Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs

Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones.Nevertheless,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.Results Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds.Analysis of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)regions.The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments.Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation.These pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid environments.By examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental adaptation.Finally,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.Conclusions In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude,and frigid environments.Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.

Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

Social-ecological perspective on the suicidal behaviour factors of early adolescents in China:a network analysis

Background In early adolescence,youth are highly prone to suicidal behaviours.Identifying modifiable risk factors during this critical phase is a priority to inform effective suicide prevention strategies.Aims To explore the risk and protective factors of suicidal behaviours(ie,suicidal ideation,plans and attempts)in early adolescence in China using a social-ecological perspective.Methods Using data from the cross-sectional project‘Healthy and Risky Behaviours Among Middle School Students in Anhui Province,China',stratified random cluster sampling was used to select 5724 middle school students who had completed self-report questionnaires in November 2020.Network analysis was employed to examine the correlates of suicidal ideation,plans and attempts at four levels,namely individual(sex,academic performance,serious physical llness/disability,history of self-harm,depression,impulsivity,sleep problems,resilience),family(family economic status,relationship with mother,relationship with father,family violence,childhood abuse,parental mental illness),school(relationship with teachers,relationship with classmates,school-bullying victimisation and perpetration)and social(social support,satisfaction with society).Results In total,37.9%,19.0%and 5.5%of the students reported suicidal ideation,plans and attempts in the past 6 months,respectively.The estimated network revealed that suicidal ideation,plans and attempts were collectively associated with a history of self-harm,sleep problems,childhood abuse,school bullying and victimisation.Centrality analysis indicated that the most influential nodes in the network were history of self-harm and childhood abuse.Notably,the network also showed unique correlates of suicidal ideation(sex,weight=0.60;impulsivity,weight=0.24;family violence,weight=0.17;relationship with teachers,weight=-0.03;school-bullying perpetration,weight=0.22),suicidal plans(social support,weight=-0.15)and suicidal attempts(relationship with mother,weight=-0.10;parental mental llness,weight=0.61).Conclusions This study identified the correlates of suicidal ideation,plans and attempts,and provided practical implications for suicide prevention for young adolescents in China.Firstly,this study highlighted the importance of joint interventions across multiple departments.Secondly,the common risk factors of suicidal ideation,plans and attempts were elucidated.Thirdly,this study proposed target interventions to address the unique influencing factors of suicidal ideation,plans and attempts.

Safety assessment of a novel marine multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 according to phenotype and whole genome-sequencing analysis

The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove microorganisms.Its safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing analysis.Results showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely found.Hyphal morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were annotated.True hyphae and phospholipase were absent.Only one retroelement(Tad1-65_BG)was found.Major biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined thresholds.GXDK6 had no resistance to common antifungal drugs.Virulence enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were absent.Acute toxicity test with mice demonstrated that GXDK6 is safe.GXDK6 has a good reproduction ability in the simulation gastrointestinal tract.GXDK6 also has a strong antioxidant ability,β-glucosidase,and inulinase activity.To sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.

Advances in microfluidic-based DNA methylation analysis

DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation studies to both clinical medicine and scientific research.Microflu-idic chips are excellent carriers for molecular analysis,and their use can provide improvements from multiple aspects.On-chip molecular analysis has received extensive attention owing to its advantages of portability,high throughput,low cost,and high efficiency.In recent years,the use of novel microfluidic chips for DNA methylation analysis has been widely reported and has shown obvious superiority to conventional methods.In this review,wefirst focus on DNA methylation and its applications.Then,we discuss advanced microfluidic-based methods for DNA methylation analysis and describe the great progress that has been made in recent years.Finally,we summarize the advantages that microfluidic technology brings to DNA methylation analysis and describe several challenges and perspectives for on-chip DNA methylation analysis.This review should help researchers improve their understanding and make progress in developing microfluidic-based methods for DNA methylation analysis.

