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Systematic beyond-DFT study of binary transition metal oxides

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npj Computational Materials 2019年第1期5卷 124-131页

作者： Subhasish Mandal Kristjan Haule Karin M.Rabe david vanderbilt Department of Physics and Astronomy Rutgers UniversityPiscatawayNJUSA

Various methods going beyond density functional theory(DFT),such as DFT+U,hybrid functionals,meta-GGAs,GW,and DFTembedded dynamical mean field theory(eDMFT),have been developed to describe the electronic structure of correlated materials,but it is unclear how accurate these methods can be expected to be when applied to a given strongly correlated *** is thus of pressing interest to compare their accuracy as they apply to different categories of *** we introduce a novel paradigm in which a chosen set of beyond-DFT methods is systematically and uniformly tested on a chosen class of *** a first application,we choose the target materials to be the binary transition metal oxides FeO,CoO,MnO,and NiO in their antiferromagnetic phase and present a head-to-head comparison of spectral properties as computed using the various *** also compare with available experimental angle-resolved photoemission spectroscopy(ARPES),inverse-photoemission spectroscopy,and with optical *** the class of compounds studied here,we find that both B3LYP and eDMFT reproduce the experiments quite well,with eDMFT doing best,in particular when comparing with the ARPES data.

关键词： materials oxides transition

The joint automated repository for various integrated simulations (JARVIS) for data-driven materials design

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npj Computational Materials 2020年第1期6卷 234-246页

作者： Kamal Choudhary Kevin F.Garrity Andrew C.E.Reid Brian DeCost Adam J.Biacchi Angela R.Hight Walker Zachary Trautt Jason Hattrick-Simpers A.Gilad Kusne Andrea Centrone Albert Davydov Jie Jiang Ruth Pachter Gowoon Cheon Evan Reed Ankit Agrawal Xiaofeng Qian Vinit Sharma Houlong Zhuang Sergei V.Kalinin Bobby G.Sumpter Ghanshyam Pilania Pinar Acar Subhasish Mandal Kristjan Haule david vanderbilt Karin Rabe Francesca Tavazza Materials Measurement Laboratory National Institute of Standards and TechnologyGaithersburgMD 20899USA Theiss Research La JollaCA 92037USA Department of Chemistry and Biochemistry University of MarylandCollege ParkMD 20742USA Physical Measurement Laboratory National Institute of Standards and TechnologyGaithersburgMD 20899USA Materials and Manufacturing Directorate Air Force Research LaboratoryWright–Patterson Air Force BaseDaytonOH 45433USA Department of Materials Science and Engineering Stanford UniversityStanfordCA 94305USA Department of Electrical and Computer Engineering Northwestern UniversityEvanstonIL 60208USA Department of Materials Science and Engineering Texas A&M UniversityTexasTX 77843USA Joint Institute for Computational Sciences University of TennesseeKnoxvilleTN 37996USA National Institute for Computational Sciences Oak Ridge National LaboratoryOak RidgeTN 37831USA School for Engineering of Matter Transport and Energy Arizona State UniversityTempeAZ 85287USA Center for Nanophase Materials Sciences Oak Ridge National LaboratoryOak RidgeTN 37831USA Materials Science and Technology Division Los Alamos National LabLos AlamosNM 87545USA Department of Mechanical Engineering Virginia TechBlacksburgVA 24061USA Department of Physics and Astronomy Rutgers UniversityPiscatawayNJ 08901USA

The Joint Automated Repository for Various Integrated Simulations(JARVIS)is an integrated infrastructure to accelerate materials discovery and design using density functional theory(DFT),classical force-fields(FF),and machine learning(ML)*** is motivated by the Materials Genome Initiative(MGI)principles of developing open-access databases and tools to reduce the cost and development time of materials discovery,optimization,and deployment.

关键词： automated JAR databases

Women in visual neural regeneration research

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Neural Regeneration Research 2025年第2期20卷 489-490页

作者： Tonia S.Rex david J.Calkins vanderbilt Eye Institute Vanderbilt University Medical CenterNashvilleTNUSA

The year 2024 marks the 60^(th)anniversary of Title IX and 25 years since the New York Times revealed bias against female faculty members at the Massachusetts Institute of *** take an opportunity here to examine the state of gender bias in a relatively new yet already prominent field,neural regeneration in the visual system,for which there is a well-defined context useful for this *** National Eye Institute(NEI)provided the first round of research funding for its Audacious Goals Initiative(AGI)on visual neural regeneration in 2013 and the last round in ***,we focus on this *** sources included PubMed,the National Science Foundation(NSF),the NEI,the Blue Ridge Institute for Medical Research and data from the major professional organization for eye and vision research,the Association for Research in Vision and Ophthalmology(ARVO).

