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Gene expression,transcription factor binding and histone modification predict leaf adaxial-abaxial polarity related genes

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Horticultural Plant Journal 2024年第4期10卷 971-982页

作者： Wei Sun Zhicheng Zhang Guusje Bonnema Xiaowu Wang Aalt Dirk jan van dijk State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China Sino-Dutch Joint Lab of Vegetable Genomics Beijing 100081China Bioinformatics Group Wageningen University and Research6708 PB Wageningenthe Netherlands Plant Breeding Wageningen University and Research6708 PB Wageningenthe Netherlands Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam1090 GE Amsterdamthe Netherlands

Leaf adaxial-abaxial(ad-abaxial)polarity is crucial for leaf morphology and function,but the genetic machinery governing this process remains *** uncover critical genes involved in leaf ad-abaxial patterning,we applied a combination of in silico prediction using machine learning(ML)and experimental analysis.A Random Forest model was trained using genes known to influence ad-abaxial polarity as ground *** expression data from various tissues and conditions as well as promoter regulation data derived from transcription factor chromatin immunoprecipitation sequencing(ChIP-seq)was used as input,enabling the prediction of novel ad-abaxial polarity-related genes and additional transcription *** to this,available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial *** on these analyses,we obtained a set of 111 novel genes which are involved in leaf ad-abaxial *** explore implications for vegetable crop breeding,we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell *** results demonstrated the utility of our computational approach for predicting candidate genes in crop *** findings expand the understanding of the genetic networks governing leaf ad-abaxial differentiation in agriculturally important vegetables,enhancing comprehension of natural variation impacting leaf morphology and development,with demonstrable breeding applications.

关键词： Machine learning Leaf polarity Arabidopsis thaliana Brassica rapa Transcription factor

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Reliability Investigation of BiCGStab and IDR Solvers for the Advection-Diffusion-Reaction Equation

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Communications in Computational Physics 2022年第6期32卷 156-188页

作者： Chris Schoutrop jan ten Thije Boonkkamp jan van dijk Department of Applied Physics Eindhoven University of TechnologyThe Netherlands Department of Mathematics and Computer Science Eindhoven University of TechnologyThe Netherlands

The reliability of BiCGStab and IDR solvers for the exponential scheme discretization of the advection-diffusion-reaction equation is *** resulting discretization matrices have real *** consider BiCGStab,IDR(S),BiCGStab(L)and various modifications of BiCGStab,where S denotes the dimension of the shadow space and L the degree of the polynomial used in the polynomial *** implementations of BiCGStab exist which are equivalent in exact arithmetic,however,not in finite precision *** modifications of BiCGStab we consider are;choosing a random shadow vector,a reliable updating scheme,and storing the best intermediate *** is shown that the Local Minimal Residual algorithm,a method similar to the“minimize residual”step of BiCGStab,can be interpreted in terms of a time-dependent advection-diffusion-reaction equation with homogeneous Dirichlet boundary conditions for the residual,which plays a key role in the convergence *** to the real eigenvalues,the benefit of BiCGStab(L)compared to BiCGStab is shown to be modest in numerical ***-sparse(*** random)shadow residual turns out to be essential for the reliability of *** reliable updating scheme ensures the required tolerance is truly *** the best intermediate solution has no significant *** is to modify BiCGStab with a random shadow residual and the reliable updating scheme,especially in the regime of large P´eclet and small Damk¨ohler *** alternative option is IDR(S),which outperforms BiCGStab for problems with strong advection in terms of the number of matrix-vector *** MATLAB code used in the numerical experiments is available on GitLab:https://***/ChrisSchoutrop/krylov-adr,a C++implementation of IDR(S)is available in the Eigen linear algebra library:http://***.

关键词： BiCGStab IDR shadow residual advection-diffusion-reaction equation

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Nonsteroidal anti-inflammatory drugs before endoscopic ultrasound guided tissue acquisition to reduce the incidence of post procedural pancreatitis

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World Journal of Gastroenterology 2024年第8期30卷 811-816页

作者： Mike de Jong Foke van Delft Christine Roozen Erwin-jan van Geenen Tanya Bisseling Peter Siersema Marco Bruno Department of Gastroenterology and Hepatology Radboud University Medical CenterNijmegen 6525 GANetherlands Department of Gastroenterology and Hepatology Erasmus University Medical CenterRotterdam 3015 GDNetherlands

Endoscopic ultrasound(EUS)with fine needle aspiration or fine needle biopsy is the gold standard for sampling tissue to diagnose pancreatic cancer and auto-immune pancreatitis or to analyze cyst *** most common reported adverse event of fine needle aspiration and/or fine needle biopsy is acute pancreatitis,which is likely induced by the same pathophysiological mechanisms as after en-doscopic retrograde cholangiopancreatography(ERCP).According to the current European Society of Gastrointestinal Endoscopy guideline,nonsteroidal anti-inflammatory drugs are administered prior to ERCP as a scientifically proven treatment to reduce post-ERCP pancreatitis incidence rate.A single suppository of diclofenac or indomethacin prior to EUS guided tissue acquisition(TA)is harm-less in healthy *** it is associated with low costs and,most important,may prevent a dreadsome complication,we strongly recommend the adminis-tration of 100 mg diclofenac rectally prior to *** will explain this recom-mendation in more detail in this review as well as the risk and pathophysiology of post-EUS TA pancreatitis.

