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

The crop Journal 2024年第3期12卷 803-813页

作者： Moritz Lell Yusheng Zhao Jochen c.Reif Leibniz Institute of Plant Genetics and crop Plant Research(IPK) Corrensstraße 3D-06466 SeelandGermany

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.

关键词： Big Data Genome-wide association study Data integration Genomic prediction Wheat

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Isolating higher yielding and more stable rice genotypes in stress environments: fine-tuning a selection method using production and resilience score indices

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Frontiers of Agricultural Science and Engineering 2024年第1期11卷 169-185页

作者： Arnauld THIRY William J.DAVIES Ian c.DODD Lancaster Environment centre Lancaster UniversityLancasterLancashire LA14YWUK

In Asia, the rice crop sustains millions of people. However, growing demand for this crop needs to be met while simultaneously reducing its water consumption to cope with the effects of climate change. Lowland cropping systems are the most common and productive but have particularly high water requirements. High-yielding rice genotypes adapted to drier environments(such as rainfed or aerobic rice ecosystems) are needed to increase the water use efficiency of cropping. Identifying these genotypes requires fast and more accurate selection methods. It is hypothesized that applying a new quantitative selection method(the score index selection method), can usefully compare rice yield responses over different years and stress intensities to select genotypes more rapidly and efficiently. Applying the score index to previously published rice yield data for 39 genotypes grown in no-stress and two stress environments, identified three genotypes(ARB 8, IR55419-04 and ARB 7) with higher and stable yield under moderate to severe stress conditions. These genotypes are postulated to be better adapted to stress environment such as upland and aerobic environments. Importantly, the score index selection method offers improved precision than the conventional breeding selection method in identifying genotypes that are well-suited to a range of stress levels within the target environment.

关键词： Aerobic rice breeding selection drought resilience production capacity index resilience capacity index stress score index upland

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Investigations of nuclear chirality at iThemba LABS

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Frontiers of physics 2024年第2期19卷 7-38页

作者： R.A.Bark E.A.Lawrie c.Liu S.Y.Wang iThemba Laboratory for Accelerator Based Sciences National Research FoundationP.O.Box 722Somerset-West 7129South Africa Department of Physics University of the Western CapePrivate Bag X177535BellvilleSouth Africa Shandong Provincial Key Laboratory of Optical Astronomy and Solar-Terrestrial Environment Institute of Space SciencesShandong UniversityWeihai 264209China

Progress in the studies of chirality in atomic nuclei at iThemba LABS is reviewed.New regions of chirality,around mass 80 and 190 have been discovered using the AFRODITE array,specifically in the nuclei^(74)As,^(78,80,82)Br,^(81)Kr,and^(193,194,198)Tl.Many phenomena have been observed,including multiple chiral bands in the same nucleus,the coexistence of octupole correlations and nuclear chirality,and the coexistence of pseudo spin and nuclear chirality.The best example of chiral degeneracy to date was found in ^(194)Tl.The level scheme of ^(106)Ag has been revisited and interpreted in terms of two-and four-quasiparticle bands.Investigations using the particle-rotor model have shown that the fingerprints of chirality in the two-quasiparticle system only can occur in an idealised model description.For systems with a higher number of quasiparticles,the calculations showed that nuclear chirality can persist.

关键词： chirality high-spin states particle-rotor model

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Targeted nanopore sequencing for the identification of novel PRMT1 circRNAs unveils a diverse transcriptional profile of this gene in breast cancer cells

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Genes & Diseases 2024年第2期11卷 589-592页

作者： Maria Papatsirou Andreas Scorilas Diamantis c.Sideris christos K.Kontos Department of Biochemistry and Molecular Biology National and Kapodistrian University of AthensPanepistimiopolisAthens GR 15701Greece

Long-read sequencing with nanopore technology has been widely utilized for the identification of the full-length sequence of RNA molecules."It is especially suitable for the identification of circular RNAs(circRNAs),which are regulatory molecules that are regarded as promising non-invasive biomarkers for various human malignancies,including breast cancer.2 The impact of circRNAs derived from the protein arginine methyltransferase 1(PRMT1)gene has not been clarified yet,even though the effect of PRMT1-mediated methylation on breast cancer cell characteristics has been well established.

