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Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

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World Journal of Gastroenterology 2021年第14期27卷 1465-1482页

作者： sarah a malik Chencan Zhu Jinyu Li Joseph F LaComb Paula I Denoya Igor Kravets Joshua D Miller Jie Yang Melissa Kramer W Richard McCombie Charles E Robertson Daniel N Frank Ellen Li Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Applied Mathematics and Statistics Stony Brook UniversityStony BrookNY 11794United States Stony Brook Cancer Center Biostatistics and Bioinformatics Shared Resource Stony Brook UniversityStony BrookNY 11794United States Department of Pathology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Surgery Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Family Population and Preventive MedicineStony Brook UniversityStony BrookNY 11794United States Cold Spring Harbor Laboratory Cancer Center Sequencing Technologies and Analysis Shared Resource Cold Spring HarborNY 11724United States Department of Medicine University of Colorado Anschutz Medical CampusAuroraCO 80045United States

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human ***-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)*** hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk *** To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection *** Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from *** 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on *** sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥*** PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach *** mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level *** confirmed increased Fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics *** coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor *** expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race *** Recent adoption of additional preoperative antibiotics as sta

关键词： Colorectal cancer Antibiotics African Continental Ancestry Group Diabetes mellitus 16S rRNA gene RNA-sequencing

Unveiling a new regulator: Vacuolar V-ATPase mediates brassinosteroid signaling in Arabidopsis

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Molecular Plant 2024年第2期17卷 227-229页

作者： Shikha malik Justin W.Walley Department of Plant Pathology Entomologyand Microbiologylowa State UniversityAmesIA 50011USA

Plant growth and development are intricately regulated by hormones such as auxins,gibberellins,jamonates,cytokinins,and brassinosteroids(BRs).BRs are a group of plant steroid hormones that play a vital role in plant growth and response to the *** regulate many biological processes including cell elongation,cell division,and male fertility,as well as abiotic and biotic stress responses.

关键词： media fertility brassinosteroid

Suppression of mature TAU isoforms prevents Alzheimer's disease-like amyloid-beta oligomer-induced spine loss in rodent neurons

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Neural Regeneration Research 2024年第8期19卷 1655-1657页

作者： sarah Buchholz Hans Zempel Institute of Human Genetics Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany Center for Molecular Medicine Cologne(CMMC) Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany

Introduction:TAU isoforms as disease mediators:The microtubule-associated protein TAU is predominantly present in the axons of neurons under physiological *** Alzheimer’s disease(AD)and related tauopathies,TAU also mislocalizes("TAU missorting")to the soma and the dendrites,where it eventually forms aggregates,the so-called neurofibrillary tangles(for review see Zimmer-Bensch and Zempel,2021;Zempel,2023).

关键词： Alzheimer Zimmer tau

Detailed analysis of the relativistic configuration of Bardeen anisotropic spheres in modified f(G)gravity

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Communications in Theoretical Physics 2024年第6期76卷 45-56页

作者： Adnan malik Ayesha Almas Tayyaba Naz Rubab Manzoor M Z Bhatti School of Mathematical Sciences Zhejiang Normal UniversityJinhuaZhejiangChina Department of Mathematics University of Management and TechnologySialkot CampusLahorePakistan National University of Computer and Emerging Sciences Lahore CampusPakistan Department of Mathematics University of Management and TechnologyJohar Town CampusLahore 54782Pakistan Department of Mathematics University of the PunjabQuaid-i-Azam CampusLahore-54590Pakistan

The aim of this work is to investigate anisotropic compact objects within the framework of f(G)modified theory of *** our present work,we utilize Krori-Barua metrics,i.e.,λ(r)=Xr^(2)+Y andβ(r)=Zr^(2).We use some matching conditions of spherically symmetric spacetime with Bardeen's model as an exterior ***,we establish some expressions of energy density and pressure components to analyze the stellar configuration of Bardeen compact stars by assuming viable f(G)*** examine the energy conditions for different stellar structures to verify the viability of our considered ***,we also investigate some other physical features,such as equilibrium condition,equation of state parameters,adiabatic index,stability analysis,mass function,surface redshift,and compactness factor,*** is worthwhile to mention here for the current study that our stellar structure in the background of Bardeen's model is more viable and stable.

