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State of machine and deep learning in histopathological applications in digestive diseases

World Journal of Gastroenterology 2021年第20期27卷 2545-2575页

作者： Soma Kobayashi Joel H Saltz Vincent W Yang Department of Biomedical Informatics Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States Department of Physiology and Biophysics Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794United States

Machine learning(ML)-and deep learning(DL)-based imaging modalities have exhibited the capacity to handle extremely high dimensional data for a number of computer vision *** these approaches have been applied to numerous data types,this capacity can be especially leveraged by application on histopathological images,which capture cellular and structural features with their highresolution,microscopic ***,these methodologies have demonstrated promising performance in a variety of applications like disease classification,cancer grading,structure and cellular localizations,and prognostic predictions.A wide range of pathologies requiring histopathological evaluation exist in gastroenterology and hepatology,indicating these as disciplines highly targetable for integration of these *** have also already been primed to consider the impact of these algorithms,as development of real-time endoscopic video analysis software has been an active and popular field of *** heightened clinical awareness will likely be important for future integration of these methods and to drive interdisciplinary collaborations on emerging *** provide an overview on the application of these methodologies for gastrointestinal and hepatological histopathological slides,this review will discuss general ML and DL concepts,introduce recent and emerging literature using these methods,and cover challenges moving forward to further advance the field.

关键词： Artificial intelligence Machine learning Deep learning Gastroenterology Hepatology Histopathology

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Calcium phosphate coatings enhance biocompatibility and degradation resistance of magnesium alloy:Correlating in vitro and in vivo studies

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Bioactive Materials 2021年第5期6卷 1223-1229页

作者： Julia Gao Yingchao Su Yi-Xian Qin Department of Biomedical Engineering Stony Brook UniversityStony BrookNY11794United States

Magnesium(Mg)and its alloys are promising biodegradable materials for orthopedic ***,one of the major problems is their rapid degradation rate with quick evolution of hydrogen *** overcome this problem,calcium phosphate(CaP)coatings have been used to improve the degradation resistance and the biocompatibility of Mg *** study focuses on the comparison and correlation of the in vitro and in vivo degradation and biocompatibility behaviors of these materials.A CaP coating consisting of dicalcium phosphate dihydrate(DCPD)was deposited on an AZ60 Mg alloy by the chemical conversion ***,the in vitro degradation testing including electrochemical and immersion tests,and in vivo implantation of the CaP coated Mg alloy were conducted to compare the degradation ***,the in vitro cell behavior and in vivo bone tissue response were also compared on both uncoated and CaP-coated Mg *** showed that the CaP coating provided the Mg alloy with significantly better biodegradation behavior and *** in vitro and in vivo biocompatibility tests exhibited good consistency while not the case for *** showed that the in vitro electrochemical test could be a quick screening tool for the biodegradation rate,while the in vitro immersion degradation rate was often 2-4 folds faster than the in vivo degradation rate.

关键词： Magnesium implants Calcium phosphate Biodegradation Cytocompatibility Bone regeneration

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Dynamic Fluid Flow Mechanical Stimulation Modulates Bone Marrow Mesenchymal Stem Cells

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Bone Research 2013年第1期1卷 98-104页

作者： Minyi Hu RobbinYeh Michelle Lien Morgan Teeratananon KunalAgarwal Yi-Xian Qin Department of Biomedical Engineering Stony Brook UniversityStony BrookNY 11794-5281USA

