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Mshpy23:a user-friendly,parameterized model of magnetosheath conditions

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Earth and Planetary Physics 2024年第1期8卷 89-104页

作者： Jaewoong Jung Hyunju Connor Andrew Dimmock Steve Sembay Andrew Read Jan Soucek NASA Goddard Space Flight center GreenbeltMDUSA Department of Astronomy University of MarylandCollege ParkMDUSA swedish Institude of Space Physics UppsalaSweden University of Leicester LeicesterUK Institute of Atmospheric Physics Academy of Sciences of the Czech Republic

Lunar Environment heliospheric X-ray Imager(LEXI)and Solar wind−Magnetosphere−Ionosphere Link Explorer(SMILE)will observe magnetosheath and its boundary motion in soft X-rays for understanding magnetopause reconnection modes under various solar wind conditions after their respective launches in 2024 and *** conditions,namely,plasma density,velocity,and temperature,are key parameters for predicting and analyzing soft X-ray images from the LEXI and SMILE *** developed a userfriendly model of magnetosheath that parameterizes number density,velocity,temperature,and magnetic field by utilizing the global Magnetohydrodynamics(MHD)model as well as the pre-existing gas-dynamic and analytic *** this parameterized magnetosheath model,scientists can easily reconstruct expected soft X-ray images and utilize them for analysis of observed images of LEXI and SMILE without simulating the complicated global magnetosphere ***,we created an MHD-based magnetosheath model by running a total of 14 OpenGGCM global MHD simulations under 7 solar wind densities(1,5,10,15,20,25,and 30 cm)and 2 interplanetary magnetic field Bz components(±4 nT),and then parameterizing the results in new magnetosheath *** compared the magnetosheath model result with THEMIS statistical data and it showed good agreement with a weighted Pearson correlation coefficient greater than 0.77,especially for plasma density and plasma ***,we compiled a suite of magnetosheath models incorporating previous magnetosheath models(gas-dynamic,analytic),and did two case studies to test the *** MHD-based model was comparable to or better than the previous models while providing self-consistency among the magnetosheath ***,we constructed a tool to calculate a soft X-ray image from any given vantage point,which can support the planning and data analysis of the aforementioned LEXI and SMILE missions.A release of the code has been uploaded to a Git

关键词： magnetosheath python modeling

Genomic selection in plant breeding:Key factors shaping two decades of progress

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Molecular Plant 2024年第4期17卷 552-578页

作者： Admas Alemu Johanna Astrand Osval A.Montesinos-López Julio Isidro y Sanchez Javier Fernandez-Gónzalez Wuletaw Tadesse Ramesh R.Vetukuri Anders S.Carlsson Alf Ceplitis JoséCrossa Rodomiro Ortiz Aakash Chawade Department of Plant Breeding Swedish University of Agricultural SciencesAlnarpSweden Lantmannen Lantbruk SvalövSweden Facultad de Telematica University de ColimaColimaColima 28040Mexico Centro de Biotecnología y Genómica de Plantas(CBGP UPM-INIA)Universidad Politécnica de Madrid(UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria(INIA)Campus de Montegancedo-UPM28223 MadridSpain International center for Agricultural Research in the Dry Areas(ICARDA) RabatMorocco International Maize and Wheat Improvement center(CIMMYT) Km 45Carretera México-VeracruzTexcocoMéxico 52640Mexico

Genomic selection,the application of genomic prediction(GP)models to select candidate individuals,has significantly advanced in the past two decades,effectively accelerating genetic gains in plant *** article provides a holistic overview of key factors that have influenced GP in plant breeding during this *** delved into the pivotal roles of training population size and genetic diversity,and their relationship with the breeding population,in determining GP *** emphasis was placed on optimizing training population *** explored its benefits and the associated diminishing returns beyond an optimum *** was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization *** density and distribution of single-nucleotide polymorphisms,level of linkage disequilibrium,genetic complexity,trait heritability,statistical machine-learning methods,and non-additive effects are the other vital *** wheat,maize,and potato as examples,we summarize the effect of these factors on the accuracy of GP for various *** search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various *** hypothesize that with ultra-high sizes of genotypic and phenotypic datasets,effective training population optimization methods and support from other omics approaches(transcriptomics,metabolomics and proteomics)coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy,making genomic selection an effective tool in plant breeding.

