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npj computational Materials 2022年第1期8卷 1434-1442页

作者： Tim Hsu Tuan Anh Pham Nathan Keilbart Stephen Weitzner James chapman Penghao Xiao S.Roger Qiu Xiao chen brandon c.wood center for Applied Scientific computing Lawrence Livermore National LaboratoryLivermoreCAUSA Materials Science Division Lawrence Livermore National LaboratoryLivermoreCAUSA Department of Physics and Atmospheric Science Dalhousie UniversityHalifaxNSCanada

Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and ***,conventional encoding does not include angular information,which is critical for describing atomic arrangements in disordered *** this work,we extend the recently proposed ALIGNN(Atomistic Line Graph Neural Network)encoding,which incorporates bond angles,to also include dihedral angles(ALIGNN-d).This simple extension leads to a memory-efficient graph representation that captures the complete geometry of atomic ***-d is applied to predict the infrared optical response of dynamically disordered cu(II)aqua complexes,leveraging the intrinsic interpretability to elucidate the relative contributions of individual structural *** and dihedral angles are found to be critical contributors to the fine structure of the absorption response,with distortions that represent transitions between more common geometries exhibiting the strongest absorption *** directions for further development of ALIGNN-d are discussed.

关键词： representation disordered absorption

fficient and universal characterization of atomic structures through a topological graph order parameter

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npj computational Materials 2022年第1期 334-345页

作者： James chapman Nir Goldman brandon c.wood Physical and Life Sciences Directorate Lawrence Livermore National LaboratoryLivermoreCAUSA Department of chemical Engineering University of CaliforniaDavisCaliforniaCA95616United States

A graph-based order parameter,based on the topology of the graph itself,is introduced for the characterization of atomistic *** order parameter is universal to any material/chemical system and is transferable to all structural *** sets of data are used to validate both the generalizability and accuracy of the algorithm:(1)liquid lithium configurations spanning up to 300 GPa,(2)condensed phases of carbon along with nanotubes and buckyballs at ambient and high temperature,(3)a diverse set of aluminum configurations including surfaces,compressed and expanded lattices,point defects,grain boundaries,liquids,nanoparticles,all at nonzero temperatures,and(4)eleven niobium oxide crystal phases generated with ab initio molecular *** compare our proposed method to existing,state-of-the-art methods for the cases of aluminum and niobium *** order parameter uniquely classifies every configuration and outperforms all studied existing methods,opening the door for its use in a multitude of complex application spaces that can require fine structure-level characterization of atomistic graphs.

关键词： parameter configuration uniquely

Microstructural impacts on ionic conductivity of oxide solid electrolytes from a combined atomistic-mesoscale approach

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npj computational Materials 2021年第1期7卷 1959-1973页

作者： Tae Wook Heo Andrew Grieder Bo Wang Marissa wood Tim Hsu Sneha A.Akhade Liwen F.Wan Long-Qing chen Nicole Adelstein brandon c.wood Materials Science Division Lawrence Livermore National LaboratoryLivermoreCA 94550USA Department of chemistry and Biochemistry San Francisco State UniversitySan FranciscoCA 94132USA Department of Materials Science and Engineering The Pennsylvania State UniversityUniversity ParkPA 16802USA center for Applied Scientific computing Lawrence Livermore National LaboratoryLivermoreCA 94550USA

Although multiple oxide-based solid electrolyte materials with intrinsically high ionic conductivities have emerged,practical processing and synthesis routes introduce grain boundaries and other interfaces that can perturb primary conduction *** directly probe these effects,we demonstrate an efficient and general mesoscopic computational method capable of predicting effective ionic conductivity through a complex polycrystalline oxide-based solid electrolyte microstructure without relying on simplified equivalent circuit *** parameterize the framework for Li_(7-x)La_(3)Zr_(2)0_(12)(LLZO)gamet solid electrolyte by combining synthetic microstructures from phase-field simulations with diffusivities from molecular dynamics simulations of ordered and disordered *** designed simulations reveal an interdependence between atomistic and mesoscopic microstructural impacts on the effective ionic conductivity of polycrystalline LLZO,quantified by newly defined metrics that characterize the com plex ionic transport *** results provide fundamental understanding of the physical origins of the reported variability in ionic conductivities based on an extensive analysis of literature data,while simultaneously outlining practical design guidance for achieving desired ionic transport properties based on conditions for which sensitivity to microstructural features is *** implications of our results are discussed,including a possible connection between ion conduction behavior and dendrite formation.

