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Batch Active Learning for Multispectral and Hyperspectral Image Segmentation Using Similarity Graphs

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Communications on Applied Mathematics and Computation 2024年第2期6卷 1013-1033页

作者： Bohan Chen Kevin Miller Andrea L.Bertozzi Jon Schwenk Department of Mathematics University of CaliforniaLos Angeles520 Portola PlazaLosAngeles90095CAUSA Oden Institute for Computational Engineering and Sciences University of Texas at Austin201 E 24th StAustin 78712TXUSA Los Alamos National Laboratory Los AlamosNM 87545USA

Graph learning,when used as a semi-supervised learning(SSL)method,performs well for classification tasks with a low label *** provide a graph-based batch active learning pipeline for pixel/patch neighborhood multi-or hyperspectral image *** batch active learning approach selects a collection of unlabeled pixels that satisfy a graph local maximum constraint for the active learning acquisition function that determines the relative importance of each pixel to the *** work builds on recent advances in the design of novel active learning acquisition functions(e.g.,the Model Change approach in arXiv:2110.07739)while adding important further developments including patch-neighborhood image analysis and batch active learning methods to further increase the accuracy and greatly increase the computational efficiency of these *** addition to improvements in the accuracy,our approach can greatly reduce the number of labeled pixels needed to achieve the same level of the accuracy based on randomly selected labeled pixels.

关键词： Image segmentation Graph learning Batch active learning Hyperspectral image

Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the singlecell level

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Molecular Plant 2021年第3期14卷 372-383页

作者： Andrew Farmer Sandra Thibivilliers Kook Hui Ryu John Schiefelbein Marc Libault National Center for Genome Resources Santa FeNM 87505USA Department of Agronomy and Horticulture Center for Plant Science InnovationUniversity of Nebraska-LincolnBeadle CenterLincolnNE 68503USA Department of Molecular Cellularand Developmental BiologyUniversity of MichiganAnn ArborMI 48109USA

Similar to other complex organisms,plants consist of diverse and specialized cell *** gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional *** a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis *** comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific ***,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell *** to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their *** reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin *** data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

关键词： single-cell RNA-seq single-nucleus ATAC-seq Arabidopsis root

Mechanistic insight into Cr(Ⅵ)retention by Si-containing ferrihydrite

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Journal of Environmental Sciences 2024年第5期139卷 217-225页

作者： Ying Hu Qiang Xue Honghan Chen Huaming Guo Kenneth C.Carroll Song Wang MOE Key Laboratory of Groundwater Circulation and Environmental Evolution School of Water Resources and EnvironmentChina University of Geosciences(Beijing)Beijing 100083China Beijing Key Laboratory of Water Resources and Environmental Engineering School of Water Resources and EnvironmentChina University of GeosciencesBeijing 100083China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China Plant&Environmental Science New Mexico State UniversityNM 88003USA Institute of Theoretical Chemistry College of ChemistryJilin UniversityChangchun 130023China

Hexavalent chromium[Cr(Ⅵ)]causes serious harm to the environment due to its high toxicity,solubility,and ***(Fh)are the main adsorbent and trapping agent of Cr(Ⅵ)in soils and aquifers,and they usually coexist with silicate(Si),forming Si-containing ferrihydrite(Si-Fh)***,the mechanism of Cr(Ⅵ)retention by Si-Fh mixtures is poorly *** this study,the behaviors and mechanisms of Cr(Ⅵ)adsorption onto Si-Fh with different Si/Fe molar ratios was *** electron microscope,Fourier transform infrared spectroscopy,X-ray diffraction,X-ray photoelectron spectroscopy,and other techniques were used to characterize Si-Fh and Cr(Ⅵ)-loading of *** results show that specific surface area of Si-Fh increases gradually with increasing Si/Fe ratios,but Cr(Ⅵ)adsorption on Si-Fh decreases with increasing Si/Fe *** is because with an increase in Si/Fe molar ratio,the point of zero charge of Si-Fh gradually decreases and electrostatic repulsion between Si-Fh and Cr(Ⅵ)***,the complexation of Cr(Ⅵ)is enhanced due to the increase in adsorbed hydroxyl(A-OH-)on Si-Fh with increasing Si/Fe molar ratio,which partly counteracts the effect of the electrostatic ***,the increase in the electrostatic repulsion has a greater impact on adsorption than the additional complexation with *** functional theory calculation further supports this observation,showing the increases in electron variation of bonding atoms and reaction energies of inner spherical complexes with the increase in Si/Fe ratio.

