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A novel method for clustering cellular data to improve classification

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Neural Regeneration Research 2025年第9期20卷 2697-2705页

作者： Diek W.Wheeler Giorgio A.Ascoli Center for Neural Informatics Structures&PlasticityKrasnow Institute for Advanced Study bioengineering department Volgenau School of Engineering George Mason University FairfaxVAUSA

Many fields,such as neuroscience,are experiencing the vast prolife ration of cellular data,underscoring the need fo r organizing and interpreting large datasets.A popular approach partitions data into manageable subsets via hierarchical clustering,but objective methods to determine the appropriate classification granularity are *** recently introduced a technique to systematically identify when to stop subdividing clusters based on the fundamental principle that cells must differ more between than within *** we present the corresponding protocol to classify cellular datasets by combining datadriven unsupervised hierarchical clustering with statistical *** general-purpose functions are applicable to any cellular dataset that can be organized as two-dimensional matrices of numerical values,including molecula r,physiological,and anatomical *** demonstrate the protocol using cellular data from the Janelia MouseLight project to chara cterize morphological aspects of neurons.

关键词： cellular data clustering dendrogram data classification Levene's one-tailed statistical test unsupervised hierarchical clustering

Axial strain enhances osteotomy repair with a concomitant increase in connexin43 expression

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Bone Research 2015年第2期3卷 83-91页

作者： Rishi R Gupta Hyunchul Kim Yu-Kwan Chan Carla Hebert Leah Gitajn David J Yoo Robert V O’Toole Adam H Hsieh Joseph P Stains department of Orthopaedics University of Maryland fischell department of bioengineering University of MarylandCollege Park

The mechanical environment is known to influence fracture healing. We speculated that connexin43 （Cx43） gap junctions, which impact skeletal homeostasis, fracture healing and the osteogenic response to mechanical load, may play a role in mediating the response of the healing bone to mechanical strain. Here, we used an established rat fracture model, which uses a 2 mm osteotomy gap stabilized by an external fixator, to examine the impact of various cyclical axial loading protocols （2%, 10%, and 30% strain） on osteotomy healing. We examined the presence of Cx43 in the osteotomy-healing environment and assessed how mechanical strain modulates Cx43 expression patterns in the callus. We demonstrated that increased cyclical axial strain results in increased radiographic and histologic bone formation. In addition, we show by immunohistochemistry that Cx43 is abundantly expressed in the healing callus, with the expression most robust in samples exposed to increased cyclical axial strain. These data are consistent with the concept that an increase in Cx43 expression by mechanical load may be part of the mechanisms by which mechanical forces enhances fracture healing.

关键词： connexin healing repair concomitant callus homeostasis assessed skeletal exposed stained

Improving localization precision of Brillouin measurements using spectral autocorre lation analysis

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Journal of Innovative Optical Health Sciences 2017年第6期10卷 35-42页

作者： Eitan Edrei Milos Nikolic Giuliano Scarcelli fischell department of bioengineering University of Maryland College ParkMaryland 20742USA

Brillouin spectroscopy is a powerful tool for measuring the mechanical properties of materials without *** sensitivity to mechanical changes that a Brillouin spectrometer can detect is determined by the precision to which a spectral peak can be *** localization precision is however fundamentally limited by the low mumber of photons within a Brillouin measurement,as wel as by intrinsic noise of the ***,we present a method to improve the spectral sensitivity of Brillouin measurements by exploiting the autocorelation function of the *** show that by performing a localization process on the autocorrelation function nearly 20%increase in localizat ion precision can be *** result is consistent bet ween our theoretical treatment,numerical simulation and experimental *** further study the efect of back-ground noise on the precision im provement for realistic scenarios.

关键词： Brillouin microscopy localization

A PERSONAL REFLECTION ON MY PH.D. ADVISOR DR. BRITTON CHANCE

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Journal of Innovative Optical Health Sciences 2011年第4期4卷 487-488页

作者： YU CHEN fischell department of bioengineering University of Maryland 2218 Jeong H.Kim Building College ParkMD 20742USA

This article briefly reflects some of my interactions with *** Chance(BC),from a perspective of his graduate student.

