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Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer thomas Stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer Science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan State Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China present address:225 S 6th St MinneapolisMN 55402USA present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA present address:Life Sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

Metabolic syndrome and the urinary microbiome of patients undergoing percutaneous nephrolithotomy

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Asian Journal of Urology 2024年第2期11卷 316-323页

作者： Ryan A.Dornbier Chirag p.Doshi Shalin C.Desai petar Bajic Michelle Van Kuiken Mark Khemmani Ahmer V.Farooq Larissa Bresler thomas M.T.Turk Alan J.Wolfe Kristin G.Baldea Loyola University Medical Center Department of UrologyMaywoodILUSA Loyola University Chicago Department of Microbiology and ImmunologyMaywoodILUSA

Objective:To identify possible stone-promoting microbes,we compared the profiles of microbes grown from stones of patients with and without metabolic syndrome(MetS).The association between MetS and urinary stone disease is well established,but the exact pathophysiologic relationship remains *** evidence suggests urinary tract dysbiosis may lead to increased nephrolithiasis ***:At the time of percutaneous nephrolithotomy,bladder urine and stone fragments were collected from patients with and without *** sample types were subjected to expanded quantitative urine culture(EQUC)and 16 S ribosomal RNA gene ***:Fifty-seven patients included 12 controls(21.1%)and 45 MetS patients(78.9%).Both cohorts were similar with respect to demographics and non-MetS *** controls had uric acid stone *** EQUC,bacteria were detected more frequently in MetS stones(42.2%)compared to controls(8.3%)(p=0.041).Bacteria also were more abundant in stones of MetS patients compared to *** validate our EQUC results,we performed 16 S ribosomal RNA gene *** 12/16(75.0%)sequence-positive stones,EQUC reliably isolated at least one species of the sequenced *** were detected in both“infectious”and“non-infectious”stone ***:Bacteria are more common and more abundant in MetS stones than control *** findings support a role for bacteria in urinary stone disease for patients with MetS regardless of stone composition.

关键词： Nephrolithiasis Urolithiasis Metabolic syndrome Urinary microbiome percutaneous nephrolithotomy

Alexa,let's train now!——A systematic review and classification approach to digital and home-based physical training interventions aiming to support healthy cognitive aging

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Journal of Sport and Health Science 2024年第1期13卷 30-46页

作者： Fabian Herold paula Theobald thomas Gronwald Navin Kaushal Liye Zou Eling D.de Bruin Louis Bherer Notger GMüller Research Group Degenerative and Chronic Diseases MovementFaculty of Health Sciences BrandenburgUniversity of PotsdamPotsdam 14476Germany Body-Brain-Mind Laboratory Shenzhen UniversityShenzhen 518060China Institute of Interdisciplinary Exercise Science and Sports Medicine MSH Medical School HamburgHamburg 20457Germany Department of Health Sciences School of Health&Human SciencesIndiana UniversityIndianapolisIN 46202USA Department of Health Sciences and Technology Institute of Human Movement Sciences and SportETH ZurichZurich 8093Switzerland Department of Neurobiology Care Sciencesand SocietyKarolinska InstituteStockholm 17177Sweden Department of Health OST-Eastern Swiss University of Applied SciencesSt.Gallen 9001Switzerland Montreal Heart Institute MontrealQC H1T 1C8Canada Department of Medicine Universite de MontrealMontrealQC H3T 1J4Canada Centre de Recherche de l'Institut Universitaire de Geriatrie de Montreal MontrealQC H3W 1W5Canada

Background:There is mounting evidence that regular physical activity is an important prerequisite for healthy cognitive ***,the finding that almost one-third of the adult population does not reach the recommended level of regular physical activity calls for further public health *** this context,digital and home-based physical training interventions might be a promising alternative to center-based intervention ***,this systematic review aimed to summarize the current state of the literature on the effects of digital and home-based physical training interventions on adult cognitive ***:In this pre-registered systematic review(pROSpERO;ID:CRD42022320031),5 electronic databases(pubMed,Web of Science,psyclnfo,SpORTDiscus,and Cochrane Library)were searched by 2 independent researchers(FH and pT)to identify eligible studies investigating the effects of digital and home-based physical training interventions on cognitive performance in *** systematic literature search yielded 8258 records(extra17 records from other sources),of which 27 controlled trials were considered *** reviewers(FH and pT)independently extracted data and assessed the risk of bias using a modified version of the Tool for the assEssment of Study qualiTy and reporting in EXercise(TESTEX scale).Results:Of the 27 reviewed studies,15 reported positive effects on cognitive and motor-cognitive outcomes(i.e.,performance improvements in measures of executive functions,working memory,and choice stepping reaction test),and a considerable heterogeneity concerning study-related,population-related,and intervention-related characteristics was noticed.A more detailed analysis suggests that,in particular,interventions using online classes and technology-based exercise devices(i.e.,step-based exergames)can improve cognitive performance in healthy older *** one-half of the reviewed studies were rated as having a high risk of bias with respect

