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Telomeric DNA breaks in human induced pluripotent stem cells trigger ATR-mediated arrest and telomerase-independent telomere damage repair

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Journal of Molecular Cell Biology 2024年第3期16卷 46-60页

作者： Katrina N.Estep John W.Tobias rafael J.fernandez Brinley M.Beveridge f.Brad Johnson Department of Pathology and Laboratory Medicine University of PennsylvaniaPhiladelphiaPA 19104USA Quantiative Biosciences Merck&Co.Inc.West PointPA 19486USA Penn Genomic Analysis Core University of PennsylvaniaPhiladelphiaPA 19104USA

Although mechanisms of telomere protection are well-defined in differentiated cells,how stem cells sense and respond to telomere dysfunction,in particular telomeric double-strand breaks(DSBs),is poorly ***,we report the DNA damage signaling,cell cycle,and transcriptome changes in human induced pluripotent stem cells(iPSCs)in response to telomere-internal *** engineer human iPSCs with an inducible TRf1-fokI fusion protein to acutely induce DSBs at *** this model,we demonstrate that TRf1-fokI DSBs activate an ATR-dependent DNA damage response,which leads to p53-independent cell cycle arrest in *** CRISPR–Cas9 to cripple the catalytic domain of telomerase reverse transcriptase,we show that telomerase is largely dispensable for survival and lengthening of TRf1-fokI-cleaved telomeres,which instead are effectively repaired by robust homologous recombination(HR).In contrast to HR-based telomere maintenance in mouse embryonic stem cells,where HR causes ZSCAN4-dependent extension of telomeres beyond their initial lengths,HR-based repair of telomeric breaks is sufficient to maintain iPSC telomeres at a normal length,which is compatible with sustained survival of the cells over several days of TRf1-fokI *** findings suggest a previously unappreciated role for HR in telomere maintenance in telomerase-positive iPSCs and reveal distinct iPSC-specific responses to targeted telomeric DNA damage.

关键词： telomeres telomerase alternative lengthening of telomeres pluripotent stem cells DNA damage double-strand breaks

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Notes for genera:Ascomycota

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fungal Diversity 2017年第5期86卷 1-594页

