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Markerless tracking enables distinction between strategic compensation and functional recovery after spinal cord injury

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Experimental Neurology 2022年 354卷 114085页

作者： Mah, Kar Men Badillo-Martinez, Abdiel Jann, Victor Bixby, John L. Lemmon, Vance P. Miami Project to Cure Paralysis University of Miami Miller School of Medicine Miami 33136 FL United States Dept. of Neurological Surgery University of Miami Miller School of Medicine Miami 33136 FL United States Institute for Data Science and Computing University of Miami Miller School of Medicine Miami 33136 FL United States Dept. of Molecular and Cellular Pharmacology University of Miami Miller School of Medicine Miami 33136 FL United States Sylvester Comprehensive Cancer Center University of Miami Miller School of Medicine Miami 33136 FL United States Neuroscience Graduate Program University of Miami Miller School of Medicine Miami 33136 FL United States University of California Berkeley United States

Injuries to the cervical spinal cord represent around 60% of all spinal cord injuries (SCIs). A major priority for patients with cervical SCIs is the recovery of any hand or arm function. The similarities between human and rodent “reach-to-eat movements” indicate that analyzing mouse forelimb reaching behavior may be a method of identifying clinically relevant treatments for people with cervical SCIs. One popular behavioral measure of forelimb functional recovery comprises the Single Pellet Retrieval Task (SPRT). The most common outcome measure for this task, however (percentage of pellets successfully retrieved), cannot readily distinguish between recovery of pre-injury motor patterns and strategic compensation. Our objective was to establish outcome measures for the SPRT that are readily adopted by different investigators and capable of measuring recovery of limb function after SCI. We used a simple semi-automated approach to high-speed tracking of mouse forepaw movements during pellet retrieval. DeepLabCut™, a machine learning based computer vision software package, was used to track individual features of the mouse forepaw, allowing a more detailed assessment of reaching behavior after SCI. Interestingly, kinematic analysis of movements pre- and post-injury illuminated persistent deficits in specific features of the reaching motor patterns, namely pronation and paw trajectory, that were poorly correlated with recovery of the ability to successfully retrieve pellets. Thus, we have developed an inexpensive method for detailed analysis of mouse reach-to-eat behavior following SCI. Further, our results suggest that binary success/fail outcome measures primarily assess an animal's ability to compensate rather than a restoration of normal function in the injured pathways and networks. © 2022 Elsevier Inc.

关键词： DeepLabCut Forelimb Machine learning Mouse kinematics Pronation Reaching Spinal cord injury

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276MO Epidemiology, treatment (tx) patterns, and clinical outcomes of patients (pts) with locally advanced or metastatic urothelial cancer (la/mUC) in Taiwan: A retrospective cohort study

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Annals of Oncology 2024年 35卷 S1511-S1511页

作者： C-T. Wu L. Young A. Lee M-Y. Ku Y-C. Hsieh H-W. Lin K-L. Lin K-P. Chou M. Kearney L-N. Chien Department of Urology Chang Gung Memorial Hospital Taoyuan City Taiwan Global Medical Unit Oncology Merck Pte. Ltd. Singapore Science Park Singapore Medical Affairs Oncology Merck Ltd. Taipei Taiwan Graduate Institute of Data Science College of Management Taipei Medical University Taipei Taiwan Program in Medical Neuroscience Taipei Medical University Taipei Taiwan Real-world Solutions IQVIA Solutions Taiwan Ltd. Taipei Taiwan Global Value Demonstration Market Access and Pricing Biopharma Global Operations Merck Healthcare KGaA Darmstadt Germany Institute of Health and Welfare Policy College of Medicine National Yang Ming Chiao Tung University Taipei Taiwan

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Molecular profiling of adult C. elegans glia across sexes by single-nuclear RNA-seq

