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rapid and flexible segmentation of electron microscopy data using few-shot machine learning

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npj Computational Materials 2021年第1期7卷 1733-1741页

作者： Sarah Akers Elizabeth Kautz Andrea Trevino-Gavito Matthew Olszta Bethany E.Matthews Le Wang Yingge Du steven r.spurgeon National Security Directorate Pacific Northwest National LaboratoryRichlandWA 99352USA Energy and Environment Directorate Pacific Northwest National LaboratoryRichlandWA 99352USA Department of Industrial Engineering and Management Sciences Northwestern UniversityEvanstonIL 60208USA Physical and Computational Sciences Directorate Pacific Northwest National LaboratoryRichlandWA 99352USA

Automatic segmentation of key microstructural features in atomic-scale electron microscope images is critical to improved understanding of structure–property relationships in many important materials and chemical ***,the present paradigm involves time-intensive manual analysis that is inherently biased,error-prone,and unable to accommodate the large volumes of data produced by modern *** more automated approaches have been proposed,many are not robust to a high variety of data,and do not generalize well to diverse microstructural features and material ***,we present a flexible,semi-supervised few-shot machine learning approach for segmentation of scanning transmission electron microscopy images of three oxide material systems:(1)epitaxial heterostructures of SrTiO_(3)/Ge,(2)La_(0.8)Sr_(0.2)FeO_(3) thin films,and(3)MoO_(3) *** demonstrate that the few-shot learning method is more robust against noise,more reconfigurable,and requires less data than conventional image analysis *** approach can enable rapid image classification and microstructural feature mapping needed for emerging high-throughput characterization and autonomous microscope platforms.

关键词： systems image enable

Machine learning for automated experimentation in scanning transmission electron microscopy

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npj Computational Materials 2023年第1期9卷 25-40页

作者： Sergei V.Kalinin Debangshu Mukherjee Kevin roccapriore Benjamin J.Blaiszik Ayana Ghosh Maxim A.Ziatdinov Anees Al-Najjar Christina Doty Sarah Akers Nageswara S.rao Joshua C.Agar steven r.spurgeon Department of Materials Science and Engineering University of TennesseeKnoxvilleTN 37996USA Computational Sciences and Engineering Division Oak Ridge National LaboratoryOak RidgeTN 37831USA Center for Nanophase Materials Sciences Oak Ridge National LaboratoryOak RidgeTN 37831USA Argonne National Laboratory Data Science and Learning DivisionChicagoIL 60439USA University of Chicago GlobusChicagoIL 60637USA National Security Directorate Pacific Northwest National LaboratoryRichlandWA 99352USA Department of Materials Science and Engineering Drexel UniversityPhiladelphiaPA 19104USA Department of Physics University of WashingtonSeattleWA 98195USA

Machine learning(ML)has become critical for post-acquisition data analysis in(scanning)transmission electron microscopy,(S)TEM,imaging and *** emerging trend is the transition to real-time analysis and closed-loop microscope *** effective use of ML in electron microscopy now requires the development of strategies for microscopy-centric experiment workflow design and ***,we discuss the associated challenges with the transition to active ML,including sequential data analysis and out-of-distribution drift effects,the requirements for edge operation,local and cloud data storage,and theory in the loop ***,we discuss the relative contributions of human scientists and ML agents in the ideation,orchestration,and execution of experimental workflows,as well as the need to develop universal hyper languages that can apply across multiple *** considerations will collectively inform the operationalization of ML in next-generation experimentation.

关键词： optimization automated execution

Eastern Asian endemic seed plant genera and their paleogeographic history throughout the Northern Hemisphere

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Journal of Systematics and Evolution 2009年第1期47卷 1-42页

作者： steven r.MANCHESTEr Kazuhiko UEMUrA Florida Museum of Natural History University of Florida National Museum of Nature and Science

We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably kn... 详细信息

ract>We review the fossil history of seed plant genera that are now endemic to eastern Asia. Although the majority of eastern Asian endemic genera have no known fossil record at all, 54 genera, or about 9%, are reliably known from the fossil record. Most of these are woody (with two exceptions), and most are today either broadly East Asian, or more specifically confined to Sino-Japanese subcategory rather than being endemic to the Sino-Himalayan area. Of the "eastern Asian endemic" genera so far known from the fossil record, the majority formerly occurred in Europe and/or North America, indicating that eastern Asia served as a late Tertiary or Quaternary refugium for taxa. Hence, many of these genera may have originated in other parts of the Northern Hemisphere and expanded their ranges across continents and former sea barriers when tectonic and climatic conditions al- lowed, leading to their arrival in eastern Asia. Although clear evidence for paleoendemism is provided by the gymnosperms Amentotaxus, Cathaya, Cephalotaxus, Cunninghamia, Cryptomeria, Glyptostrobus, Ginkgo, Ketel-eeria, Metasequoia, Nothotsuga, Pseudolarix, Sciadopitys, and Taiwania, and the angiosperms Cercidiphyllum, Choerospondias, Corylopsis, Craigia, Cyclocarya, Davidia, Dipelta, Decaisnea, Diplopanax, Dipteronia, Em-menopterys, Eucommia, Euscaphis, Hemiptelea, Hovenia, Koelreuteria, Paulownia, Phellodendron, Platycarya, Pteroceltis, rehderodendron, Sargentodoxa, Schizophragma, Sinomenium, Tapiscia, Tetracentron, Toricellia, Trapella, and Trochodendron, we cannot rule out the possibility that neoendemism plays an important role especially for herbaceous taxa in the present-day flora of Asia, particularly in the Sino-Himalayan region. In addition to reviewing paleobotanical occurrences from the literature, we document newly recognized fossil occurrences that expand the geographic and stratigraphic ranges previously known for Dipelta, Pteroceltis, and Toricellia.