关键词： PRMT1 breast cancer

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characterization of Arroyo Verde Epithermal Deposit:Paragenesis,Mineral Geochemistry,Geochronology and Fluid Inclusions in Lower chon Aike Volcanism,Argentina

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Journal of Earth Science 2024年第1期35卷 62-84页

作者： cecilia Pavón Pivetta Leonardo Benedini Paulo Marcos Ma.Agustina cócola Mercedes Virginia Barros Daniel Gregori Leonardo Strazzere Anderson costa dos Santos Mauro c.Geraldes Instituto Geologico del Sur(INGEOSUR) Universidad Nacional del Sur(UNS)-Consejo Nacional de Investigaciones Cientificas y Tecnicas(CONICET)Bahia Blanca 8000Argentina Dpto.de Geologia Universidad Nacional del Sur(UNS)Bahia Blanca 8000Argentina Universidad Nacional de Rio Negro Instituto de Investigacion en Paleobiologia y GeologiaGeneral Roca 8332Argentina Universidade do Estado do Rio de Janeiro Faculdade de GeologiaDepartamento de Mineralogia e Petrologia igneaRiodeJaneiro20559-900Brazil Geobiotec Departamento de GeocienciasUniversidade de AveiroAveiro 3800-002Portuga

Arroyo Verde epithermal deposit,in the North Patagonia region of Argentina,is located within the Lower chon Aike volcanism and is developed between 192.6±2.5 Ma(mineralization host rock)and 189.5±2.6 Ma(overlying lava).Marifil volcanic complex is the host rock for these veins,veinlets and breccias.This particular small deposit has developed low to intermediate sulphidation characteristics,with gangue mineral textures associated with several ore minerals.Electron probe microanalysis determines electrum,silver minerals such as acanthite,and tetrahedrite,related Ag-cu minerals like jalpaite,mckinstryite,stromeyerite,and base metals like chalcopyrite,sphalerite,galena and pyrite.Fluid inclusions in quartz of two out of five events indicate that these Low Jurassic veins were formed due to subtle boiling and dilution mechanisms and by low-salinity(3.4 wt.%to 6.7 wt.%Nacl Eq)magmatic-hydrothermal fluid at 225 to 310℃.The fluid inclusion measurements that indicate boiling(Event 3)were plotted,and based on this data,we interpret that the Arroyo Verde deposit has been eroded between 550 and 700 m.This particular character has not been previously recorded for other sectors of the eastern north Patagonian region.

关键词： epithermal deposit Ag minerals mineral geochemistry fluid inclusions chon Aike geochronology

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The anti-inflammatory effects of exercise on autoimmune diseases:A 20-year systematic review

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Journal of Sport and Health Science 2024年第3期13卷 353-367,I0001页

作者： Beibei Luo Dao Xiang Xiaorong Ji Xuan chen Rui Li Shuxin Zhang Yujun Meng David c.Nieman Peijie chen School of Exercise and Health Shanghai University of SportShanghai 200438China Shanghai Key Laboratory of Human Performance Shanghai University of SportShanghai 200438China Department of Diving and Hyperbaric Medicine Naval Medical CenterShanghai 200433China National Key Laboratory of Immunity and Inflammation Naval Medical UniversityShanghai 200433China Human Performance Laboratory Appalachian State UniversityNorth Carolina Research CampusKannapolisNC 28081USA Research Institute for Doping control Shanghai University of SportShanghai 200438China

