Jove-Journal of Visualized Experiments最新文献_第10页

Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA). 微型生物反应器阵列（MBRA）组装和使用的更新协议。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68788

Jason D Pizzini, Firas S Midani, Robert A Britton

{"title":"Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).","authors":"Jason D Pizzini, Firas S Midani, Robert A Britton","doi":"10.3791/68788","DOIUrl":"https://doi.org/10.3791/68788","url":null,"abstract":"The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Convolutional Neural Network-based Framework for Brain Tumor Classification and Segmentation using Magnetic Resonance Images. 基于卷积神经网络的脑肿瘤磁共振图像分类与分割框架。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68428

Ambuj Kathuria, Deepali Gupta, Mudita Uppal

{"title":"Convolutional Neural Network-based Framework for Brain Tumor Classification and Segmentation using Magnetic Resonance Images.","authors":"Ambuj Kathuria, Deepali Gupta, Mudita Uppal","doi":"10.3791/68428","DOIUrl":"https://doi.org/10.3791/68428","url":null,"abstract":"Early diagnosis of brain tumors is critical for optimization of the prognosis and treatment selection of the patient. Accurate segmentation and categorization of brain tumors are essential to create specialist treatment techniques. As MRI utilization for brain diagnosis increases and computer vision technology also improves, having a good and effective model to identify and categorize tumors based on MRI scans remains challenging. To address this problem, the authors suggested a deep learning-based technique to segment and classify brain tumors from different datasets. Image preprocessing employed nine augmentation methods to enhance model performance. Segmentation of MRI was done by using a U-Net model. The developed classification model based on InceptionV3 and DenseNet201 predicts the existence of the tumor and categorizes it into Glioma, Meningioma, and Pituitary. With 99.15% accuracy, InceptionV3 is higher than DenseNet201's 98.75% in tumor classification. Additional tumor classification was performed by Clustering as HGG and LGG on the basis of Inception-ResNet-v2. Tumor grades (1-4) are identified with 96.64% accuracy by Inception-ResNet-v2. An autonomous system integrates hybrid models with GPT-4.0 to generate reports. Hence, this novel framework could very well be suitable for clinics when used for automatically identifying and separating brain tumors utilizing input images captured from MRI scans.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Flexible Procedure for Performing Telomere FISH and Immunofluorescence in Cells Expressing Fluorescent Proteins. 在表达荧光蛋白的细胞中执行端粒FISH和免疫荧光的灵活程序。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68977

Sarah F Clatterbuck Soper, Paul S Meltzer

{"title":"A Flexible Procedure for Performing Telomere FISH and Immunofluorescence in Cells Expressing Fluorescent Proteins.","authors":"Sarah F Clatterbuck Soper, Paul S Meltzer","doi":"10.3791/68977","DOIUrl":"https://doi.org/10.3791/68977","url":null,"abstract":"Visualizing telomeres using fluorescence in situ hybridization (TelFISH) has long been an essential tool in telomere biology experiments. Combining TelFISH with immunofluorescence (IF) is also a well-established method (IF-TelFISH), for example, in identifying telomere dysfunction-induced foci, where telomeres co-localize with 53BP1. More recently, native telomere FISH (nTelFISH) has become an important tool for assaying Alternative Lengthening of Telomeres, a telomere maintenance mechanism used in some tumor cells. Expressing fluorescent proteins is also an essential tool in cell biology, allowing visualization of proteins and structures that may remain undetectable by other methods. Because FISH buffers denature proteins, performing the assay in cells with an expressed fluorescent protein (FP) results in loss of FP signal. A method for integrating IF and telomere FISH in cells with an expressed fluorescent protein that preserves the FP signal even after FISH is described here. Alternatives are provided for denaturing and native telomere FISH in combination with several IF and FP scenarios. Taken together, this protocol offers a flexible framework for exploring telomere biology in both normal and tumor cells.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ultrasound Tissue Characterization of Human Achilles Tendon by Stability Quantification of Echo Patterns. 回声模式稳定性定量的人体跟腱超声组织表征。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68543