作者： Nalin N.Wijayawardene Kevin D.Hyde Kunhiraman C.Rajeshkumar david L.Hawksworth Hugo Madrid Paul M.Kirk Uwe Braun Rajshree V.Singh Pedro W.Crous Martin Kukwa Robert Lücking Cletus P.Kurtzman Andrey Yurkov danny Haelewaters Andre´Aptroot H.Thorsten Lumbsch Einar Timdal damien Ertz Javier Etayo Alan J.L.Phillips Johannes Z.Groenewald Moslem Papizadeh Laura Selbmann Monika C.dayarathne Gothamie Weerakoon E.B.Gareth Jones Satinee Suetrong Qing Tian rafael f.castanda-ruiz Ali H.Bahkali Ka-Lai Pang Kazuaki Tanaka Dong Qin dai Jariya Sakayaroj Martina Hujslová Lorenzo Lombard Belle D.Shenoy Ave Suija Sajeewa S.N.Maharachchikumbura Kasun M.Thambugala Dhanushka N.Wanasinghe Bharati O.Sharma Subhash Gaikwad Gargee Pandit Laura Zucconi Silvano Onofri Eleonora Egidi Huzefa A.Raja Rampai Kodsueb Marcela E.S.Caceres Sergio Perez-Ortega Patrícia O.fiuza Josiane Santana Monteiro Larissa N.Vasilyeva Roger G.Shivas Maria Prieto Mats Wedin Ibai Olariaga Adebola Azeez Lateef Yamini Agrawal Seyed Abolhassan Shahzadeh fazeli Mohammad Ali Amoozegar Guo Zhu Zhao Walter P.Pfliegler Gunjan Sharma Magdalena Oset Mohamed A.Abdel-Wahab Susumu Takamatsu Konstanze Bensch Nimali Indeewari de Silva AndréDe Kesel Anuruddha Karunarathna Saranyaphat Boonmee Donald H.Pfister Yong-Zhong Lu Zong-Long Luo Nattawut Boonyuen Dinushani A.daranagama Indunil C.Senanayake Subashini C.Jayasiri Milan C.Samarakoon Xiang-Yu Zeng Mingkwan Doilom Luis Quijada Sillma Rampadarath Gabriela Heredia Asha J.Dissanayake Ruvishika S.Jayawardana Rekhani H.Perera Li Zhou Tang Chayanard Phukhamsakda Margarita Hernańdez-Restrepo Xiaoya Ma Saowaluck Tibpromma Luis f.P.Gusmao darshani Weerahewa Samantha C.Karunarathna Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand World Agroforestry Centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China Mushroom Research foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand National fungal Culture Collection of India(NfCCI) Biodiversity and Palaeobiology(Fungi)GroupAgharkar Research InstitutePuneMaharashtra 411004India Royal Botanic Gardens KewRichmondSurrey TW93DSUK Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Jilin Agricultural University Changchun 130118JilinPeople’s Republic of China Centro de Geno´mica y Bioinforma´tica Facultad de CienciasUniversidad Mayor de ChileCamino La Pira´mide 5750HuechurabaSantiagoChile Martin-Luther-Universita¨t Institut fu¨r BiologieBereich Geobotanik und Botanischer GartenHerbariumNeuwerk 2106099 Halle(Saale)Germany Westerdijk fungal Biodiversity Institute Uppsalalaan 83584 CT UtrechtThe Netherlands Department of Plant Taxonomy and Nature Conservation Faculty of BiologyUniversity of Gdan´skWita Stwosza 5980-308 Gdan´skPoland Botanic Garden and Botanical Museum Königin-Luise-Str.6-814195 BerlinGermany Mycotoxin Prevention and Applied Microbiology Research Unit National Center for Agricultural Utilization ResearchAgricultural Research ServiceU.S.Department of AgriculturePeoriaIL 61604USA Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B38124 BrunswickGermany farlow Reference Library and Herbarium of Cryptogamic Botany Harvard University22 Divinity AvenueCambridgeMA 02138USA Department of Organismic and Evolutionary Biology Harvard University22 Divinity AvenueCambridgeMA 02138USA ABL Herbarium G.v.d.Veenstraat 1073762 XK SoestThe Netherlands Science&Education The Field Museum1400

Knowledge of the relationships and thus the classification of fungi,has developed rapidly with increasingly widespread use of molecular techniques,over the past 10–15 years,and continues to *** genera have been found to be polyphyletic,and their generic concepts have subsequently been *** names have thus been introduced for species which are phylogenetically distinct from the type species of particular *** ending of the separate naming of morphs of the same species in 2011,has also caused changes in fungal generic *** order to facilitate access to all important changes,it was desirable to compile these in a single *** present article provides a list of generic names of Ascomycota(approximately 6500 accepted names published to the end of 2016),including those which are *** and summaries of the changes since the last edition of‘Ainsworth&Bisby’s Dictionary of the fungi’in 2008 are *** notes include the number of accepted species,classification,type species(with location of the type material),culture availability,life-styles,distribution,and selected publications that have appeared since *** work is intended to provide the foundation for updating the ascomycete component of the"Without prejudice list of generic names of fungi"published in 2013,which will be developed into a list of protected generic *** will be subjected to the XIXth International Botanical Congress in Shenzhen in July 2017 agreeing to a modification in the rules relating to protected lists,and scrutiny by procedures determined by the Nomenclature Committee for fungi(NCf).The previously invalidly published generic names Barriopsis,Collophora(as Collophorina),Cryomyces,Dematiopleospora,Heterospora(as Heterosporicola),Lithophila,Palmomyces(as Palmaria)and Saxomyces are validated,as are two previously invalid family names,Bartaliniaceae and *** species of Lalaria,which were invalidly published are trans

关键词： Article 59 Classification One name Pleomorphic fungi Taxonomy

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Mathematical modeling for estimating influenza vaccine efficacy:A case study of the Valencian Community,Spain.