A Review on Sources,Extractions and Analysis Methods of a Sustainable Biomaterial:Tannins

Condensed and hydrolysable tannins are non-toxic natural polyphenols that are a commercial commodity industrialized for tanning hides to obtain leather and for a growing number of other industrial applications mainly to substitute petroleum-based products.They are a definite class of sustainable materials of the forestry industry.They have been in operation for hundreds of years to manufacture leather and now for a growing number of applications in a variety of other industries,such as wood adhesives,metal coating,pharmaceutical/medical applications and several others.This review presents the main sources,either already or potentially commercial of this forestry by-materials,their industrial and laboratory extraction systems,their systems of analysis with their advantages and drawbacks,be these methods so simple to even appear primitive but nonetheless of proven effectiveness,or very modern and instrumental.It constitutes a basic but essential summary of what is necessary to know of these sustainable materials.In doing so,the review highlights some of the main challenges that remain to be addressed to deliver the quality and economics of tannin supply necessary to fulfill the industrial production requirements for some materials-based uses.

Lagrangian coherent structure analysis on transport of Acetes chinensis along coast of Lianyungang,China

Spatial heterogeneity or“patchiness”of plankton distributions in the ocean has always been an attractive and challenging scientific issue to oceanographers.We focused on the accumulation and dynamic mechanism of the Acetes chinensis in the Lianyungang nearshore licensed fishing area.The Lagrangian frame approaches including the Lagrangian coherent structures theory,Lagrangian residual current,and Lagrangian particle-tracking model were applied to find the transport pathways and aggregation characteristics of Acetes chinensis.There exist some material transport pathways for Acetes chinensis passing through the licensed fishing area,and Acetes chinensis is easy to accumulate in the licensed fishing area.The main mechanism forming this distribution pattern is the local circulation induced by the nonlinear interaction of topography and tidal flow.Both the Lagrangian coherent structure analysis and the particle trajectory tracking indicate that Acetes chinensis in the licensed fishing area come from the nearshore estuary.This work contributed to the adjustment of licensed fishing area and the efficient utilization of fishery resources.

Iron and ferritin effects on intensive care unit mortality:A metaanalysis

BACKGROUND The effect of serum iron or ferritin parameters on mortality among critically ill patients is not well characterized.AIM To determine the association between serum iron or ferritin parameters and mortality among critically ill patients.METHODS Web of Science,Embase,PubMed,and Cochrane Library databases were searched for studies on serum iron or ferritin parameters and mortality among critically ill patients.Two reviewers independently assessed,selected,and abstracted data from studies reporting on serum iron or ferritin parameters and mortality among critically ill patients.Data on serum iron or ferritin levels,mortality,and demographics were extracted.RESULTS Nineteen studies comprising 125490 patients were eligible for inclusion.We observed a slight negative effect of serum ferritin on mortality in the United States population[relative risk(RR)1.002;95%CI:1.002-1.004].In patients with sepsis,serum iron had a significant negative effect on mortality(RR=1.567;95%CI:1.208-1.925).CONCLUSION This systematic review presents evidence of a negative correlation between serum iron levels and mortality among patients with sepsis.Furthermore,it reveals a minor yet adverse impact of serum ferritin on mortality among the United States population.

Telomerase-related advances in hepatocellular carcinoma:A bibliometric and visual analysis

