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MethylGenotyper:Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data

Genomics, Proteomics & Bioinformatics 2024年第3期22卷 43-54页

作者： Yi Jiang Minghan Qu Minghui Jiang Xuan Jiang Shane Fernandez Tenielle Porter simon M.Laws Colin L.Masters Huan Guo Shanshan Cheng Chaolong Wang Ministry of Education Key Laboratory of Environment and Health School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Department of Epidemiology and Biostatistics School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Centre for Precision Health Edith Cowan UniversityPerthWA 6027Australia Collaborative Genomics and Translation Group School of Medical and Health SciencesEdith Cowan UniversityPerthWA 6027Australia Curtin Medical School BentleyWA 6102Australia The Florey Institute of Neuroscience and Mental Health University of MelbourneMelbourneVIC 3052Australia Department of Occupational and Environmental Health School of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China

Epigenome-wide association studies(EWAS)are susceptible to widespread confounding caused by population structure and genetic ***,kinship estimation is challenging in EWAS without genotyping ***,we proposed MethylGenotyper,a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms(SNPs)directly from commercial DNA methylation *** modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization *** conducted extensive simulations to demonstrate the performance of the *** applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples,we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%,enabling the identification of 255 pairs of close ***,we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse *** also implemented MethylGenotyper in a publicly available R package(https://***/Yi-Jiang/MethylGenotyper)to facilitate future large-scale EWAS.

关键词： DNA methylation Genotype calling Genetic relatedness Population structure Epigenome-wide association study

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Leadership and Top Management Influence on Total Quality Management Implementation in the Ghanaian Construction Industry

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Journal of Building Construction and Planning Research 2024年第2期12卷 37-51页

作者： Ansah Samuel Kwame Tekpe Emmanuel Ametepey simon Ofori Department of Construction Technology and Management Cape Coast Technical University Cape Coast Ghana Department of Building Technology Koforidua Technical University Koforidua Ghana

This study aims to determine the key and underlying Leadership and Top Management (LTM) factors that have a significant impact on sustaining the implementation of Total Quality Management (TQM) within the construction industry in Ghana. The research methodology employed in this study was a quantitative technique. Questionnaires were distributed to 641 participants within construction industry in Ghana. Questionnaires retrieved for the analysis were 536. Three steps approached were used for the data analysis. These include Exploratory Factor Analysis (EFA), Confirmatory Factor Analysis (CFA), and Structural Equation Modeling (SEM) analysis. After conducting the EFA and CFA, SEM was also used to analyze the construct validity. The SEM analysis helps to determine four key indicator variables for the leadership and top management construct. These include Leadership/Top Management approach to employees’ management, Leadership/Top Management understanding of TQM, Leadership/Top Management empowerment of employees to resolve quality issues, and Leadership/Top Management endorsement of TQM. All the four indicator variables were found to be good of fit and closely associated with the dependent variable. The study adds to the body of knowledge by using EFA, CFA and SEM techniques to establish key leadership and top management factors affecting TQM implementation in Ghana’s construction industry. The findings in general suggested that leadership and top Management factors identified have a direct positive impact on sustaining TQM implementation in the Ghanaian construction industry. Consequently, the leadership and top management factors identified in this study can help improve TQM in the Ghanaian construction industry.

关键词： Construction Industry Leadership Top management Total Quality Management

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关于全球高等教育研究未来的若干思考

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中国高教研究 2024年第8期 9-13页

作者： simon Marginson 沈文钦(译) 王嘉璐(译) 牛津大学教育系牛津OX12JD 全球高等教育研究中心北京大学教育学院

制度化的高等教育研究起源于20世纪60年代的美国,其中马丁·特罗和伯顿·克拉克作为开创者作出了独特的贡献。20世纪80年代以来,新自由主义的崛起、全球化的发展、技术的膨胀成为高等教育系统的突出特征,高等教育研究需要对这些发展及... 详细信息

