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Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

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Journal of Pharmaceutical Analysis 2024年第5期14卷 733-743页

作者： Alongkorn Kurilung Suphitcha Limjiasahapong Khwanta Kaewnarin Pattipong Wisanpitayakorn Narumol Jariyasopit Kwanjeera Wanichthanarak Sitanan Sartyoungkul Stephen Choong Chee Wong Nuankanya Sathirapongsasuti Chagriya Kitiyakara Yongyut Sirivatanauksorn Sakda Khoomrung Siriraj Center of Research Excellent in Metabolomics and Systems Biology(SiCORE-MSB) Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Siriraj Metabolomics and Phenomics Center Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Department of Biomedical informatics University of Arkansas for Medical SciencesLittle RockAR72205USA SingHealth Duke-NUS institute of Biodiversity Medicine National Cancer Centre Singapore168583Singapore Waters Pacific Pte. Ltd.Singapore117528Singapore Program in Translational Medicine Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkok10400Thailand Chakri Naruebodindra medical institute Faculty of Medicine Ramathibodi HospitalMahidol UniversitySamut Prakan10540Thailand Department of Medicine Ramathibodi HospitalMahidol UniversityBangkok10400Thailand Department of Biochemistry Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Center of Excellence for Innovation in Chemistry(PERCH-CIC) Faculty of ScienceMahidol UniversityBangkok10400Thailand

The collision cross-sections(CCS)measurement using ion mobility spectrometry(IMS)in combination with mass spectrometry(MS)offers a great opportunity to increase confidence in metabolite ***,owing to the lack of sensitivity and resolution,IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites(VLMs250 Da).Here,we describe an analytical method using ultrahigh-performance liquid chromatography(UPLC)coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine *** experimental CCS values,along with mass spectral properties,were reported for the 174 *** experimental data included the mass-to-charge ratio(m/z),retention time(RT),tandem MS(MS/MS)spectra,and CCS *** the studied metabolites,263 traveling wave ion mobility spectrometry(TWIMS)-derived CCS values(TWCCSN2)were reported for the first time,and more than 70%of these were CCS values of *** TWCCSN2 values were highly repeatable,with inter-day variations of<1%relative standard deviation(RSD).The developed method revealed excellent TWCCSN2 accuracy with a CCS difference(DCCS)within±2%of the reported drift tube IMS(DTIMS)and TWIMS CCS *** complexity of the urine matrix did not affect the precision of the method,as evidenced by DCCS within±1.92%.According to the Metabolomics Standards Initiative,55 urinary metabolites were identified with a confidence level of *** these 55 metabolites,53(96%)were *** larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values,which clearly increased metabolite identification confidence.

关键词： Very low-molecular-weight metabolites Traveling wave ion mobility Collision cross-section Human urine

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Modeling the dynamical behavior of the interaction of T-cells and human immunodeficiency virus with saturated incidence

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Communications in Theoretical Physics 2024年第3期76卷 1-14页

作者： Salah Boulaaras Rashid Jan Amin Khan Ali Allahem Imtiaz Ahmad Salma Bahramand Department of Mathematics College of ScienceQassim UniversityBuraydah51452Saudi Arabia institute of Energy Infrastructure(IEI) Department of Civil EngineeringCollege of EngineeringUniversiti Tenaga Nasional(UNITEN)Putrajaya CampusJalan IKRAM-UNITEN43000 KajangSelangorMalaysia Department of Mathematics University of SwabiSwabi 23561Pakistan Department of Mathematics College of SciencesQassim UniversitySaudi Arabia institute of informatics and Computing in Energy(IICE) Universiti Tenaga NasionalKajangSelangorMalaysia Department of Political Science Bacha Khan University CharsaddaCharsadda 24420KPK Pakistan

