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Comparison of methods for deriving phenotypes from incomplete observation data with an application to age at puberty in dairy cattle

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journal of Animal Science and Biotechnology 2024年第2期15卷 535-545页

作者： melissa A.Stephen Chris R.Burke jennie E.Pryce Nicole m.Steele Peter R.Amer Susanne meier Claire V.C.Phyn Dorian j.Garrick DairyNZ Ltd 605 Ruakura RoadHamilton 3240New Zealand AL Rae Centre for Genetics and Breeding-massey University RuakuraHamilton 3214New Zealand Agriculture Victoria Research AgriBioCentre for AgriBioscienceBundooraVictoria 3083Australia School of Applied Systems Biology La Trobe UniversityBundooraVictoria 3083Australia AbacusBio DunedinNew Zealand

Background many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure *** include time-dependent traits such as reproductive status,or *** measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound *** we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example *** We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New *** used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three *** methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation *** Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was *** sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to *** estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring *** Our results indicate that using

关键词： Cattle Gibbs sampler markov-chain monte Carlo(mCmC) Puberty

Network analyses:Inhibition of androgen receptor signaling reduces inflammation in the lung through AR-mAF-IL6 signaling axes

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Genes & Diseases 2024年第3期11卷 140-143页

作者： Albert R.Wang Andrew m.Baschnagel Zijian Ni Sean R.Brennan Hypatia K.Newton Darya Buehler Christina Kendziorski Randall j.Kimple Gopal lyer Department of Human Oncology University of Wisconsin School of Medicine and Public HealthUniversity of WisconsinMadisonWI 53705USA Department of Biomedical Engineering University of Wisconsin-MadisonMadisonWI 53705USA University of Wisconsin Carbone Cancer Center MadisonWI 53705USA Department of Biostatistics and medical Informatics University of Wisconsin-MadisonMadisonWI 53706USA Department of Biology Tufts UniversityMedfordMA 02155USA Department of Pathology and Laboratory medicine University of Wisconsin School of Medicine and Public HealthUniversity of WisconsinMadisonWI 53705USA

Androgen receptor(AR)is a major transcription factor that plays a role in inflammatory response including interleukin-6(IL6)signaling.1 While AR regulation through paracrine loop signaling in prostate tissue is well-studied,its impact through an IL6 autocrine loop in the lung has not been wellstudied despite the organ's response to respiratory viral *** inhibition and RNA knockdown of AR identified a bZIP transcription factor mAF to be a common target of inflammation using these perturbations in lung cells.

关键词： inflammation lung respiratory

粉末冶金Al-5.6Zn-2mg合金在热压缩过程中加工硬化特性及本构模型的比较

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journal of Central South University 2024年第2期31卷 346-368页

作者： KATIKA Harikrishna DAmODA R.K. DAVIDSON m.j. SEETHARAm R. KASAGANI Veera Venkata Nagaraju Department of mechanical Engineering National Institute of TechnologyWarangal 506004India Department of mechanical Engineering The Indian Institute of Information Technology Design and ManufacturingKurnool 518007India

在300~5000℃、应变速率为0.1~0.0001 s−1的条件下,在万能试验机上对Al-5.6Zn-2mg铝合金进行热压缩试验,以确定动态再结晶开始时的加工硬化速率曲线σ_(c)(ε_(c))l以及关键特征σ_(c)(ε_(c))l、σ_(p)(ε_(p))和σ_(ss)与Z系数之间的... 详细信息

在300~5000℃、应变速率为0.1~0.0001 s−1的条件下,在万能试验机上对Al-5.6Zn-2mg铝合金进行热压缩试验,以确定动态再结晶开始时的加工硬化速率曲线σ_(c)(ε_(c))l以及关键特征σ_(c)(ε_(c))l、σ_(p)(ε_(p))和σ_(ss)与Z系数之间的相关性。使用了四个本构模型,Arrhenius模型、改进的johnson-Cook模型(mjC)、改进的Zerilli-Armstrong模型(mZA)和开发的人工神经网络(ANN)。结果表明,ANN型模型和Arrhenius模型的相对误差的绝对平均值最低,分别为0.486%和3.36%,mZA型模型和mjC型模型的相对误差的绝对平均值较高,分别为8.84%和3.93%。由于Arrhenius模型能够处理各种因素之间的非线性关系,因此它被认为是最合适的预测模型,但在材料性质未知或实验数据有限的情况下,mjC模型可能是一种更简单的替代方法。mZA模型不适合估计热压缩时的流变应力。此外,训练最好的神经网络模型的预测性能最好,相对误差的绝对平均值为0.486%,R值为0.99。