关键词： genomic selection genetic gain genomic prediction optimization deep learning training population optimization

TMB相关免疫浸润调控评分(MOTIF)预测免疫治疗响应并指导联合增效

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Science Bulletin 2024年第6期69卷 803-822页

作者：钱政宇潘艺芊李薛鑫陈衍行吴灏祥刘泽先 Martin Kosar Jiri Bartek 王梓贤徐瑞华 Department of medical Oncology Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerResearch Unit of Precision Diagnosis and Treatment for Gastrointestinal CancerChinese Academy of Medical SciencesGuangzhou 510060China Science for Life Laboratory Division of Genome BiologyDepartment of Medical Biochemistry and BiophysicsKarolinska InstituteStockholm S-17121Sweden Department of General Surgery The Fourth Affiliated HospitalChina Medical UniversityShenyang 110032China Bioinformatics Platform Sun Yat-sen University Cancer CenterGuangzhou 510060China Zhejiang University-University of Edinburgh Institute Zhejiang University School of MedicineHaining 314400China Edinburgh medical School Biomedical SciencesCollege of Medicine and Veterinary MedicineThe University of EdinburghEdinburgh EH11LTUK Danish Cancer Society Research center Copenhagen DK-2100Denmark Laboratory of Artificial Intelligence and Data Science Sun Yat-sen University Cancer CenterGuangzhou 510060China

Patients with high tumor mutational burden(TMB)levels do not consistently respond to immune checkpoint inhibitors(ICIs),possibly because a high TMB level does not necessarily result in adequate infiltration of CD8^(+)T *** bulk ribonucleic acid sequencing(RNA-seq)data from 9311 tumor samples across 30 cancer types,we developed a novel tool called the modulator of TMB-associated immune infiltration(MOTIF),which comprises genes that can determine the extent of CD8^(+)T cell infiltration prompted by a certain TMB *** confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity *** analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors,we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8^(+)T cell *** pretreatment RNA-seq data from 13 ICI-treated cohorts,we validated the use of MOTIF in predicting CD8^(+)T cell infiltration and ICI *** the components of MOTIF,we identified EMC3 as a negative regulator of CD8^(+)T cell infiltration,which was validated via in vivo ***,MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8^(+)T cell infiltration and improve ICI efficacy.

关键词： Tumor mutational burden Immunotherapy Cancer-immunity cycle Treatment efficacy prediction CD8^(+)T cell infiltration Combination therapy

SIL1 improves cognitive impairment in APP23/PS45 mice by regulating amyloid precursor protein processing and Aβ generation

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Zoological Research 2024年第4期45卷 845-856页

作者： Qunxian Wang Yanshuang Jiang Zijun Meng Xiangjun Dong Dongjie Hu Liangye Ji Weihui Zhou Weihong Song Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400000China Second Affiliated Hospital and Yuying Children’s Hospital Institute of AgingKey Laboratory of Alzheimer’s Disease of Zhejiang ProvinceWenzhou Medical UniversityWenzhouZhejiang 325000China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)WenzhouZhejiang 325001China

SIL1,an endoplasmic reticulum(ER)-resident protein,is reported to play a protective role in Alzheimer’s disease(AD).However,the effect of SIL1 on amyloid precursor protein(APP)processing remains *** this study,the role of SIL1 in APP processing was explored both in vitro and in *** the in vitro experiment,SIL1 was either overexpressed or knocked down in cells stably expressing the human swedish mutant *** the in vivo experiment,AAV-SIL1-EGFP or AAV-EGFP was microinjected into APP23/PS45 mice and their wild-type *** blotting(WB),immunohistochemistry,RNA sequencing(RNA-seq),and behavioral experiments were performed to evaluate the relevant *** indicated that SIL1 expression decreased in APP23/PS45 *** of SIL1 significantly decreased the protein levels of APP,presenilin-1(PS1),and C-terminal fragments(CTFs)of APP in vivo and in ***,knockdown of SIL1 increased the protein levels of APP,β-site APP cleavage enzyme 1(BACE1),PS1,and CTFs,as well as APP mRNA expression in 2EB2 ***,SIL1 overexpression reduced the number of senile plaques in APP23/PS45 ***,Y-maze and Morris Water maze tests demonstrated that SIL1 overexpression improved cognitive impairment in APP23/PS45 *** findings indicate that SIL1 improves cognitive impairment in APP23/PS45 mice by inhibiting APP amyloidogenic processing and suggest that SIL1 is a potential therapeutic target for AD by modulating APP processing.