BACKGROUND As a critical early event in hepatocellular carcinogenesis,telomerase activation might be a promising and critical biomarker for hepatocellular carcinoma(HCC)patients,and its function in the genesis and treatment of HCC has gained much attention over the past two decades.AIM To perform a bibliometric analysis to systematically assess the current state of research on HCC-related telomerase.METHODS The Web of Science Core Collection and PubMed were systematically searched to retrieve publications pertaining to HCC/telomerase limited to“articles”and“reviews”published in English.A total of 873 relevant publications related to HCC and telomerase were identified.We employed the Bibliometrix package in R to extract and analyze the fundamental information of the publications,such as the trends in the publications,citation counts,most prolific or influential writers,and most popular journals;to screen for keywords occurring at high frequency;and to draw collaboration and cluster analysis charts on the basis of coauthorship and co-occurrences.VOSviewer was utilized to compile and visualize the bibliometric data.RESULTS A surge of 51 publications on HCC/telomerase research occurred in 2016,the most productive year from 1996 to 2023,accompanied by the peak citation count recorded in 2016.Up to December 2023,35226 citations were made to all publications,an average of 46.6 citations to each paper.The United States received the most citations(n=13531),followed by China(n=7427)and Japan(n=5754).In terms of national cooperation,China presented the highest centrality,its strongest bonds being to the United States and Japan.Among the 20 academic institutions with the most publications,ten came from China and the rest of Asia,though the University of Paris Cité,Public Assistance-Hospitals of Paris,and the National Institute of Health and Medical Research(INSERM)were the most prolific.As for individual contributions,Hisatomi H,Kaneko S,and Ide T were the three most prolific authors.Kaneko S ranked first by H-index,G-index,and overall publication count,while Zucman-Rossi J ranked first in citation count.The five most popular journals were the World Journal of Gastroenterology,Hepatology,Journal of Hepatology,Oncotarget,and Oncogene,while Nature Genetics,Hepatology,and Nature Reviews Disease Primers had the most citations.We extracted 2293 keywords from the publications,120 of which appeared more than ten times.The most frequent were HCC,telomerase and human telomerase reverse transcriptase(hTERT).Keywords such as mutational landscape,TERT promoter mutations,landscape,risk,and prognosis were among the most common issues in this field in the last three years and may be topics for research in the coming years.CONCLUSION Our bibliometric analysis provides a comprehensive overview of HCC/telomerase research and insights into promising upcoming research.

Micro segment analysis of supercritical methane thermal-hydraulic performance and pseudo-boiling in a PCHE straight channel

The printed circuit heat exchanger(PCHE) is receiving wide attention as a new kind of compact heat exchanger and is considered as a promising vaporizer in the LNG process. In this paper, a PCHE straight channel in the length of 500 mm is established, with a semicircular cross section in a diameter of 1.2 mm.Numerical simulation is employed to investigate the flow and heat transfer performance of supercritical methane in the channel. The pseudo-boiling theory is adopted and the liquid-like, two-phase-like, and vapor-like regimes are divided for supercritical methane to analyze the heat transfer and flow features.The results are presented in micro segment to show the local convective heat transfer coefficient and pressure drop. It shows that the convective heat transfer coefficient in segments along the channel has a significant peak feature near the pseudo-critical point and a heat transfer deterioration when the average fluid temperature in the segment is higher than the pseudo-critical point. The reason is explained with the generation of vapor-like film near the channel wall that the peak feature related to a nucleateboiling-like state and heat transfer deterioration related to a film-boiling-like state. The effects of parameters, including mass flow rate, pressure, and wall heat flux on flow and heat transfer were analyzed.In calculating of the averaged heat transfer coefficient of the whole channel, the traditional method shows significant deviation and the micro segment weighted average method is adopted. The pressure drop can mainly be affected by the mass flux and pressure and little affected by the wall heat flux. The peak of the convective heat transfer coefficient can only form at high mass flux, low wall heat flux, and near critical pressure, in which condition the nucleate-boiling-like state is easier to appear. Moreover,heat transfer deterioration will always appear, since the supercritical flow will finally develop into a filmboiling-like state. So heat transfer deterioration should be taken seriously in the design and safe operation of vaporizer PCHE. The study of this work clarified the local heat transfer and flow feature of supercritical methane in microchannel and contributed to the deep understanding of supercritical methane flow of the vaporization process in PCHE.

Semi-analytical solution for drained expansion analysis of a hollow cylinder of critical state soils

The expansion of a thick-walled hollow cylinder in soil is of non-self-similar nature that the stress/deformation paths are not the same for different soil material points.As a result,this problem cannot be solved by the common self-similar-based similarity techniques.This paper proposes a novel,exact solution for rigorous drained expansion analysis of a hollow cylinder of critical state soils.Considering stress-dependent elastic moduli of soils,new analytical stress and displacement solutions for the nonself-similar problem are developed taking the small strain assumption in the elastic zone.In the plastic zone,the cavity expansion response is formulated into a set of first-order partial differential equations(PDEs)with the combination use of Eulerian and Lagrangian descriptions,and a novel solution algorithm is developed to efficiently solve this complex boundary value problem.The solution is presented in a general form and thus can be useful for a wide range of soils.With the new solution,the non-self-similar nature induced by the finite outer boundary is clearly demonstrated and highlighted,which is found to be greatly different to the behaviour of cavity expansion in infinite soil mass.The present solution may serve as a benchmark for verifying the performance of advanced numerical techniques with critical state soil models and be used to capture the finite boundary effect for pressuremeter tests in small-sized calibration chambers.