关键词： microstructure solid conductivity

Multiple sclerosis is at a checkpoint: advancing the program

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Neural Regeneration Research 2025年第3期20卷 811-812页

作者： brandon c.Smith Jessica L.Williams Department of Neurosciences Lerner Research InstituteCleveland ClinicClevelandOHUSA Department of Biological Geologicaland Environmental SciencesCleveland State UniversityClevelandOHUSA

Multiple sclerosis(MS) is a chronic inflammatory and demyelinating disease of the central nervous system(cNS). Patients with MS experience sensory and motor function loss due to myelin and/or axon damage perpetuated b... 详细信息

关键词： Hauser sclerosis damage

Activation of stress-response genes by retrograde signaling-mediated destabilization of nuclear importin IMPα-9 and its interactor TPR2

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Molecular Plant 2024年第6期17卷 884-899页

作者： Liping Zeng Maria Fernanda Gomez Mendez Jingzhe Guo Jishan Jiang Bailong Zhang Hao chen brandon Le Haiyan Ke Katayoon Dehesh Department of Botany and Plant Sciences Institute of Integrative Genome BiologyUniversity of CaliforniaRiversideRiversideCA 92521USA School of Medicine University of CaliforniaRiversideRiversideCA 92521USA

Stress-induced retrograde signal transmission from the plastids to the nucleus has long puzzled plant *** address this,we performed a suppressor screen of the ceh1 mutant,which contains elevated 2-c-methyl-d-erythritol-2,4-cyclopyrophosphate(MEcPP)levels,and identified the gain-of-function mutant impα-9,which shows reversed dwarfism and suppressed expression of stress-response genes in the ceh1 background despite heightened *** genetic and biochemical analyses established that the accumulation of MEcPP initiates an upsurge in Arabidopsis SKP1-like 1(ASK1)abundance,a pivotal component in the proteasome degradation *** increase in ASK1 prompts the degradation of IMPα-***,we uncovered a protein-protein interaction between IMPα-9 and TPR2,a transcriptional co-suppressor and found that a reduction in IMPα-9 levels coincides with a decrease in TPR2 ***,the interaction between IMPα-9 and TPR2 was disrupted in impα-9 mutants,highlighting the critical role of a single amino acid alteration in maintaining their *** of their interaction results in the reversal of MEcPP-associated *** immunoprecipitation coupled with sequencing analyses revealed that TPR2 binds globally to stress-response genes and suggested that IMPα-9 associates with the *** function together to suppress the expression of stress-response genes under normal conditions,but this suppression is alleviated in response to stress through the degradation of the suppressing *** biological relevance of our discoveries was validated under high light stress,marked by MEcPP accumulation,elevated ASK1 levels,IMPα-9 degredation,reduced TPR2 abundance,and subsequent activation of a network of stress-response *** summary,our study collectively unveils fresh insights into plant adaptive mechanisms,highlighting intricate interactions among retrograde signaling,the proteasome,and nuclear transport machinery.

关键词： plastidial retrograde signal MEcPP ASK1 impα-9 TPR2

RNA m^(6)A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression

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Genes & Diseases 2024年第1期11卷 382-396页

作者： Zheng Zhang Keren Zhou Li Han Andrew Small Jianhuang Xue Huilin Huang Hengyou Weng Rui Su brandon Tan chao Shen Wei Li Zhicong Zhao Ying Qing Xi Qin Kitty Wang Keith Leung Mark Boldin chun-Wei chen David Ann Zhijian Qian Xiaolan Deng Jianjun chen Zhenhua chen Department of Systems Biology Beckman Research Institute of City of HopeMonroviaCA 91016USA Irell and Manella Graduate School of Biological Sciences Beckman Research Institute of City of HopeDuarteCA 91010USA Gehr Family center for Leukemia Research City of HopeDuarteCA 91010USA Sun Yat-sen University cancer center State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangzhouGuangdong 510060China Guangzhou Laboratory GuangzhouGuangdong 510005China Bioland Laboratory GuangzhouGuangdong 51005China Department of Liver Surgery Renji HospitalShanghai Jiao Tong University School of MedicineShanghai 200127China Department of Diabetes complications and Metabolism Beckman Research Institute of City of HopeDuarteCA 91010USA Department of Biochemistry and Molecular Biology University of FloridaGainesvilleFL 32603USA Tongji Hospital Affiliated to Tongji University Frontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China School of Pharmacy China Medical UniversityShenyangLiaoning 110001China

