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microstructure segmentation with deep learning encoders pre-trained on a large microscopy dataset

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npj Computational materials 2022年第1期8卷 1905-1916页

作者： joshua Stuckner Bryan Harder Timothy m.Smith materials and Structures Division NASA Glenn Research Center21000 Brookpark RdClevelandOH44135USA

This study examined the improvement of microscopy segmentation intersection over union accuracy by transfer learning from a large dataset of microscopy images called *** neural network encoder architectures were trained on over 100,000 labeled microscopy images from 54 material *** pre-trained encoders were then embedded into multiple segmentation architectures including UNet and DeepLabV3+to evaluate segmentation performance on created benchmark microscopy *** to ImageNet pre-training,models pre-trained on microNet generalized better to out-of-distribution micrographs taken under different imaging and sample conditions and were more accurate with less training *** training with only a single Ni-superalloy image,pre-training on microNet produced a 72.2%reduction in relative intersection over union *** results suggest that transfer learning from large in-domain datasets generate models with learned feature representations that are more useful for downstream tasks and will likely improve any microscopy image analysis technique that can leverage pre-trained encoders.

关键词： union intersection image

Same Concept Different Outcomes:Sugars Determine Circadian Clock Protein Fate in Animals and Plants

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molecular Plant 2020年第3期13卷 360-362页

作者： Wei Liu joshua m.Gendron Department of molecular Cellular and Developmental BiologyYale UniversityNew HavenCT 06511USA

most eukaryotes have a self-sustaining circadian clock that senses environmental cues and the internal metabolic state and then imposes daily temporal organization of the *** clock,by nature,regulates the daily creation and destruction of a large quantity of RNA and proteins,including those at the core of the oscillator *** a transcriptional-translational feedback loop maintains the rhythmicity of the oscillator,various post-translational modifications(PTms)of clock proteins play fundamental roles in keeping the pace of the circadian clock near 24 *** maintain circadian clock pacing,PTms act to ensure the rapid,efficient,and precise activation,inactivation,and finally destruction of core clock proteins(Hirano et al.,2016).

关键词： maintain oscillator precise

Exotic parrots breeding in urban tree cavities: nesting requirements, geographic distribution, and potential impacts on cavity nesting birds in southeast Florida

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Avian Research 2019年第4期10卷 459-468页

作者： joshua m.Diamond michael S.Ross Florida International University Earth & Environment

Background:Exotic parrots have established breeding populations in southeast Florida,including several species that nest in tree *** aimed to determine the species identity,nest site requirements,relative nest abundance,geographic distribution,and interactions of parrots with native cavity-nesting bird ***:We searched miami-Dade County,Florida,and nearby areas for natural cavities and holes excavated by woodpeckers,recording attributes of potential nest *** inspected all cavities with an elevated video inspection system to determine occupancy by parrots or other *** mapped nearly 4000 citizen science observations of parrots in our study area corresponding to our study period,and used these to construct range maps,comparing them to our nesting ***:Not all parrots reported or observed in our study area were actively *** parrots were observed at tree cavities,which previous studies have suggested is evidence of reproduction,but our inspections with an elevated video inspection system suggest they never initiated nesting *** parrot species did successfully nest in tree cavities,Red-masked Parakeets(Psittacara erythrogenys)and Orange-winged Parrots(Amazona amazonica)being the most common(n=7 and 6 nests,respectively).These two parrots had similar nesting requirements,but Orange-winged Parrots use nests with larger entrance holes,which they often *** analysis of nests combined with citizen science data indicate that parrots are limited to developed *** most common parrots were less abundant cavity nesters than the native birds which persist in miami’s urban areas,and far less abundant than the invasive European Starling(Sturnus vulgaris).Conclusions:Exotic parrots breeding elsewhere in the world have harmed native cavity-nesting birds through interference competition,but competitive interference in southeast Florida is minimized by the urban affinities of parrots in this ***

关键词： Amazona Cavity nest webs Invasive species Parakeets Psittacara Urban ecology

Cost-Effectiveness of Interventions for Alternate Food to Address Agricultural Catastrophes Globally

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International Journal of Disaster Risk Science 2016年第3期7卷 205-215页

作者： David C.Denkenberger joshua m.Pearce Global Catastrophic Risk Institute Department of Civil and Architectural Engineering Tennessee State University Department of materials Science and Engineering Michigan Technological University Department of Electrical and Computer Engineering Michigan Technological University