Identification of cell surface markers for acute myeloid leukemia prognosis based on multi-model analysis

Given the extremely high inter-patient heterogeneity of acute myeloid leukemia(AML),the identification of biomarkers for prognostic assessment and therapeutic guidance is critical.Cell surface markers(CSMs)have been shown to play an important role in AML leukemogenesis and progression.In the current study,we evaluated the prognostic potential of all human CSMs in 130 AML patients from The Cancer Genome Atlas(TCGA)based on differential gene expression analysis and univariable Cox proportional hazards regression analysis.By using multi-model analysis,including Adaptive LASSO regression,LASSO regression,and Elastic Net,we constructed a 9-CSMs prognostic model for risk stratification of the AML patients.The predictive value of the 9-CSMs risk score was further validated at the transcriptome and proteome levels.Multivariable Cox regression analysis showed that the risk score was an independent prognostic factor for the AML patients.The AML patients with high 9-CSMs risk scores had a shorter overall and event-free survival time than those with low scores.Notably,single-cell RNA-sequencing analysis indicated that patients with high 9-CSMs risk scores exhibited chemotherapy resistance.Furthermore,PI3K inhibitors were identified as potential treatments for these high-risk patients.In conclusion,we constructed a 9-CSMs prognostic model that served as an independent prognostic factor for the survival of AML patients and held the potential for guiding drug therapy.

Perception of dental appearance and aesthetic analysis among patients,laypersons and dentists

BACKGROUND Current concepts of beauty are increasingly subjective,influenced by the viewpoints of others.The aim of the study was to evaluate divergences in the perception of dental appearance and smile esthetics among patients,laypersons and dental practitioners.The study goals were to evaluate the influence of age,sex,education and dental specialty on the participants’judgment and to identify the values of different esthetic criteria.Patients sample included 50 patients who responded to a dental appearance questionnaire(DAQ).Two frontal photographs were taken,one during a smile and one with retracted lips.Laypersons and dentists were asked to evaluate both photographs using a Linear Scale from(0-10),where 0 represent(absolutely unaesthetic)and 10 represent(absolutely aesthetic).One-way analysis of variance(ANOVA)and t-test analysis were measured for each group.Most patients in the sample expressed satisfaction with most aspects of their smiles and dental appearance.Among laypersons(including 488 participants),47 pictures“with lips”out of 50 had higher mean aesthetic scores compared to pictures“without lips”.Among the dentist sample,90 dentists’perception towards the esthetic smile and dental appearance for photos“with lips”and“without lips”were the same for 23 out of 50 patients.Perception of smile aesthetics differed between patients,laypersons and dentists.Several factors can contribute to shape the perception of smile aesthetic.AIM To compare the perception of dental aesthetic among patients,laypersons,and professional dentists,to evaluate the impact of age,sex,educational background,and income on the judgments made by laypersons,to assess the variations in experience,specialty,age,and sex on professional dentists’judgment,and to evaluate the role of lips,skin shade and tooth shade in different participants’judgments.METHODS Patients sample included 50 patients who responded to DAQ.Two frontal photographs were taken:one during a smile and one with retracted lips.Laypersons and dentists were asked to evaluate both photographs using a Linear Scale from(0-10),where 0 represent(absolutely unaesthetic)and 10 represent(absolutely aesthetic).One-way ANOVA and t-test analysis were measured for each group.RESULTS Most patients in the sample expressed satisfaction with most aspects of their smiles and dental appearance.Among laypersons(including 488 participants),47 pictures“with lips”out of 50 had higher mean aesthetic scores compared to pictures“without lips”.Whereas among the dentist sample,90 dentists’perception towards the esthetic smile and dental appearance for photos“with lips”and“without lips”were the same for 23 out of 50 patients.Perception of smile aesthetics differed between patients,laypersons and dentists.CONCLUSION Several factors can contribute to shape the perception of smile aesthetic.