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Developmental cell 2025年

作者： Maria D Purice Elgene J A Quitevis R Sean Manning Liza J Severs Nina-Tuyen Tran Violet Sorrentino Connor Finkbeiner Feinan Wu Michael Zager Manu Setty Aakanksha Singhvi Division of Basic Sciences Fred Hutchinson Cancer Center Seattle WA 98109 USA. Division of Basic Sciences Fred Hutchinson Cancer Center Seattle WA 98109 USA Herbold Computational Biology Program Public Health Sciences Division Fred Hutchinson Cancer Center Seattle WA 98109 USA. Molecular and Cell Biology Graduate Program Fred Hutchinson Cancer Center and University of Washington Seattle WA 98109 USA. Herbold Computational Biology Program Public Health Sciences Division Fred Hutchinson Cancer Center Seattle WA 98109 USA Department of Genome Sciences University of Washington Seattle WA 98109 USA. Genomics and Bioinformatics Shared Resource Fred Hutchinson Cancer Center Seattle WA 98109 USA. Data Visualization Core Fred Hutchinson Cancer Center Seattle WA 98109 USA. Translational Data Science IRC Fred Hutchinson Cancer Center Seattle WA 98109 USA. Electronic address: msetty@***. Department of Neurobiology and Biophysics University of Washington School of Medicine Seattle WA 98195 USA. Electronic address: asinghvi@***.

A comprehensive understanding of nervous system function requires molecular insight into the diversity and sex dimorphism of both its component cell types, glia and neurons. Here, we present a single-nuclear RNA sequencing (RNA-seq) census of all neuroectoderm-derived glia in the adult C. elegans nervous system, across sexes. By iteratively coupling computational modeling and custom analytics with in vivo validations, we uncovered molecular markers for all glia, as well as class-specific and pan-glial molecular signatures. These identified that each glia is functionally heterogeneous across the nervous system and variably sex dimorphic between sexes. Thus, this glial transcriptome (***) offers deep mechanistic insights into glial biology brain wide. Complementing the existing C. elegans neuronal transcriptome and mapped connectome, it also enables single-cell and molecular resolution insight into the entire nervous system of an adult metazoan.

关键词： C. elegans glia cell-type classification cellular heterogeneity dense core vesicles glia glial transcriptome sexual dimorphism snRNA-seq

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Analyzing important factors in e-commerce for sustainable industry

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IOP Conference Series: Earth and Environmental science 2021年第1期794卷

作者： Yulius Lie Kartika Purwandari Bharuno Mahesworo Reza Rahutomo Anzaludin Samsinga Perbangsa Hery Harjono Muljo Bens Pardamean Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Accounting Information Systems Program Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The rapid growth of e-commerce for sustainable industry in Indonesia leads to competition for customer acquisition. Instead of gaining loyalty, customers are trapped in a price war and take advantage to compare and choose the one with the best offer. This study aims to analyze important factors of an online retailer to determine customer loyalty in the productive age group. This study contributes to design a questionnaire that can be utilized in analyzing customer loyalty to a retailer in e-commerce (popularly known as the term e-tailer). The questionnaire can be distributed through the Internet to gather demography, population, and e-loyalty factors. Questionnaire design is proposed containing three parts: Part A – Demography, Part B – Targeted Population, and Part C - e-Loyalty Factors. While Part A records basic information and Part B validates, Part C records respondent's assessment to an e - tailer. Therefore, the outcome delivers a data engineering method to help e-tailers determine important factors to gain customer loyalty.

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The dynamic effect of trading between China and Taiwan under exchange rate fluctuations

Humanities and Social Sciences Communications

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Humanities and Social sciences Communications 2023年第1期10卷 1-9页

作者： Tzu-Yi Yang Chieh Liu Yu-Tai Yang Ssu-Han Chen Graduate Program of International Business Communication Department of Foreign Languages and Literature National Ilan University No. 1 Section 1 Shennong Rd Yilan City Yilan County 260 Taiwan Department of Aeronautical and Opto-Mechatronic Engineering Vanung University No.1 Vanung Rd. ChungLi Taoyuan 32061 Taiwan Department of Industrial Engineering and Management Center for Artificial Intelligence & Data Science Ming Chi University of Technology No.84 Gungjuan Rd. Taishan Dist. New Taipei City 24301 Taiwan

As an export-oriented economy, Taiwan’s export income can be easily influenced by internal and international economic factors, including the industrial production index (IPI) and the exchange rate. With China being Taiwan’s largest recipient, Taiwan’s export income from China is extremely important to Taiwan’s economy. Therefore, this research investigates the nonlinear relationship between the IPI of Taiwan and Taiwan’s export income from China with the application of a panel smooth transition regression (PSTR) model. In addition, the currency exchange rate of RMB to NTD, which is the transfer variable, is used to examine the dynamic effect. The research period is monthly data ranging from January 2001 to February 2022. The empirical results show that the effect of the IPI of Taiwan on Taiwan’s export income with China is dynamic. Moreover, with the existence of a threshold value, its influence changes as the currency exchange rate of RMB to NTD varies over time. Finally, regardless of whether the currency exchange rate of RMB to NTD is above or below the threshold value, as the IPI of Taiwan increases, Taiwan’s export income from China also increases, differing only in the degree of increase.