制度化的高等教育研究起源于20世纪60年代的美国,其中马丁·特罗和伯顿·克拉克作为开创者作出了独特的贡献。20世纪80年代以来,新自由主义的崛起、全球化的发展、技术的膨胀成为高等教育系统的突出特征,高等教育研究需要对这些发展及其效应进行深入分析。在新的时代背景下,高等教育系统自身面临新的挑战,这主要包括毕业生的结果与机会公平、大学生就业、高等教育的社会价值以及如何促进更加多元的声音和主题等方面。随着东亚高等教育体系的崛起,世界高等教育格局正在发生重大变迁,世界各国需要增进彼此的理解,通过他者思考以理解自身的高等教育体系和世界高等教育体系是必不可少的。

关键词：高等教育研究多样性人力资本

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Photoelectrochemical Iron-Catalyzed C(sp^(3))-H Borylation of Alkanes in a Position-Selective Manner

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CCS Chemistry 2024年第6期6卷 1430-1438页

作者： Wen Wei Bin Wang simon L.Homölle Jinbin Zhu Yanjun Li Tristan von Münchow Isaac Maksso Lutz Ackermann Institut für Organische und Biomolekulare Chemie Georg-August-Universität Göttingen37077 Göttingen

Catalytic C-H borylation is of prime topical importance,since easily available feedstock chemicals can thereby be transformed into valuable transient functional groups in the absence of directing ***,we disclose an iron-catalyzed C(sp^(3))-H borylation of simple,non-prefunctionalized alkanes,providing access to value-added products in a single step by means of *** power of merging photo-and electrochemistry was mirrored by ample scope and exceedingly mild reaction ***,an outstanding position-selectivity in favor of primary C(sp^(3))-H proved viable within the photoelectrochemical borylation through a chemo-selective anodic overoxidation *** ferro-photoelectrochemistry strategy avoids toxic precious transition metals,enabling C(sp^(3))-H borylations in a site-selective fashion.

关键词： photoelectrocatalysis C(sp^(3))-H borylation iron catalysis position-selectivity chlorine radical

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Proterozoic to Phanerozoic case studies of laser ablation microanalysis for microbial carbonate U–Pb geochronology

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Geoscience Frontiers 2024年第2期15卷 30-40页

作者： Yuxiang Jiang simon V.Hohl Xiangtong Huang Shouye Yang State Key Laboratory of Marine Geology School of Ocean and Earth SciencesTongji UniversityShanghai 200092China

Some of the earliest bio-sedimentary records of life on Earth are represented by microbial carbonates,which are also critical geochemical archives of ancient seawater chemistry and the environmental circumstances in which they *** paleo-microbial environments on Earth and potentially other planets requires precise determination of the depositional ages of these ***(abiogenic)carbonate geochemistry communities can now use developments in in-situ laser ablation U-Pb dating using inductively coupled plasma mass spectrometry(LA-ICP-MS).Due to the effects of impurity mixing and diagenesis,microbial carbonates have received little geochronological study despite their broad relevance for understanding ancient seawater’s environmental conditions and geochemical *** study demonstrates using time-of-flight mass spectrometry(TOF-MS)to perform quick,quantitative elemental mapping before U-Pb spot dating to improve experiment success rates and data reliability and offers four practical application examples.

关键词： Stromatolite Microbial carbonate Carbonate geochronology In-situ LA-ICP-MS ICP-Time Of Flight-MS Trace element mapping

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Advancing Malaria Prediction in Uganda through AI and Geospatial Analysis Models

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Journal of Geographic Information System 2024年第2期16卷 115-135页

作者： Maria Assumpta Komugabe Richard Caballero Itamar Shabtai simon Peter Musinguzi Center for Information Systems & Technology Claremont Graduate University Claremont California USA Department of Information Technology Faculty of Business and ICT University of Kisubi Entebbe Uganda Faculty of Health Sciences University of Kisubi Entebbe Uganda Department of Agriculture Production Faculty of Agriculture Kyambogo University Kyambogo Uganda Department of Agriculture and Natural Sciences Faculty of Agriculture Uganda Martyrs University Kampala Uganda