关键词： Alzheimer’s disease SIL1 APP processing Cognitive impairment

Why ecosystem characteristics predicted from remotely sensed data are unbiased and biased at the same time-and how this affects applications

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Forest Ecosystems 2024年第1期11卷 24-31页

作者： Goran Ståhl Terje Gobakken Svetlana Saarela Henrik J.Persson Magnus Ekstrom Sean P.Healey Zhiqiang Yang Johan Holmgren Eva Lindberg Kenneth Nystrom Emanuele Papucci Patrik Ulvdal Hans OleØrka Erik Næsset Zhengyang Hou Håkan Olsson Ronald E.McRoberts Department of Forest Resource Management Swedish University of Agricultural Sciences90183UmeåSweden Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life SciencesÅsNorway USDA Forest Service Rocky Mountain Research StationOgdenUTUSA The Key Laboratory for Silviculture and Conservation of Ministry of Education Beijing Forestry UniversityBeijing100083China Department of Forest Resources University of MinnesotaSt.PaulMNUSA

Remotely sensed data are frequently used for predicting and mapping ecosystem characteristics,and spatially explicit wall-to-wall information is sometimes proposed as the best possible source of information for ***,wall-to-wall information typically relies on model-based prediction,and several features of model-based prediction should be understood before extensively relying on this type of *** such feature is that model-based predictors can be considered both unbiased and biased at the same time,which has important implications in several areas of *** this discussion paper,we first describe the conventional model-unbiasedness paradigm that underpins most prediction techniques using remotely sensed(or other)auxiliary *** this point of view,model-based predictors are typically ***,we show that for specific domains,identified based on their true values,the same model-based predictors can be considered biased,and sometimes severely *** suggest distinguishing between conventional model-bias,defined in the statistical literature as the difference between the expected value of a predictor and the expected value of the quantity being predicted,and design-bias of model-based estimators,defined as the difference between the expected value of a model-based estimator and the true value of the quantity being *** show that model-based estimators(or predictors)are typically design-biased,and that there is a trend in the design-bias from overestimating small true values to underestimating large true ***,we give examples of applications where this is important to acknowledge and to potentially make adjustments to correct for the design-bias *** argue that relying entirely on conventional model-unbiasedness may lead to mistakes in several areas of application that use predictions from remotely sensed data.

关键词： Bias Model-based inference Design-based inference

Ground-based and additional science support for SMILE

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Earth and Planetary Physics 2024年第1期8卷 275-298页

作者： J.A.Carter M.Dunlop C.Forsyth K.Oksavik E.Donovon A.Kavanagh S.E.Milan T.Sergienko R.C.Fear D.G.Sibeck M.Connors T.Yeoman X.Tan M.G.G.T.Taylor K.McWilliams J.Gjerloev R.Barnes D.D.Billet G.Chisham A.Dimmock M.P.Freeman D.-S.Han M.D.Hartinger S.-Y.W.Hsieh Z.-J.Hu M.K.James L.Juusola K.Kauristie E.A.Kronberg M.Lester J.Manuel J.Matzka I.McCrea Y.Miyoshi J.Rae L.Ren F.Sigernes E.Spanswick K.Sterne A.Steuwer T.Sun M.-T.Walach B.Walsh C.Wang J.Weygand J.Wild J.Yan J.Zhang Q.-H.Zhang Planetary Sciences Group School of Physics and AstronomyUniversity of LeicesterUniversity RoadLeicesterLE17RHUK Rutherford Appleton Laboratory Space Science Technology Facilities CouncilOxfordshireUK School of Space and Environment Beihang UniversityBeijing 100191China Key Laboratory of Space Environment Monitoring and Information Processing Ministry of Industry and Information TechnologyBeijing 100017China Department of Space and Climate Physics UCLMullard Space Science LaboratoryHolmbury St.MaryDorkingSurreyRH56NTUK Birkeland Centre for Space Science Department of Physics and Technology.University of BergenBergenNorway Department of Physics and Astronomy University of Calgary2500 University DriveCalgaryAlbertaCanada T2N 1N4 British Antarctic Survey CambridgeUK swedish Institute of Space Physics KirunaSweden West Highfield Campus University of SouthamptonUniversity RoadSO171BJUK Goddard Space Flight center NASAGreenbeltMarylandUSA Athabasca University AthabascaCanada ESTEC European Space AgencyNetherlands University of Saskatchewan SaskatoonCanada The Johns Hopkins University Applied Physics Laboratory LaurelMarylandUSA swedish Institude of Space Physics UppsalaSE 75121Sweden Tongji University Shanghai 200092China center for Space Plasma Physics Space Science Institute4765 Walnut Street Suite BBoulderColorado80301USA Polar Research Institute of China Shanghai 200136China Finnish Meteorological Institute(FMI) Finland Department of Earth and Environmental Sciences(Geophysics) Ludwig Maximilian University of Munich(LMU)MunichTheresienstr.41MunichD-80333Germany Canadian Space Agency MontrealCanada GFZ German Research Centre for Geosciences PotsdamGermany Nagoya University Institute for Space Earth Environment ResearchCenter for Integrated Data ScienceNagoyaAichiJP 464-8601 Northumbria University Newcastle upon TyneTyne and WearUK NE18ST National Space Science center Chinese Academy SciencesBeijing 100190China Arctic Geophysics University Centre in Svalbard