The literature suggests there is about a 1 % risk per year of a 10 % global agricultural shortfall due to catastrophes such as a large volcanic eruption, a medium asteroid or comet impact, regional nuclear war, abrupt climate change, and extreme weather causing multiple breadbasket failures. This shortfall has an expected mortality of about 500 million people. To prevent such mass starvation, alternate foods can be deployed that utilize stored biomass. This study developed a model with literature values for variables and, where no values existed,used large error bounds to recognize uncertainty. Then monte Carlo analysis was performed on three interventions: planning, research, and development. The results show that even the upper bound of USD 400 per life saved by these interventions is far lower than what is typically paid to save a life in a less-developed country. Furthermore, every day of delay on the implementation of these interventions costs 100–40,000 expected lives(number of lives saved multiplied by the probability that alternate foods would be required). These interventions plus training would save 1–300 million expected lives. In general, these solutions would reduce the possibility of civilization collapse, could assist in providing food outside of catastrophic situations, and would result in billions of dollars per year of return.

关键词： Agricultural catastrophe Alternate food Global catastrophic risk Intervention cost-effectiveness

Coronavirus Disease 2019 and Liver Injury:A Retrospective Analysis of Hospitalized Patients in New York City

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Journal of Clinical and Translational Hepatology 2021年第4期9卷 551-558页

作者： joshua m.Bender Howard J.Worman Department of medicine Vagelos College of Physicians&SurgeonsColumbia UniversityNew YorkNYUSA Department of Pathology and Cell Biology Vagelos College of Physicians&SurgeonsColumbia UniversityNew YorkNYUSA

Background and Aims:Coronavirus disease 2019(COVID-19)is a global threat,affecting more than 100 million people and causing over 2 million *** laboratory test abnormalities are an extrapulmonary manifestation of COVID-19,yet characterization of hepatic injury is *** objective was to further characterize and identify causes of liver injury in patients with ***:We conducted a retrospective cohort study of 551 patients hospitalized with COVID-19 at NewYork-Presbyterian Hospital/Columbia University Irving medical Center between march 1,2020 and may 31,*** analyzed patient demographics,liver laboratory test results,vital signs,other relevant test results,and clinical outcomes(mortality and intensive care unit admission).Results:Abnormal liver laboratory tests were common on hospital admission for COVID-19 and the incidence increased during *** those with elevated serum alanine aminotransferase and/or alkaline phosphatase activities on admission,58.2%had a cholestatic injury pattern,35.2%mixed,and 6.6%*** liver disease was not associated with outcome;however,abnormal direct bilirubin or albumin on admission were associated with intensive care unit stay and *** average,patients who died had greater magnitudes of abnormalities in all liver laboratory tests than those who *** hepatitis was a mechanism of severe hepatocellular injury in some ***:Liver laboratory test abnormalities are common in hospitalized patients with COVID-19,and some are associated with increased odds of intensive care unit stay or *** hepatocellular injury is likely attributable to secondary effects such as systemic inflammatory response syndrome,sepsis,and ischemic hepatitis.

关键词： Aminotransferase Bilirubin Ischemic hepatitis SARS-CoV-2

Probing Electrocatalytic CO_(2) Reduction at Individual Cu Nanostructures via Optically Targeted Electrochemical Cell microscopy

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Journal of Analysis and Testing 2019年第2期3卷 140-149页

作者： joshua D.Walmsley joshua W.Hill Partha Saha Caleb m.Hill Department of Chemistry University of WyomingLaramieWY 82071USA

Optically targeted electrochemical cell microscopy(OTECCm)was applied to measure electrocatalytic rates at individual Cu nanoparticles(NPs)under electrolyte conditions relevant to CO_(2) *** electrocatalytic responses from individual NPs were found to exhibit a wide variation in behavior,with significant NP-to-NP variations in the magnitude of electrocata-lytic currents and necessary overpotentials being *** of these quantities with metrics of NP size suggest no significant variations in the inherent electrocatalytic activity of the NPs with *** element simulations of diffusion in this system demonstrate the observed diffusion-limited currents are significantly smaller than expected,attributable to the presence of a significant amount of residual ligand on the surface of the Cu NPs,which were prepared via an organic phase *** results presented here further demonstrate the promise of techniques which employ correlated optical and electrochemical measurements,such as OTECCm,for studying electrocatalysis at individual NPs.