Background:The anti-inflammatory effect of exercise may be an underlying factor in improving several autoimmune diseases.The aim of this systematic review was to examine the evidence on the role of exercise training in mitigating inflammation in adolescents and adults with autoimmune disease.Methods:PubMed,Web of Science,and Embase databases were systematically reviewed for related studies published between January 1,2003,and August 31,2023.All randomized and non-randomized controlled trials of exercise interventions with autoimmune disease study participants that evaluated inflammation-related biomarkers were included.The quality of evidence was assessed using the Tool for the assEssment of Study qualiTy and reporting in EXercise scale and cochrane bias risk tool.Results:A total of 14,565 records were identified.After screening the titles,abstracts,and full texts,87 were eligible for the systematic review.These studies were conducted in 25 different countries and included a total of 2779 participants(patients with autoimmune disease,in exercise or control groups).Overall,the evidence suggests that inflammation-related markers such as c-reactive protein,interleukin 6,and tumor necrosis factor a were reduced by regular exercise interventions.Regular exercise interventions combined with multiple exercise modes were associated with greater benefits.conclusion:Regular exercise training by patients with autoimmune disease exerts an anti-inflammatory influence.This systematic review provides support for the promotion and development of clinical exercise intervention programs for patients with autoimmune disease.Most patients with autoimmune disease can safely adopt moderate exercise training protocols,but changes in inflammation biomarkers will be modest at best.Acute exercise interventions are ineffective or even modestly but transiently pro-inflammatory.

关键词： Autoimmune diseases cytokines Inflammation Physical activity Training

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Glucagon-like peptide 1 receptor activation:anti-inflammatory effects in the brain

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Neural Regeneration Research 2024年第8期19卷 1671-1677页

作者： Yolanda Diz-chaves Zainab Maastor carlos Spuch José Antonio Lamas Lucas c.González-Matías Federico Mallo Biomedical Research centre(cINBIO) Laboratory of EndocrinologyUniversity of VigoGalicia Sur Health Research InstituteVigoSpain Translational Neuroscience Research Group Galicia Sur Health Research InstituteCIBERSAMHospitalÁlvaro CunqueiroSala InvestigaciónEstrada Clara CampoamorVigoSpain Biomedical Research centre(cINBIO) Laboratory of NeuroscienceUniversity of VigoGalicia Sur Health Research InstituteVigoSpain

The glucagon-like peptide 1 is a pleiotropic hormone that has potent insulinotropic effects and is key in treating metabolic diseases such as diabetes and obesity.Glucagon-like peptide 1 exerts its effects by activating a membrane receptor identified in many tissues,including diffe rent brain regions.Glucagon-like peptide 1 activates several signaling pathways related to neuroprotection,like the support of cell growth/survival,enhancement promotion of synapse formation,autophagy,and inhibition of the secretion of proinflammatory cytokines,microglial activation,and apoptosis during neural morphogenesis.The glial cells,including astrocytes and microglia,maintain metabolic homeostasis and defe nse against pathogens in the central nervous system.After brain insult,microglia are the first cells to respond,followed by reactive astrocytosis.These activated cells produce proinflammato ry mediators like cytokines or chemokines to react to the insult.Furthermore,under these circumstances,mic roglia can become chro nically inflammatory by losing their homeostatic molecular signature and,consequently,their functions during many diseases.Several processes promote the development of neurological disorders and influence their pathological evolution:like the formation of protein aggregates,the accumulation of abnormally modified cellular constituents,the formation and release by injured neurons or synapses of molecules that can dampen neural function,and,of critical impo rtance,the dysregulation of inflammato ry control mechanisms.The glucagonlike peptide 1 receptor agonist emerges as a critical tool in treating brain-related inflammatory pathologies,restoring brain cell homeostasis under inflammatory conditions,modulating mic roglia activity,and decreasing the inflammato ry response.This review summarizes recent advances linked to the anti-inflammato ry prope rties of glucagon-like peptide 1 receptor activation in the brain related to multiple sclerosis,Alzheimer’s disease,Parkinson’s disease,vascular dementia,or chronic migrai

关键词： astrocytes brain glucagon-like peptide 1 receptor inflammation microglia

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cancer-associated fibroblasts express cD1d and activate invariant natural killer T cells under cellular stress

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cellular & Molecular Immunology 2024年第1期21卷 91-94页

作者： Shengduo Pei Jonas Sjölund Yueyun Pan Kristian Pietras Mikael c.I.Karlsson Department of Microbiology Tumor and Cell BiologyKarolinska InstitutetStockholmSweden Division of Translational cancer Research Department of Laboratory MedicineLund University Cancer CentreLund UniversityLundSweden

Invariant natural killer T(iNKT)cells are part of the family of unconventional T cells,and they recognize glycolipid antigens presented on the MHc class I like molecule cD1^([1]).In humans there are five cD1 molecules named cD1a to cD1e,whereas mice use only cD1d for lipid presentation.Functionally,iNKT cells can elicit both cytotoxicity similarly to conventional cD8 T cells and secrete cytokines that influence the adaptive immune response including providing direct T cell help to B cells^([2]).In the context of tumors,they can use both release of granzyme B and use Fas-mediated mechanisms for killing of tumor cells.As iNKT cells use a restricted TcR repertoire and cD1 molecules are non-heterogenous the risk of graft vs host disease is limited and thus these T cells have been an attractive option for off the shelf immunotherapy to treat cancer^([3]).