关键词：加工硬化速率曲线本构建模热压缩 EBSD分析流变曲线

Provenance and tectonic setting of sandstones of the Lomas Coloradas Formation, Cabullona Group, Sonora, méxico: Constraints on petrography and geochemistry

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journal of Palaeogeography 2024年第4期13卷 839-861页

作者： j.madhavaraju D.G.Noriega-montoya E.Ramirez-montoya C.m.Gonz alez-Le on john S.Armstrong-Altrin Estaci on Regional del Noroeste Instituto de GeologíaUniversidad Nacional Aut onoma de Mexico Ingeniería en Geociencias Universidad Estatal de Sonora Posgrado en Ciencias de la Tierra Estaci on Regional del NoroesteInstituto de GeologíaUniversidad Nacional Aut onoma de Mexico Universidad Nacional Aut onoma de mexico Instituto de Ciencias del Mar y LimnologíaUnidad de Procesos Oce anicos y CosterosCiudad Universitaria

The sedimentary rocks of the Cabullona Group are well exposed in the Cabullona Basin of northeastern Sonora, mexico, which represent syntectonic sedimentation associated with Laramide-style deformation during the Campanian-early maastrichtian. The sandstones of the Lomas Coloradas Formation deposited at the upper part of the Cabullona Group. Petrography and geochemical(major, trace, and rare earth elements) studies were carried out on the sandstones to interpret the palaeoweathering, provenance,and tectonic setting of the Lomas Coloradas Formation sandstones. most of the sandstone modal analysis data plotted in the QFL and Qm FLt ternary diagrams fall into the fields of dissected arcs and recycled orogens,respectively. Geochemically the sandstones are classified as litharenites while few samples plot into the arkosic field. The chondrite-normalized REE diagrams for sandstones have LREE-enriched, relatively flat HREE patterns with negative Eu anomalies. CIA values and the A-CN-K diagram indicate a low intensity of chemical weathering in the source area. The tectonic setting diagram suggests both arc and rift settings for the studied sandstones. The bivariate and ternary diagrams and elemental ratios suggest a felsic source for the Lomas Coloradas Formation. The average REE patterns of the studied sandstones are comparable with REE patterns of the granite from the Caborca block, the rhyolite and granite of the Tarahumara Formation, and the mesozoic felsic volcanic rocks. The modeled mixture of 40% Proterozoic granite, 30% Triassic arc, 10% jurassic arc, and 20% Laramide arc represents the probable source rocks for the Lomas Coloradas Formation.

关键词： Provenance Petrography Geochemistry Lomas Coloradas Formation Cabullona Group méxico

The NORE1A/RASSF5 Tumor Suppressor Forms a Complex with GSK-3β to Regulate β-Catenin

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journal of Biosciences and medicines 2024年第8期12卷 60-75页

作者： m. Lee Schmidt Howard Donninger Geoffrey j. Clark Department Pharmacology and Toxicology University of Louisville Louisville USA US Worldmeds LouisvilleUSA Department of medicine University of Louisville Louisville USA Experimental Therapeutics Program James Graham Brown Cancer Center University of Louisville Louisville USA