关键词： Hexavalent chromium Ferrihydrite Si/Fe ratio Cr(Ⅵ)Adsorption

Temporal variability and sources of PFAS in the Rio Grande,New Mexico through an arid urban area using multiple tracers and highfrequency sampling

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Emerging Contaminants 2024年第3期10卷 205-220页

作者： Kimberly R.Beisner Rebecca E.Travis David A.Alvarez Larry B.Barber Jacob A.Fleck Jeramy R.Jasmann U.S.Geological Survey 6700 Edith Blvd NEAlbuquerqueNM87113USA U.S.Geological Survey 4200 New Haven RoadColumbiaMO65201USA U.S.Geological Survey 3215 Marine St.BoulderCO80303USA U.S.Geological Survey 6000 J St.Placer Hall.SacramentoCA95819USA

Per-and polyfluoroalkyl substances(PFAS)are ubiquitous in the environment but sources are not well defined for temporal and spatial aspects within an urban environment,and especially for an arid urban environment subject to seasonal short term high-intensity precipitation events.A focused diel sampling was conducted in the summer of 2021 to assess the temporal and spatial variability of PFAS in the Rio Grande near Albuquerque,New Mexico and showed an order of magnitude increase of PFAS as it flows through the Albuquerque urban *** samples were collected at two different locations on the Rio Grande in addition to wastewater treatment plant(WWTP)effluent that discharges directly to the Rio Grande between the sampling ***-term high-intensity precipitation events occurred during the study period and mobilized PFAS from urban *** organic matter composed of tryptophan-like organic substances and refined fuel and fuel byproducts,characteristic of an urban signature,were also related to the precipitation *** PFAS in discharge from the WWTP was consistent over a 24-h period with slight differences in some *** presence on the Rio Grande downstream of the WWTP was evidenced by a gadolinium anomaly as well as increases in several other trace elements,total dissolved nitrogen,and fluorescence indicators,in addition to *** varied depending on source contribution,where urban runoff was associated with PFOA,PFOS,and PFBA,whereas PFHxA and PFPeA were associated with wastewater *** addition,passive polar organic chemical integrative samplers(POCIS)using hydrophilic-lipid balance(HLB)sorption media were deployed for a month at two locations on the Rio Grande to assess longer term PFAS *** POCIS results show some compounds(PFPeA and PFHpA)were greater than the average concentration from discrete samples,whereas other compounds(PFHxA,PFOA,PFDA,and PFNA)were lower in the POCIS,and PFOS was very simila

关键词： wastewater Rio runoff

Diffusion tensor imaging in the courtroom:Distinction between scientific specificity and legally admissible evidence

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World Journal of Clinical Cases 2023年第19期11卷 4477-4497页

作者： Jennifer Christine van Velkinburgh Mark D Herbst Stewart M Casper Science Communication Filipodia Publishing LLCSanta FeNM 87505United States Diagnostic Radiology Independent Diagnostic Radiology IncSt PetersburgFL 33711United States Personal Injury Law Casper&DeToledo LLCStamfordCT 06905United States