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Infectious Disease Modelling 2024年第3期9卷 744-762页

作者： Carlos Andreu-Vilarroig rafael J.Villanueva Gilberto González-Parra Instituto de Matemática Multidisciplinar Universitat Politècnica de ValènciaValenciaSpain Department of Mathematics New Mexico TechSocorroNMUSA

Vaccine efficacy and its quantification is a crucial concept for the proper design of public health vaccination *** this work we proposed a mathematical model to estimate the efficacy of the influenza vaccine in a real-word *** particular,our model is a SEIR-type epidemiological model,which distinguishes vaccinated and unvaccinated ***,its dynamics is governed by a nonlinear system of ordinary differential equations,where the non-linearity arises from the effective contacts between susceptible and infected *** key aspects of this study is that we use a vaccine distribution over time that is based on real data specific to the elderly people in the Valencian Community and the calibration process takes into account that over one influenza season a specific proportion of the population becomes infected with *** consider the effectiveness of the vaccine,the model incorporates a parameter,the vaccine attenuation factor,which is related with the vaccine efficacy against the influenza *** this framework,in order to calibrate the model parameters and to obtain an influenza vaccine efficacy estimation,we considered the 2016–2017 influenza season in the Valencian Community,Spain,using the influenza reported cases of vaccinated and *** order to ensure the model identifiability,we choose to deterministically calibrate the parameters for different scenarios and we find the one with the minimum error in order to determine the vaccine *** calibration results suggest that the influenza vaccine developed for 2016–2017 influenza season has an efficacy of approximately 76.7%,and that the risk of becoming infected is five times higher for an unvaccinated individual in comparison with a vaccinated *** estimation partially agrees with some previous studies related to the influenza *** study presents a new integrated mathematical approach to study the influenza vaccine efficacy and gives f

关键词： Mathematical modeling Epidemiology SEIR Vaccine efficacy Influenza Valencian community

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Structural foundation and Geometry of the Material Singularity (and Its Quantum Entanglement)

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Journal of High Energy Physics, Gravitation and Cosmology 2024年第3期10卷 1095-1137页

作者： rafael Cañete Mesa Independent Researcher Seville Spain

In this paper we develop and study, as the second part of one more general development, the energy transmutation equation for the material singularity, previously obtained through the symmetrisation of a wave packet, that is, we develop the correlation between the terms of this equation, which accounts for the formation of matter from a previous vibrational state, and the different possible energy species. These energetic species are ascribed, in a simplified form, to the equation E¯ω=E¯k+E¯f, which allows us, through its associated phase factor, to gain an insight into the wave character of the kinetic energy and thus to attain the basis of the matter-wave, and all sorts of related phenomenologies, including that concerning quantum entanglement. The formation of the matter was previously identified as an energetic process, analogous to the kinetic one, in which finally the inertial mass is consolidated as a mass in a different phase, now, in addition, the mass of the material singularity is identified as a volumetric density of waves of toroidal geometry created in the process of singularisation or energy transfer between species, which makes it possible to establish the real relation or correspondence between the corpuscular and photonic energy equation (E=mc2=hν), i.e. to explain through m the intimate sense of the first equivalence, which explains what νis in the second one.

关键词： Standard Model Wave-Packet Material Singularity Wave-Particle Dualism Wave Symmetrisation Matter-Wave Energetic Transmutation Quantum Entanglement

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The Use of Secondary Grape Biomass in Beef Cattle Nutrition on Carcass Characteristics, Quality and Shelf Life of Meat

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food and Nutrition Sciences 2024年第6期15卷 447-469页

作者： Vitor L. Molosse Guilherme L. Deolindo rafael V. P. Lago Bruna Klein Claiton A. Zotti Marcelo Vedovato Marcylene V. da Silveira Priscila M. Copetti Maria R. C. Schetinger Juscivete f. favero Eliana L. fiorentin Aleksandro S. da Silva Universidade do Estado de Santa Catarina (UDESC) Chapec Brazil Department of Animal Science UDESC Chapec Brazil Department of Animal Science Universidade do Oeste de Santa Catarina Xanxere Brazil Dean Lee Research and Extension Center Louisiana State University Alexandria LA USA Department of Biochemistry Universidade Federal de Santa Maria Santa Maria Brazil Department of Medicina Veterinria UNOCHAPEC Chapec Brasil