NORE1A (RASSF5) is a tumor suppressor of the RASSF family that is often down-regulated in human tumors. NORE1A has multiple roles in controlling cellular homeostasis, one of them being regulating levels of β-catenin by binding and modulating the ubiquitin ligase substrate recognition factor β-TrCP. β-catenin is a major executor of the Wnt pathway. The ubiquitin SCF-β-TrCP ligase complex acts on a phospho-degron site in β-catenin that can be phosphorylated by GSK-3β. We now show that in addition to binding β-TrCP, NORE1A also promotes the phosphorylation of the β-catenin phospho-degron by complexing with the kinase GSK-3β. Indeed, NORE1A enhances the formation of a GSK-3β/β-TrCP complex. A structural mutant of NORE1A that retains β-TrCP binding but will no longer interact with GSK-3β inhibits the β-catenin degrading action of NORE1A. The GSK-3β interaction with NORE1A plays an important role in the biology of NORE1A as a GSK-3β inhibitor blocks NORE1A induced senescence. Thus, we identify a new role for the tumor suppressor NORE1A: The regulation of GSK-3β. GSK-3β has many other substrates including multiple transcription factors and co-activators such as p53 and the Hippo component TAZ. The work implies that NORE1A may be able to influence all of them via this new kinase scaffolding interaction.

关键词： RAS NORE1A RASSF5 GSK-3β Beta Catenin HIPPO

Surface engineering with ionic polymers on membranes for boron removal

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Frontiers of Chemical Science and Engineering 2024年第5期18卷 61-69页

作者： Xiting Zhang Chenyi Fang j Paul Chen Sui Zhang Department of Chemical and Biomolecular Engineering National University of SingaporeSingapore 117576Singapore Department of Civil and Environmental Engineering National University of SingaporeSingapore 119260Singapore College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China

Removal of boric acid from seawater and wastewater using reverse osmosis membrane technologies is imperative and yet remains inadequately addressed by current commercial *** research efforts performed post-modification of reverse osmosis membranes to enhance boron rejection,which is usually accompanied by substantial sacrifice in water *** study delves into the surface engineering of low-pressure reverse osmosis membranes,aiming to elevate boron removal efficiency while maintaining optimal salt rejection and water *** were modified by the self-polymerization and co-deposition of dopamine and polystyrene sulfonate at varying ratios and *** surfaces became smoother and more hydrophilic after *** optimum membrane exhibited a water permeability of 9.2±0.1 L·m^(-2)·h^(-1)·bar^(-1),NaCl rejection of 95.8%±0.3%,and boron rejection of 49.7%±0.1% and 99.6%±0.3% at neutral and alkaline pH,*** water permeability is reduced by less than 15%,while the boron rejection is 3.7 times higher compared to the blank *** research provides a promising avenue for enhancing boron removal in reverse osmosis membranes and addressing water quality concerns in the desalination process.

关键词： membrane low-pressure reverse osmosis boron surface engineering

SARS-CoV-2 triggers Dickkopf-1(Dkk-1)modulation of T helper cells and lung pathology in mice

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Genes & Diseases 2024年第4期11卷 9-12页

作者： Yifan Wu Freedom m.Green Stephen A.Shaw Lauren j.Bonilla Shannon E.Ronca maria Elena Bottazzi Farrah Kheradmand jill E.Weatherhead Department of Pathology&Immunology One Baylor PlazaHoustonTX 77030USA Department of Pediatrics One Baylor PlazaHoustonTX 77030USA Department of medicine One Baylor PlazaHoustonTX 77030USA National School of Tropical medicine One Baylor PlazaHoustonTX 77030USA molecular Virology&microbiology One Baylor PlazaHoustonTX77030USA Biologyof Inflammation Center Baylor College of MedicineOne BaylorPlazaHoustonTX77030USA michael E.DeBakey VA Center for Translational Research on Inflammatory Diseases HoustonTX 77030USA

Severe acute respiratory syndrome coronavirus 2(SARSCov-2)is the etiologic agent of the coronavirus disease 19(COVID-19)*** viral infections like SARS-CoV-2,a robust anti-viral type 1 immune response,including upregulation of type 1 CD4+T helper cells(Th1),is required for effective viral clearance while minimizing end-organ pathology and collateral tissue damage.