Interest and uptake of science and medicine peer-reviewed literature by readers outside of a paper’s topical subject,field or even discipline is *** the application of knowledge from one field or discipline to others can stimulate innovative solutions to problems facing modern society,it is also fraught with danger for *** the practice of law in the United States,academic papers are submitted to the courts as evidence in personal injury litigation from both the plaintiff(complainant)and *** transcendence of an academic publication over disciplinary boundaries is immediately met with the challenge of application by a group that inherently lacks in-depth knowledge on the scientific method,the practice of evidence-based medicine,or the publication process as a structured and internationally synthesized process involving peer review and guided by ethical standards and norms.A modern-day example of this is the ongoing conflict between the sensitivity of diffusion tensor imaging(DTI)and the legal standards for admissibility of evidence in litigation cases of mild traumatic brain injury(mTBI).In this review,we amalgamate the peer-reviewed research on DTI in mTBI with the court’s rationale underlying decisions to admit or exclude evidence of DTI abnormalities to support claims of brain *** found that the papers which are critical of the use of DTI in the courtroom reflect a primary misunderstanding about how diagnostic biomarkers differ legally from relevant and admissible *** clinical use of DTI to identify white matter abnormalities in the brain at the chronic stage is a valid methodology both clinically as well as forensically,contributes data that may or may not corroborate the existence of white matter damage,and should be admitted into evidence in personal injury trials if supported by a *** also delve into an aspect of science publication and peer review that can be manipulated by scientists and clinicians to

关键词： Diffuse axonal injury Mild brain injury Magnetic resonance imaging Neuroimaging Medicolegal Litigation Medical jurisprudence Ethics Peer review Publishing

Radiation force and torque on a two-dimensional circular cross-section of a non-viscous eccentric layered compressible cylinder in acoustical standing waves

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Chinese Physics B 2021年第2期30卷 355-366页

作者： F G Mitri Santa Fe NM 87508USA

The purpose of this study is to develop an analytical formalism and derive series expansions for the time-averaged force and torque exerted on a compound coated compressible liquid-like cylinder,insonified by acoustic standing waves having an arbitrary angle of incidence in the polar(transverse)*** host medium of wave propagation and the eccentric liquid-like cylinder are *** computations illustrate the theoretical analysis with particular emphases on the eccentricity of the cylinder,the angle of incidence and the dimensionless size parameters of the inner and coating cylindrical fluid *** method to derive the acoustical scattering,and radiation force and torque components conjointly uses modal matching with the addition theorem,which adequately account for the multiple wave interaction effects between the layer and core fluid *** results demonstrate that longitudinal and lateral radiation force components ***,an axial radiation torque component is quantified and computed for the non-absorptive compound cylinder,arising from geometrical asymmetry considerations as the eccentricity *** computational results reveal the emergence of neutral,positive,and negative radiation force and torque depending on the size parameter of the cylinder,the eccentricity,and the angle of incidence of the insonifying ***,based on the law of energy conservation applied to scattering,numerical verification is accomplished by computing the extinction/scattering energy *** results may find some related applications in fluid dynamics,particle trapping,mixing and manipulation using acoustical standing waves.

关键词： radiation force radiation torque liquid compound cylinder multiple scattering acoustical standing waves

Investigating the therapeutic efficacy of psilocybin in advanced cancer patients: A comprehensive review and meta-analysis

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World Journal of Clinical Oncology 2024年第7期15卷 908-919页

作者： Husam Bader Husam Farraj Joud Maghnam Yazan Abu Omar Department of Internal Medicine University of MichiganAnn ArborMI 48109United States Department of Internal Medicine University of New MexicoAlbuquerqueNM 87106United States Faculty of Medicine AL-Balqa Applied UniversityAl-Salt 19110Jordan

