male sterile (MS-4) of alfalfa.
De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal
Authors: Suranjika Sandhya , Pradhan Seema , Nayak Soumya Shree , Parida Ajay 
Published: April 2022

Abstract
Background
The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers.

Results
We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis.

Conclusions
The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement.
Ropivacaine inhibits wound healing by suppressing the proliferation and migration of keratinocytes via the PI3K/AKT/mTOR Pathway
Authors: Wu Xiaoyang , Sun Quanyu , He Simeng , Wu Ya , Du Shihan , Gong Lirong , Yu Jianbo , Guo Haifeng 
Published: April 2022

AbstractBackgroundAfter surgery, millions of people suffer from delayed healing or wound dehiscence with subsequent severe complications, even death. Previous studies have reported that ropivacaine exhibits anti-proliferative and anti-migratory activities on numerous cells. Whether ropivacaine is able to influence the proliferation and migration of keratinocytes is still unclear. This study aimed to investigate the effect of ropivacaine on keratinocytes and its underlying molecular mechanism.MethodsAdult male Sprague–Dawley rats were allocated to establish wound healing models with or without 0.75% ropivacaine treatment and assessed the epidermal thickness by HE staining. HaCaT cells were cultured to evaluate the effect of ropivacaine on wound healing. The cell proliferation, apoptosis status and migration were detected in vitro. Moreover, western blotting was used to examine expression to with PI3K/AKT/mTOR signaling pathways for molecular studies and the changes in inflammatory factors (IL-6, IL-10, TNF-α) were detected by ELISA.ResultsIn the present study, we found that ropivacaine delayed wound closure in vivo. In vitro experiments, it was demonstrated that ropivacaine significantly inhibited the proliferation and migration of HaCaT cells via the suppression of PI3K/AKT/mTOR signaling pathway. Activation of PI3K/AKT/mTOR signaling pathway reversed the effects of ropivacaine on the proliferation and migration of HaCaT cells. Furthermore, ropivacaine contributed to the release of pro-inflammatory cytokines (IL-6 and TNF-α) and inhibited the secretion of anti-inflammatory cytokines of keratinocytes (IL-10).ConclusionsOur research demonstrated that ropivacaine treatment showed a more decreased wound closure rate. Mechanistically, we found that ropivacaine suppressed the proliferation and migration of keratinocytes and altered the expression of cytokines by inhibiting PI3K/AKT/mTOR pathway.
How parents express their worry in calls to a medical helpline: a mixed methods study
Authors: Gren Caroline , Pedersen Maria Kjøller , Hasselager Asbjørn Børch , Folke Fredrik , Ersbøll Annette Kjær , Cortes Dina , Egerod Ingrid , Gamst-Jensen Hejdi 
Published: April 2022

AbstractBackgroundTelephone triage is used globally in out-of-hours primary care, to prioritize who needs urgent assessment. Even though children rarely are severely ill, calls about sick children are among the most prevalent, mainly due to parental worry. Pediatric calls are considered challenging, as the call-handler must rely on parents’ second-hand information. We aimed to investigate if parents’ worry can be used as a predictor of severe illness, and if the content of the calls varies between different grades of worry.MethodsIn a convergent mixed methods study design we asked patients to rate their degree-of-worry before talking to a call-handler. We used quantitative data of degree-of-worry, triage- and patient outcome in pediatric calls (n = 2857), and the qualitative content from 54 calls with subsequent hospitalization ≥24 h.ResultsHigh degree-of-worry was associated with hospitalization ≥24 h (OR 3.33, 95% CI 1.53–7.21). Qualitative findings both confirmed and expanded knowledge of degree-of-worry. Worry was the predominant cause for contact overall, and was mainly triggered by loss-of-control. In calls with high degree-of-worry, the prevalence of loss-of-control was especially high, and the parents had additionally often contacted healthcare services recently. Parents with a foreign accent often rated their worry as high, and these callers were often ignored or interrupted. Calls with low degree-of-worry seemed to occur early during the disease.ConclusionHigh degree of parental worry was associated with severe illness. At the end of calls, call-handlers should ensure that the parent has regained control of the situation to reach increased reassurance and to prevent renewed unnecessary contact. Safety-netting is crucial, as many parents made contact early during the illness and deterioration may develop later. The scoring of parental degree-of-worry may be used as an indicator of potentially severe illness and can easily be implemented at out-of-hours call-centers globally.Trial registrationOriginal study registered atclinicaltrials.gov(NCT02979457).
Combined impact of lifestyle-related factors on total mortality among the elder Chinese: a prospective cohort study
Authors: Lian Zhiwei , Zhu Chunsu , Yuan Haowen , Chen Ying 
Published: April 2022

Abstract
Background
The combined impact of healthy lifestyle factors on total mortality among elder Chinese is unclear. This study aimed to investigate the overall impact of lifestyle factors on total mortality in a senior Chinese population, and determine whether these associations were consistent in the presence of different characteristics, including physical comorbidities.

Methods
The Chinese Longitudinal Healthy Longevity Survey (CLHLS) is a large population-based prospective cohort study in 22 of 31 provinces from mainland China. We included 15,163 adults aged ≥65 years recruited from 1998- to 2002 and followed-up until 2014. A healthy lifestyle score was calculated considering five lifestyle factors (exercise, smoking, dietary diversity, body mass index and drinking). The scores ranged from zero to five points and were classified into the following three categories: unhealthy (0-1 point), intermediate (2-3 points) and healthy (4-5 points). Cox proportional hazards regression analyses were used to assess the associations between the combined healthy lifestyle score and total mortality, adjusting for demographic characteristics and physical comorbidities, as appropriate. Stratification analyses and interaction analyses were further performed.

Results
Among the 15,163 participants, the mean age (SD) was 86.2 (11.6) years. During an average follow-up period of 12.5 (SD = 3.9) years, 9655 deaths occurred. The adjusted hazard ratios (HRs) of total mortality decreased as the number of healthy lifestyle factors increased. Compared to the unhealthy lifestyle group, the healthy lifestyle group had a HR and 95% CI of 0.78 and 0.72-0.83. The population attributable risk of total death among those without a healthy lifestyle was 25.2%. A healthier lifestyle pattern was associated with a lower total mortality risk among individuals with different severities of physical comorbidities, although the associations were stronger among those with fatal physical comorbidities (p-interaction < .001).

Conclusions
In this large-scale study, a healthier lifestyle measured by regular exercise participation, never smoking, never drinking, good dietary diversity and normal weight, was inversely associated with total mortality, regardless of physical comorbidity status. These findings support the necessity of multiple lifestyle modifications to prevent premature death in both general elderly populations and those with physical comorbidities.