关键词： pathology acute respiratory

Integrated Single-cell multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 67-88页

作者： manickam Ashokkumar Wenwen mei jackson j.Peterson Yuriko Harigaya David m.murdoch David m.margolis Caleb Kornfein Alex Oesterling Zhicheng Guo Cynthia D.Rudin Yuchao jiang Edward P.Browne Department of medicine University of North Carolina at Chapel HillChapel HillNC 27599USA HIV Cure Center University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Biostatistics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of microbiology and Immunology University of North Carolina at Chapel HillChapel HillNC 27599USA Department of Genetics University of North Carolina at Chapel HillChapel HillNC 27599USA Department of medicine Duke UniversityDurhamNC 27708USA Department of Computer Science Duke UniversityDurhamNC 27708USA Department of Statistics Texas A&M UniversityCollege StationTX 77843USA Department of Biology Texas A&M UniversityCollege StationTX 77843USA Department of Biomedical Engineering Texas A&M UniversityCollege StationTX 77843USA

Despite the success of antiretroviral therapy,human immunodeficiency virus(HIV)cannot be cured because of a reservoir of latently infected cells that evades *** understand the mechanisms of HIV latency,we employed an integrated single-cell RNA sequencing(scRNA-seq)and single-cell assay for transposase-accessible chromatin with sequencing(scATAC-seq)approach to simultaneously profile the transcriptomic and epigenomic characteristics of~125,000 latently infected primary CD4^(+)T cells after reactivation using three different latency reversing *** expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor(TF)activities across the cell *** identified cellular transcripts and TFs whose expression/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%-79%accurate at predicting viral ***,we validated the role of two candidate HIV-regulating factors,FOXP1 and GATA3,in viral *** data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.

关键词： HIV latency reversal Primary CD4þT cell Single-cell multiomics HIV-regulating factor machine learning

This work was supported by the European Research Council Advanced Grant(ETAP-742985 to *** j.F.)and by the ministry of Science and Technology(grant 110-2636-B-005-001 to K.-j.L.).

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Plant Communications 2024年第1期5卷 130-147页

作者： Yu Zhang Yuan Fu Wenfei Xian Xiuli Li Yong Feng Fengjiao Bu Yan Shi Shiyu Chen Robin van Velzen Kai Battenberg Alison m.Berry marco G.Salgado Hui Liu Tingshuang Yi Pascale Fournier Nicole Alloisio Petar Pujic Hasna Boubakri m.Eric Schranz Pierre-marc Delaux Gane Ka-Shu Wong Valerie Hocher Sergio Svistoonoff Hassen Gherbi Ertao Wang Wouter Kohlen Luis G.Wall martin Parniske Katharina Pawlowski Philippe Normand jeffrey j.Doyle Shifeng Cheng Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Biosystematics Group Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Department of Plant Sciences University of CaliforniaDavisDavisCA 95616USA Department of Ecology Environment and Plant SciencesStockholm University10691 StockholmSweden Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Universite´de Lyon Universite´Lyon 1CNRSUMR5557Ecologie MicrobienneINRAUMR 141843 bd du 11 novembre 191869622 VilleurbanneFrance Laboratoire de Recherche en Sciences Ve´ge´tales(LRSV) Universite´de ToulouseCNRSUPS24 chemin de Borde RougeAuzevilleBP4261731326 Castanet TolosanFrance Department of Biological Sciences University of AlbertaEdmontonAB T6G 2E9Canada French National Research Institute for Sustainable Development(IRD) UMR LSTM(IRD/CIRAD/INRAe/Montpellier University/Supagro)-Campus International BaillarguetTA A-82/J34398 Montpellier Cedex 5France National Key Laboratory of Plant molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologySIBSChinese Academy of SciencesShanghaiChina Laboratory of molecular Biology Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Laboratory of Biochemistry Microbiology and Soil Biological InteractionsDepartment of Science and TechnologyNational University of QuilmesCONICETBernalArgentina Faculty of Biology GeneticsLMU MunichGroßhaderner Strasse 2-482152 MartinsriedGermany School of Integrative Plant Science Sections of Plant Biology and Plant Breeding&GeneticsCornell UniversityIthacaNY 14853USA State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Univer

Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume *** species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time ***,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the ***,much remains to be learned about nodulation,especially outside of ***,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of *** phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the *** transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response *** 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage *** study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC ***-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in ***,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

关键词： nitrogen-fixing root-nodule symbiosis two competing hypotheses phylogenomics phylotranscrip-tomics conserved non-coding elements convergence deep homology