关键词： Pancreatitis Endoscopic ultrasound Tissue acquisition Nonsteroidal antiinflammatory drugs Pancreatic cancer

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Epidemiology of insertional and midportion Achilles tendinopathy in runners:A prospective cohort study

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Journal of Sport and Health Science 2024年第2期13卷 256-263页

作者： Wenbo Chen Kyra L.A.Cloosterman Sita M.A.Bierma-Zeinstra Marienke van Middelkoop Robert-jan de Vos Department of Orthopaedic Surgery and Sports Medicine Erasmus MC University Medical CenterRotterdam 3015GDthe Netherlands Department of General Practice Erasmus MC University Medical CenterRotterdam 3015GDthe Netherlands Department of Sports Medicine Huashan HospitalFudan UniversityShanghai 200040China

Background:Achilles tendinopathy(AT)is a common problem among *** is only limited evidence for risk factors for AT,and most studies have not defined the AT *** study has compared the incidence and risk factors between insertional AT and midportion AT,though they are considered *** study aimed to assess incidence and risk factors of AT based on data from a large prospective *** secondary aim was to explore differences in risk factors between insertional and midportion ***:Participants were recruited from among registered runners at registration for running *** were completed at baseline,1 month before the event,1 week before the event,and 1 month after the *** concerning demographics,training load,registered events,and running-related injuries were collected at *** follow-up questionnaires collected information about new injuries.A pain map was used to diagnose midportion and insertional *** primary outcome was the incidence of *** logistic regression analysis was applied to identify risk factors for the ***:We included 3379 participants with a mean follow-up of 20.4 *** incidence of AT was 4.2%.The proportion of insertional AT was 27.7%and of midportion AT was 63.8%;the remaining proportion was a combined type of insertional and midportion *** had a significantly higher incidence(5%,95%confidence interval(95%CI):4.1%-6.0%)than women(2.8%,95%CI:2.0%-3.8%).AT in the past12 months was the most predominant risk factor for new-onset AT(odds ratio(OR)=6.47,95%CI:4.27-9.81).This was similar for both subcategories of AT(insertional:OR=5.45,95%CI:2.51-11.81;midportion:OR=6.96,95%CI:4.24-11.40).Participants registering for an event with a distance of 10/10.55 km were less likely to develop a new-onset AT(OR=0.59,95%CI:0.36-0.97)or midportion AT(OR=0.47,95%CI:0.23-0.93).Higher age had a significant negative association with insertional AT(OR=0.97,95%CI:0.9

关键词： Achilles tendon injury Incidence Risk factor Running-related injury

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Elevated fluid and glycosaminoglycan content in the Achilles tendon contribute to higher intratendinous pressures:Implications for Achilles tendinopathy

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Journal of Sport and Health Science 2024年第6期13卷 863-871页

作者： Lauren Pringels Gert-jan van Valckenborgh Patrick Segers Amelie Chevalier Hedwig Stepman Evi Wezenbeek Arne Burssens Luc vanden Bossche Department of Physical and Rehabilitation Medicine Ghent University HospitalGhent 9000Belgium Department of Rehabilitation Sciences and Physiotherapy Ghent UniversityGhent 9000Belgium Department of Electronics and Information Systems Ghent UniversityGhent 9000Belgium Department of Electromechanics University of AntwerpAntwerp 2020Belgium Department of Laboratory Medicine Ghent University HospitalGhent 9000Belgium Department of Orthopedic Surgery Ghent University HospitalGhent 9000Belgium