The joint European Space Agency and Chinese Academy of Sciences Solar wind Magnetosphere Ionosphere Link Explorer(SMILE)mission will explore global dynamics of the magnetosphere under varying solar wind and interplanetary magnetic field conditions,and simultaneously monitor the auroral response of the Northern Hemisphere *** these large-scale responses with medium and fine-scale measurements at a variety of cadences by additional ground-based and space-based instruments will enable a much greater scientific impact beyond the original goals of the SMILE ***,we describe current community efforts to prepare for SMILE,and the benefits and context various experiments that have explicitly expressed support for SMILE can offer.A dedicated group of international scientists representing many different experiment types and geographical locations,the Ground-based and Additional Science Working Group,is facilitating these *** include constructing an online SMILE Data Fusion Facility,the discussion of particular or special modes for experiments such as coherent and incoherent scatter radar,and the consideration of particular observing strategies and spacecraft *** anticipate growing interest and community engagement with the SMILE mission,and we welcome novel ideas and insights from the solar-terrestrial community.

关键词： magnetosphere ionosphere magnetosphere-ionosphere coupling ground-based experimentation SMILE conjunctions missions

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard

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Zoological Research 2024年第3期45卷 464-467页

作者： Hai-Meng Li Bo-Yang Liu Min-Hui Shi Le Zhang Shang-Chen Yang Sunil Kumar Sahu Liang-Yu Cui Shan-Lin Liu Nicolas Dussex Yue Ma Dan Liu Wei-Yao Kong Hao-Rong Lu Yue Zhao Love Dalén Huan Liu Tian-Ming Lan Guang-Shun Jiang Yan-Chun Xu College of Wildlife and Protected Area Northeast Forestry UniversityHarbinHeilongjiang 150040China State Key Laboratory of Agricultural Genomics BGI ResearchShenzhenGuangdong 518083China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China BGI Research WuhanHubei 430074China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China Centre for Palaeogenetics Svante Arrhenius väg 20CStockholm 10691Sweden Department of Zoology Stockholm UniversityStockholm 10691Sweden Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryStockholm 10691Sweden Heilongjiang Siberian Tiger Park HarbinHeilongjiang 150000China Jinlin Provincial Academy of Forestry Science ChangchunJilin 130033China China National GeneBank BGI ResearchShenzhenGuangdong 518120China Guangdong Provincial Key Laboratory of Genome Read and Write BGI ResearchShenzhenGuangdong 518083China BGI Life Science Joint Research center Northeast Forestry UniversityHarbinHeilongjiang 150040China Feline Research center of National Forestry and Grassland Administration College of Wildlife and Protected AreaNortheast Forestry UniversityHarbinHeilongjiang 150040China National Forestry and Grassland Administration Research center of Engineering Technology for Wildlife Conservation and Utilization HarbinHeilongjiang 150040China

DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(*** orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator ***,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated ***,all extant big cats are categorized as endangered or threatened according to their conservation *** tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal *** tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the *** spatial and temporal niche partitioning,interspecific competition between these two species is ***,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.

