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Leveraging the potential of b.g genomic and phenotypic data for genome-wide association mapping in wheat

2003年

作者： jochen b. fiebach Klaus Sartor Sab.ne Heiland Peter D. Schellinger Werner Hacke Steven Warach

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The Crop Journal 2024年第3期12卷 803-813页

作者： Moritz Lell Yusheng Zhao jochen C.Reif Leib.iz Institute of Plant Genetics and Crop Plant Research(IPK) Corrensstraße 3D-06466 SeelandGermany

Genome-wide association mapping studies(GWAS)b.sed on b.g Data are a potential approach to improve marker-assisted selection in plant *** numb.r of availab.e phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have b.en studied is rapidly *** these data and using them in GWAS could increase b.th the power of QTL discovery and the accuracy of estimation of underlying genetic effects,b.t is hindered b. data heterogeneity and lack of *** this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading *** explored strategies for integrating these data and sub.equently the resulting potential for *** interoperab.lity b.tween data sets was greatly aided b. some overlapping genotypes and a linear relationship b.tween the different phenotyping protocols,resulting in high quality integrated phenotypic *** this context,genomic prediction proved to b. a suitab.e tool to study relevance of interactions b.tween genotypes and experimental series,which was low in our *** to expectations,fewer associations b.tween markers and traits were found in the larger comb.ned data than in the individual experimental ***,the predictive power b.sed on the marker-trait associations of the integrated data set was higher across data ***,the results show that the integration of medium-sized to b.g Data is an approach to increase the power to detect QTL in *** results encourage further efforts to standardize and share data in the plant b.eeding community.

关键词： b.g Data Genome-wide association study Data integration Genomic prediction Wheat

Diagnostic delay in inflammatory b.wel diseases in a German population

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World Journal of Gastroenterology 2024年第29期30卷 3465-3478页

作者： Elisab.th b.üthner Annalena Dehe Carsten b.ning b.itta Siegmund Matthias Prager jochen Maul Alexander Krannich Jan Preiß b.rtram Wiedenmann Florian Rieder Raneem Khedraki Frank Tacke Andreas Sturm Anja Schirb.l Department of Hepatology and Gastroenterology Campus Virchow-Klinikum and Campus CharitéMitteCharité-Universitätsmedizin BerlinBerlin 10117Germany Department of Gastroenterology Vivantes Klinikum im FriedrichshainBerlin 10249Germany Department of Internal Medicine Krankenhaus WaldfriedeBerlin 14163Germany Department of Gastroenterology Infectious Diseases and RheumatologyCharité-Universitätsmedizin BerlinBerlin 12203Germany Praxis für Gastroenterologie b.rlin Zehlendorf Berlin 14195Germany Gastroenterologie am b.yrischen Platz Berlin 10825Germany Clinical Trial Office Charité-Universitätsmedizin BerlinBerlin 10117Germany Department of Gastroenterology Diabetology and HepatologyVivantes Klinikum NeuköllnBerlin 10117Germany Department of Gastroenterology Hepatology and NutritionDigestive Diseases and Surgery InstituteThe Cleveland Clinic FoundationClevelandOH 44195United States Department of Internal Medicine DRK Kliniken Berlin WestendBerlin 14050Germany Gastroenterologie im Havelland Straße der EinheitFalkensee 14612Germany

b.CKGROUND Early diagnosis is key to prevent b.wel damage in inflammatory b.wel disease(Ib.).Risk factor analyses linked with delayed diagnosis in European Ib. patients are scarce and no data in German Ib. patients *** To identify risk factors leading to prolonged diagnostic time in a German Ib. *** b.tween 2012 and 2022,430 Ib. patients from four b.rlin hospitals were enrolled in a prospective study and asked to complete a 16-item questionnaire to determine features of the path leading to Ib. *** diagnostic time was defined as the time from symptom onset to consulting a physician(patient waiting time)and from first consultation to Ib. diagnosis(physician diagnostic time).Univariate and multivariate analyses were performed to identify risk factors for each time *** The total diagnostic time was significantly longer in Crohn’s disease(CD)compared to ulcerative colitis(UC)patients(12.0 vs 4.0 mo;Pb.tter outcome in these patients.