关键词： killer cD1d cancer

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Mathematical modeling and simulations of stress mitigation by coating polycrystalline particles in lithium-ion batteries

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Applied Mathematics and Mechanics(English Edition) 2024年第6期45卷 947-962页

作者： N.IQBAL J.cHOI S.F.SHAH c.LEE S.LEE Department of Mechanical Roboticsand Energy EngineeringDongguk University-SeoulSeoul 04620Republic of Korea

A chemo-mechanical model is developed to investigate the effects on the stress development of the coating of polycrystalline Ni-rich LiNixMnyco_(z)O_(2)(x>0.8)(NMc)particles with poly(3,4-ethylenedioxythiophene)(PEDOT).The simulation results show that the coating of primary NMc particles significantly reduces the stress generation by efficiently accommodating the volume change associated with the lithium diffusion,and the coating layer plays roles both as a cushion against the volume change and a channel for the lithium transport,promoting the lithium distribution across the secondary particles more homogeneously.Besides,the lower stiffness,higher ionic conductivity,and larger thickness of the coating layer improve the stress mitigation.This paper provides a mathematical framework for calculating the chemo-mechanical responses of anisotropic electrode materials and fundamental insights into how the coating of NMc active particles mitigates stress levels.

关键词： lithium-ion battery(LIB) polycrystalline particle coating finite element simulation Ni-rich LiNixMnyco_(z)O_(2)(x>0.8)(NMc)

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Theoretical and experimental study of a bi-stable piezoelectric energy harvester under hybrid galloping and band-limited random excitations

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Applied Mathematics and Mechanics(English Edition) 2024年第3期45卷 461-478页

作者： Haitao LI Tianyu ZHENG Weiyang QIN Ruilan TIAN Hu DING J.c.JI Liqun cHEN Department of Engineering Mechanics North University of ChinaTaiyuan 030051China Department of Engineering Mechanics Northwestern Polytechnical UniversityXi'an 710072China Department of Engineering Mechanics Shijiazhuang Tiedao UniversityShijiazhuang 050043China Shanghai Key Laboratory of Mechanics in Energy Engineering Shanghai Frontier Science Center of MechnoinformaticsShanghai Institute of Applied Mathematics and MechanicsSchool of Mechanics and Engineering ScienceShanghai UniversityShanghai 200072China School of Mechanical and Mechatronic Engineering University of Technology SydneyNew South Wales 2007Australia

In the practical environment,it is very common for the simultaneous occurrence of base excitation and crosswind.Scavenging the combined energy of vibration and wind with a single energy harvesting structure is fascinating.For this purpose,the effects of the wind speed and random excitation level are investigated with the stochastic averaging method(SAM)based on the energy envelope.The results of the analytical prediction are verified with the Monte-carlo method(McM).The numerical simulation shows that the introduction of wind can reduce the critical excitation level for triggering an inter-well jump and make a bi-stable energy harvester(BEH)realize the performance enhancement for a weak base excitation.However,as the strength of the wind increases to a particular level,the influence of the random base excitation on the dynamic responses is weakened,and the system exhibits a periodic galloping response.A comparison between a BEH and a linear energy harvester(LEH)indicates that the BEH demonstrates inferior performance for high-speed wind.Relevant experiments are conducted to investigate the validity of the theoretical prediction and numerical simulation.The experimental findings also show that strong random excitation is favorable for the BEH in the range of low wind speeds.However,as the speed of the incoming wind is up to a particular level,the disadvantage of the BEH becomes clear and evident.

关键词： bi-stability inter-well response galloping band-limited random

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