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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 Sciences Sino-Dutch Joint Lab of Vegetable Genomics Bioinformatics Group Wageningen University and Research Plant Breeding Wageningen University and Research Biosystems Data Analysis Swammerdam Institute for Life SciencesUniversity of Amsterdam

Leaf adaxial-abaxial(ad-abaxial) polarity is crucial for leaf morphology and function, but the genetic machinery governing this process remains unclear. To 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 truth.Gene 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 factors. Parallel to this, available and newly-obtained transcriptome data enabled us to identify genes differentially expressed across leaf ad-abaxial sides. Based on these analyses, we obtained a set of 111 novel genes which are involved in leaf ad-abaxial specialization. To explore implications for vegetable crop breeding, we examined the conservation of expression patterns between Arabidopsis and Brassica rapa using single-cell transcriptomics. The results demonstrated the utility of our computational approach for predicting candidate genes in crop species. Our 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

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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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 investigated.The resulting discretization matrices have real eigenvalues.We 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 part.Several implementations of BiCGStab exist which are equivalent in exact arithmetic,however,not in finite precision arithmetic.The modifications of BiCGStab we consider are;choosing a random shadow vector,a reliable updating scheme,and storing the best intermediate solution.It 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 analysis.Due to the real eigenvalues,the benefit of BiCGStab(L)compared to BiCGStab is shown to be modest in numerical experiments.Non-sparse(e.***.uniform random)shadow residual turns out to be essential for the reliability of BiCGStab.The reliable updating scheme ensures the required tolerance is truly achieved.Keeping the best intermediate solution has no significant effect.Recommendation 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 numbers.An alternative option is IDR(S),which outperforms BiCGStab for problems with strong advection in terms of the number of matrix-vector products.The 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

Dysregulation of IL-34 ligation to SDC-1 mitigates collagen-induced arthritis

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Cellular & Molecular Immunology 2022年第9期19卷 1070-1072页

作者： Anja Meyer Ryan Sienes Brian Zanotti katrien van Raemdonck Karol Palasiewicz Daniel P.Mass Michael V.Volin Shiva Shahrara Jesse Brown VA Medical Center ChicagoILUSA Department of Medicine Division of RheumatologyThe University of Illinois at ChicagoChicagoILUSA Department of Microbiology and Immunology Midwestern UniversityDowners GroveILUSA Department of Orthopedic Surgery The University of Illinois at ChicagoChicagoILUSA

IL-34 is a novel biomarker for rheumatoid arthritis(RA),as its serum levels are linked to C-reactive protein,erythrocyte sedimentation rate,rheumatoid factor(RF),IL-6 and radiographic progression[1,2].IL-34 reprograms naïve circulating M0 cells into glycolytic(CD14^(+)CD86^(+)GLUT1^(high))M34 macrophages(MΦs)by binding to its pathogenic receptor,SDC-1,which controls the activation of its coreceptor/M-CSFR[3].Glycolytic M34 MΦs are primed to differentiate into osteoclasts through SDC-1 ligation[3].

关键词： CD86 GLUT1 sedimentation

Liquid metal thermal hydraulics R&D at European scale:achievements and prospects

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Frontiers in Energy 2021年第4期15卷 842-853页

作者： Ferry ROELOFS Antoine GERSCHENFELD katrien van TICHELEN Nuclear Research and Consultancy Group(NRG) Westerduinweg 31755 LEPettenThe Netherlands CEA DES UniversitéParis-SaclayF-91191 Gif-sur-YvetteFrance SCK CEN Boeretang 2002400 MolBelgium

A significant role for a future nuclear carbonfree energy production is attributed to fast reactors,mostly employing a liquid metal as a coolant.This paper summarizes the efforts that have been undertaken in collaborative projects sponsored by the European Commission in the past 20 years in the fields of liquid-metal heat transfer modeling,fuel assembly and core thermal hydraulics,pool and system thermal hydraulics,and establishment of best practice guidelines and verification,validation,and uncertainty quantification(UQ).The achievements in these fields will be presented along with the prospects on topics which will be studied collaboratively in Europe in the years to come.These prospects include further development of heat transfer models for applied computational fluid dynamics(CFD),further analysis of the consequences of fuel assembly blockages on coolant flow and temperature,analysis of the thermal hydraulic effects in deformed fuel assemblies,extended validation of three-dimensional pool thermal hydraulic CFD models,and further development and validation of multi-scale system thermal hydraulic methods.