关键词： Cretaceous eastern Asia endemic paleobotany phytogeography Tertiary

Pathophysiology and treatment of Barrett's esophagus

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World Journal of Gastroenterology 2010年第30期16卷 3762-3772页

作者： Daniel S Oh steven r DeMeester Department of Surgery The University of Southern CaliforniaKeck School of MedicineLos AngelesCA 90033United States

Gastroesophageal reflux disease (GErD) affects an estimated 20% of the population in the United States. About 10%-15% of patients with GErD develop Barrett’s esophagus, which can progress to adenocarcinoma, currently the most prevalent type of esophageal cancer. The esophagus is normally lined by squamous mucosa, therefore, it is clear that for adenocarcinoma to develop, there must be a sequence of events that result in transformation of the normal squamous mucosa into columnar epithelium. This sequence begins with gastroesophageal reflux, and with continued injury metaplastic columnar epithelium develops. This article reviews the pathophysiology of Barrett’s esophagus and implications for its treatment. The effect of medical and surgical therapy of Barrett’s esophagus is compared.

关键词： Gastroesophageal reflux disease Barrett’s esophagus Lower esophageal sphincter Esophageal motility Proton pump inhibitors Antireflux surgery

Long-term antifibrotic action of interferon-γ treatment in patients with chronic hepatitis B virus infection

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Hepatobiliary & Pancreatic Diseases International 2011年第2期10卷 151-157页

作者： Peter r Mertens steven Dooley Department of Nephrology and Hypertension Otto-von-Guericke-University First Affiliated Hospital Zhejiang University School of Medicine Molecular Hepatology-Alcohol Dependent Diseases II. Medical Clinic Faculty of Medicine at MannheimUniversity of Heidelberg

BACKGrOUND:The first priority in treating fibrosis is to eliminate the causes that result in liver injury,e.g.,hepatitis B and C ***,in many liver diseases the cause is either unknown or *** present study was designed to investigate the long-term antifibrotic effect of interferon-gamma(IFN-γ)treatment in patients chronically infected with hepatitis B virus. METHODS:A total of 42 patients,30 treated with IFN-γand 12 controls,were enrolled from an original clinical trial(Clin Gastroenterol Hepatol 2005;3:819.).Three serial liver biopsies that were obtained at the initiation and end of IFN-γtreatment as well as 4 to 6 years after treatment discontinuation were assessed according to the modified Chevallier scoring system. rESULTS:Twenty-five out of 30 IFN-γ-treated patients were followed up until 4 to 6 years after the treatment was stopped. However,all controls were excluded from follow-up due to death,loss and elevated virus level within 2 ***-five IFN-γ-treated patients had stable serum liver function and liver fibrosis indices without any further antiviral or anti-fibrotic *** inflammatory and fibrotic scores were found after nine months of IFN-γtreatment according to the modified Chevallier scoring system(inflammation:11.8±6.5 at the beginning of IFN-γtreatment vs.9.2±4.1 after 9 months, Prosis:15.0±7.3 at baseline vs.12.6±6.8 after 9 months, Prd serial liver biopsy 4 to 6 years after treatment discontinuation,and the fibrotic score was increased(14.2±8.3 vs.11.9±7.6 after 9 months, Preatment significantly improves the fibrosis score in patients with chronic HBV *** majority of patients demonstrate stable serum biochemical indices and quality of ***,they do not show a long-term benefit according to histological criteria. Given the limited sample size,long-term IFN-γtreatment regimens should be assessed in further

关键词： hepatic stellate cells hepatitis B virus liver fibrosis inflammation interferon-gamma

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Testosterone and benign prostatic hyperplasia

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Asian Journal of Andrology 2015年第2期17卷 212-216,I0007页

作者： Thomas r Jarvis Bilal Chughtai steven A Kaplan Department of Urology Weill Cornell Medical College New York USA.