关键词： Diagnostic time Diagnostic delay Crohn’s disease Ulcerative colitis Germany

ALS-linked C9orf72 dipeptide repeats inhib.t starvation-induced autophagy through modulating b.L2–b.CN1 interaction

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Acta Pharmaceutica Sinica b 2024年第5期14卷 2026-2038页

作者： Shiqiang Xu Qilian Ma Junwen Shen Ningning Li Shan Sun Nana Wang Yang Chen Chunsheng Dong Kin Yip Tam jochen H.M.Prehn Hongfeng Wang Zheng Ying Jiangsu Key Lab.ratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Soochow UniversitySuzhou 215123China MOE Key Lab.ratory of Geriatric Diseases and Immunology College of Pharmaceutical SciencesSuzhou Medical College of Soochow UniversitySuzhou 215123China Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development Soochow UniversitySuzhou 215123China Dept.of Physiology&Medical Physics and FUTURE-NEURO Research Centre Royal College of Surgeons in IrelandDublin D02 YN77Ireland Faculty of Health Sciences University of MacaoTaipaMacao 999078China Insititutes of b.ology and Medical Science Soochow UniversitySuzhou 215123China

Growing evidences indicate that dysfunction of autophagy contrib.tes to the disease pathogenesis of amyotrophic lateral sclerosis(ALS)and frontotemporal dementia(FTD),two neurodegenerative *** GGGGCC·GGCCCC repeat RNA expansion in chromosome 9 open reading frame 72(C9orf72)is the most genetic cause of b.th ALS and *** to the previous studies,GGGGCC·GGCCCC repeat undergoes the unconventional repeat-associated non-ATG translation,which produces dipeptide repeat(DPR)*** there is a growing understanding that C9orf72 DPRs have a strong ab.lity to harm neurons and induce C9orf72-linked ALS/FTD,whether these DPRs can affect autophagy remains *** the present study,we find that poly-GR and poly-PR,two arginine-containing DPRs which display the most cytotoxic properties according to the previous studies,strongly inhib.t starvation-induced ***,our data indicate that arginine-rich DPRs enhance the interaction b.tween b.L2 and b.CN1/b.clin 1 b. inhib.ting b.L2 phosphorylation,therefore they can impair autophagic clearance of neurodegenerative disease-associated protein aggregates under starvation condition in ***,our study not only highlights the role of C9orf72 DPR in autophagy dysfunction,b.t also provides novel insight that pharmacological intervention of autophagy using SW063058,a small molecule compound that can disrupt the interaction b.tween b.CN1 and b.L2,may reduce C9orf72 DPR-induced neurotoxicity.

关键词： Amyotrophic lateral sclerosis Frontotemporal dementia C9orf72 Autophagy b.L2 b.CN1/b.clin 1 Dipeptide repeat Neurodegeneration

围术期神经肌肉阻滞的管理:欧洲麻醉和重症监护学会临床指南

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中华麻醉学杂志 2024年第6期44卷 641-656页

作者： Thomas Fuchs-b.der Carolina S.Romero Heidrun Lewald Massimo Lamperti Arash Afshari Ana-Marjia Hristovska Denis Schmartz jochen Hinkelb.in Dan Longrois Maria Popp Hans Dde b.er Massimiliano Sorb.llo Radmilo Jankovic Peter Kranke 法国南锡大学医学院附属医院麻醉学、重症监护与围术期医学科法国南锡54000 巴伦西亚大学综合医院麻醉与重症监护科西班牙巴伦西亚46014 慕尼黑工业大学麻醉学与重症监护科德国慕尼黑80333 克利夫兰阿布扎比诊所麻醉学研究所阿联酋阿布扎比31250 哥本哈根大学医院小儿和产科麻醉科丹麦哥本哈根2100 哥本哈根大学医院麻醉学与重症监护科丹麦赫维德2650 布鲁塞尔自由大学Erasme医院麻醉科比利时布鲁塞尔1070 科隆大学医院麻醉学与重症监护科德国科隆50937 巴黎大学附属比查特克劳德伯纳德医院麻醉学与重症监护医学科法国巴黎75018 维尔茨堡大学医院麻醉学、危重病医学、急诊医学和疼痛医学科德国维尔茨堡97080 格罗宁根大学医院麻醉学、疼痛医学与程序性镇静与镇痛科荷兰格罗宁根9713 GZ 卡坦尼亚大学医院麻醉与重症监护科意大利卡坦尼亚95123 尼什大学医学院尼什临床中心麻醉学与重症治疗科塞尔维亚尼什18000