关键词： habitat Panthera resolved

Recent advances and future directions in preclinical research of argininevasopressin(AVP) receptor blocker conivaptan in the context of stroke

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Neural Regeneration Research 2016年第3期11卷 392-393页

作者： Emil Zeynalov Susan M.Jones swedish medical center Neurotrauma Research Department Englewood

Stroke is a major cause of mortality and permanent *** onset of stroke is followed by life-threatening pathophysiological responses including brain edema,elevation of intracranial pressure,disruption of blood-brain barrier（BBB）,brain infarct and permanent tissue *** edema develops due to accumulation of water in intracellular and extracellular compartments of the brain,

关键词： edema permanent disability intracranial elevation blocker infarct disruption advances mortality

Psychiatric comorbidities in epilepsy:population co-occurrence,genetic correlations and causal effects

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General Psychiatry 2024年第1期37卷 103-111页

作者： Viktor H Ahlqvist Christina Dardani Paul Madley-Dowd Harriet Forbes Jessica Rast Caichen Zhong Renee M Gardner Christina Dalman Kristen Lyal cRAIG Newschaffer Torbjorn Tomson Michael Lundberg Daniel Berglind Neil M Davies Brian K Lee Cecilia Magnusson Dheeraj Rai Department of Global Public Health Karolinska InstitutetStockholmSweden medical Research Council Integrative Epidemiology Unit Bristol Medical SchoolUniversity of BristolBristolUK Centre for Academic Mental Health Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK Faculty of Epidemiology and Population Health London School of Hygiene and Tropical MedicineLondonUK A.J.Drexel Autism Institute Drexel UniversityPhiladelphiaPAUSA Department of Epidemiology and Biostatistics School of Public HealthDrexel UniversityPhiladelphiaPAUSA College of Health and Human Development Pennsylvania State UniversityState CollegePAUSA Department of Clinical Neuroscience Karolinska InstitutetStockholmSweden Centre for Epidemiology and Community Medicine Region StockholmStockholmSweden K.G Jebsen center for Genetic Epidemiology Department of Public Health and NursingNorwegian University of Science and TechnologyTrondheimNorway Division of Psychiatry University Collge LondonLondonUK Department of Statistical Sciences University Cllge LondonLondonK NIHR Biomedical Research Centre University of BristoBristolUK Avon and Wiltshire Partnership NHS Mental Health TrustBristolUK

Background Psychiatric comorbidities are common in patients with *** for the co-occurrence of psychiatric conditions and epilepsy remain poorly *** We aimed to triangulate the relationship between epilepsy and psychiatric conditions to determine the extent and possible origins of these *** Using nationwide swedish health registries,we quantified the lifetime prevalence of psychiatric disorders in patients with *** then used summarydata from genome-wide association studies to investigate whether the identified observational associations could be attributed to a shared underlying genetic aetiology using cross-trait linkage disequilibrium score ***,we assessed the potential bidirectional relationships using two-sample Mendelian *** In a cohort of 7628495 individuals,we found that almost half of the 94435 individuals diagnosed with epilepsy were also diagnosed with a psychiatric condition in their lifetime(adjusted lifetime prevalence,44.09%;95%confidence interval(Cl)43.78%to 44.39%).We found evidence for a genetic correlation between epilepsy and some neurodevelopmental and psychiatric *** example,we observed a genetic correlation between epilepsy and attention-deficit/hyperactivity disorder(r,=0.18,95%Cl 0.09 to 0.27,p<0.001)—a correlation that was more pronounced in focal epilepsy(r=0.23,95%CI 0.09 to 0.36,p<0.001).Findings from Mendelian randomisation using common genetic variants did not support bidirectional effects between epilepsy and neurodevelopmental or psychiatric *** Psychiatric comorbidities are common in patients with *** correlations may partially explain some comorbidities;however,there is little evidence of a bidirectional relationship between the genetic liability of epilepsy and psychiatric *** findings highlight the need to understand the role of environmental factors or rare genetic variations in the origins of psy

关键词： epilepsy Psychiat lifetime