关键词： liquid metal thermal hydraulics Europe

Integrity of the hip capsule measured with magnetic resonance imaging after capsular repair or unrepaired capsulotomy in hip arthroscopy

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World Journal of Orthopedics 2022年第4期13卷 400-407页

作者： Niels H Bech Lode A van dijk Sheryl de Waard Gwendolyn Vuurberg Inger N Sierevelt Gino MMJ Kerkhoffs Daniël Haverkamp Department of Orthopedic Surgery Amsterdam University Medical CenterAmsterdam 1105 AZNetherlands Department of Orthopedic Surgery Xpert Orthopedic Surgery ClinicAmsterdam 1101 EANetherlands Department of Orthopedic Surgery Tergooi ZiekenhuisHilversum 1213 XZNetherlands Department of Radiology and Nuclear Medicine Rijnstate HospitalArnhem 6815 ADNetherlands Department of Radiology and Nuclear Medicine Amsterdam University Medical CenterAmsterdam 1105 AZNetherlands Centre for Orthopaedic Research Spaarne ZiekenhuisHoofddorp 2134 TMNetherlands Academic Center for Evidence-Based Sports Medicine Amsterdam University Medical CenterAmsterdam 1105 AZNetherlands Amsterdam Collaboration on Health and Safety in Sports Amsterdam UMC/IOC Research CenterAmsterdam 1105 AZNetherlands

BACKGROUND Current literature shows no clear answer on the question how to manage the capsule after hip arthroscopy.Regarding patient reported outcome measures there seems to be no difference between capsular repair or unrepaired capsulotomy.AIM To evaluate and compare the integrity of the hip capsule measured on a magnetic resonance imaging(MRI)scan after capsular repair or unrepaired capsulotomy.METHODS A case series study was performed;a random sample of patients included in a trial comparing capsular repair vs unrepaired capsulotomy had a postoperative MRI scan.The presence of a capsular defect and gap size were independently evaluated on MRI.RESULTS A total of 28 patients(29 hips)were included.Patient demographics were comparable between treatment groups.There were 2 capsular defects in the capsular repair group and 7 capsular defects in the unrepaired capsulotomy group(P=0.13).In the group of patients with a defect,median gap sizes at the acetabular side were 5.9 mm(range:2.7-9.0)in the repaired and 8.0 mm(range:4.5-18.0)in the unrepaired group(P=0.462).At the muscular side gap sizes were 6.6 mm(range:4.1-9.0)in the repaired group and 11.5 mm(range:3.0-18.0)in the unrepaired group(P=0.857).The calculated Odds ratio(OR)for having a capsular defect with an increasing lateral center-edge(CE)angle was 1.12(P=0.06).The OR for having a capsular defect is lower in the group of patients that underwent a labral repair with an OR of 0.1(P=0.05).CONCLUSION There is no significant difference in capsular defects between capsular repair or unrepaired capsulotomy.Regarding clinical characteristics our case series shows that a larger CE angle increases the likelihood of a capsular defect and the presence of a labral repair decreases the likelihood of a capsular defect.

关键词： Hip Arthroscopy Magnetic resonance imaging Capsule Thickness

A Review of Self-healing Metals: Fundamentals, Design Principles and Performance

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Acta Metallurgica Sinica(English Letters) 2020年第9期33卷 1167-1179页

作者： Shasha Zhang Niels van dijk Sybrand van der Zwaag College of Materials and Technology Nanjing University of Aeronautics and AstronauticsNanjing 211106China Key Laboratory of Materials Preparation and Protection for Harsh Environment(Nanjing University of Aeronautics and Astronautics) Ministry of Industry and Information TechnologyNanjing 211106China Fundamental Aspects of Materials and Energy Group Faculty of Applied SciencesDelft University of TechnologyMekelweg 152629 JB DelftThe Netherlands Novel Aerospace Materials Group Faculty of Aerospace EngineeringDelft University of TechnologyKluyverweg 12629 HS DelftThe Netherlands School of Materials Science and Engineering Tsinghua UniversityBeijing 100084China

Self-healing metals possess the capability to autonomously repair structural damage during service. While self-healing concepts remain challenging to be realized in metals and metallic systems due to the small atomic volume of the mobile atoms, the slow diffusion unless at high temperatures and the strong isotropic metallic bonds, the scientific interest has increased sharply and promising progress is obtained. This article provides a comprehensive and updated review on the developments and limitations associated with the various modes of potentially healable damage induced in metals and alloys, i.e., stressinduced damage, irradiation-induced damage in bulk materials and contact damage in corrosion protective coatings. The spontaneous intrinsic healing mechanisms not requiring external assistance other than the material operating at the right temperature and an assisted healing mechanism with external intervention are reviewed. Promising strategies to achieve self-healing in metals are identified. Finally, we give some prospects for future research directions in self-healing metals.