Osteoblasts are derived from mesenchymal stem cells （MSCs）, which initiate and regulate bone formation. New strategies for osteoporosis treatments have aimed to control the fate of MSCs. While functional disuse decreases MSC growth and osteogenic potentials, mechanical signals enhance MSC quantity and bias their differentiation toward osteoblastogenesis. Through a non-invasive dynamic hydraulic stimulation （DHS）, we have found that DHS can mitigate trabecular bone loss in a functional disuse model via rat hindlimb suspension （HLS）. To further elucidate the downstream cellular effect of DHS and its potential mechanism underlying the bone quality enhancement, a longitudinal in vivo study was designed to evaluate the MSC populations in response to DHS over 3, 7, 14, and 21 days. Five-month old female Sprague Dawley rats were divided into three groups for each time point： age-matched control, HLS, and HLS＋DHS. DHS was delivered to the right mid-tibiae with a daily ＂10 min on-5 min off-10 min on＂ loading regime for five days/week. At each sacrifice time point, bone marrow MSCs of the stimulated and control tibiae were isolated through specific cell surface markers and quantified by flow cytometry analysis. A strong time-dependent manner of bone marrow MSC induction was observed in response to DHS, which peaked on day 14. After 21 days, this effect of DHS was diminished. This study indicates that the MSC pool is positively influenced by the mechanical signals driven by DHS. Coinciding with our previous findings of mitigation of disuse bone loss, DHS induced changes in MSC number may bias the differentiation of the MSC population towards osteoblastogenesis, thereby promoting bone formation under disuse conditions. This study provides insights into the mechanism of time-sensitive MSC induction in response to mechanical loading, and for the optimal design of osteovorosis treatments.

关键词： bone adaptation mechanical loading noninvasive stimulation osteoporosis osteopenia

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Noise-resilient quantum power flow

iEnergy

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iEnergy 2023年第1期2卷 63-70页

作者： Fei Feng Yi-Fan Zhou Peng Zhang Department of Electrical and Computer Engineering Stony Brook UniversityStony BrookNY 11794USA

Quantum power flow(QPF)offers an inspiring direction for overcoming the computation challenge of power flow through quantum ***,the practical implementation of existing QPF algorithms in today’s noisy-intermediate-scale quantum(NISQ)era remains limited because of their sensitivity to *** paper establishes an NISQ-QPF algorithm that enables power flow computation on noisy quantum *** main contributions include:(1)a variational quantum circuit(VQC)-based alternating current(AC)power flow formulation,which enables QPF using short-depth quantum circuits;(2)NISQ-compatible QPF solvers based on the variational quantum linear solver(VQLS)and modified fast decoupled power flow;and(3)an error-resilient QPF scheme to relieve the QPF iteration deviations caused by noise;(3)a practical NISQ-QPF framework for implementable and reliable power flow analysis on noisy quantum *** simulation tests validate the accuracy and generality of NISQ-QPF for solving practical power flow on IBM’s real,noisy quantum computers.

关键词： Quantum AC power flow quantum computing variational quantum linear solver fast decoupled load flow noisy-intermediate-scale quantum device

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POWER OF DUAL-WAVELENGTH APPROACHES IN STUDYING PHYSIOLOGICAL AND FUNCTIONAL CHANGES OF INTACT HEART AND IN VIVO BRAIN

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Journal of Innovative Optical Health Sciences 2011年第3期4卷 261-268页

作者： ZHONGCHI LUO CONGWU DU Department of Biomedical Engineering SUNY at stony brook Stony BrookNY 11794USA Medical Department Brookhaven National Laboratory UptonNY 11973-5000USA Department of Anesthesiology SUNY at Stony Brook Life Science BuildingRoom 002 Stony BrookNY 11794USA

Since the dual-wavelength spectrophotometer was developed,it has been widely used for studying biological samples and applied to extensive investigations of the electron transport in respiration and redox cofactors,redox state,metabolic control,and the generation of reactive oxygen species in ***,we discuss some extension of dual-wavelength approaches in our research to study the physiological and functional changes in intact hearts and in vivo ***,we aimed at(1)making nonratiometricfluorescent indicator become ratiometricfluorescence function for investigation of Ca^(2+) dynamics in live tissue;(2)eliminating the effects of physiological changes on measurement of intracellular calcium;(3)permitting simultaneous imaging of multiple physiological *** animal models of the perfused heart and transiently ischemic insult of brain are used to validate these approaches for physiological applications.