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Association between a priori and a posteriori dietary patterns and the risk of type 2 diabetes: a representative cohort study in Taiwan

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Journal of Nutritional science 2023年 12卷 e16-e16页

作者： Rong Lin Kuo-Liong Chien Ming-Chieh Tsai Yi-Jie Wang Le-Yin Hsu Division of Endocrinology Department of Internal Medicine Far Eastern Memorial Hospital New Taipei City Taiwan Institute of Epidemiology and Preventive Medicine National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan Division of Endocrinology Department of Internal Medicine MacKay Memorial Hospital Tamsui Branch New Taipei City Taiwan Department of Dietetics National Taiwan University Hospital Taipei Taiwan Graduate Program of Data Science National Taiwan University and Academia Sinica Taipei Taiwan

The present study aimed to investigate the relationship between dietary patterns and the risk of type 2 diabetes mellitus (T2DM) among Taiwanese individuals. data were collected using a nationwide cohort study (2001–15) from the Triple-High database. Dietary intake was assessed using the twenty-group food frequency questionnaire and used to calculate alternate Mediterranean diet (aMED) and Dietary Approaches to Stop Hypertension (DASH) scores. Principal component analysis (PCA) and partial least-squares (PLS) regression were used to derive dietary patterns, with incident T2DM as the outcome. Multivariable-adjusted hazard ratios and 95 % confidence intervals were calculated using time-dependent Cox proportional hazards (Cox PH) regression analysis, and subgroup analyses were performed. A total of 4705 participants were enrolled in the study, and 995 had newly developed T2DM during the median 5⋅28-year follow-up period (30⋅7 per 1000 person-years). Six dietary patterns were extracted (PCA: Western, prudent, dairy and plant-based; PLS: health-conscious, fish-vegetable and fruit-seafood). The highest aMED score quartile had a 25 % (hazard ratio 0⋅75; 95 % CI 0⋅61, 0⋅92; P = 0⋅039) lower risk of T2DM than the lowest quartile. This association remained significant after adjustment (adjusted hazard ratio 0⋅74; 95 % CI 0⋅60, 0⋅91; P = 0⋅010), and no effect modifier was found for aMED. The DASH scores, PCA and PLS dietary patterns were not significant after adjustment. In conclusion, high adherence to a MED-type dietary pattern by Taiwanese foods was associated with a lower risk of T2DM in the Taiwanese population, regardless of unhealthy lifestyle habits.

关键词： Dietary patterns Mediterranean diet Partial least-squares regression Principal component analysis Type 2 diabetes mellitus

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Transfer Learning from Chest X-Ray Pre-trained Convolutional Neural Network for Learning Mammogram data 3

Transfer Learning from Chest X-Ray Pre-trained Convolutional...

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3rd International Conference on Computer science and Computational Intelligence, ICCSCI 2018

作者： Pardamean, Bens Cenggoro, Tjeng Wawan Rahutomo, Reza Budiarto, Arif Karuppiah, Ettikan Kandasamy Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia NVIDIA Corporation United States

Breast cancer is one of the deadliest cancer for female nowadays. Despite of the rapid advancement in medical image analysis with the rise of deep learning, development of breast cancer detection system is limited due to relatively small size of the publicly available mammogram dataset. In this paper, we discover an effective configuration for transfer learning from Chest X-Ray pre-trained Convolutional Neural Network to overcome the small-size mammogram dataset problem. We found that the best configuration achieve 90.38% validation accuracy for modified. © 2018 The Authors. Published by Elsevier Ltd.

关键词： Deep learning

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Crowdsourcing annotation system of object counting dataset for deep learning algorithm 2

Crowdsourcing annotation system of object counting dataset f...

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2nd International Conference on Eco Engineering Development 2018, ICEED 2018

作者： Cenggoro, Tjeng Wawan Tanzil, Fidelson Aslamiah, Ayu Hidayah Karuppiah, Ettikan Kandasamy Pardamean, Bens Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia NVIDIA Corporation Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Deep Learning is currently the state-of-the-art technique for various Computer Vision tasks, including object counting. Despite of its high performance, Deep Learning requires a gigantic amount of training data to show its best result. Getting this massive data in reasonable time requires a proper strategy such as crowdsourcing. However, in case of object counting, we found no crowdsourcing system able to effectively collect necessary data. To tackle this problem, we develop a crowdsourcing system to annotate image for object counting dataset. This system is also equipped with validation system to ensure the quality of collected dataset. © 2018 Institute of Physics Publishing. All rights reserved.