关键词： Britton Chance reflection

Antiviral therapy for hepatitis B virus infection is beneficial for the prognosis hepatocellular carcinoma

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维普期刊数据库

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World Journal of Gastrointestinal Oncology 2025年第1期17卷 1-9页

作者： Hui Wan Yu-Xin Zhang Guan-Yue Shan Jun-Ya Cheng Duan-Rui Qiao Yi-Ying Liu Wen-Na Shi Hai-Jun Li Institute of Translational Medicine The First Hospital of Jilin UniversityChangchun 130061Jilin ProvinceChina department of bioengineering Pharmacy School of Jilin UniversityChangchun 130061Jilin ProvinceChina Institute of Liver Diseases Institute of Translational MedicineThe First Hospital of Jilin UniversityChangchun 130061Jilin ProvinceChina

In this editorial,we comment on the article by Mu et al,published in the recent issue of the World Journal of Gastrointestinal *** pay special attention to the immune tolerance mechanism caused by hepatitis B virus(HBV)infection,the pathogenesis of hepatocellular carcinoma(HCC),and the role of antiviral therapy in treating HCC related to HBV *** infection leads to systemic innate immune tolerance by directly inhibiting pattern recognition receptor recognition and antiviral signaling pathways,as well as by inhibiting the immune functions of macrophages,natural killer cells and dendritic *** addition,HBV leads to an immunosuppressive cascade by expressing inhibitory molecules to induce exhaustion of HBV-specific cluster of differentiation 8+T cells,ultimately leading to long-term viral *** loss of immune cell function caused by HBV infection ultimately leads to ***-term antiviral therapy can improve the prognosis of patients with HCC and prevent tumor recurrence and metastasis.

关键词： Hepatitis B virus Hepatocellular carcinoma Hepatitis B virus-DNA Immune tolerance Antiviral therapy

OPTIMIZATION OF DESIGN PARAMETERS FOR FLUORESCENCE LAMINAR OPTICAL TOMOGRAPHY

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Journal of Innovative Optical Health Sciences 2011年第3期4卷 309-323页

作者： CHAO-WEI CHEN YU CHEN fischell department of bioengineering and Electrical and Computer Engineering 2218 Jeong H.Kim Building University of Maryland College ParkMD 20742USA

Laminar optical tomography(LOT)is a mesoscopic tomographic imaging technique ranging between confocal microscopy and diffuse optical tomography(DOT).Fluorescence LOT(FLOT)provides depth-resolved molecular information with 100-200μm resolution over 2-3mm *** this study,we use Monte Carlo simulation and singular-value analysis(SVA)to optimize the source-detector configurations for potential enhancement of FLOT imaging *** effects of different design parameters,including source incidence and detector collection angles,detector number,and sampling density,are *** results indicate that angled incidence/detection configuration might improve the imaging resolution and depth sensitivity,especially for low-scattering *** the number of detectors and the number of scanning steps will also result in enhanced imaging *** also demonstrate that the optimal imaging performance depends upon the background scattering coe±*** result might provide an optimization strategy for FLOT or LOT experimental setup.

关键词： Laminar optical tomography(LOT) fluorescence laminar optical tomography(FLOT) singular value analysis(SVA) image reconstruction

Unleashing the Potential of Electroactive Hybrid Biomaterials and Self‑Powered Systems for Bone Therapeutics

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维普期刊数据库

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Nano-Micro Letters 2025年第2期17卷 463-497页

作者： Shichang Liu Farid Manshaii Jinmiao Chen Xinfei Wang Shaolei Wang Junyi Yin Ming Yang Xuxu Chen Xinhua Yin Yunlei Zhou Honghui Hospital Xi’an Jiaotong UniversityXi’an 710018People’s Republic of China department of bioengineering Henry Samueli School of Engineering and Applied ScienceUniversity of California Los AngelesLos Angeles 90095USA Hangzhou Institute of Technology Xidian UniversityHangzhou 311231People’s Republic of China

The incidence of large bone defects caused by traumatic injury is increasing worldwide,and the tissue regeneration process requires a long recovery time due to limited self-healing *** bioelectrical phenomena have been well recognized as critical biophysical factors in bone remodeling and *** by bioelectricity,electrical stimulation has been widely considered an external intervention to induce the osteogenic lineage of cells and enhance the synthesis of the extracellular matrix,thereby accelerating bone *** ongoing advances in biomaterials and energy-harvesting techniques,electroactive biomaterials and self-powered systems have been considered biomimetic approaches to ensure functional recovery by recapitulating the natural electrophysiological microenvironment of healthy bone *** this review,we first introduce the role of bioelectricity and the endogenous electric field in bone tissue and summarize different techniques to electrically stimulate cells and ***,we highlight the latest progress in exploring electroactive hybrid biomaterials as well as self-powered systems such as triboelectric and piezoelectric-based nanogenerators and photovoltaic cell-based devices and their implementation in bone tissue ***,we emphasize the significance of simulating the target tissue’s electrophysiological microenvironment and propose the opportunities and challenges faced by electroactive hybrid biomaterials and self-powered bioelectronics for bone repair strategies.