In the last forty years,the rise of HIV has undoubtedly become a major concern in the field of public health,imposing significant economic burdens on affected ***,it becomes imperative to undertake comprehensive investigations into the mechanisms governing the dissemination of HIV within the human *** this work,we have devised a mathematical model that elucidates the intricate interplay between CD4^(+)T-cells and viruses of HIV,employing the principles of fractional *** production rate of CD4^(+)T-cells,like other immune cells depends on certain factors such as age,health status,and the presence of infections or ***,we incorporate a variable source term in the dynamics of HIV infection with a saturated incidence rate to enhance the precision of our *** introduce the fundamental concepts of fractional operators as a means of scrutinizing the proposed HIV *** facilitate a deeper understanding of our system,we present an iterative scheme that elucidates the trajectories of the solution pathways of the *** show the time series analysis of our model through numerical findings to conceptualize and understand the key factors of the *** addition to this,we present the phase portrait and the oscillatory behavior of the system with the variation of different input *** information can be utilized to predict the long-term behavior of the system,including whether it will converge to a steady state or exhibit periodic or chaotic oscillations.

关键词： HIV infection fractional-calculus dynamics of HIV iterative scheme dynamical behaviour mathematical model fractional derivatives

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Significance of ipsilateral breast tumor recurrence after breast conserving treatment: role of surgical removal

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Chinese Journal of Cancer Research 2013年第1期25卷 22-31页

作者： Romano Demicheli Ilaria Ardoino Federico Ambrogi Roberto Agresti Elia Biganzoli Scientific Directorate IRCCS National Cancer Institute medical Statistics and biometry University of Milan Breast Surgery IRCCS National Cancer Institute medical Statistics and biometry IRCCS National Cancer Institute

Objective： To analyze the pattern over time （dynamics） of further recurrence and death after ipsilateral breast tumor recurrence （IBTR） in breast cancer patients undergoing breast conserving treatment （BCT）. Methods： A total of 338 evaluable patients experiencing IBTR were extracted from a database of 3,293 patients undergoing BCT. The hazard rates for recurrence and mortality throughout 10 years of follow-up after IBTR were assessed and were compared to the analogous estimates associated to the primary treatment. Results： In a time frame with the time origin at the surgical treatment for IBTR, the hazard rate for further recurrence displays a bimodal pattern （peaks at the second and at the sixth year）. Patients receiving mastectomy for IBTR reveal recurrence and mortality dynamics similar to that of node positive （N＋） patients receiving mastectomy as primary surgery, apart from the first two-three years, when IBTR patients do worse. If the patients with time to IBTR longer than 2.5 years are considered, differences disappear. Conclusions： The recurrence and mortality dynamics following IBTR surgical removal is similar to the corresponding dynamics following primary tumor removal. In particular, patients with time to IBTR in excess of 2.5 years behave like N＋ patients following primary tumor removal. Findings may be suitably explained by assuming that the surgical manoeuvre required by IBTR treatment is able to activate a sudden growing phase for tumor foci most of which, as suggested by the systemic model of breast cancer, would have reached the clinical level according to their own dynamics.

关键词： Breast cancer IBTR recurrence dynamics effects of surgery conservative surgery tumor homeostasis

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Changes in the adult sex ratio of six duck species breeding populations over two decades

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Avian Research 2024年第2期15卷 202-210页

作者： Monika Homolkova Petr Musil Diego Pavon-Jordan Dorota Gajdosova Zuzana Musilova Sarka Neuzilova Jan Zouhar Department of Ecology Faculty of Environmental SciencesCzech University of Life Sciences PragueKamýcka 129CZ-16521Prague–SuchdolCzech Republic Department of Terrestrial Ecology Norwegian Institute for Nature Research(NINA)PO Box 5685 TorgardenTrondheimN-7485Norway Department of Econometrics Faculty of Informatics and StatisticsUniversity of Economicsnam.W.Churchilla 4CZ-13067Prague 3Czech Republic