The resurgence of locally acquired malaria cases in the USA and the persistent global challenge of malaria transmission highlight the urgent need for research to prevent this disease. Despite significant eradication efforts, malaria remains a serious threat, particularly in regions like Africa. This study explores how integrating Gregor’s Type IV theory with Geographic Information Systems (GIS) improves our understanding of disease dynamics, especially Malaria transmission patterns in Uganda. By combining data-driven algorithms, artificial intelligence, and geospatial analysis, the research aims to determine the most reliable predictors of Malaria incident rates and assess the impact of different factors on transmission. Using diverse predictive modeling techniques including Linear Regression, K-Nearest Neighbor, Neural Network, and Random Forest, the study found that;Random Forest model outperformed the others, demonstrating superior predictive accuracy with an R2 of approximately 0.88 and a Mean Squared Error (MSE) of 0.0534, Antimalarial treatment was identified as the most influential factor, with mosquito net access associated with a significant reduction in incident rates, while higher temperatures correlated with increased rates. Our study concluded that the Random Forest model was effective in predicting malaria incident rates in Uganda and highlighted the significance of climate factors and preventive measures such as mosquito nets and antimalarial drugs. We recommended that districts with malaria hotspots lacking Indoor Residual Spraying (IRS) coverage prioritize its implementation to mitigate incident rates, while those with high malaria rates in 2020 require immediate attention. By advocating for the use of appropriate predictive models, our research emphasized the importance of evidence-based decision-making in malaria control strategies, aiming to reduce transmission rates and save lives.

关键词： Malaria Predictive Modeling Geospatial Analysis Climate Factors Preventive Measures

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Below-Moho Earthquakes of Tibet, Himalaya, the Indian Foreland, and Worldwide: How, Where and Why?

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Acta Geologica Sinica(English Edition) 2024年第S1期 27-29页

作者： simon L.KLEMPERE WANG Shiqi SONG Xiaohan Jackie R.HARRIS Hitank KASAUNDHAN LIANG Xiaofeng Department of Geophysics Stanford University Department of Geology Carleton College Research School of Earth Sciences Australian National University Institute of Geology and Geophysics Chinese Academy of Sciences

We seek to understand lithospheric rheology by mapping continental earthquake depths relative to Moho depth, across the entire India/Asia convergent orogen, and eventually worldwide. Such mapping has particular value in geothermometry, and potentially in identifying regions of delamination. How: We are extending our Sn/Lg method beyond amplitude ratios of regional seismic phases measured on arrays(array Sn/Lg method, Wang and Klemperer, 2021) to include frequency proxies for earthquake depth relative to Moho(Wang & Klemperer, 2024a, b; Harris et al., 2024).

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Exploring a New Lifetime Distribution for Modelling the Waiting Time of Bank Customers

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Journal of Applied Mathematics and Physics 2024年第1期12卷 194-209页

作者： simon A. Ogumeyo Jacob C. Ehiwario Festus C. Opone Department of Mathematics Delta State University of Science and Technology Ozoro Nigeria Department of Statistics University of Delta Agbor Nigeria Department of Statistics Delta State University of Science and Technology Ozoro Nigeria

The fitting of lifetime distribution in real-life data has been studied in various fields of research. With the theory of evolution still applicable, more complex data from real-world scenarios will continue to emerge. Despite this, many researchers have made commendable efforts to develop new lifetime distributions that can fit this complex data. In this paper, we utilized the KM-transformation technique to increase the flexibility of the power Lindley distribution, resulting in the Kavya-Manoharan Power Lindley (KMPL) distribution. We study the mathematical treatments of the KMPL distribution in detail and adapt the widely used method of maximum likelihood to estimate the unknown parameters of the KMPL distribution. We carry out a Monte Carlo simulation study to investigate the performance of the Maximum Likelihood Estimates (MLEs) of the parameters of the KMPL distribution. To demonstrate the effectiveness of the KMPL distribution for data fitting, we use a real dataset comprising the waiting time of 100 bank customers. We compare the KMPL distribution with other models that are extensions of the power Lindley distribution. Based on some statistical model selection criteria, the summary results of the analysis were in favor of the KMPL distribution. We further investigate the density fit and probability-probability (p-p) plots to validate the superiority of the KMPL distribution over the competing distributions for fitting the waiting time dataset.