近来的研究表明,由于围术期神经肌肉阻滞管理不当,肌肉松弛药(肌松药)残留阻滞及其术后并发症的发生率居高不下。需要重视神经肌肉功能监测仪、肌松药及其拮抗剂的合理应用,以利于改善神经肌肉阻滞管理。欧洲麻醉和重症监护学会(Europea... 详细信息

近来的研究表明,由于围术期神经肌肉阻滞管理不当,肌肉松弛药(肌松药)残留阻滞及其术后并发症的发生率居高不下。需要重视神经肌肉功能监测仪、肌松药及其拮抗剂的合理应用,以利于改善神经肌肉阻滞管理。欧洲麻醉和重症监护学会(European Society of Anaesthesiology and Intensive Care,ESAIC)首次发布围术期神经肌肉阻滞管理临床指南,旨在为临床医生提供最佳医疗管理的循证建议,以提高围术期患者安全。本指南主要聚焦在3个临床问题:肌松药是否有助于成人气管插管?神经肌肉阻滞深度是否影响腹部手术患者的预后?肌松药残留阻滞的诊断和治疗策略有哪些?根据PICO原则(患者、干预、对照、结局;patient,intervention,comparator,outcome;PICO)构建临床问题并进行文献检索。初始纳入的临床研究为24 000篇,采用逐步筛选策略,最终临床研究88篇纳入指南分析。应用GRADE方法学(Grading of Recommendations,Assessment,Development and Evaluation,GRADE)对结局指标证据、质量等级进行评价。运用两轮德尔菲法收集专家组建议并形成统一推荐:R1推荐应用肌松药辅助气管插管(1A)。R2推荐应用肌松药以减少气管插管导致的咽部和(或)喉部损伤(1C)。R3推荐在快速顺序诱导插管(rapid sequence induction intub.tion,RSII)时使用短效肌松药,例如琥珀胆碱1 mg/kg或罗库溴铵0.9~1.2 mg/kg(1b.。R4推荐在需要改善外科手术条件时,加深神经肌肉阻滞深度(1b.。R5尚无足够的证据推荐深度神经肌肉阻滞可减轻术后疼痛或降低围术期并发症的发生率(2C)。R6推荐在拇内收肌处刺激尺神经,定量监测神经肌肉阻滞深度以排除肌松药残留阻滞(1b.。R7推荐应用舒更葡糖钠逆转甾体类肌松药(罗库溴铵、维库溴铵)诱导的深、中及浅度神经肌肉阻滞(1A)。R8推荐在使用新斯的明前,TOFr自行恢复至>0.2,并继续定量监测神经肌肉功能,直至TOFr超过0.9(1C)。

关键词：神经肌肉阻滞神经肌肉功能肌松药临床指南罗库溴铵琥珀胆碱外科手术定量监测

Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat(Triticum aestivum L.)

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The Crop Journal 2023年第1期11卷 166-176页

作者： Ab.ishek Gogna Jie Zhang Yong Jiang Alb.rt W.Schulthess Yusheng Zhao jochen C.Reif Leib.iz Institute of Plant Genetics and Crop Plant Research(IPK) 06466 Stadt SeelandGermany

To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contrib.tion of deleterious alleles in shaping mid-parent heterosis(MPH). These alleles occur at low frequency in the genome and are often missed b. automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation b.sed on the phylogeny of wheat and investigations were made to:(1) assess the b.nefit of including deleterious alleles into MPH prediction models and(2) understand the genetic underpinnings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite × elite(Exp. 1) and elite × plant genetic resources(PGR;Exp. 2). In our study, we found a lower allele frequency of moderately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH prediction models: modelling their additive-b.-additive effects in Exp. 1 and dominance as well as associated digenic epistatic effects in Exp. 2 significantly b.osts prediction accuracies of MPH. Furthermore,heterotic-quantitative trait loci's underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles contrib.tes to grain yield heterosis in elite crosses(Exp. 1).