We determined whether the inclusion of 100 g/kg dry matter of grape pomace silage (GPS) and grape pomace bran (GPB) as substitutes for other traditional fiber sources in the diet of steers (Charolais x Nellore) would improve carcass characteristics, meat quality and composition, and shelf life. Twenty-four animals (248 ± 19.32 kg of initial body weight) were fed a high concentrate diet for 121 days. Carcass characteristics were measured, and the longissimus dorsi muscle was analyzed for fatty acid (fA) profile and composition. The meat was sliced and stored in air-permeable packages for 10 days. On each sampling day (d 1, 3, 7, and 10), oxidative stability, bacterial load, lipid and protein oxidation, and staining were analyzed. The experimental diets influenced the pH of cold carcasses only. The GPS group had a higher pH than the control. The GPS and GPB groups showed improved oxidant status (i.e., lower lipid peroxidation and concentrations of reactive oxygen species were in the meat of both groups than in control). On the first day of storage, the antioxidant enzyme glutathione S-transferase activity was more significant in the meat of the GPS and GPB groups than in the control. The bacterial loads in the meat were attenuated by GPS inclusion;there were lower total coliform counts and a trend toward lower counts for enterobacteria in the control group. The diets altered the fA profile of the meat;i.e., the GPB diet allowed for a more significant amount of the n-6 omegas in the meat, while the GPS diet showed a tendency for a more significant amount of n-6 and 9 omegas. Both diets (GPS and GPB) increased the amounts of long-chain fAs. The GPS diet decreased saturated fA levels. We conclude that the dietary treatments GPS and GPB are a promising alternative to maintain meat quality standards throughout in real-world retail conditions. These treatments gave rise to an improvement in the nutritional value of the meat due to the more significant amounts of fAs that im

关键词： Animal Nutrition Antioxidant Biomass Grape Meat Quality Microbiology Residue

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促进慢性阻塞性肺疾病哮喘患者自我监控空气质量的护理干预措施: 整合性综述

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International Journal of Nursing Sciences 2024年第1期11卷 46-56页

作者： Bruna f.Sebastiao Raquel M.Hortelao Sara S.Granadas Jose M.faria Joana R.Pinto Helga rafael Henriques Nursing School of Lisbon LisbonPortugal Hospital Center of Central Lisbon Portugal CUf Tejo Hospital LisbonPortugal University Hospital Center of Northern Lisbon LisbonPortugal Nursing Research Innovation and Development Centre of Lisbon(CIDNUR)LisbonPortugal

目的哮喘-慢性阻塞性肺疾病肺重叠症(Asthma-chronie obst ructive pulmonary disease overlap,A-CO)患者的生活质量较低,肺功能较差,病情经常加重。由于暴露于污染环境会加重其症状,增加发病率和病死率,环境管理对其至关重要。旨在通... 详细信息

目的哮喘-慢性阻塞性肺疾病肺重叠症(Asthma-chronie obst ructive pulmonary disease overlap,A-CO)患者的生活质量较低,肺功能较差,病情经常加重。由于暴露于污染环境会加重其症状,增加发病率和病死率,环境管理对其至关重要。旨在通过系统性综述,寻找证据,以指导制订护理干预措施,促进ACO患者对空气质量的自我管理。方法2023年3月 ,系统检索CINAHL、Medline、Academie Search Complete .Scopus、WebofScience、Cochrane图书馆、乔安娜布里格斯研究所(JoannaBriggsInstitute,JBI)循证实践数据库,以及GoogleScholar。对纳人研究进行数据提取和综合,并对护理干预措施进行分类。采用JBI研究质量评估工具进行方法学质量评估。结果共纳入5篇来自不同国家的研究。促进ACO患者自我监控空气质量的干预措施包括:警觉性干预措施(医务人员定期巡诊、进行症状评估),监测干预措施(监测室内外诱发因素) ,教育干预措施(空气质量警报、避免接触过敏原),以及相关政策的影响,如无烟政策和改善空气质量的综合战略。尽管这些研究报告了不同的干预措施,方法质量也存在差异,但这些干预措施显示了预防患者病情恶化、尽量减少急诊就诊和住院治疗的潜力。这些关键点可作为护理干预措施的关键组成部分。结论有必要采取全面措施,让护士参与促进患者自我监控空气质量的多学科团队.提高认识、制订和实施护理干预,从而使ACO患者受益。同时,需要进--步开展研究,以扩大证据基础并完善这些干预措施。