Chiara Busso, Marta Andrighetti, Elisabetta Quilico, Kristen M Meiburger, Marco A Minetto

引用次数: 0

Dual Encoder-Decoder-Encoder with Adversarial Training for Unsupervised Traffic Accident Detection in Surveillance Videos. 基于对抗性训练的双编码器-解码器-编码器在监控视频中的无监督交通事故检测。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68731

Sneha Kandacharam, B Rajathilagam, Shriram K Vasudevan

{"title":"Dual Encoder-Decoder-Encoder with Adversarial Training for Unsupervised Traffic Accident Detection in Surveillance Videos.","authors":"Sneha Kandacharam, B Rajathilagam, Shriram K Vasudevan","doi":"10.3791/68731","DOIUrl":"https://doi.org/10.3791/68731","url":null,"abstract":"To enhance road safety and improve emergency response, traffic incidents should be detected in real-world surveillance footage as quickly as possible. Existing systems largely depend on manual monitoring, which is time-consuming and prone to error. Automated accident detection remains challenging due to the substantial class imbalance: normal driving situations are overrepresented, whereas accidents are rare and diverse. In such cases, traditional computer vision systems often cannot reliably differentiate between normal and abnormal events. This study addresses the problem by developing a deep learning architecture based on a dual encoder-decoder-encoder (EDE) framework. The model uses two shared encoder-decoder pipelines to map image distributions to specified latent distributions in both directions. This framework enables the system to model common traffic behavior patterns and become more sensitive to changes that may indicate dangerous or unusual events. A two-phase training technique is proposed to further improve anomaly detection. In the first phase, the model learns to reconstruct images of normal driving, using reconstruction loss to characterize normal behavior. In the second phase, a generative adversarial mechanism is introduced: reconstructed latent vectors from one EDE are passed to the other, generating synthetic images and latent spaces. This process amplifies differences between real and synthetic outputs, making the system more responsive to subtle signs of potential anomalies. The dual-EDE architecture and adversarial training methodology represent a substantial advance over current methods by modeling both normal and pathological behavior. Experimental results on real-world traffic surveillance datasets demonstrate that the proposed method significantly improves the detection of accidents and unsafe driving behaviors, both in terms of accuracy and robustness.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Production and Testing of Moisture Behavior and Thermal Properties of Rapeseed Straw and Ganoderma resinaceum Mycelium Bio-Composites. 油菜籽秸秆与灵芝菌丝体生物复合材料的制备及热湿性能测试

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68375

Francisco Ortega Exposito, Catharina Adriana Rovers

{"title":"Production and Testing of Moisture Behavior and Thermal Properties of Rapeseed Straw and Ganoderma resinaceum Mycelium Bio-Composites.","authors":"Francisco Ortega Exposito, Catharina Adriana Rovers","doi":"10.3791/68375","DOIUrl":"https://doi.org/10.3791/68375","url":null,"abstract":"This research aimed to address the growing demand for sustainable construction materials by developing mycelium bio-composites as innovative, biobased insulation. Utilizing local agricultural lignocellulosic residual by-products bound by mycelium, they offer a promising circular alternative to fossil-based materials. This manuscript is a condensed view of the Mythic project, focused on optimizing growth techniques and material properties to ensure technical feasibility. In the growth optimization phase, a novel inoculation method using reclaimed cellulose, instead of grain kernel-based inoculants, significantly improved growth speed and substrate colonization, reducing incubation times and aligning with industrial production needs. Material property optimization focused on thermal properties, fire resistance, and moisture behavior -- key attributes for insulation materials. Mycelium bio-composites achieved thermal conductivity values of 0.034-0.039 W/m·K, comparable to conventional insulators. The moisture behaviour properties are considered to be sufficient for its use as insulation. Hydrophobic properties were enhanced through a coating, improving durability in humid conditions. These innovations ensure that mycelium bio-composites meet industry benchmarks for various applications.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mining Spatial Transcriptomics Datasets using DeepSpaceDB. 利用DeepSpaceDB挖掘空间转录组学数据集。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68892