关键词： Dual-wavelength optical spectroscope and biomedical imaging heart brain Rhod2 fluorescence

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s cascade reinforcement likely when sympatric tnd allopatric populations exchange migrants？

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Current Zoology 2016年第2期62卷 155-167页

作者： Roman YUKILEVICH Fumio AOKI Department of Biology Union College Schenectady NY 12308 Department of Ecology and Evolution Stony Brook University Stony Brook NY 11794

When partially reproductively isolated species come back into secondary contact, these taxa may diverge in mating preferences and sexual cues to avoid maladaptive hybridization, a process known as reinforcement. This phenomenon often leads to reproductive character displacement （RCD） between sympatric and allopatric populations of reinforcing species that differ in their exposure to hybridization. Recent discussions have reinvigorated the idea that RCD may give rise to additional speciation between conspecific sympatric and allopatric populations, dubbing the concept ＂cascade reinforcement.＂ Despite some empirical studies supporting cascade reinforcement, we still know very little about the conditions for its evolution. In the present article, we address this question by developing an individual-based population genetic model that explicitly simulates cascade reinforcement when one of the hybridizing species is split into sympatric and allopatric populations. Our results show that when sympatric and allopatric populations reside in the same environment and only differ in their exposure to maladaptive hybridization, migration between them generally inhibits the evolution of cascade by spreading the reinforcement alleles from sympatry into allopatry and erasing RCD. Under these conditions, cascade reinforcement only evolved when migration rate between sympatric and allopatric populations was very low. This indicates that stabilizing sexual selection in allopatry is generally ineffective in preventing the spread of reinforcement alleles. Only when sympatric and allopatric populations experienced divergent ecological selection did cascade reinforcement evolve in the presence of substantial migration. These predictions clarify the conditions for cascade reinforcement and facilitate our understanding of existing cases in nature.

关键词： Dobzhansky-Muller incompatibilities hybrid zones reproductive character displacement reproductive isolation secondary contact sexual isolation speciation

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Hyaluronic acid and its biomedical applications:A review

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Engineered Regeneration 2020年第1期1卷 102-113页

作者： Matthew Dovedytis Zhuo Jie Liu Samuel Bartlett Department of Biomedical Engineering Stony Brook UniversityStony BrookNew York 11794United States

Hyaluronic acid is a naturally occurring biopolymer possessing numerous functions within the body including wound repair,cell migration,and cell *** to its versatility,hyaluronic acid has been a major component of biomedical research and has seen application in several fields such as tissue engineering and cancer treatments through a multitude of different *** review aims to outline hyaluronic acid’s role in the healing process while focusing on its myriad of forms and applications in the biomedical world.

关键词： Hyaluronic acid Wound healing Hydrogel Tissue engineering Regenerative medicine

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Advancements in microRNA based cancer therapeutics

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临床检验杂志 2014年第1期32卷 1-8页

作者： Andrew FESLER Jingfang JU Department of Pathology Stony Brook MedicineStony Brook University

Research efforts on non-coding RNAs have grown exponentially in the past *** are now beginning to witness the achievements that have been made in better understanding the roles of miRNAs in human diseases such as cancer and cardiovascular *** show great promise as biomarkers for cancer diagnosis and *** addition,miRNAs,due to their critical function as either oncogenes or tumor suppressor genes and their broad impact on target genes and pathways,have great potential as therapeutic agents for novel cancer drug *** miRNA molecules and mimics are getting close to clinical *** this review,we summarize and highlight some of the important findings relating to miRNA and anticancer therapeutic development.