关键词：空气质量哮喘哮喘-慢阻肺重叠慢性病慢性阻塞性肺疾病护理自我管理

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Localization on Certain Grothendieck Categories

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Acta Mathematica Sinica,English Series 2009年第3期25卷 379-392页

作者： f. castan■O-IGLESIAS N.CHIfAN C.N■ST■SESCU Departamento de Estadística y Matemática Aplicada Universidad de Almería Department of Mathematics University of Galati facultatea de Matematicǎ

Using categorical techniques we obtain some results on localization and colocalization theory in Grothendieck categories with a set of small projective generators. In particular, we give a sufficient condition for such category to be semiartinian. for semiartinian Grothendieck categories where every simple object has a projective cover, we obtain that every localizing subcategory is a TTf-class. In addition, some applications to semiperfect categories are obtained.

关键词： Grothendieck category localization colocalization semiartinian category semiperfect category

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The role of rhizobacteria in rice plants: Growth and mitigation of toxicity

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Journal of Integrative Agriculture 2018年第12期17卷 2636-2647页

作者： Marcela C f Rêgo Aline f Cardoso Thayná da C ferreira Marta C C de filippi Telma f V Batista rafael G Viana Gisele B da Silva Plant Protection Laboratory Institute of Agrarian Sciences Federal Rural University of Amazon Phytopathology Laboratory Brazilian Enterprise for Agricultural Research-Rice and Beans

Allelopathic compounds reduce the growth and productivity of upland rice plants, especially in consecutive plantations. The rhizobacteria Pseudomonas fluorescens BRM-32111 and Burkholderia pyrrocinia BRM-32113 have been recorded as growth promoters in rice. This study was developed to understand the effect of the application of rhizobacteria on upland rice plants in consecutive plantations. Experiments were conducted in a completely randomized design with four replications of four treatments: rice seed inoculated with P. fluorescens BRM-32111, rice seed inoculated with B. pyrrocinia BRM-32113(both sown on soil with rice residue), non-inoculated plants sown on soil with rice residue(control with residue(WR)), and non-inoculated plants on soil with no residue(NR). Roots and seedling growth were adversely affected by allelopathic compounds in control WR plants. Plants inoculated with rhizobacteria P. fluorescens BRM-32111 or B. pyrrocinia BRM-32113 induced an increase of 88% in biomass, 3% in the leaf area, 40% in length, 67% in root biomass, 21% in chlorophyll a, 53% in chlorophyll(a+b), 50% in rate of carbon assimilation(A), 227% in A/rubisco carboxylation efficiency(Ci) and 63% in water use efficiency(WUE) compared to control WR plants. These results indicate that rhizobacteria P. fluorescens BRM-32111 and B. pyrrocinia BRM-32113 increase the tolerance of rice plants to stress from allelochemicals. There are possible practical agricultural applications of these results for mitigating the effects of environmental allelochemistry on upland rice.

关键词： allelopathy B.pyrrocinia P.fluorescens rhizobacteria rice

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Retention of eucalyptus harvest residues reduces soil compaction caused by deep subsoiling

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Journal of forestry Research 2022年第2期33卷 643-651页

作者： Raphael Oliveira de Melo AymbiréAngeletti da fonseca Nairam félix de Barros Raphael Bragança Alves fernandes rafael da Silva Teixeira Iago Nery Melo Ricardo Previdente Martins Soil Science Department Universidade Federal de ViçosaViçosaMinas GeraisBrazil BRACELL Company AlagoinhasBahiaBrazil