Despite all efforts,long-term changes in the adult sex ratios of breeding duck populations are still unclear;this uncertainty is especially true for male-bias populations,which are often under the scrutiny of researchers lacking convenient results for the active protection of endangered *** with male-bias populations are usually strongly affected by a decline in population size that leads to a higher extinction *** this study,we examined our long-term data of the abundance of breeding populations in six duck species(Mallard Anas platyrhynchos,Gadwall Mareca strepera,Red-crested Pochard Netta rufina,Common Pochard Aythya ferina,Tufted Duck Aythya fuligula,and Common Goldeneye Bucephala clangula)from fishponds in South Bohemia,Czechia,between 2004 and *** evidence was used to assess long-term changes in the adult sex ratio in these breeding populations and investigate the possible effects of the NAO index(North Atlantic Oscillation index)on them,indicating climate conditions in *** determined a long-term decrease of the proportion of females in the breeding season in two of the six examined species:Common Pochard and Red-crested Pochard,which is driven by the long-term increase in the number of males in contrast to the decreasing or stable number of females likely caused by different migration behaviours between females and *** the case of Common Pochard,in breeding populations,we estimated 60-65%of males in the early 2000s rising to 75-80%in the early ***,we establish no significant effects linked to climate conditions of the previous winter in these species as a crucial cause of the changes of the proportion of females in the breeding population.

关键词： Adult sex ratio Breeding population Population dynamics Red-listed species Waterfowl Winter weather conditions

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Are dogs not susceptible to retroviral infections?

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动物疾病（英文） 2024年第3期4卷 217-223页

作者： Jorge Casseb João Henrique Campos Luciano Rodrigo Lopes Laboratory of Investigation in Dermatology and Immunodeficiencies Department of DermatologyUniversity of São Paulo Medical SchoolSão PauloSPBrazil Igen-institute of Immunogenetics São PauloSPBrazil Bioinformatics and Biomedical Data Science Division Health Informatics DepartmentUniversidade Federal de São Paulo-UNIFESP.Rua Botucatu 862Prédio Leal Pradotérreo Vila Clementino CEP 04023-062 São PauloSPBrazil

Retroviruses have been proven to cause infections and diseases in a series of mammalian hosts but not in ***,this letter discussed the dog susceptibility to retrovirus infection,encompassing arguments to understand why dogs may have not been infected by retroviruses thus *** potential resistance of retrovirus in dogs enables this provocative short communication to discuss this question,looking at some evolutive *** lineage of canids has shown,throughout its evolutionary history,a smaller accumulation of retroviruses in canid genomes,classified as endogenous *** this context,the genomes of canids seem to offer obstacles,which have been evolu-tionarily conserved,in the face of retroviral infection.

关键词： Retrovirus dogs Endogenous retrovirus

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Convergence Towards the Population Cross-Diffusion System from Stochastic Many-Particle System

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Communications in Mathematical Research 2024年第1期40卷 43-63页

作者： Yue Li Li Chen Zhipeng Zhang Department of Mathematics Nanjing UniversityNanjing 210093P.R.China institute for Analysis and Scientific Computing Vienna University of TechnologyWiedner Hauptstrafβe 8-10Vienna 1040Austria School of Business informatics and Mathematics University of MannheimMannheim 68131Germany

In this paper,we derive rigorously a non-local cross-diffusion system from an interacting stochastic many-particle system in the whole *** convergence is proved in the sense of probability by introducing an intermediate particle system with a mollified interaction potential,where the mollification is of algebraic *** main idea of the proof is to study the time evolution of a stopped process and obtain a Gronwall type estimate by using Taylor's expansion around the limiting stochastic process.