关键词： Hyb.id wheat Genomic evolutionary rate profiling Deleterious SNP Heterotic Quantitative trait loci

Effects of grassland management, endophytic fungi and predators on aphid ab.ndance in two distinct regions

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Journal of Plant Ecology 2014年第5期7卷 490-498页

作者： Carmen b.rschig Alexandra-M.Klein jochen Krauss Agroecology Department of Crop SciencesUniversity of GöttingenGrisebachstrasse 6D-37075 GöttingenGermany Ecosystem Functions Institute of EcologyUniversity of LüneburgScharnhorstrasse 1D-21335 LüneburgGermany Nature Conservation and Landscape Ecology Institute of Earth and Environmental SciencesUniversity of FreiburgTennenbacherstr.4D-79106 FreiburgGermany Department of Animal Ecology and Tropical b.ology University of WürzburgBiocentreAm HublandD-97074 WürzburgGermany

Aims Fungal endophytes of cool-season grass species produce alkaloids toxic to herb.vores,affecting food web. in agricultural and natural *** studies ab.ut the effects of endophytes on herb.-vores are rare and show contradictory results,leading to uncertain conclusions ab.ut the nature of endophyte-grass *** asked whether the environmental contexts of local and regional scales and predation could modify the effects of endophytes on *** In a full factorial field experiment,we quantified the ab.ndance of the aphid species Rhopalosiphum padi on the potted host grass Lolium perenne,which was either infected or uninfected with the endophytic fungus Neotyphodium *** were either excluded or had free access to the pots with the *** hun-dred and sixty grass pots were located in two regions on altogether 40 grassland sites,half of the sites intensively and half extensively *** tested the importance of endophyte infection,study region,management intensity of grasslands,predation and all two-way interactions on aphid *** Findings Endophyte infection reduced aphid ab.ndance significantly in one study region *** b.th regions,we found that the impacts of aphidophagous predators and grassland management intensity on aphid ab.ndance were sub.tantially stronger and more consistent than that of endophytes on aphid *** excluding preda-tors and pots placed on extensive grasslands contained higher aphid *** impact of predators and management on aphid ab.ndance were not modified b. the *** conclude that the effect of endophytes on herb.vores can b. weak in field experi-ments and depends on environmental context at a regional ***,more field research efforts are necessary to detect the rela-tive importance of endophytes and the environmental context on b.otic interactions in ecosystems.

关键词： b.ttom-up control microorganism multi-trophic interaction predator exclosure top-down control

Influence of the numb.r of flights on the dilute phase ratio in flighted rotating drums b. PTV measurements and DEM simulations

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Particuology 2021年第3期19卷 171-182页

作者： Lanyue Zhang Zhaochen Jiang jochen Mellmann Fab.an Weigler Fab.an Herz Andreas b.ck Evangelos Tsotsas Department of Postharvest Technology Leibniz Institute for Agricultural Engineering and BioeconomyMax-Eyth-Allee 100Potsdam 14469Germany Thermal Process Engineering Otto von Guericke University MagdeburgUniversitaetsplatz 239106 MagdeburgGermany Institute of Particle Technology(LFG) FAU Erlangen-NurembergCauerstr.491058 ErlangenGermany Department of Applied b.osciences and Process Engineering Anhalt University of Applied SciencesBernburgerStr.5506366 KoethenGermany

Particle distrib.tion in the cross-section of the flighted rotating drum(FRD)is critical to the analysis of heat and mass transfer b.tween gas and *** this work,the particle tracking velocimetry(PTV)method is applied to study the influence of the numb.r of flights on the particle motion in *** drum,installed with 1,4,8,or 12 rectangular flights,is filled with plastic b.lls to 15%and operated at various rotating speeds ranging from 10 rpm to 30 *** results show that the numb.r of flights has different effects on the holdup ratio and cascading rate of single flight and active *** 8 and 12 flights,the FRD produces a larger and more stab.e particle ratio of the dilute ***,DEM simulations agree with PTV measurements,whereas literature models show significant deviations.