关键词： Brain Cognition Digital health Exercise-cognition physical activity

Efficient scar-free knock-ins of several kilobases in plants by engineered CRISpR-Cas endonucleases

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Molecular plant 2024年第5期17卷 824-837页

作者： Tom Schreiber Anja prange petra Schafer thomas Iwen Ramona Grutzner Sylvestre Marillonnet Aurelie Lepage Marie Javelle Wyatt paul Alain Tissier Department of Cell and Metabolic Biology Leibniz Institute of Plant BiochemistryWeinberg 306120 Halle(Saale)Germany Limagrain Centre de RechercheRoute d’EnnezatCS 9012663720 ChappesFrance

In plants and mammals,non-homologous end-joining is the dominant pathway to repair DNA doublestrand breaks,making it challenging to generate knock-in *** this study,we identified two groups of exonucleases from the herpes virus and the bacteriophage T7 families that conferred an up to 38-fold increase in homology-directed repair frequencies when fused to Cas9/Cas12a in a tobacco mosaic virus-based transient assay in Nicotiana *** achieved precise and scar-free insertion of several kilobases of DNA both in transient and stable transformation *** Arabidopsis thaliana,fusion of Cas9 to a herpes virus family exonuclease led to 10-fold higher frequencies of knock-ins in the first generation of *** addition,we demonstrated stable and heritable knock-ins in wheat in 1%of the primary *** together,our results open perspectives for the routine production of heritable knock-in and gene replacement events in plants.

关键词： homology-directed repair knockin gene replacement CRISpR-Cas 50 exonuclease plants

Another SSOR Iteration Method

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American Journal of Computational Mathematics 2024年第2期14卷 248-256页

作者： thomas Smotzer John Buoni Department of Mathematics and Statistics Youngstown State University Youngstown Ohio USA

Kellogg gave a version of the peaceman-Radford method. In this paper, we introduce a SSOR iteration method which uses Kellogg’s method. The new algorithm has some advantages over the traditional SSOR algorithm. A Cyc... 详细信息

关键词： Matrix Splitting SSOR Iteration KSSOR Iteration Method Kellogg-Type SSOR Iteration Cyclic Reduction

MEMS-actuated terahertz metamaterials driven by phase-transition materials

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Frontiers of Optoelectronics 2024年第2期17卷 23-32页

作者： Zhixiang Huang Weipeng Wu Eric Herrmann Ke Ma Zizwe A.Chase thomas A.Searles M.Benjamin Jungfleisch Xi Wang Department of Materials Science and Engineering College of EngineeringUniversity of DelawareNewarkDE 19716USA Department of physics and Astronomy College of Arts and SciencesUniversity of DelawareNewarkDE 19716USA Department of Electrical and Computer Engineering College of EngineeringUniversity of Illinois ChicagoChicagoIL 60607USA

The non-ionizing and penetrative characteristics of terahertz(THz)radiation have recently led to its adoption across a variety of *** effectively utilize THz radiation,modulators with precise control are *** most recent THz modulators manipulate the amplitude,frequency,or phase of incident THz radiation,considerably less progress has been made toward THz polarization *** methods for polarization control suffer from high driving voltages,restricted modulation depth,and narrow band capabilities,which hinder device performance and broader ***,an ideal THz modulator that offers high modulation depth along with ease of processing and operation is *** this paper,we propose and realize a THz metamaterial comprised of microelectromechanical systems(MEMS)actuated by the phase-transition material vanadium dioxide(VO_(2)).Simulation and experimental results of the three-dimensional metamaterials show that by leveraging the unique phase-transition attributes of VO_(2),our THz polarization modulator offers notable advancements over existing designs,including broad operation spectrum,high modulation depth,ease of fabrication,ease of operation condition,and continuous modulation *** enhanced features make the system a viable candidate for a range of THz applications,including telecommunications,imaging,and radar systems.

关键词： Metamaterials MEMS THz VO_(2) phase-transition material

Attitudes,beliefs,behaviours and perspectives on barriers and enablers of Australian general practitioners towards non-drug interventions:a national survey

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Family Medicine and Community Health 2024年第1期12卷 1-8页

作者： Loai Albarqouni Hannah Greenwood Caroline Dowsett Tammy Hoffmann Rae thomas paul Glasziou Institute for Evidence-based Healthcare Faculty of Health Sciences&MedicineBond UniversityRobinaQueenslandAustralia Tropical Australian Academic Health Centre TownsvilleQueenslandAustralia