Causal Analysis Between Rice Growth and Cadmium Accumulation and Transfer under Arbuscular Mycorrhizal Inoculation

Cadmium(Cd)contamination in rice has been a serious threat to human health.To investigate the effects of arbuscular mycorrhizal fungi(AMF)on the Cd translocation in rice,a controlled pot experiment was conducted.The results indicated that AMF significantly increased rice biomass,with an increase of up to 40.0%,particularly in root biomass by up to 68.4%.Notably,the number of prominent rice individuals also increased,and their plasticity was enhanced following AMF inoculation.AMF led to an increase in the net photosynthetic rate and antioxidant enzyme activity of rice.In the AMF treatment group,the Cd concentration in the rice roots was significantly higher(19.1%‒68.0%)compared with that in the control group.Conversely,the Cd concentration in the rice seeds was lower in the AMF treatment group,indicating that AMF facilitated the sequestration of Cd in rice roots and reduced Cd accumulation in the seeds.Path coefficients varied across different treatments,suggesting that AMF inoculation reduced the direct impact of soil Cd concentration on the total Cd accumulation in seeds.The translocation of Cd was consistently associated with simultaneous growth dilution and compensatory accumulation as a result of mycorrhizal effects.Our study quantitatively analyzed this process through path analysis and clarified the causal relationship between rice growth and Cd transfer under the influence of AMF.

Model reduction of fractional impedance spectra for time–frequency analysis of batteries, fuel cells, and supercapacitors

Joint time–frequency analysis is an emerging method for interpreting the underlying physics in fuel cells,batteries,and supercapacitors.To increase the reliability of time–frequency analysis,a theoretical correlation between frequency-domain stationary analysis and time-domain transient analysis is urgently required.The present work formularizes a thorough model reduction of fractional impedance spectra for electrochemical energy devices involving not only the model reduction from fractional-order models to integer-order models and from high-to low-order RC circuits but also insight into the evolution of the characteristic time constants during the whole reduction process.The following work has been carried out:(i)the model-reduction theory is addressed for typical Warburg elements and RC circuits based on the continued fraction expansion theory and the response error minimization technique,respectively;(ii)the order effect on the model reduction of typical Warburg elements is quantitatively evaluated by time–frequency analysis;(iii)the results of time–frequency analysis are confirmed to be useful to determine the reduction order in terms of the kinetic information needed to be captured;and(iv)the results of time–frequency analysis are validated for the model reduction of fractional impedance spectra for lithium-ion batteries,supercapacitors,and solid oxide fuel cells.In turn,the numerical validation has demonstrated the powerful function of the joint time–frequency analysis.The thorough model reduction of fractional impedance spectra addressed in the present work not only clarifies the relationship between time-domain transient analysis and frequency-domain stationary analysis but also enhances the reliability of the joint time–frequency analysis for electrochemical energy devices.

Metagenomic analysis revealing the metabolic role of microbial communities in the free amino acid biosynthesis of Monascus rice vinegar during fermentation

Free amino acid(FAA)is the important component of vinegar that infl uences quality perception and consumer acceptance.FAA is one of the major metabolites produced by microorganisms;however,the microbial metabolic network on FAA biosynthesis remains unclear.Through metagenomic analysis,this work aimed to elucidate the roles of microbes in FAA biosynthesis during Monascus rice vinegar fermentation.Taxonomic profiles from functional analyses showed 14 dominant genera with high contributions to the metabolism pathways.The metabolic network for FAA biosynthesis was then constructed,and the microbial distribution in different metabolic pathways was illuminated.The results revealed that 5 functional genera were closely involved in FAA biosynthesis.This study illuminated the metabolic roles of microorganisms in FAA biosynthesis and provided crucial insights into the functional attributes of microbiota in vinegar fermentation.