关键词： Electroactive biomaterials Self-powered bioelectronics Bone regeneration Bone tissue

Gene therapy for spinal muscular atrophy:perspectives on the possibility of optimizing SMN1 delivery to correct all neurological and systemic perturbations

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Neural Regeneration Research 2025年第7期20卷 2011-2012页

作者： Sharon J.Brown Rafael J.Yáñez-Muñoz Heidi R.Fuller School of Pharmacy and bioengineering Keele UniversityKeeleUK Wolfson Center for Inherited Neuromuscular Disease TORCH BuildingRJAH Orthopaedic HospitalOswestryUK *** Center of Gene and Cell TherapyDepartment of Biological SciencesSchool of Life Sciences and the EnvironmentRoyal Holloway University of LondonEghamUK

Spinal muscular atrophy(SMA)is a genetic condition that results in selective lower motor neuron loss with concomitant muscle weakness and *** genetic cause of SMA was understood in 1995 when loss or impairment of the survival motor neuron 1(SMN1)gene was identified as the main contributing factor(Lefebvre et al.,1995).This,in combination with the discovery that humans have a“back-up”gene,SMN2,which can produce low levels(approximately 10%)of the full-length functional SMN protein,has led to the generation of SMA-specific gene *** was traditionally classified according to age of symptom onset and developmental milestones achieved,with life expectancy and severity varying between ***,SMN2 copy number is used as a proxy for the prediction of disease severity,with higher SMN2 copy number typically being associated with reduced severity of SMA,although this relationship is not absolute:some individuals with low SMN2 copy number have less severe SMA phenotypes and vice ***,the etiology of SMA is further complicated by other factors,such as non-typical nucleotide variants and SMN2-independent modifiers of disease severity.

关键词： atrophy traditionally absolute

Temporal dynamics of neonatal hypoxic-ischemic encephalopathy injuries on magnetic resonance imaging

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Neural Regeneration Research 2025年第11期20卷 3144-3150页

作者： Holly Flyger Samantha J.Holdsworth Alistair J.Gunn Laura Bennet Hamid Abbasi Mātai Medical Research Institute Tairāwhiti GisborneNew Zealand department of Anatomy&Medical Imaging Faculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand Center for Brain Research The University of AucklandAucklandNew Zealand Auckland bioengineering Institute The University of AucklandAucklandNew Zealand

Moderate to severe perinatal hypoxic-ischemic encephalopathy occurs in~1 to 3/1000 live births in high-income countries and is associated with a significant risk of death or neurodevelopmental *** assessment is important to help identify highrisk infants,to help families,and to support appropriate interventions.A wide range of monitoring tools is available to assess changes over time,including urine and blood biomarkers,neurological examination,and *** present,magnetic resonance imaging is unique as although it is expensive and not suited to monitoring the early evolution of hypoxic-ischemic encephalopathy by a week of life it can provide direct insight into the anatomical changes in the brain after hypoxic-ischemic encephalopathy and so offers strong prognostic information on the long-term outcome after hypoxic-ischemic *** review investigated the temporal dynamics of neonatal hypoxic-ischemic encephalopathy injuries,with a particular emphasis on exploring the correlation between the prognostic implications of magnetic resonance imaging scans in the first week of life and their relationship to long-term outcome prediction,particularly for infants treated with therapeutic hypothermia.A comprehensive literature search,from 2016 to 2024,identified 20 pertinent *** review highlights that while the optimal timing of magnetic resonance imaging scans is not clear,overall,it suggests that magnetic resonance imaging within the first week of life provides strong prognostic *** challenges limit the timing consistency,particularly the need for intensive care and clinical ***,although most reports examined the prognostic value of scans taken between 4 and 10 days after birth,there is evidence from small numbers of cases that,at times,brain injury may continue to evolve for weeks after *** suggests that in the future it will be important to explore a wider range of times after hypo

关键词： magnetic resonance imaging neonatal hypoxic-ischemic encephalopathy neurodevelopmental outcomes prognostic biomarkers in neuroimaging scan timing therapeutic hypothermia