As the most common internal modification of mRNA,Ne-methyladenosine(m^(6)A)and its regulators modulate gene expression and play critical roles in various biological and patholog-ical processes including *** was reported previously that m^(6)A methyltransferase(writer),methyltransferase-like 3(METTL3)adds m^(6)A in primary microRNAs(pri-miRNAs)and fa-cilitates its processing into precursor miRNAs(pre-miRNAs).However,it is unknown whether m^(6)A modification also plays a role in the maturation process of pre-miRNAs and(if so)whether such a function contributes to ***,we found that YTHDF2 is aberrantly overexpressed in acute myeloid leukemia(AML)patients,especially in relapsed patients,and plays an onco-genic role in ***,YTHDF2 promotes expression of miR-126-3p(also known as miR-126,as it is the main product of precursor miR-126(pre-miR-126)),a miRNA that was reported as an oncomiRNA in AML,through facilitating the processing of pre-miR-126 into mature ***,YTHDF2 recognizes m^(6)A modification in pre-miR-126 and recruits AGO2,a regulator of pre-miRNA processing,to promote the maturation of ***2 posi-tively and negatively correlates with miR-126 and miR-126's downstream target genes,respec-tively,in AML patients,and forced expression of miR-126 could largely rescue YTHDF2/Ythdf2 depletion-mediated suppression on AML cell growth/proliferation and leukemogenesis,indi-cating that miR-126 is a functionally important target of YTHDF2 in ***,our studies not only reveal a previously unappreciated YTHDF2/miR-126 axis in AML and highlight the ther-apeutic potential of targeting this axis for AML treatment,but also suggest that m^(6)A plays a role in pre-miRNA processing that contributes to tumorigenesis.

关键词： AML miR-126 N^(6)-methyladenosine Pre-miRNA maturation YTHDF2

AdsorbML: a leap in efficiency for adsorption energy calculations using generalizable machine learning potentials

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npj computational Materials 2023年第1期9卷 565-573页

作者： Janice Lan Aini Palizhati Muhammed Shuaibi brandon M.wood Brook Wander Abhishek Das Matt Uyttendaele c.Lawrence Zitnick Zachary W.Ulissi Fundamental AI Research(FAIR) Meta AIMetaMenlo ParkCAUSA Department of chemical Engineering Carnegie Mellon UniversityPittsburghPAUSA Scott Institute for Energy Innovation Carnegie Mellon UniversityPittsburghPAUSA

computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications.A common task for many computational methods is the need to accurately compute the adsorption energy for an adsorbate and a catalyst surface of ***,the identification of low-energy adsorbate-surface configurations relies on heuristic methods and researcher *** the desire to perform high-throughput screening increases,it becomes challenging to use heuristics and intuition *** this paper,we demonstrate machine learning potentials can be leveraged to identify low-energy adsorbate-surface configurations more accurately and *** algorithm provides a spectrum of trade-offs between accuracy and efficiency,with one balanced option finding the lowest energy configuration 87.36%of the time,while achieving a~2000×speedup in *** standardize benchmarking,we introduce the Open catalyst Dense dataset containing nearly 1000 diverse surfaces and~100,000 unique configurations.

关键词： adsorption configuration energy

Phylogenetic endemism of the orchids of Megamexico reveals complementary areas for conservation

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Plant Diversity 2022年第4期44卷 351-359页

作者： brandon E.Gutierrez-Rodríguez Marilyn Vasquez-cruz Victoria Sosa Instituto de Ecología Ac Carretera Antigua a Coatepec 351El Haya91073 XalapaVeracruzMexico Unidad de Genomica Avanzada Laboratorio Nacional de Genomica para La BiodiversidadCentro de Investigaciony Estudios Avanzados IrapuatoLibramiento Norte Carretera Leon Km.9.636821 IrapuatoGuanajuatoMexico

Orchid diversity provides a unique opportunity to further our understanding of biotic and abiotic factors linked to patterns of richness,endemism,and phylogenetic endemism in many ***,orchid diversity is consistently threatened by illegal trade and habitat ***,we identified areas critical for orchid conservation in the biogeographic province of *** this purpose,we evaluated orchid endemism,phylogenetic diversity,and phylogenetic endemism within Megamexico and characterized orchid life *** results indicate that the majority of the regions with the highest estimates of endemism and phylogenetic endemism are in southern Mexico and northern central America,mostly located on the Pacific side of *** the most important orchid lineages,several belong to epiphytic lineages such as Pleurothallidinae,Laeliinae and *** also found that species from diverse and distantly related lineages converge in montane forests where suitable substrates for epiphytes ***,the southernmost areas of phylogenetic diversity and endemism of Megamexico are in unprotected ***,we conclude that the most critical areas for orchid conservation in Megamexico are located in southern Mexico and northern central *** recommend that these areas should be given priority by the Mexican system of natural protected areas as complementary conservation areas.