Achilles tendon;Achilles tendinopathy;Intratendinous pressure;Glycosaminoglycans;Tendon fluid Background:Tendinopathy alters the compositional properties of the Achilles tendon by increasing fluid and glycosaminoglycan *** has been speculated that these changes may affect intratendinous pressure,but the extent of this relationship remains ***,we aimed to investigate the impact of elevated fluid and glycosaminoglycan content on Achilles tendon intratendinous pressure and to determine whether hyaluronidase(HYAL)therapy can intervene in this potential ***:Twenty paired fresh-frozen cadaveric Achilles tendons were mounted in a tensile-testing machine and loaded up to 5%*** resting(at 0%strain)and dynamic pressure(at 5%strain)were assessed using the microcapillary infusion ***,intratendinous pressure was measured under native conditions before and after infusion of 2 mL physiological ***,80 mg of glycosaminoglycans were administered bilaterally to the paired *** right tendons were additionally treated with 1500 units of ***,both groups were retested,and the glycosaminoglycan content was ***:It was found that both elevated fluid and glycosaminoglycan content resulted in higher intratendinous resting and dynamic pressures(p<0.001).HYAL treatment induced a 2.3-fold reduction in glycosaminoglycan content(p=0.002)and restored intratendinous ***:The results of this study demonstrated that elevated fluid and glycosaminoglycan content in Achilles tendinopathy contribute to increased intratendinous resting and dynamic pressures,which can be explained by the associated increased volume and reduced permeability of the tendon matrix,*** degrades glycosaminoglycans sufficiently to lower intratendinous pressures and may,therefore,serve as a promising treatment.

关键词： Achilles tendon Achilles tendinopathy Intratendinous pressure Glycosaminoglycans Tendon fluid

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Littoral landforms of Lake Hulun and Lake Buir(China and Mongolia):Wind-driven hydro-sedimentary dynamics and resulting clastics distribution

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Journal of Palaeogeography 2024年第2期13卷 309-326页

作者： Li Wang Mathieu Schuster Shi-Wei Xin Florin Zainescu Xin-Yu Xue Joep Storms jan-Hendrik May Alexis Nutz Helena van der Vegt Guilherme Bozetti Zai-Xing Jiang School of Energy Resources China University of Geosciences(Beijing)Beijing100083China Universite de Strasbourg CNRSENGEESInstitut Terre et Environnement de StrasbourgUMR 70635 Rue DescartesStrasbourgFrance Tamsag Mongolia(XIX)Ltd. PetroChinaDaqing 163000China CEREGE Aix-Marseille UniversitéCNESIRDCollege de FranceINRAAix en ProvenceFrance School of Marine Science Sun Yat-sen UniversityZhuhai 519083China Delft University of Technology Department of Geoscience and EngineeringDelfthe Netherlands School of Geography Earth and Atmospheric SciencesUniversity of Melbourne253 Elgin St.CarltonVIC 3053Australia Deltares Delfthe Netherlands SCMF Faculty of GeographyUniversity of Bucharest1 N.Balcescu Blv.BucharestRomania

Two rectangular-shaped lakes,Lake Hulun and Lake Buir,located at the boundary between China and Mongolia,only c.75 km apart and therefore experiencing similar wind fields,have been studied based on satellite images and field surveys in order to compare their geomorphological and sedimentological *** wind-driven hydrodynamics,which have a significant effect on the development of littoral landforms and on sediment distribution,have been discussed for the two similar lakes that experienced a prevailing wind perpendicular to their long axis.A conceptual model related to wind-driven water bodies and sediment distribution is ***-influenced to wave-dominated deltas,beaches,spits,and eolian dune deposits develop around these two lakes,with a strikingly similar distribution *** features locally inform the longshore drift and help reconstruct the water circulation induced by wind *** the NW prevailing wind regime,the spits developed on the SW coast with a NW—SE extension,which was influenced by the NW—SE longshore *** same influence was observed in the delta extension in the NE *** differences lie in the presence of fan deltas in the NW region of Lake Hulun,but not in Lake ***,the width of the beach and eolian deposits on the downwind coast of Lake Hulun is three times greater than that of Lake Buir which were caused by the differences in sediment supply and wind fetch between the two *** Hulun and Lake Buir provide two reliable examples to understand the relationship among the wind field,provenance,hydrodynamics,landforms,and asymmetrical distribution of clastics in elongated *** also represent relevant modern analogs,which may also be of guiding significance to wind-driven sand body prediction in lacustrine basins.

关键词： Wind-driven lakes Fetch Sedimentary facies Hydrodynamics Geomorphology Spits Shoreline Lake Hulun Lake Buir

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作者： (荷)简·梵·迪克(jan van dijk)

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城市空间何以影响城市产业选择?——以荷兰埃因霍温的空间演变为例

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国际城市规划 2024年第3期39卷 137-144页

作者：陈悦特里·范戴克邵甬澳门科技大学人文艺术学院中国澳门荷兰格罗宁根大学空间科学学院城市规划系同济大学建筑与城市规划学院高密度人居环境生态与节能教育部重点实验室

城市空间是否可以主动地影响产业转型?本文从完整的历史演变视角考察城市空间与产业之间的互动关系,引入路径依赖方法来构建城市与产业互动演变的分析框架,并应用该框架对荷兰的工业城市埃因霍温展开实证研究,详细分析该城市在三个历史... 详细信息