关键词： neural visual Times

The Dallas Donation after Circulatory Death Transplantation Summit:expanding donation after circulatory death procedures through process improvement,broader utilization,and innovation

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Hepatobiliary Surgery and Nutrition 2024年第5期13卷 824-836,I0009页

作者： Michele Finotti Anji Wall Anthony D’Alessandro Gary Schwartz Chris Sonnenday david Goldberg Ashish Shah Peter Friend Jeff P.Orlowski Greg McKenna Steve Newton Brad Adams William C.Chapman Amit Mathur Marwan Abouljoud Tim Pruett Amelia Hessheimer James F.Trotter Sumeet K.Asrani Giuliano Testa Simmons Transplant Institute Baylor University Medical CenterDallasTXUSA Hepatobiliary and General Surgery Unit Regional Hospital TrevisoDISCOGUniversity of PaduaPaduaItaly Division of Transplantation Department of SurgeryUniversity of Wisconsin School of Medicine and Public HealthMadisonWIUSA Department of Thoracic Surgery and Lung Transplantation Baylor University Medical CenterCenter for Advanced Heart and Lung DiseaseDallasTXUSA Department of Surgery University of MichiganAnn ArborMIUSA Division of Digestive Health and Liver Diseases Department of MedicineUniversity of Miami Miller School of MedicineMiamiFLUSA Department of Cardio-Thoracic Surgery Vanderbilt University Medical CenterNashvilleTNUSA Nuffield Department of Surgical Sciences University of OxfordOxfordUK LifeShare Transplant Donor Services of Oklahoma Oklahoma CityOKUSA Administration Baylor University Medical CenterDallasTXUSA Southwest Transplant Alliance DallasTXUSA Department of Surgery/Transplantation Washington UniversitySt.LouisMOUSA Division of Transplant Surgery Department of SurgeryMayo Clinic ArizonaAlix School of MedicinePhoenixAZUSA Divisions of Transplant and Hepatobiliary Surgery Henry Ford HospitalDetroitMIUSA Department of Surgery University of MinnesotaMinneapolisMNUSA General and Digestive Surgery Hospital Universitario La PazIdiPAZMadridSpain

Despite a significant increase in utilization over the past decade,the number of donation after circulatory death(DCD)organs that are procured and transplanted in the United States(US)remains well below its *** is still room for expansion,as utilizing DCD organs to the fullest extent is currently the most viable solution to the persistent mismatch between supply and demand in *** convened a multidisciplinary transplantation summit to examine various aspects of DCD,with faculty members from around the world with clinical and academic interest in DCD donation and transplantation,including abdominal and cardiothoracic surgeons,organ procurement organization directors,hepatologists,and *** conference focused on identifying barriers to DCD organ utilization and strategies to overcome these *** divide the barriers to DCD utilization into three mains categories:(Ⅰ)policy and process variation;(II)logistical and transportation challenges;and(Ⅲ)higher risk perceptions related to DCD *** each barrier,we proposed a variety of solutions,providing an overview of the status of DCD donation in the US and suggestions on how to increase the use of *** is a specific focus on ex situ machine perfusion,normothermic regional perfusion,and other opportunities to expand DCD utilization without negatively impacting recipient outcomes.

关键词： Donation after circulatory death donation(DCD donation) marginal graft donor pool machine perfusion(MP)

Emerging treatments for complex perianal fistula in Crohn's disease

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World Journal of Gastroenterology 2009年第34期15卷 4263-4272页

作者： Carlos Taxonera david A Schwartz Damián García-Olmo Inflammatory Bowel Disease Unit Department of GastroenterologyHospital Clínico Inflammatory Bowel Disease Center Vanderbilt University Medical Center Department of General Surgery "La Paz"University Hospital