Nupura Prabhune, Yilin Du, Afeefa Zainab, Satoru Ebihara, Shinji Takeoka, Shinpei Kawaoka, Alexis Vandenbon

{"title":"Mining Spatial Transcriptomics Datasets using DeepSpaceDB.","authors":"Nupura Prabhune, Yilin Du, Afeefa Zainab, Satoru Ebihara, Shinji Takeoka, Shinpei Kawaoka, Alexis Vandenbon","doi":"10.3791/68892","DOIUrl":"https://doi.org/10.3791/68892","url":null,"abstract":"Spatial transcriptomics is a rapidly evolving technology that enables the capture of gene expression patterns in tissue samples while preserving positional information. It has wide-ranging applications in biological research and bioinformatics, allowing researchers to investigate and track spatial variations in gene expression across different tissues, conditions, and diseases. With spatial transcriptomics data analysis gaining traction, the number of publicly available datasets is rising. However, spatial transcriptomics remains a highly specialized experimental technique, with significant technical and financial constraints. To facilitate access to spatial data, we have recently developed DeepSpaceDB, a comprehensive and dynamic database for spatial transcriptomics data exploration. This article presents detailed workflows outlining the components of the database and its navigation with the help of a few examples. First, the analysis of a mouse brain sample is demonstrated, exploring quality indicators, spatially variable genes and pathways, and gene expression variations between the hippocampus and hypothalamus. Next, the identification and annotation of differentially expressed genes associated with immune activity is further explored by comparing metastatic regions of colorectal origin with distant areas of healthy tissue in murine livers. DeepSpaceDB, with its advanced tools and interactive features, serves as a valuable resource for spatial transcriptomics research, enabling deeper exploration of tissue organization and disease biology.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Robotic-assisted Lateral Pancreaticojejunostomy for Chronic Pancreatitis. 机器人辅助外侧胰空肠造口术治疗慢性胰腺炎。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68371

Michael P Sestito, Kathryn H Schwartzman, Britney Niemann, Carl R Schmidt, Brian A Boone

{"title":"Robotic-assisted Lateral Pancreaticojejunostomy for Chronic Pancreatitis.","authors":"Michael P Sestito, Kathryn H Schwartzman, Britney Niemann, Carl R Schmidt, Brian A Boone","doi":"10.3791/68371","DOIUrl":"10.3791/68371","url":null,"abstract":"Chronic pancreatitis is a debilitating, benign inflammatory disorder that significantly alters a patient's quality of life. Pancreatic drainage procedures have long been demonstrated to be safe and feasible using laparoscopic and open surgical approaches but have largely been replaced by pancreaticoduodenectomy. Over the past several decades, perioperative outcomes using the robotic platform in hepatobiliary surgery have been rapidly improving and, in many cases, surpassing outcomes in open and laparoscopic approaches. In appropriately selected patients with pancreatic duct obstruction and without an inflammatory mass at the head of the pancreas, there remains a role for parenchymal-sparing operations that relieve recurrent pancreatitis but also limit endocrine and exocrine insufficiency. We present a robotic-assisted lateral pancreaticojejunostomy for a patient with recurrent pancreatitis in the setting of a pancreatic duct stricture. The intention of this manuscript is to provide fellowship-trained hepatobiliary surgeons with a concise and adoptable method for performing robotic-assisted lateral pancreatojejunostomy. This article demonstrates critical aspects of the operation performed in a minimally invasive, robotic fashion to treat recurrent acute/chronic pancreatitis.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advancements in the Metabolic Profiling of Three-Dimensional Brain Tumor Spheroids for Drug Screening. 用于药物筛选的三维脑肿瘤球体代谢谱研究进展。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68833

Lijing Yang, Xiaojuan Ma, Decao Yang, Jiagui Song, Jianling Yang, Yan Sun, Yan Wang, Lixiang Xue