BACKGROUND Psilocybin,a naturally occurring psychedelic compound found in certain species of mushrooms,is known for its effects on anxiety and *** has recently gained increasing interest for its potential therapeutic effects,particularly in patients with advanced *** systematic review and meta-analysis aim to evaluate the effects of psilocybin on adult patients with advanced *** To investigate the therapeutic effect of psilocybin in patients with advanced *** A comprehensive search of electronic databases was conducted in PubMed,Cochrane Central Register of Controlled Trials,and Google Scholar for articles published up to February *** reference lists of the included studies were also searched to retrieve possible additional *** A total of 7 studies met the inclusion criteria for the systematic review,comprising 132 *** results revealed significant improvements in quality of life,pain control,and anxiety relief following psilocybin-assisted therapy,specifically results on anxiety *** effect sizes indicated statistically significant reductions in symptoms of anxiety at both 4 to 4.5 months[35.15(95%CI:32.28-38.01)]and 6 to 6.5 months[33.06(95%CI:28.73-37.40)].Post-administration compared to baseline assessments(P<0.05).Additionally,patients reported sustained improvements in psychological well-being and existential distress fo-llowing psilocybin *** The findings provided compelling evidence for the potential benefits of psilocybin-assisted therapy in improving quality of life,pain control,and anxiety relief in patients with advanced cancer.

关键词： Quality of life Advanced cancer Psilocybin Systemic review Meta analysis

Three-dimensional simulation of liquid injection,film formation and transport,in fluidized beds

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Particuology 2009年第5期7卷 337-346页

作者： Paul Zhao Peter J. O'Rourke Dale Snider CPFD Software LLCAlbuquerqueNM 87111USA CFD d'OR Software and Consulting LLCLos AlamosNM 87544USA

Liquid injection, and film formation and transport in dense-phase gas-solids fluidized beds are numerically simulated in three dimensions using a collisional exchange model that is based on the mechanism that collisions cause transfer of liquid mass, momentum, and energy between particles. In the model, each of the particles is represented by a solid core and a liquid film surrounding the core. The model is incorporated in the framework of the commercial code Barracuda developed by CPFD Software. The commercial software is an advanced CFD-based computational tool where the particles are treated as discrete entities, calculated by the MP-PIC method, and tracked using the Lagrangian method. Details of the collisional liquid transfer model have been previously presented in O＇Rourke, Zhao, and Snider （2009）; this paper presents new capabilities and proof-testing of the collision model and a new method to better quantify the penetration length. Example calculations of a fluidized bed without liquid injection show the expected effect of collisions on the reduction of granular temperature （fluctuational kinetic energy） of the bed. When applied to liquid injection into a dense-phase fluidized bed under different conditions, the model predicts liquid penetration lengths comparable to the experiments. In addition, the simulation reveals for the first time the dynamic mixing of the liquid droplets with the bed particles and the transient distribution of the droplets inside the bed.

关键词： MP-PIC Liquid injection Fluidized bed Particle collisions CPFD Jet penetration

Deep material network via a quilting strategy: visualization for explainability and recursive training for improved accuracy

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npj Computational Materials 2023年第1期9卷 1023-1038页

作者： Dongil Shin Ryan Alberdi Ricardo A.Lebensohn Rémi Dingreville Center for Integrated Nanotechnologies Sandia National LaboratoriesAlbuquerqueNM 87185USA Simulation Modeling Sciences Sandia National LaboratoriesAlbuquerqueNM 87185USA Theoretical Division Los Alamos National LaboratoryLos AlamosNM 87845USA

Recent developments integrating micromechanics and neural networks offer promising paths for rapid predictions of the response of heterogeneous materials with similar accuracy as direct numerical *** deep material network is one such approaches,featuring a multi-layer network and micromechanics building blocks trained on anisotropic linear elastic *** trained,the network acts as a reduced-order model,which can extrapolate the material’s behavior to more general constitutive laws,including nonlinear behaviors,without the need to be ***,current training methods initialize network parameters randomly,incurring inevitable training and calibration ***,we introduce a way to visualize the network parameters as an analogous unit cell and use this visualization to“quilt”patches of shallower networks to initialize deeper networks for a recursive training *** result is an improvement in the accuracy and calibration performance of the network and an intuitive visual representation of the network for better explainability.

关键词： networks Deep network