关键词： Crowdsourcing

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A Geoelectric Approach for Karst Groundwater Analysis

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Amallia Ferhat Taufik Seizarsyah Mohammad Prasanto Bimantio Nanda Satya Nugraha Dian Pratama Putra Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Agribusiness Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Geophysical Engineering Department Universitas Pembangunan Nasional 'Veteran' Yogyakarta Indonesia Agricultural Crop Technology Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Forestry Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Agricultural Engineering Department Institute of Agricultural STIPER Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Artesian well is one of the major efforts to obtain water source for fulfilling water demands in Eroniti Conservation park, Ponjong, Yogyakarta by drilling deep into several soil layers. Vertical Electrical Sounding (VES) method is the most common approach to determine the existence of groundwater. The method probes layers of rock below the ground surface based on their electrical properties, since the electrical resistivity of each layer is theoretically different. This study aims to utilize the VES approach for investigating the properties of the rock layers in the area to explore groundwater sources. We install six different VES points in the observation area using Schlumberger electrode configuration. The methodology of the work consists of three steps: the planning of the placement of the sounding points, the measurement step performed by a unit of IRIS SYSCAL Resistivity meter, and the data analysis and interpretation. Employing the resistivity analysis, we conclude that the observed region consists of Mediterranean soil as a result of weathering of limestone as well as lithology of the limestone. Furthermore, there are two types of aquifer found in the area: a perched aquifer found 27 meters below the ground surface of VES point 1 and a confined aquifer 166 meters below the ground surface of VES point 2 and 6.

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Association of vaccine-specific regulatory T cells with reduced antibody response to repeated influenza vaccination

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European journal of immunology 2023年第12期53卷 e2350525页

作者： Pin-Hung Lin Po-Ju Hsiao Ching-Fu Pan Ming-Tsan Liu Jann-Tay Wang Chi Ching Fang-Yi Wu Yi-Hsuan Lin Yu-Chan Yang Le-Yin Hsu Hung-Chih Yang Un-In Wu Graduate Institute of Microbiology College of Medicine National Taiwan University Taipei Taiwan. Department of Medical Research National Taiwan University Hospital Taipei Taiwan. Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan. Department of Internal Medicine College of Medicine National Taiwan University Taipei Taiwan. Center for Diagnostics and Vaccine Development Centers for Disease Control Taipei Taiwan. Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei Taiwan. Graduate Program of Data Science National Taiwan University and Academia Sinica Taipei Taiwan. Department of Medicine National Taiwan University Cancer Center Taipei Taiwan.

Repeated annual influenza vaccinations have been associated with reduced vaccine-induced antibody responses. This prospective study aimed to explore the role of vaccine antigen-specific regulatory T (Treg) cells in antibody response to repeated annual influenza vaccination. We analyzed pre- and postvaccination hemagglutination inhibition (HI) titers, seroconversion rates, seroprotection rates, vaccine antigen hemagglutinin (HA)-specific Treg cells, and conventional T (Tconv) cells. We compared these parameters between vaccinees with or without vaccine-induced seroconversion. Our multivariate logistic regression revealed that prior vaccination was significantly associated with a decreased likelihood of achieving seroconversion for both H1N1(adjusted OR, 0.03; 95% CI, 0.01-0.13) and H3N2 (adjusted OR, 0.09; 95% CI, 0.03-0.30). Furthermore, individuals who received repeated vaccinations had significantly higher levels of pre-existing HA-specific Treg cells than those who did not. We also found that vaccine-induced fold-increases in HI titers and seroconversion were negatively correlated with pre-existing HA-specific Treg cells and positively correlated with the ratio of Tconv to Treg cells. Overall, our findings suggest that repeated annual influenza vaccination is associated with a lower vaccine-induced antibody response and a higher frequency of vaccine-specific Treg cells. However, a lower frequency of pre-existing Treg cells correlates with a higher postvaccination antibody response.

关键词： Influenza Regulatory T cells Repeated vaccination Seroconversion Seroprotection

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