关键词： Electrochemistry Electrochemical microscopy Nanoparticles CO_(2)reduction

Estimating underground mine ventilation friction factors from low density 3D data acquired by a moving LiDAR

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International Journal of mining Science and Technology 2018年第4期28卷 650-655页

作者： Curtis Watson joshua marshall mining Systems Laboratory The Robert M.Buchan Department of Mining Queen's University

Ventilation system analysis for underground mines has remained mostly unchanged since the Atkinson method was made popular by mc Elroy in 1935. Data available to ventilation technicians and engineers is typically limited to the quantity of air moving through any given heading. Because computer-aided modelling, simulation, and ventilation system design tools have improved, it is now important to ensure that developed models have the most accurate information possible. This paper presents a new technique for estimating underground drift friction factors that works by processing 3 D point cloud data obtained by using a mobile Li DAR. Presented are field results that compare the proposed approach with previously published algorithms, as well as with manually acquired measurements.

关键词： mine ventilation mine design mobile mapping Roughness estimation Friction factors LiDAR3D point clouds

Potential gains from spatially-explicit coordinated planning between two large public ownerships in minnesota

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Forest Ecosystems 2019年第2期6卷 102-118页

作者： joshua J. Bixby Howard m. Hoganson Yu Wei Geospatial Systems Engineer USDA Forest Service Chief’s Information Office Duluth MN USA Department of Forest Resources and North Central Research and Outreach Center University of MN Grand Rapids MN USA Department of Forest and Rangeland Stewardship Colorado State University Fort Collins CO USA

Background: many forested landscapes throughout the world involve a mix of public forest ownerships. This study explores how coordinated planning between two large public ownerships in minnesota impact landscape-level trade-offs between timber production and production of core area of older forest (COF) for the region. COF is an important metric for wildlife habitat. Emphasis is on better understanding potential gains from both coordinated planning at the site-level where ownerships share stand boundaries and from coordinated planning at a broader policy level involving assumed values of COF by the public. The study area involves over 300,000 ha, 150,000 analysis units and a 100-year planning horizon. methods: The concept of influence zones in modeling spatial interdependencies is described and implemented. The estimated total area of COF is assumed an important landscape metric for forest wildlife habitat condition for each forest planning period. COF has a surrounding buffer protecting it from edge effects. Differences are recognized between COF condition requirements and condition requirements for its surrounding buffer. A spatially-explicit harvest scheduling model is applied in conjunction with moving-windows techniques of GIS to find near-optimal management schedules for the large landscape. multiple model runs are examined to help better understand both potential gains from coordinated planning and the tradeoffs between timber and COF production. Results: Results demonstrate the ability to incorporate detailed site-level COF production into management scheduling models for broad, landscape-level planning. For the study area and the assumed COF definitions, substantially larger gains are possible by coordinating COF value assumptions across ownerships, as compared to possible gains from coordinating on-the-ground management activities in areas involving shared stand boundaries. Although a general map of the study area shows a definite intertwining mosaic of ow

关键词： Core area Interior space Trade-off analysis multiple objective planning Landscape planning Harvest scheduling Patch size Production possibilities frontier

Crystallization kinetics of Sn_(40)Se_(60) thin films for phase change memory applications

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Journal of Semiconductors 2015年第6期36卷 17-20页

作者： joshua m.Kundu Patrick m.Karimi Walter K.Njoroge Department of Physics Kenyatta University

The crystallization kinetics of Sn4oSe6o thin films has been successfully investigated using sheet resis- tance versus temperature measurements. Thermal evaporation was used to deposit the films on ordinary glass sub- strates. The crystallization temperature for Sn4oSe60 thin film was found to be 156.6 -t- 0.3 ~C. In the as-deposited state, the sheet resistance was found to be 195 mf2/[2, this value declined to 1560 f2/[2] upon annealing. The value of activation energy obtained from the Kissinger plot was 0.62 ＋ 0.07 eV. From the results obtained, SnaoSe60 is a promising alloy for PCm application because of its high electrical contrast, high crystallization temperature, and relatively high activation energy.

关键词： crystallization temperature activation energy electrical contrast phase change memory