The use of testosterone to treat the symptoms of late-onset hypogonadal men has increased recently due to patient and physician awareness. However, concerns regarding the effect of testosterone on the prostate, in particular any possible effect on the risk of prostate cancer have prompted further research in this regard. Surprisingly, numerous retrospective or small, randomized trials have pointed to a possible improvement in male lower urinary tract symptoms （LUTS） in patients treated with testosterone. The exact mechanism of this improvement is still debated but may have a close relationship to metabolic syndrome. For the clinician, the results of these studies are promising but do not constitute high levels of evidence. A thorough clinical examination （including history, examination and laboratory testing of testosterone） should be undertaken before considering the diagnosis of late-onset hypogonadism or instigating treatment for it. Warnings still remain on the testosterone supplement product labels regarding the risk of urinary retention and worsening LUTS, and these should be explained to patients.

关键词： benign prostatic hyperplasia lower urinary tract symptoms metabolic syndrome X testosterone urinary bladder neck obstruction

Validity of continuous-failure-state unloading triaxial tests as a means to estimate the residual strength of rocks

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Journal of rock Mechanics and Geotechnical Engineering 2021年第4期13卷 717-726页

作者： Gabriel Walton steven Gaines Leandro r.Alejano Department of Geology and Engineering Geology Colorado School of MinesGoldenCO80401USA Natural resources Canada CanmetMININGOttawaOntarioK1A 1M1Canada Department of Natural resources and Environmental Engineering Universidad de VigoVigo36310Spain

The residual strength of rocks and rock masses is an important parameter to be constrained for analysis and design purposes in many rock engineering applications.A residual strength envelope in principal stress space is typically developed using residual strength data obtained from compression tests on many different specimens of the same rock *** this study,we examined the potential for use of the continuous-failure-state testing concept as a means to constrain the residual strength envelope using a limited number of ***,cylindrical specimens of three rock types(granodiorite,diabase,and Stanstead granite)were unloaded at the residual state such that a full residual strength envelope for each individual specimen was *** a residual strength model that introduces a single new strength parameter(the residual strength index,or rSI),the results of the continuous-failurestate unloading tests were compared to conventionally obtained residual strength ***,the continuous-failure-state residual strength data were found to be consistent with the conventional residual strength ***,it was identified that the primary factor limiting an accurate characterization of the residual strength for a given rock type is not the amount of data for a given specimen,but the variety of specimens available to characterize the inherent variability of the rock unit of ***,the use of continuous-failure-state testing for estimation of the residual strength of a rock unit is only recommended when the number of specimens available for testing is very limited(i.e.<5).

关键词： residual strength Continuous-failure-state testing Compression testing Brittle rock mechanics

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Oral microbiome: possible harbinger for children’s health

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International Journal of Oral Science 2020年第2期12卷 89-101页

作者： Jin Xiao Kevin A.Fiscella steven r.Gill Eastman Institute for Oral Health University of Rochester Medical CenterRochesterNYUSA Department of Family Medicine University of Rochester Medical CenterRochesterNYUSA Department of Microbiology and Immunology University of Rochester Medical CenterRochesterNYUSA Genomics research Center University of Rochester Medical CenterRochesterNYUSA

The human microbiome functions as an intricate and coordinated microbial network,residing throughout the mucosal surfaces of the skin,oral cavity,gastrointestinal tract,respiratory tract,and reproductive *** oral microbiome encompasses a highly diverse microbiota,consisting of over 700 microorganisms,including bacteria,fungi,and *** our understanding of the relationship between the oral microbiome and human health has evolved,we have identified a diverse array of oral and systemic diseases associated with this microbial community,including but not limited to caries,periodontal diseases,oral cancer,colorectal cancer,pancreatic cancer,and inflammatory bowel *** potential predictive relationship between the oral microbiota and these human diseases suggests that the oral cavity is an ideal site for disease diagnosis and development of rapid point-of-care *** oral cavity is easily accessible with a non-invasive collection of biological *** can envision a future where early life salivary diagnostic tools will be used to predict and prevent future disease via analyzing and shaping the infant’s oral *** this review,we present evidence for the establishment of the oral microbiome during early childhood,the capability of using childhood oral microbiome to predict future oral and systemic diseases,and the limitations of the current evidence.

关键词： diagnosis salivary biome

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Fertility control of rodent pests: recent developments from lab to field

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Integrative Zoology 2022年第6期17卷 960-963页

作者： Lyn A.HINDS steven r.BELMAIN CSIrO Health and Biosecurity CanberraACTAustralia Natural resources Institute University of GreenwichKentUK

This special issue of Integrative Zoology(the official journal of the International Society of Zoological Science and the Institute of Zoology,Chinese Academy of Sciences)comprises a series of papers,aspects of which were presented at the 23rd International Congress of Zoology,a virtual meeting for participants between November 22 and 24,*** symposium topic at the virtual conference was“Fertility control of rodent pests for better agriculture,ecosystems and human health.”

关键词： ecosystems journal pests