关键词： Stochastic particle systems cross-diffusion system mean-field limit population dynamics

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Microsnoop: A generalist tool for microscopy image representation

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The Innovation 2024年第1期5卷 109-117页

作者： Dejin Xun Rui Wang Xingcai Zhang Yi Wang Pharmaceutical informatics institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China State Key Lab of Computer-Aided Design&Computer Graphics Zhejiang UniversityHangzhou 310058China John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Innovation institute for Artificial Intelligence in Medicine of Zhejiang University Hangzhou 310018China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314100China

Accurate profiling of microscopy images from small scale to high throughput is an essential procedure in basic and applied biological ***,we present Microsnoop,a novel deep learning–based representation tool trained on large-scale microscopy images using masked self-supervised *** can process various complex and heterogeneous images,and we classified images into three categories:single-cell,full-field,and batch-experiment *** benchmark study on 10 high-quality evaluation datasets,containing over 2,230,000 images,demonstrated Microsnoop’s robust and state-ofthe-art microscopy image representation ability,surpassing existing generalist and even several custom *** can be integrated with other pipelines to perform tasks such as superresolution histopathology image and multimodal ***,Microsnoop can be adapted to various hardware and can be easily deployed on local or cloud computing *** will regularly retrain and reevaluate the model using communitycontributed data to consistently improve Microsnoop.

关键词： hardware image representation

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Prevalence and risk factors of nonalcoholic fatty liver disease in patients with inflammatory bowel diseases:A cross-sectional and longitudinal analysis

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World Journal of Gastroenterology 2020年第46期26卷 7367-7381页

作者： Peter Hoffmann Victoria Jung Rouven Behnisch Annika Gauss Department of Gastroenterology and Hepatology University Hospital HeidelbergHeidelberg 69120Germany institute of medical biometry and informatics University Hospital HeidelbergHeidelberg 69120Germany

BACKGROUND Nonalcoholic fatty liver disease(NAFLD)is common in the German population,with an even higher prevalence in inflammatory bowel disease *** To investigate the risk factors for NAFLD in inflammatory bowel disease *** This monocentric retrospective study with a cross-sectional and a longitudinal part included 694 *** criteria were diagnosed inflammatory bowel disease,age≥18 years,availability of at least one abdominal *** with infectious or suspected alcoholic fatty liver disease were *** was defined by increased echogenicity at liver *** characteristics,disease activity and medications were analyzed as potential risk *** influencing the course of NAFLD were identified by a generalized linear mixed *** Forty-eight percent of Crohn’s disease(CD)patients and 44%of ulcerative colitis patients suffered from *** occurrence was associated with greater age,hypertension and body mass index(BMI)in both groups,and with higher disease activity and dyslipidemia in CD.2467 ultrasound results were included in the longitudinal *** factors for NAFLD were age,BMI,higher disease activity,bowel resection(s),endoscopic activity and azathioprine use in CD;and BMI and endoscopic activity in ulcerative *** NAFLD was highly prevalent in this cohort of German inflammatory bowel disease *** risk increased mainly with rising age and *** analysis provides a rationale for non-invasive liver screening in inflammatory bowel disease patients.

关键词： Crohn’s disease Ulcerative colitis Inflammatory bowel disease Nonalcoholic fatty liver disease Nonalcoholic steatohepatitis Ultrasound

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Predictors of functional benefit of hepatitis C therapy in a‘real-life’cohort

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World Journal of Gastroenterology 2018年第7期24卷 852-861页

作者： Niels Steinebrunner Kerstin Stein Catharina Sandig Thomas Bruckner Wolfgang Stremmel Anita Pathil Department of Internal Medicine IV University Hospital HeidelbergHeidelberg 69120Germany Department of Gastroenterology Hepatology and Infectious DiseasesUniversity Hospital of MagdeburgMagdeburg 39120Germany Department of medical biometry Institute of Medical Biometry and Informatics(IMBI)Heidelberg 69120Germany