关键词： Metal Self-healing Creep behavior Fatigue damage Irradiation Coating

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Enhanced reversibility of the magnetoelastic transition in(Mn,Fe)2(P,Si)alloys via minimizing the transition-induced elastic strain energy

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Journal of Materials Science & Technology 2022年第8期103卷 165-176页

作者： Xuefei Miao Yong Gong Fengqi Zhang Yurong You Luana Caron Fengjiao Qian Wenhui Guo Yujing Zhang Yuanyuan Gong Feng Xu Niels van dijk Ekkes Brück MIIT Key Laboratory of Advanced Metallic and Intermetallic Materials Technology School of Materials Science and EngineeringNanjing University of Science and TechnologyNanjing 210094China Fundamental Aspects of Materials and Energy Department of Radiation Science and TechnologyDelft University of TechnologyMekelweg 15DelftJB 2629Netherlands Department of Physics Bielefeld UniversityBielefeld 33501Germany Helmholtz-Zentrum Berlin für Materialien und Energie Berlin 12489Germany College of Physics Nanjing University of Aeronautics and AstronauticsNanjing 210016China

Magnetocaloric materials undergoing reversible phase transitions are highly desirable for magnetic refrigeration applications.(Mn,Fe)_(2)(P,Si)alloys exhibit a giant magnetocaloric effect accompanied by a magnetoelastic transition,while the noticeable irreversibility causes drastic degradation of the magnetocaloric properties during consecutive cooling cycles.In the present work,we performed a comprehensive study on the magnetoelastic transition of the(Mn,Fe)_(2)(P,Si)alloys by high-resolution transmission electron microscopy,in situ field-and temperature-dependent neutron powder diffraction as well as density functional theory calculations(DFT).We found a generalized relationship between the thermal hysteresis and the transition-induced elastic strain energy for the(Mn,Fe)_(2)(P,Si)family.The thermal hysteresis was greatly reduced from 11 to 1 K by a mere 4 at.%substitution of Fe by Mo in the Mn_(1.15)Fe_(0.80)P_(0.45)Si_(0.55)alloy.This reduction is found to be due to a strong reduction in the transition-induced elastic strain energy.The significantly enhanced reversibility of the magnetoelastic transition leads to a remarkable improvement of the reversible magnetocaloric properties,compared to the parent alloy.Based on the DFT calculations and the neutron diffraction experiments,we also elucidated the underlying mechanism of the tunable transition temperature for the(Mn,Fe)_(2)(P,Si)family,which can essentially be attributed to the strong competition between the covalent bonding and the ferromagnetic exchange coupling.The present work provides not only a new strategy to improve the reversibility of a first-order magnetic transition but also essential insight into the electron-spin-lattice coupling in giant magnetocaloric materials.

关键词： Magnetocaloric effect (Mn Fe)2(P Si) Hysteresis Neutron diffraction

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A Single Active Trehalose-6-P Synthase （TPS） and a Family of Putative Regulatory TPS-Like Proteins in Arabidopsis

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Molecular Plant 2010年第2期3卷 406-419页

作者： Lies vandesteene Matthew Ramon katrien Le Roy Patrick van Dijck Filip Rolland Laboratory of Functional Biology Plant Metabolic Signaling Group Institute of Botany and Microbiology KU Leuven Kasteelpark Arenberg 31-bus 2438 B-3001 Heverlee Belgium Department of Molecular Biology Harvard Medical School Massachusetts General Hospital Boston USA Laboratory of Molecular Plant Physiology Institute of Botany and Microbiology KU Leuven Belgium Department of Molecular Microbiology VIB Leuven Belgium Laboratory of Molecular Cell Biology Institute of Botany and Microbiology KU Leuven Belgium

Higher plants typically do not produce trehalose in large amounts, but their genome sequences reveal large families of putative trehalose metabolism enzymes. An important regulatory role in plant growth and development is also emerging for the metabolic intermediate trehalose-6-P （T6P）. Here, we present an update on Arabidopsis trehalose me- tabolism and a resource for further detailed analyses. In addition, we provide evidence that Arabidop$is encodes a single trehalose-6-P synthase （TPS） next to a family of catalytically inactive TPS-like proteins that might fulfill specific regulatory functions in actively growing tissues.

关键词： Trehalose metabolism TPS Arabidopsis.