城市空间是否可以主动地影响产业转型?本文从完整的历史演变视角考察城市空间与产业之间的互动关系,引入路径依赖方法来构建城市与产业互动演变的分析框架,并应用该框架对荷兰的工业城市埃因霍温展开实证研究,详细分析该城市在三个历史时期的三次成功的产业转型过程,尤其重点分析城市空间在产业转型中发挥的积极作用。通过研究发现:城市空间在每个关键节点都影响着城市的产业选择,且在不同时代以不同形式影响着产业选择。因此,对于面临产业转型的中国城市而言,应当冷静地审视自身的产业发展历史和固有的城市空间条件,或许可以从中发现适合本城市的产业转型方向。

关键词：产业转型城市空间城市演变路径依赖埃因霍温

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维生素D代谢物有助于母猪分娩过程

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国外畜牧学（猪与禽） 2024年第1期44卷 12-13页

作者： Katia Pedrosa Kathrin Buehler jan Dirk van der Klis 张相鑫(译) 王晶晶(校) 孟祥光(制图) 不详

维生素D是一种重要的营养物质,母猪在妊娠后期和哺乳期对其需要量非常高。本文概述了维生素D对母猪分娩的影响,提出可以在常规添加维生素D之外补充1,25-二羟基维生素D3糖苷,以缩短分娩时间,减少分娩过程中的人为干预,减少死胎数。

关键词：维生素D 1 25-二羟基维生素D3糖苷分娩

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Impact of black cherry on pedunculate oak vitality in mixed forests:Balancing benefits and concerns

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Forest Ecosystems 2023年第6期10卷 690-699页

作者： Ellen Desie Bart Muys jan den Ouden Bart Nyssen Rita Sousa-Silva Leon van den Berg Arnold van den Burg Gert-jan van Duinen Koenraad van Meerbeek Maaike Weijters Karen vancampenhout Division Forest Nature and LandscapeKU Leuven Campus GeelKleinhoefstraat 4B-2240 GeelBelgium Division Forest Nature and LandscapeKU LeuvenCelestijnenlaan 200EBox 2411B-3001 LeuvenBelgium KU Leuven Plant Institute B-3001 LeuvenBelgium Forest Ecology and Management Group Wageningen UniversityP.O.Box 47Wageningenthe Netherlands Bosgroep Zuid-Nederland Huisvenseweg 145591 VD Heezethe Netherlands Young Academy for Sustainability Research University of Freiburg79104 Freiburg im BreisgauGermany Aquatic Ecology&Environmental Biology Radboud University NijmegenHeyendaalseweg 1356525 AJ Nijmegenthe Netherlands Biosphere/Zoological Museum Netherlands Onderlangs 176731 BK Otterlothe Netherlands Stichting Bargerveen Toernooiveld 16525 ED Nijmegenthe Netherlands B-WARE Research Centre/Radboud University Nijmegen Toernooiveld 16525 ED Nijmegenthe Netherlands

The vitality of European forests continues to decline due to new pests and diseases,climate-change related disturbances and high loads of atmospheric nitrogen *** soil health is a major factor underpinning the low vitality of West-European *** tree species with soil ameliorative traits is proposed as an avenue to counteract soil acidification and improve overall forest *** we evaluate the impact of black cherry(Prunus serotina Ehrh.),a known rich litter species,on the vitality of neighboring pedunculate oak(Quercus robur L.)in ten mixed forests on sand in Germany,Belgium and the *** found that black cherry admixture increases foliar N and P to a surplus whereas it causes deficiencies in foliar Mg,thereby resulting in an overall negative effect on oak foliar nutrient ***,defoliation of oak leaves by herbivory decreases with the proximity of black *** structural equation modelling(SEM),we tested the hypothesized‘improved soil health’*** analyses showed that black cherry admixture leads to lower accumulation in the humus layer,resulting in higher soil base saturation which has a positive effect on foliar Ca yet a negative effect on total ***,the SEM illustrated that herbivory of oak leaves decreases when black cherry is admixed,both via dilution and improved soil *** effects of black cherry on oak vitality via“improved soil health”in our SEM are however small in comparison to direct ***,our study showed that the combined positive and negative impacts of black cherry on oak vitality are limited,which tempers the potential benefits of using the rich litter species to counteract oak decline via improved soil health–yet,the concern of black cherry as an invasive alien species negatively affecting the vitality of mature pedunculate oak trees may also be exaggerated.

关键词： Rich litter species Black cherry Nutrient cycling Insect herbivory Dilution effect Humus type Pedunculate oak Plant-soil interaction

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