Complex perianal fistulas have a negative impact on the quality of life of sufferers and should be *** diagnosis,characterization and classification of the fistulas are essential to optimize ***, in the case of patients whose fistulas are associated with Crohn's disease,complete closure is particularly difficult to *** medical treatments(antibiotics, thiopurines and other immunomodulatory agents,and, more recently,anti-tumor necrosis factor-αagents such as infliximab)have been tried with varying degrees of *** medical(including infliximab)and less aggressive surgical therapy(drainage and seton placement)offer the best outcomes in complex Crohn's fistulas while more aggressive surgical procedures such as fistulotomy or fistulectomy may increase the risk of *** review will focus on emerging novel treatments for perianal disease in Crohn's patients. These include locally applied infliximab or tacrolimus, fistula plugs,instillation of fibrin glue and the use of adult expanded adipose-derived stem cell *** welldesigned controlled studies are required to confirm the effectiveness of these emerging treatments.

关键词： Crohn's disease Perianal fistula Drug therapy Topical administration Infliximab Adalimumab Adipose tissue Stem cells

Randomness in the Hybrid Modeling and Simulation of Insulin Secretion Pathways in Pancreatic Islets

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Tsinghua Science and Technology 2015年第5期20卷 441-452页

作者： Yang Pu david C.Samuels Layne T.Watson Yang Cao the Department of Computer Science Virginia Polytechnic Institute and State University the Department of Molecular Physiology and Biophysics Vanderbilt University

Insulin secreted by pancreatic islet ˇ-cells is the principal regulating hormone of glucose *** of insulin secretion may cause glucose to accumulate in the blood, and result in diabetes *** deterministic models of the insulin secretion pathway have been developed, the stochastic aspect of this biological pathway has not been explored. The first step in this direction presented here is a hybrid model of the insulin secretion pathway, in which the delayed rectifying KCchannels are treated as stochastic events. This hybrid model can not only reproduce the oscillation dynamics as the deterministic model does, but can also capture stochastic dynamics that the deterministic model does not. To measure the insulin oscillation system behavior, a probability-based measure is proposed and applied to test the effectiveness of a new remedy.

关键词： insulin secretion mathematical modeling hybrid model and simulation stochastic dynamics

Extracellular matrix remodelling in obesity and metabolic disorders

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Life Metabolism 2023年第4期2卷 7-21页

作者： Vishal Musale david H.Wasserman Li Kang Division of Systems Medicine School of MedicineUniversity of DundeeDundee DD19SYUnited Kingdom Department of Molecular Physiology and Biophysics Mouse Metabolic Phenotyping CenterVanderbilt UniversityNashvilleTN 37235United States

Obesity causes extracellular matrix (ECM) remodelling which can develop into serious pathology and fibrosis, having metabolic effects in insulin-sensitive tissues. The ECM components may be increased in response to overnutrition. This review will focus on specific obesity-associated molecular and pathophysiological mechanisms of ECM remodelling and the impact of specific interactions on tissue metabolism. In obesity, a complex network of signalling molecules such as cytokines and growth factors has been implicated in fibrosis. Increased ECM deposition contributes to the pathogenesis of insulin resistance at least in part through the activation of cell surface integrin receptors and CD44 signalling cascades. These cell surface receptors transmit signals to the cell adhesome which orchestrates an intracellular response that adapts to the extracellular environment. Matrix proteins, glycoproteins, and polysaccharides interact through ligand-specific cell surface receptors that interact with the cytosolic adhesion proteins to elicit specific actions. Cell adhesion proteins may have catalytic activity or serve as scaffolds. The vast number of cell surface receptors and the complexity of the cell adhesome have made study of their roles challenging in health and disease. Further complicating the role of ECM-cell receptor interactions is the variation between cell types. This review will focus on recent insights gained from studies of two highly conserved, ubiquitous axes and how they contribute to insulin resistance and metabolic dysfunction in obesity. These are the collagen-integrin receptor-IPP (ILK-PINCH-Parvin) axis and the hyaluronan-CD44 interaction. We speculate that targeting ECM components or their receptor-mediated cell signalling may provide novel insights into the treatment of obesity-associated cardiometabolic complications.