{"title":"Advancements in the Metabolic Profiling of Three-Dimensional Brain Tumor Spheroids for Drug Screening.","authors":"Lijing Yang, Xiaojuan Ma, Decao Yang, Jiagui Song, Jianling Yang, Yan Sun, Yan Wang, Lixiang Xue","doi":"10.3791/68833","DOIUrl":"https://doi.org/10.3791/68833","url":null,"abstract":"Brain tumors, especially gliomas, are challenging to treat because of their aggressive nature, complex tumor microenvironment, and resistance to conventional therapies. Traditional two-dimensional (2D) cell cultures often fail to replicate the true tumor environment, leading to inaccurate predictions of drug efficacy. Extracellular flux analysis technology, typically used for real-time metabolic analysis in 2D cultures, measures key metabolic parameters, such as the extracellular acidification rate (ECAR) and oxygen consumption rate (OCR), providing insights into cellular metabolism. The use of 3D models represents a significant advancement, as they more accurately mimic the in vivo tumor environment. The extracellular flux analyzer was adapted to three-dimensional (3D) glioma cell models, enabling the analysis of critical metabolic pathways, including glycolysis and oxidative phosphorylation, in a more physiologically relevant context. U87 cells were seeded at appropriate densities in a 96-well low-attachment plate and cultured for 5 days. On day 5, 3D spheroid formation was observed via high-content imaging. The successfully formed spheroids were then transferred to a metabolic assay plate coated with poly-L-lysine for metabolic analysis. To improve the accuracy of these measurements, high-content imaging systems assess 3D cell size, allowing for precise normalization of extracellular flux data and minimizing metabolic variations due to differences in cell size. This integrated approach provides a more reliable analysis of glioma cell metabolic responses to drug treatments, revealing potential mechanisms of drug resistance. Ultimately, this methodology offers valuable insights into the metabolic dynamics of gliomas and supports the development of novel, clinically relevant therapeutic strategies.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acupoint Application as a Traditional Chinese Medicine Treatment for Fatigue Associated with Chronic Obstructive Pulmonary Disease. 穴位贴敷中药治疗慢性阻塞性肺疾病伴发疲劳。

IF 1.2 4区综合性期刊

Jove-Journal of Visualized Experiments Pub Date : 2025-09-05 DOI: 10.3791/68744

Xiyang Zhang, Ke Chen, Hualing Wang, Linsen Gu, Xiyu Cao, Feifei Yang, Shishuang Yu, Yi Zhu, Liuying Li

{"title":"Acupoint Application as a Traditional Chinese Medicine Treatment for Fatigue Associated with Chronic Obstructive Pulmonary Disease.","authors":"Xiyang Zhang, Ke Chen, Hualing Wang, Linsen Gu, Xiyu Cao, Feifei Yang, Shishuang Yu, Yi Zhu, Liuying Li","doi":"10.3791/68744","DOIUrl":"https://doi.org/10.3791/68744","url":null,"abstract":"Chronic obstructive pulmonary disease (COPD) is characterized by persistent respiratory symptoms and progressive airflow obstruction. Research has found that the prevalence of COPD is high and continues to rise globally and regionally. COPD has now become a major cause of death and disability worldwide. Fatigue is a subjective discomfort of the body and weakness that is closely related to physical and mental state and is a common symptom in patients with COPD. Fatigue can lead to limitations in daily functioning and decreased health-related quality of life, which in turn can severely affect the prognosis of COPD. At present, pulmonary rehabilitation is the main non-drug treatment for COPD fatigue, but patient compliance and participation are insufficient, the long-term maintenance effect is limited, and economic and time costs are high, so it is important to seek safer and more effective treatments. Acupoint application (AA), as one of the classic external treatment methods in traditional Chinese medicine, is characterized by its minimal side effects, ease of operation and dissemination, multi-target synergistic effects, and low economic costs. Preliminary findings show their role in improving the clinical symptoms of fatigue in COPD.This study will provide a detailed presentation of the process of using AA therapy to treat COPD and the observed trends, aiming to offer a reference for non-pharmacological treatment approaches.","PeriodicalId":48787,"journal":{"name":"Jove-Journal of Visualized Experiments","volume":" 223","pages":""},"PeriodicalIF":1.2,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145126144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0