关键词： KM-Transformation Power Lindley Distribution Data Fitting Moments Quantiles

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Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

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Molecular Plant 2024年第8期17卷 1307-1327页

作者： Yaming Liu Dario Esposto Lisa K.Mahdi Andrea Porzel Pauline Stark Hidayat Hussain Anja Scherr-Henning simon Isfort Ulschan.Bathe Ivan F.Acosta Alga Zuccaro Gerd U.Balcke Alain Tissier Department of Cell and Metabolic Biology Leibniz Institute of Plant BiochemistryHalleGermany Institute for Plant Sciences Cluster of Excellence on Plant Sciences(CEPLAS)Cologne BiocenterUniversity of CologneCologneGermany Department of Bioorganic Chemistry Leibniz Institute of Plant BiochemistryHalleGermany Max Planck Institute for Plant Breeding Research CologneGermany Horticultural Sciences University of FloridaGainesvilleFLUSA.

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense *** include the induction of a cocktail of defense metabolites that typically restrict pathogen ***,we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana(Bs)and Fusarium graminearum(Fg)at the metabolite *** identify hordedanes,a previously undescribed set of labdane-related diterpenoids with antimicrobial properties,as critical players in these *** of barley roots by Bs and Fg elicits hordedane synthesis from a 60o-kb gene *** reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes,including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid(19-OH-HTA).Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but,unexpectedly,show reduced Bs *** contrast,colonization by Fusarium graminearum,another fungal pathogen of barley and wheat,is 4-fold higher in the mutants completely lacking ***,19-OH-HTA enhances both germination and growth of Bs,whereas it inhibits other pathogenic fungi,including *** of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of *** together,these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

关键词： barley Hordeum vulgare diterpenoid phytoalexins gene cluster pathogenic fungi Bipolaris sorokininiana Fusarium graminearum

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Meldonium-induced steatosis is associated with increased delta 6 desaturation and reduced elongation of n-6 polyunsaturated fatty acids

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Liver Research 2024年第3期8卷 152-164页

作者： Bodil Bjørndal Siri Lunde Tungland Pavol Bohov Magne OSydnes simon N.Dankel Lise Madsen Rolf K Berge Department of Clinical Science University of BergenBergenNorway Department of Sports Physical Activity and FoodWestern Norway University of Applied SciencesBergenNorway Department of Chemistry Bioscience and Environmental EngineeringUniversity of StavangerStavangerNorway Department of Clinical Medicine University of BergenBergenNorway Department of Heart Disease Haukeland University HospitalBergenNorway

Background and objective Metabolic associated fatty liver disease(MAFLD)is associated with abnormal lipid *** dysfunction is considered an important factor in the onset of MAFLD,whereas altered fatty acid composition has been linked to the severity of the *** acid(TTA),shown to induce mitochondrial proliferation and alter the fatty acid composition,was used to delay the accumulation of hepatic *** study aimed to evaluate how impaired mitochondrial fatty acid beta-oxidation affects fatty acid composition by incorporating meldonium into a high-carbohydrate *** C57BL/6 mice(n=40)were fed high-carbohydrate diets supplemented with meldonium,TTA,or a combination of meldonium and TTA for 21 *** levels were determined in liver samples,and fatty acid composition was measured in both liver and plasma ***,desaturase and elongase activities were *** hepatic activities and gene expression levels of enzymes involved in fatty acid metabolism were measured in liver samples,whereas carnitines,their precursors,and acylcarnitines were measured in plasma *** The meldonium-induced depletion of L-carnitine and mitochondrial fatty acid oxidation was confirmed by reduced plasma levels of L-carnitine and *** component analyses of the hepatic fatty acid composition revealed clustering dependent on meldonium and *** meldonium-induced increase in hepatic triacylglycerol levels correlated negatively with estimated activities of elongases and was associated with higher estimated activities of delta-6 desaturase(D6D;C18:4n-3/C18:3n-3 and C18:3n-6/C18:2n-6),and increased circulating levels of C18:4n-3 and C18:3n-6(gamma-linolenic acid).TTA mitigated meldonium-induced triacylglycerol levels by 80%and attenuated the estimated D6D activities,and elongation of n-6 polyunsaturated fatty acids(PUFAs).TTA also attenuated the meldonium-mediated reduction of C24:1n-

关键词： Steatosis Fatty acid composition Fatty acid oxidation Meldonium Desaturase Elongasen-6 polyunsaturated fatty acid

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