关键词： microRNA therapeutics cancer stem cell resistance

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Two fully automated data-driven 3D whole-breast segmentation strategies in MRI for MR-based breast density using image registration and U-Net with a focus on reproducibility

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Visual Computing for Industry,Biomedicine,and Art 2022年第1期5卷 303-314页

作者： Jia Ying Renee Cattell Tianyun Zhao Lan Lei Zhao Jiang Shahid M.Hussain Yi Gao H‑H.Sherry Chow Alison T.Stopeck Patricia A.Thompson Chuan Huang Department of Biomedical Engineering Stony Brook UniversityStony BrookNY 11794USA Department of Radiation Oncology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794USA Department of Medicine Northside Hospital GwinnettLawrencevilleGA 30046USA Program of Public Health Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794USA Department of Radiology Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794USA Department of Biomedical Informatics Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794USA School of Biomedical Engineering Health Science CenterShenzhen UniversityShenzhen 518060China University of Arizona Cancer Center TucsonAZ 85719USA Department of Medicine Renaissance School of MedicineStony Brook UniversityStony BrookNY 11794USA stony brook Cancer Center Stony Brook UniversityStony BrookNY 11794USA Department of Medicine Cedar Sinai CancerCedars Sinai Medical CenterLos AngelesCA 90048USA

Presence of higher breast density(BD)and persistence over time are risk factors for breast cancer.A quantitatively accurate and highly reproducible BD measure that relies on precise and reproducible whole-breast segmentation is *** this study,we aimed to develop a highly reproducible and accurate whole-breast segmentation algorithm for the generation of reproducible BD *** datasets of volunteers from two clinical trials were *** MR images were acquired on 3T Siemens Biograph mMR,Prisma,and Skyra using 3D Cartesian six-echo GRE sequences with a fat-water separation *** whole-breast segmentation strategies,utiliz-ing image registration and 3D U-Net,were *** segmentation was performed.A task-based analysis was performed:a previously developed MR-based BD measure,MagDensity,was calculated and assessed using automated and manual *** mean squared error(MSE)and intraclass correlation coefficient(ICC)between MagDensity were evaluated using the manual segmentation as a *** test-retest reproducibility of MagDensity derived from different breast segmentation methods was assessed using the difference between the test and retest measures(Δ_(2-1)),MSE,and *** results showed that MagDensity derived by the registration and deep learning segmentation methods exhibited high concordance with manual segmentation,with ICCs of 0.986(95%CI:0.974-0.993)and 0.983(95%CI:0.961-0.992),*** test-retest analysis,MagDensity derived using the regis-tration algorithm achieved the smallest MSE of 0.370 and highest ICC of 0.993(95%CI:0.982-0.997)when compared to other segmentation *** conclusion,the proposed registration and deep learning whole-breast segmentation methods are accurate and reliable for estimating *** methods outperformed a previously developed algorithm and manual segmentation in the test-retest assessment,with the registration exhibiting superior performance for highly reproducibl

关键词： Breast cancer Breast density Breast segmentation Image registration Deep learning

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Normal Crossings Singularities for Symplectic Topology:Structures

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Acta Mathematica Sinica,English Series 2024年第1期40卷 107-160页

作者： Mohammad FARAJZADEH-TEHRANI Mark MCLEAN Aleksey ZINGER The University of Iowa MacLean HallIowa CityIA 52241 Department of Mathematics Stony Brook UniversityStony BrookNY 11794

Our previous papers introduce topological notions of normal crossings symplectic divisor and variety,show that they are equivalent,in a suitable sense,to the corresponding geometric notions,and establish a topological smoothability criterion for normal crossings symplectic *** present paper constructs a blowup,a complex line bundle,and a logarithmic tangent bundle naturally associated with a normal crossings symplectic divisor and determines the Chern class of the last *** structures have applications in constructions and analysis of various moduli *** a corollary of the Chern class formula for the logarithmic tangent bundle,we refine Aluffi’s formula for the Chern class of the tangent bundle of the blowup at a complete intersection to account for the torsion and extend it to the blowup at the deepest stratum of an arbitrary normal crossings divisor.

关键词： Normal crossings divisor Chern class Logarithmic tangent bundle

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