Inferring Mycobacterium Tuberculosis Drug Resistance and Transmission using Whole-genome Sequencing in a High TB-burden Setting in China

Objective China is among the 30 countries with a high burden of tuberculosis(TB)worldwide,and TB remains a public health concern.Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China.However,molecular epidemiological studies of Kashgar are lacking.Methods A population-based retrospective study was conducted using whole-genome sequencing(WGS)to determine the characteristics of drug resistance and the transmission patterns.Results A total of 1,668 isolates collected in 2020 were classified into lineages 2(46.0%),3(27.5%),and 4(26.5%).The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid(7.4%,124/1,668),streptomycin(6.0%,100/1,668),and rifampicin(3.3%,55/1,668).The rate of rifampicin resistance was 1.8%(23/1,290)in the new cases and 9.4%(32/340)in the previously treated cases.Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains,respectively:18.6%vs.8.7 or 9%,P<0.001.The estimated proportion of recent transmissions was 25.9%(432/1,668).Multivariate logistic analyses indicated that sex,age,occupation,lineage,and drug resistance were the risk factors for recent transmission.Despite the low rate of drug resistance,drug-resistant strains had a higher risk of recent transmission than the susceptible strains(adjusted odds ratio,1.414;95%CI,1.023–1.954;P=0.036).Among all patients with drug-resistant tuberculosis(DR-TB),78.4%(171/218)were attributed to the transmission of DR-TB strains.Conclusion Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

Application of Isogeometric Analysis Method in Three-Dimensional Gear Contact Analysis

Gears are pivotal in mechanical drives,and gear contact analysis is a typically difficult problem to solve.Emerging isogeometric analysis(IGA)methods have developed new ideas to solve this problem.In this paper,a threedimensional body parametric gear model of IGA is established,and a theoretical formula is derived to realize single-tooth contact analysis.Results were benchmarked against those obtained from commercial software utilizing the finite element analysis(FEA)method to validate the accuracy of our approach.Our findings indicate that the IGA-based contact algorithmsuccessfullymet theHertz contact test.When juxtaposed with the FEA approach,the IGAmethod demonstrated fewer node degrees of freedomand reduced computational units,all whilemaintaining comparable accuracy.Notably,the IGA method appeared to exhibit consistency in analysis accuracy irrespective of computational unit density,and also significantlymitigated non-physical oscillations in contact stress across the tooth width.This underscores the prowess of IGA in contact analysis.In conclusion,IGA emerges as a potent tool for addressing contact analysis challenges and holds significant promise for 3D gear modeling,simulation,and optimization of various mechanical components.

Bibliometric analysis of microphthalmos and anophthalmos over 20 years:from 2004 to 2023

AIM:To conduct a bibliometric analysis of studies on microphthalmos and anophthalmos(M/A),explore research hotspots,and provide information on future research interests in this field to benefit clinicians and researchers.METHODS:Totally 751 publications related to M/A from the year 2004 to 2023 were collected from the Web of Science Core Collection database.These publications consist of both original and review articles,that are composed in English.The contributions of different countries,institutions,journals,and authors were analyzed,and network analysis was conducted by using Microsoft Excel 2021,VOSviewer,and R Studio to visualize research hotspots.RESULTS:Among all publications included,the highest number of publications came from USA(218,29.03%).China followed with 99 publications(13.18%),and England with 86 publications(11.45%).The publications from the USA had the highest frequency of citations,with 16699 citations,and the highest H-index of 49.The American Journal of Medical Genetics Part A(43,5.73%)published the largest number of papers,and the University of London had the most publications(41,5.46%).The genetic and molecular mechanisms of M/A were still unclear and the clinical intervention for M/A had gained a lot of attention as an emerging area of interest.CONCLUSION:Data have been gathered on the yearly count of published materials and citations,as well as the rise in publication trends,the efficiency of regions or countries,authors,journals,and organizations,along with the high-cited publications in M/A.The recent trend of research has shifted from genetic mechanisms to different clinical phenotypes and corresponding clinical interventions,which can give direction to future research.