关键词： Bardeen compact stars f(G)modified gravity Krori-Barua potential

Psychological consequences of a diagnosis of infertility in men:a systematic analysis

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Asian Journal of Andrology 2024年第1期26卷 10-19页

作者： sarah N Biggs Jane Halliday Karin Hammarberg Reproductive Epidemiology Murdoch Children's Research InstituteMelbourne 3052Australia Department of Paediatrics University of MelbourneMelbourne 3052Australia Public Health and Preventative Medicine Monash UniversityMelbourne 3004Australia Victorian Assisted Reproductive Treatment Authority Melbourne 3000Australia

Almost half of infertility cases involve male *** the consequence of a diagnosis of male infertility,as a sole or partial contributor to the couples'infertility,to the mental health of men is required to ensure clinical care meets their psychological *** aim of this systematic analysis was to synthesize the evidence regarding whether men diagnosed with male factor infertility experience greater psychological distress than(1)men described as fertile and(2)men in couples with other infertility *** databases were searched using a combination of Medical Subject Headings(MeSH)headings and keywords relating to male infertility and psychological *** search yielded 1016 unique publications,of which 23 were included:8 case-control,14 prospective cohort,and 1 data linkage *** aspects of psychological distress were identified depression,anxiety,self-esteem,quality of life,fertility-related stress,general psychological stress or well-being,and psychiatric ***-control studies reported that men with male factor infertility have more symptoms of depression,anxiety and general psychological distress,worse quality of some aspects of life,and lower self-esteem than *** men with male factor infertility were compared to men in couples with other causes of infertility,there were few differences in the assessed aspects of psychological *** methodological limitations within the studies,this systematic analysis suggests that the experience of infertility,irrespective of its cause,negatively affects men's mental health and demonstrates the need for assisted reproduction technology(ART)providers to consider men undergoing assisted reproduction as individuals with their own unique support needs.

关键词： anxiety depression infertility male mental health quality of life

Improved Dwarf Mongoose Optimization Algorithm for Feature Selection:Application in Software Fault Prediction Datasets

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Journal of Bionic Engineering 2024年第4期21卷 2000-2033页

作者： Abdelaziz I.Hammouri Mohammed A.Awadallah malik ShBraik Mohammed Azmi Al-Betar Majdi Beseiso Department of Computer Science Al-Balqa Applied UniversityAl-Salt19117Jordan Department of Scientific Research and Graduate Studies University of Prince Mugrin42241MedinaSaudi Arabia Department of Computer Science Al-Aqsa UniversityGaza4051Palestine Artificial Intelligence Research Center(AIRC) Ajman UniversityAjmanUnited Arab Emirates Department of Information Technology Al-Huson University CollegeAl-Balqa Applied UniversityAl-HusonIrbid21110Jordan

Feature selection(FS)plays a crucial role in pre-processing machine learning datasets,as it eliminates redundant features to improve classification accuracy and reduce computational *** paper presents an enhanced approach to FS for software fault prediction,specifically by enhancing the binary dwarf mongoose optimization(BDMO)algorithm with a crossover mechanism and a modified positioning updating *** proposed approach,termed iBDMOcr,aims to fortify exploration capability,promote population diversity,and lastly improve the wrapper-based FS process for software fault prediction *** gained superb performance compared to other well-esteemed optimization methods across 17 benchmark *** ranked first in 11 out of 17 datasets in terms of average classification ***,iBDMOcr outperformed other methods in terms of average fitness values and number of selected features across all *** findings demonstrate the effectiveness of iBDMOcr in addressing FS problems in software fault prediction,leading to more accurate and efficient models.

关键词： Dwarf mongoose optimization algorithm Optimization Feature selection Classification

Advances in Zika virus vaccines and therapeutics:A systematic review

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Asian Pacific Journal of Tropical Medicine 2024年第3期17卷 97-109页

作者： Shiza malik Khalid Muhammad Omar Ahsan Muhammad Tahir Khan Ranjit Sah Yasir Waheed Bridging Health Foundation Rawalpindi 46000Pakistan Department of Biology College of SciencesUAE University15551Al AinUnited Arab Emirates Department of Medicine Foundation University Medical CollegeFoundation University IslamabadIslamabad 44000Pakistan INTI International University Persiaran Perdana BBN Putra Nilai71800 NilaiNegeri SembilanMalaysia Institute of Molecular Biology and Biotechnology the University of LahoreKM Defence RoadLahore 58810Pakistan Zhongjing Research and Industrialization Institute of Chinese Medicine Zhongguancun Scientific ParkNanyang 473006China Department of Microbiology Tribhuvan University Teaching HospitalInstitute of MedicineKathmandu 44600Nepal Department of Microbiology Dr.D.Y.Patil Medical CollegeHospital and Research CentreDr.D.Y.Patil VidyapeethPune 411018MaharashtraIndia Department of Public Health Dentistry Dr.D.Y.Patil Dental College and HospitalDr.D.Y.Patil VidyapeethPune 411018MaharashtraIndia Gilbert and Rose-Marie Chagoury School of Medicine Lebanese American UniversityByblos 1401Lebanon