AIM To define predictors of functional benefit of direct-acting antivirals(DAAs) in patients with chronic hepatitis C virus(HCV) infection and liver *** We analysed a cohort of 199 patients with chronic HCV genotype 1, 2, 3 and 4 infection involving previously treated and untreated patients with compensated(76%) and decompensated(24%) liver cirrhosis at two tertiary centres in Germany. Patients were included withtreatment initiation between February 2014 and August 2016. All patients received a combination regimen of one or more DAAs for either 12 or 24 wk. Predictors of functional benefit were assessed in a univariable as well as multivariable model by binary logistic regression *** Viral clearance was achieved in 88%(175/199) of patients. Sustained virological response(SVR) 12 rates were as follows: among 156 patients with genotype 1 infection the SVR 12 rate was 90%(n = 141); among 7 patients with genotype 2 infection the SVR 12 rate was 57%(n = 4); among 30 patients with genotype 3 infection the SVR 12 rate was 87%(n = 26); and among 6 patients with genotype 4 infection the SVR 12 rate was 67%(n = 4). Follow-up MELD scores were available for 179 patients. A MELD score improvement was observed in 37%(65/179) of patients, no change of MELD score in 41%(74/179) of patients, and an aggravation was observed in 22%(40/179) of patients. We analysed predictors of functional benefit from antiviral therapy in our patients beyond viral eradication. We identified the Child-Pugh score, the MELD score, the number of platelets and the levels of albumin and bilirubin as significant factors for functional *** Our data may contribute to the discussion of potential risks and benefits of antiviral therapy with individual patients infected with HCV and with advanced liver disease.

关键词： functional benefit direct acting antiviral hepatitis C cirrhosis real-life data

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Accelerated Particle Swarm Optimization Algorithm for Efficient Cluster Head Selection in WSN

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Computers, Materials & Continua 2024年第6期79卷 3585-3629页

作者： Imtiaz Ahmad Tariq Hussain Babar Shah Altaf Hussain Iqtidar Ali Farman Ali institute of Computer Sciences and Information Technology The University of AgriculturePeshawarPakistan School of Computer Science and Technology Zhejiang Gongshang UniversityHangzhouChina College of Technological Innovation Zayed UniversityDubaiUnited Arab Emirates School of Computer Science and Technology Chongqing University of Posts and TelecommunicationsChongqing400065China Department of Applied AI School of ConvergenceCollege of Computing and InformaticsSungkyunkwan UniversitySeoul03063South Korea

Numerous wireless networks have emerged that can be used for short communication ranges where the infrastructure-based networks may fail because of their installation and *** of them is a sensor network with embedded sensors working as the primary nodes,termed Wireless Sensor Networks(WSNs),in which numerous sensors are connected to at least one Base Station(BS).These sensors gather information from the environment and transmit it to a BS or gathering *** have several challenges,including throughput,energy usage,and network lifetime *** strategies have been applied to get over these *** may,therefore,be thought of as the best way to solve such ***,it is crucial to analyze effective Cluster Head(CH)selection to maximize efficiency throughput,extend the network lifetime,and minimize energy *** paper proposed an Accelerated Particle Swarm Optimization(APSO)algorithm based on the Low Energy Adaptive Clustering Hierarchy(LEACH),Neighboring Based Energy Efficient Routing(NBEER),Cooperative Energy Efficient Routing(CEER),and Cooperative Relay Neighboring Based Energy Efficient Routing(CR-NBEER)*** the help of APSO in the implementation of the WSN,the main methodology of this article has taken *** simulation findings in this study demonstrated that the suggested approach uses less energy,with respective energy consumption ranges of 0.1441 to 0.013 for 5 CH,1.003 to 0.0521 for 10 CH,and 0.1734 to 0.0911 for 15 *** sending packets ratio was also raised for all three CH selection scenarios,increasing from 659 to *** number of dead nodes likewise dropped for the given combination,falling between 71 and *** network lifetime was deemed to have risen based on the results found.A hybrid with a few valuable parameters can further improve the suggested APSO-based *** to underwater,WSN can make use of the proposed *** overall results have been evaluated and

关键词： Wireless sensor network cluster head selection low energy adaptive clustering hierarchy accelerated particle swarm optimization

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