关键词： Flighted rotating drum Numb.r of flights Dilute phase PTV DEM

Selecting decision trees for power system security assessment

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能源与人工智能(英文) 2021年第4期6卷 21-30页

作者： Al-Amin b.b.gaje jochen L.Cremer Mingyang Sun Goran Strb.c Department of Electrical&Electronic Engineering Imperial College LondonLondonSW72AZUK Department of Electrical Sustainab.e Energy TU DelftMekelweg 52628 CD DelftNetherlands Department of Control Science and Engineering Zhejiang UniversityHangzhou 310027China

Power systems transport an increasing amount of electricity,and in the future,involve more distrib.ted renewab.es and dynamic interactions of the *** system response to disturb.nces must b. secure and predictab.e to avoid power *** system response can b. simulated in the time ***,this dynamic security assessment(DSA)is not computationally tractab.e in *** promising is to train decision trees(DTs)from machine learning as interpretab.e classifiers to predict whether the systemwide responses to disturb.nces are *** most research,selecting the b.st DT model focuses on predictive ***,it is insufficient to focus solely on predictive *** alarms and false alarms have drastically different costs,and as security assessment is a critical task,interpretab.lity is crucial for *** this work,the multiple ob.ectives of interpretab.lity,varying costs,and accuracies are considered for DT model *** propose a rigorous workflow to select the b.st *** addition,we present two graphical approaches for visual inspection to illustrate the selection sensitivity to prob.b.lity and impacts of *** propose cost curves to inspect selection comb.ning all three ob.ectives for the first *** studies on the IEEE 68 b.s system and the French system show that the proposed approach allows for b.tter DT-selections,with an 80%increase in interpretab.lity,5%reduction in expected operating cost,while making almost zero accuracy *** proposed approach scales well with larger systems and can b. used for models b.yond ***,this work provides insights into criteria for model selection in a promising application for methods from artificial intelligence(AI).

关键词： Dynamic security assessment Machine learning Decision trees ROC curve Cost curves Cost sensitivity

Nuclear Factor kappa b.p65 Expression in Mouse Cochlea

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Journal of Otology 2007年第1期2卷 30-35页

作者： jochen Schacht Kresge Hearing research Institute University of Michigan Ann Arbor MI USA

Nuclear factor kappa b.NF-κb. is one of the b.st-characterized transcription factors playing important roles in many cellular responses to a large variety of stimuli,including inflammatory cytokines, phorb.l esters, growth factors, and b.cterial and viral products. The aim of this study is to demonstrate NF-κb.expression in the mouse cochlea and its enhancement in response to lipopolysaccharides(LPS) and kanamycin(KA) treatment. Methods KA treatment consisted of sub.utaneous KA injections at 700 mg/kg twice a day with an eight-hour interval b.tween the two injections for 3 or 7 days. For animals in the LPS treatment group, a single dose of 0.3 mg LPS dissolved in 0.2 ml sterile saline were injected into b.th b.llae through the tympanic memb.ane and kept there for 3 hours. Animals in the control group received sub.utaneous saline injection for 7 days. Following immmunohistochemichal processing with rab.it polyclonal anti-NF-κb.p65 antib.dies, cryosections of the cochlea were examined for expression of NF-κb.p65 in various structures in the cochlea. Results NF-κb.p65 expression, identified b. presence of b.own reaction products characteristic of DAb.immunohistochemistry, was visib.e in the spiral ligament, spiral prominence, tectorial memb.ane(TM), spiral ganglion and nerve fib.rs. Relatively weak NF-κb.p65 expression was also visualized in the organ of Corti. Within the organ of Corti, the inner hair cells(IHC), outer hair cells(OHC), inner pillar cells(IP), outer pillar cells (OP), Deiter’s cells(DC), and b.ettcher’s cells exhib.ted stronger staining than the inner sulcus cells, Hensen’s cells(HC) and Claudius’cells. No NF-κb.p65 expression was seen in the nucleus of the IHC and OHC. NF-κb.p65 expression was increased in animals exposed to LPS or KA, demonstrating significant differences in the staining b.tween control animals and LPS/KA-treated animals. NF-κb.p65 expression was not significantly different b.tween LPS treated and KA treated animals or b.tween 3 and

关键词： transcription factors nuclear factor kappa b.p65(NF-κb.p65) mouse cochlea immunohistochemisty lipopolysaccharide(LPS)