Eucalyptus harvesting,forwarding and soil tillage operations are among the main causes for compaction of forest soils,with potential impacts on *** concern is especially important in areas with soils that are naturally compacted(fragipans and duripans).In these soils,tillage operations include the use of subsoilers that can reach depths of more than one meter and require heavy tractors that exert high pressure on the *** of the ways to try to minimize the effect of this compaction is by retaining harvest *** objective of this study was to evaluate the impacts of eucalyptus harvesting on soil physical attributes,as well as to determine the potential of different types of residue management to reduce compaction from the soil tillage *** experiments were conducted in the same area with a Yellow *** the first experiment,compaction caused by mechanized harvesting with harvester+forwarder was *** the second experiment,different managements of harvest residues were examined as potential modifiers of soil compaction during tillage for new *** this,three managements systems were tested:(1)retention of all harvest residues and litter from the previous rotation(HR+L),(2)retention of litter from the previous rotation(L),and(3)removal of harvest residues and litter from the previous rotation(WR).Before and after harvest,sampling was carried out in the planting rows and inter-rows,and after tillage,samples were collected in the traffic line of the subsoiler-tractor *** both experiments,undisturbed soil samples were collected from the center of the 0-10,10-20,20-40,40-60,and 60-100 cm layers to determine soil density and total *** each period and site of evaluation,mechanical resistance to penetration up to the 60-cm depth was also *** harvesting operation increased soil density at 0-10 and 60-100 cm depths only in the *** of harvest residues and litter(HR+L)after harvesting avoi

关键词： Soil penetration resistance Harvester+forwarder Soil tillage Soil density Cohesive soils

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Predicting major adverse cardiovascular events after orthotopic liver transplantation using a supervised machine learning model:A cohort study

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World Journal of Hepatology 2024年第2期16卷 193-210页

作者： Jonathan Soldera Leandro Luis Corso Matheus Machado Rech Vinícius Remus Ballotin Lucas Goldmann Bigarella fernanda Tomé Nathalia Moraes rafael Sartori Balbinot Santiago Rodriguez Ajacio Bandeira de Mello Brandão Bruno Hochhegger Post Graduate Program at Acute Medicine and Gastroenterology University of South WalesCardiff CF371DLUnited Kingdom Postgraduate Program in Pathology Federal University of Health Sciences of Porto Alegre(UFCSPA)Porto Alegre 90050-170Brazil Department of Engineering Universidade de Caxias do SulCaxias do Sul 95070-560Brazil School of Medicine Universidade de Caxias do SulCaxias do Sul 95070-560Brazil Postgraduate Program in Hepatology Federal University of Health Sciences of Porto Alegre(UFCSPA)Porto Alegre 90050-170Brazil

BACKGROUND Liver transplant(LT)patients have become older and *** rate of post-LT major adverse cardiovascular events(MACE)has increased,and this in turn raises 30-d post-LT *** cardiac stress testing loses accuracy when applied to pre-LT cirrhotic *** To assess the feasibility and accuracy of a machine learning model used to predict post-LT MACE in a regional *** This retrospective cohort study involved 575 LT patients from a Southern Brazilian academic *** developed a predictive model for post-LT MACE(defined as a composite outcome of stroke,new-onset heart failure,severe arrhythmia,and myocardial infarction)using the extreme gradient boosting(XGBoost)machine learning *** addressed missing data(below 20%)for relevant variables using the k-nearest neighbor imputation method,calculating the mean from the ten nearest neighbors for each *** modeling dataset included 83 features,encompassing patient and laboratory data,cirrhosis complications,and pre-LT cardiac *** performance was assessed using the area under the receiver operating characteristic curve(AUROC).We also employed Shapley additive explanations(SHAP)to interpret feature *** dataset was split into training(75%)and testing(25%)*** was evaluated using the Brier *** followed Transparent Reporting of a Multivariable Prediction Model for Individual Prognosis or Diagnosis guidelines for ***-learn and SHAP in Python 3 were used for all *** supplementary material includes code for model development and a user-friendly online MACE prediction *** Of the 537 included patients,23(4.46%)developed in-hospital MACE,with a mean age at transplantation of 52.9 *** majority,66.1%,were *** XGBoost model achieved an impressive AUROC of 0.89 during the training *** model exhibited accuracy,precision,recall,and f1-score values of 0.84,0.85,0.80,and 0.79,***

关键词： Liver transplantation Major adverse cardiac events Machine learning Myocardial perfusion imaging Stress test

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