关键词： Epiphytes Geophytes Orchids Phylogenetic endemism Weighted endemism

Effects of medium chain triglycerides on hepatic fatty acid oxidation in clofibrate-fed newborn piglets

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Animal Nutrition 2023年第1期12卷 334-344页

作者： Jinan Zhao brandon Pike Jin Huang Zhihua Feng Jack Odle Xi Lin Laboratory of Developmental Nutrition Department of Animal SciencesNorth Carolina State UniversityRaleighNC 27695USA Zinpro corporation Eden PrairieMN 55344USA college of Biological Engineering Henan University of TechnologyZhengzhou450001China college of Animal Science and Technology Agricultural University of HebeiBaoding071001China

To investigate whether increasing tricarboxylic acid(TcA)cycle activity and ketogenic capacity would augment fatty acid(FA)oxidation induced by the peroxisome proliferator-activated receptor-alpha(PPARα)agonist clofibrate,suckling newborn piglets(n=54)were assigned to 8 groups following a 2(±clofibrate)×4(glycerol succinate[SUc],triglycerides of 2-methylpentanoic acid[T2M],valeric acid[Tc5]and hexanoic acid[Tc6])factorial *** group was fed an isocaloric milk formula containing either 0%or 0.35%clofibrate(wt/wt,dry matter basis)with 5%SUc,T2M,Tc5 or Tc6 for 5 *** 6 pigs served as newborn *** acid oxidation was examined in fresh homogenates of liver collected on d 6 using[1-^(14)c]palmitic acid(1 mM)as a substrate(0.265μci/μmol).Measurements were performed in the absence or presence of L-carnitine(1 mM)or inhibitors of 3-hydroxy-3-methylglutaryl-coA synthase(L659699,1.6μM)or acetoacetate-coA deacylase(iodoacetamide,50μM).Without clofibrate stimulation,^(14)c accumulation in cO_(2) was higher from piglets fed diets containing T2M and Tc5 than SUc,but similar to those fed *** clofibrate stimulation,accumulation also was higher in homogenates from piglets fed Tc5 than all other dietary *** between clofibrate and carnitine or the inhibitors were observed(P=0.0004)for acid soluble products(ASP).In vitro addition of carnitine increased^(14)c-ASP(Pclofibrate *** percentage of^(14)c in cO_(2) was higher(P=0.0023)in Tc5 than in the control *** these results we suggest that dietary supplementation of anaplerotic and ketogenic FA could impact FA oxidation and modify the metabolism of acetyl-coA(product ofβ-oxidation)via alteration of TcA cycle activity,but the modification has no significant impact on the hepatic FA oxidative capacity induced by PPARα.In addition,the availability of carnitine is a critical element to maintain FA oxidation during the neonatal perio

关键词： PPARα clofibrate Newborn piglets Medium chain triglyceride(McT) Hepatic fatty acid oxidation

clinical classification of symptomatic heterotopic pancreas of the stomach and duodenum:A case series and systematic literature review

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World Journal of Gastroenterology 2022年第14期28卷 1455-1478页

作者： Michael T Le compte brandon Mason Keenan J Robbins Motoyo Yano Deyali chatterjee Ryan c Fields Steven M Strasberg William G Hawkins Department of Surgical Oncology University of North CarolinaRaleighNC 27608United States Department of Radiology Stillwater Medical CenterStillwaterOK 74074United States Department of General Surgery Washington University St.LouisSt.LouisMO 63110-8109United States Department of Radiology Mayo ClinicPhoenixAZ 8505United States Department of Pathology and Immunology MD Anderson Cancer CenterHoustonTX 77030United States Department of Surgical Oncology Washington University School of MedicineSt.LouisMO 63110-8109United States Section of Hepatobiliary-Pancreatic and GI Surgery Washington University St.LouisSt.LouisMO 63110United States

BAcKGROUND Heterotopic pancreas(HP)is an aberrant anatomic malformation that occurs most commonly in the upper gastrointestinal *** the majority of heterotopic pancreatic lesions are asymptomatic,many manifest severe clinical symptoms which require surgical or endoscopic *** of the clinical manifestations and symptoms of HP is limited due to the lack of large volume studies in the *** purpose of this study is to review symptomatic cases at a single center and compare these to a systematic review of the literature in order to characterize common clinical manifestations and treatment of this *** To classify the common clinical manifestations of heterotopic *** A retrospective review was conducted of pathologic samples containing heterotopic pancreas from *** was limited to HP of the upper gastrointestinal tract due to the frequency of presentation in this *** patients were identified from review of the medical records and clinical symptoms were *** were compared to a systematic review of the literature utilizing Pub Med and Embase searches for papers pertaining to heterotopic *** describing symptomatic presentation of HP were selected for *** including demographics,symptoms,presentation and treatment were compiled and *** Twenty-nine patient were identified with HP at a single center,with six of these identified has having clinical *** manifestations included,gastrointestinal bleeding,gastric ulceration with/without perforation,pancreatitis,and gastric outlet *** review of the literature yielded 232 publications detailing symptomatic cases with only 20 studies describing ten or more *** and multi-patient studies were combined to form a cohort of 934 symptomatic *** majority of patients presented with abdominal pain(67%)combined with one of the following clinical catego

关键词： Heterotopic pancreas Ectopic pancreas Aberrant pancreas Pancreatic rest Groove pancreatitis