关键词： extracellular matrix fibrosis insulin resistance obesity metabolism

A candidate targeting molecule of insulin-like growth factor-Ⅰ receptor for gastrointestinal cancers

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World Journal of Gastroenterology 2010年第46期16卷 5779-5789页

作者： Yasushi Adachi Hiroyuki Yamamoto Hirokazu Ohashi Takao Endo david P Carbone Kohzoh Imai Yasuhisa Shinomura First Department of Internal Medicine Sapporo Medical University Department of Internal Medicine Sapporo Shirakabadai Hospital vanderbilt-Ingram Cancer Center and Departments of Medicine and Cell Biology Vanderbilt University

Advances in molecular research in cancer have brought new therapeutic strategies into clinical *** new group of targets is tyrosine kinase receptors,which can be treated by several strategies,including small molecule tyrosine kinase inhibitors(TKIs) and monoclonal antibodies(mAbs).Aberrant activation of growth factors/receptors and their signal pathways are required for malignant transformation and progression in gastrointestinal(GI) *** concept of targeting specif ic carcinogenic receptors has been validated by successful clinical application of many new *** I insulin-like growth factor(IGF) receptor(IGF-IR) signaling potently stimulates tumor progression and cellular differentiation,and is a promising new molecular target in human *** this review,we focus on this promising therapeutic target,*** IGF/IGF-IR axis is an important modifier of tumor cell proliferation,survival,growth,and treatment sensitivity in many malignant diseases,including human GI *** studies demonstrated that downregulation of IGF-IR signals reversed the neoplastic phenotype and sensitized cells to anticancer *** results were mainly obtained through our strategy of adenoviruses expressing dominant negative IGF-IR(IGF-IR/dn) against gastrointestinal cancers,including esophagus,stomach,colon,and *** also summarize a variety of strategies to interrupt the IGFs/IGF-IR axis and their preclinical *** mAbs and TKIs targeting IGF-IR have entered clinical trials,and early results have suggested that these agents have generally acceptable safety profiles as single *** summarize the advantages and disadvantages of each strategy and discuss the merits/demerits of dual targeting of IGF-IR and other growth factor receptors,including Her2 and the insulin receptor,as well as other alternatives and possible drug ***,IGF-IR might be a candidate for a molecular therapeutic target in human GI carcino

关键词： Dominant negative Gastrointestinal cancer Insulin like growth factor-I receptor Monoclonal anti-body Tyrosine kinase inhibitor

Bacterial biota in reflux esophagitis and Barrett's esophagus

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World Journal of Gastroenterology 2005年第46期11卷 7277-7283页

作者： Zhiheng Pei Liying Yang Richard M Peek Jr Steven M Levine david T Pride Martin J Blaser Departments of Pathology and Medicine New York University School of Medicine New York NY 10016 the United States of America and Department of Veterans Affairs New York Harbor Health System New York NY 10010United States Department of Pathology New York University School of Medicine New York NY 10016 United States Jr Department of Medicine Vanderbilt University School of Medicine Nashville TN 37212United States Department of Medicine New York University School of Medicine New York NY 10016 United States Departments of Medicine and Microbiology New York University School of Medicine New York NY 10016United States Departments of Medicine and Microbiology New York University School of Medicine New York NY 10016the United States of America and Department of Veterans AffairsNew York Harbor Health System New York NY 10010 United States

AIM： To identify the bacterial flora in conditions such as Barrett＇s esophagus and reflux esophagitis to determine if they are similar to normal esophageal flora. METHODS： Using broad-range 16S rDNA PCR, esophageal biopsies were examined from 24 patients [9 with normal esophageal mucosa, 12 with gastroesophageal reflux disease （GERD）, and 3 with Barrett＇s esophagus]. Two separate broad-range PCR reactions were performed for each patient, and the resulting products were cloned. In one patient with Barrett＇s esophagus, 99 PCR clones were analyzed. RESULTS： Two separate clones were recovered from each patient （total = 48）, representing 24 different species, with 14 species homologous to known bacteria, 5 homologous to unidentified bacteria, and 5 were not homologous （〈97% identity） to any known bacterial 16S rDNA sequences. Seventeen species were found in the reflux esophagitis patients, 5 in the Barrett＇s esophagus patients, and 10 in normal esophagus patients. Further analysis concentrating on a single biopsy from an individual with Barrett＇s esophagus revealed the presence of 21 distinct bacterial species. Members of four phyla were represented, including Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Microscopic examination of each biopsy demonstrated bacteria in intimate association with the distal esophageal epithelium, suggesting that the presence of these bacteria is not transitory. CONCLUSION： These findings provide evidence for a complex, residential bacterial population in esophageal reflux-related disorders. While much of this biota is present in the normal esophagus, more detailed comparisons may help identify potential disease associations.

关键词： Bacterial biota Esophagus 16S rDNA PCR