Zika virus(ZIKV)is the causative agent of a viral infection that causes neurological complications in newborns and adults *** wide transmission route and alarming spread rates are of great concern to the scientific *** trials have been conducted to develop treatment options for ZIKV *** review highlights the latest developments in the fields of vaccinology and pharmaceuticals developments for ZIKV infection.A systematic and comprehensive approach was used to gather relevant and up-to-date data so that inferences could be made about the gaps in therapeutic *** results indicate that several therapeutic interventions are being tested against ZIKV infection,such as DNA vaccines,subunit vaccines,live-attenuated vaccines,virus-vector-based vaccines,inactivated vaccines,virus-like particles,and mRNA-based *** addition,approved anti-ZIKV drugs that can reduce the global burden are *** many vaccine candidates for ZIKV are at different stages of development,none of them have received Food and Drug Authority approval for use up to *** issue of side effects associated with these drugs in vulnerable newborns and pregnant women is a major obstacle in the therapeutic pathway.

关键词： Zika virus Infection Therapeutics Antiviral agents Vaccines Therapies Treatment Novel therapeutic Clinical management

The Combination of Achnatherum inebrians Extracts and Soil Microorganisms Inhibited Seed Germination and Seedling Growth in Elymus nutans

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Phyton-International Journal of Experimental Botany 2024年第3期93卷 567-580页

作者： Rui Zhang Taixiang Chen Zhenjiang Chen Hao Chen Xuekai Wei malik Kamran Chunjie Li State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems Key Laboratory of Animal Husbandry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland AgricultureMinistry of EducationWest Gansu Province Prataculture Technology Innovation CenterCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou730020China Center for Grassland Research National Forestry and Grassland AdministrationCaFBeijing100091China

In a greenhouse experiment,the effects of soil microorganisms and extracts of Achnatherum inebrians on the seed germination and seedling growth of Elymus nutans were *** results showed that both the extracts from aboveground and belowground parts of *** signiﬁcantly inhibited the germination rate,germination potential,germination index,vigor index,seedling height,root length,and fresh weight of ***,but increased malondialdehyde content,catalase,peroxidase and superoxide dismutase activity of *** seedlings(p<0.05).The allelopathy of aqueous extracts of the aboveground parts of *** was stronger than that of the *** extracts of the aboveground parts of *** decreased seed germination rate,germination potential,germination index,vigor index,seedling length,root length,and seedling fresh weight by 10.45%-74.63%,24.18%-32.50%,19.03%-73.36%,37.83%-88.41%,21.42%-53.14%,2.65%-40.21%,and 20.45%-61.36%,respectively,and malondialdehyde content,peroxidase,catalase,and superoxide dismutase activity increased by 8.09%-62.24%,27.83%-86.47%,22.90%-93.17%,and 11.15%-75.91%,*** above indexes were higher in live soil than in sterilized *** microorganisms increased the allelopathy of *** seed germination rate,germination potential,germination index,vigor index,seedling length,and seedling fresh weight of *** planted in live soil decreased by 8.22%-48.48%,10.00%-51.85%,8.19%-53.26%,16.43%-60.03%,12.91%-28.81%,and 9.09%-22.86%compared with sterilized soil,*** content,peroxidase,catalase,and superoxide dismutase activity of *** planted in live soil increased by 53.91%-81.06%,15.71%-57.34%,33.33%-86.31%,and 9.78%-52.51%compared with sterilized soil,*** existence of soil microorganisms enhanced the allelopathy of the secondary metabolites of ***.A combination of microorganisms and aqueous extracts from the aboveground parts of *** had the s

关键词： Achnatherum inebrians water immersion liquid aqueous leachate precipitate allelopathy Elymus nutans soil microorganisms

Virus-like nanoparticle vaccines for inducing long-lasting immunity against infectious diseases

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National Science Review 2024年第4期11卷 13-15页

作者： Yi-Nan Zhang sarah Auclair Jiang Zhu Department of Integrative Structural and Computational Biology The Scripps Research Institute Department of Immunology and Microbiology The Scripps Research Institute

Prophylactic vaccines that can generate long-lasting protective immune responses are needed for many infectious diseases. Efficient vaccination requires vaccine antigens to be retained and presented to B cells in lymp...

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