Background Many guidelines recommend non-drug interventions(NDIs)for managing common conditions in primary ***,compared with drug interventions,NDIs are less widely known,promoted and *** aim to(1)examine general practitioners’(Gps’)knowledge,attitudes and practices for NDIs,including their use of the Royal Australian College of General practitioners(RACGp)Handbook of Non-Drug Interventions(HANDI),and(2)identify factors influencing their use of NDIs and *** We conducted a web-based cross-sectional survey of practicing Gp members in Australia during October-November *** survey contained five sections:characteristics of Gp;knowledge and use of NDIs;attitudes towards NDIs;barriers and enablers to using HANDI;and suggestions of NDIs and ideas to improve the uptake of NDIs in primary *** Of the 366 Gps who completed the survey,242(66%)were female,and 248(74%)were≥45 years *** in three Gps reported that they regularly(‘always’)recommend NDIs to their patients when appropriate(34%),whereas one-third of Gps were unaware of HANDI(39%).Gps identified several factors that improve the uptake of HANDI,including‘access and integration of HANDI in clinical practice’,‘content and support to use in practice’and‘awareness and training’.Conclusions While many Gps are aware of the effectiveness of NDIs and often endorse their use,obstacles still prevent widespread adoption in primary *** results of this survey can serve as a foundation for developing implementation strategies to improve the uptake of effective evidence-based NDIs in primary care.

关键词： enable survey sectional

气体流量和喷嘴直径对鼓泡塔内气泡大小和形状分布的影响

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Transactions of Nonferrous Metals Society of China 2024年第5期34卷 1710-1720页

作者：闫红杰张河杨刘柳 thomas ZIEGENHEIN 周萍中南大学能源科学与工程学院长沙410083 TIV Consultancy 7th Pl Road 131285281 TempeArizonaUnited States

通过高速摄影结合图像处理算法,研究气体流量和喷嘴直径对气泡尺寸和纵横比分布的影响。结果表明,在所有喷嘴直径下,气泡当量直径的概率密度呈现双峰分布,其中第一个峰值接近直径为1.5~2 mm的小气泡区域,另一个峰值位于较大的气泡区域... 详细信息

通过高速摄影结合图像处理算法,研究气体流量和喷嘴直径对气泡尺寸和纵横比分布的影响。结果表明,在所有喷嘴直径下,气泡当量直径的概率密度呈现双峰分布,其中第一个峰值接近直径为1.5~2 mm的小气泡区域,另一个峰值位于较大的气泡区域。将气体流量从0.1 L/min增加到0.2 L/min会导致大气泡的概率密度更高,表明气泡聚并现象普遍存在。当气体流量增加至1.2L/min时,峰值对应的气泡直径变小,并且气泡破裂占主导地位。对于直径为1~2 mm的气泡,形状受气体流量的影响较小,而3~9 mm的气泡在所有气体流量下气泡纵横比概率密度分布的峰值均位于纵横比E=0.5处。Iguchi和Chihara提出的模型能更好地预测气泡脱离直径随气体流量的增大的变化。

关键词：气泡尺寸分布气泡直径气泡纵横比气体流量喷嘴直径鼓泡塔

A chromosome-scale genome assembly of Rauvolfia tetraphylla facilitates identification of the complete ajmaline biosynthetic pathway

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plant Communications 2024年第4期5卷 129-132页

作者： Enzo Lezin Ines Carqueijeiro Clement Cuello Mickael Durand Hans JJansen Valentin Verges Caroline Birer Williams Audrey Oudin thomas Duge de Bernonville Julien petrignet Noemie Celton Benoit St-pierre Nicolas papon Chao Sun Ron p.Dirks Sarah Ellen O’Connor Michael Krogh Jensen Sebastien Besseau Vincent Courdavault Biomole´cules et Biotechnologies Vegetales EA2106Universite´de Tours37200 ToursFrance Future Genomics Technologies 2333 BE Leidenthe Netherlands Laboratoire Synthe se et Isolement de Molecules BioActives(SIMBA EA 7502)Universitede Tours37200 ToursFrance Laboratoire de Cytoge´netique Constitutionnelle CHRU de Tours-Hopital Bretonneau37044 ToursFrance University Angers University BrestIRFSFR ICAT49000 AngersFrance Institute of Medicinal plant Development Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 2800China Department of Natural product Biosynthesis Max Planck Institute for Chemical Ecology07745 JenaGermany Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark100193 Kgs LyngbyDenmark present address:Limagrain Center de RechercheRoute d’EnnezatChappesFrance These authors contributed equally to this article

Dear Editor,Rauvolfia tetraphylla(aka the Devil pepper)(Supplemental Figure 1)is a well-known medicinal plant that produces monoterpenoid indole alkaloids(MIAs).This MIA biosynthesis occurs in several organs,including leaves,stems,fruit,and roots,which accumulate the famous antiarrhythmic ajmaline(Kumar et al.2016a,2016b;Kumara et al.,2019).MIAs are natural products notably involved in plant adaptation to the environment and defense against *** mainly results from their high biological activities,which also explain their pharmacological properties.

关键词： properties. Figure roots