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A mountable toilet system for personalized health monitoring via the analysis of excreta (vol 15, pg 561, 2020)

NATURE BIOMEDICAL engineering 2020年第6期4卷 662-662页

作者： Park, Seung-min Won, Daeyoun D. Lee, Brian J. Escobedo, Diego Esteva, Andre Aalipour, Amin Ge, T. Jessie Kim, Jung Ha Suh, Susie Choi, Elliot H. Lozano, Alexander X. Yao, Chengyang Bodapati, Sunil Achterberg, Friso B. Kim, Jeesu Park, Hwan Choi, Youngjae Kim, Woo Jin Yu, Jung Ho Bhatt, Alexander M. Lee, Jong Kyun Spitler, Ryan Wang, Shan X. Gambhir, Sanjiv S. Department of Radiology Stanford University School of Medicine Stanford CA USA Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford CA USA Department of Surgery Seoul Song Do Hospital Seoul Republic of Korea Cancer Immunology Laboratory Seoul Song Do Hospital Seoul Republic of Korea Department of Surgery Leiden University Medical Center Leiden the Netherlands Department of Creative IT Engineering Pohang University of Science and Technology (POSTECH) Pohang Republic of Korea Precision Health and Integrated Diagnostic Center (PHIND) Stanford University School of Medicine Palo Alto CA USA Department of Materials Science and Engineering Stanford University Stanford CA USA Department of Bioengineering Stanford University Stanford CA USA Canary Center at Stanford for Cancer Early Detection Stanford University School of Medicine Palo Alto CA USA Salesforce Research Palo Alto CA USA Department of Urology Stanford University School of Medicine Stanford CA USA Department of Pharmacology Case Western Reserve University School of Medicine Cleveland OH USA Faculty of Medicine University of Toronto Toronto Ontario Canada Department of Electrical Engineering Stanford University Stanford CA USA College of Medicine The Catholic University of Korea Seoul Republic of Korea

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： Diagnosis

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Silicone breast implant modification review: Overcoming capsular contracture

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Biomaterials Research 2018年第1期22卷 319-327页

作者： Shin, Byung Ho Kim, Byung Hwi Kim, Sujin Lee, Kangwon Choy, Young Bin Heo, Chan Yeong Seoul National University College of Medicine Department of Biomedical Engineering Seoul 03080 South Korea Seoul National University Department of Transdisciplinary Studies Graduate School of Convergence Science and Technology Seoul 08826 South Korea Seoul National University Interdisciplinary Program for Bioengineering College of Engineering Seoul 08826 South Korea Seoul National University Department of Plastic and Reconstructive Surgery College of Medicine Seoul 03080 South Korea Seoul National University Bundang Hospital Department of Plastic and Reconstructive Surgery Seongnam 13620 South Korea Seoul National University Institute of Medical and Biological Engineering Medical Research Center Seoul 03080 South Korea Advanced Institutes of Convergence Technology Suwon Gyeonggi-do 16229 South Korea

Background: Silicone implants are biomaterials that are frequently used in the medical industry due to their physiological inertness and low toxicity. However, capsular contracture remains a concern in long-term transplantation. To date, several studies have been conducted to overcome this problem. This review summarizes and explores these trends. Main body: First, we examined the overall foreign body response from initial inflammation to fibrosis capsule formation in detail and introduced various studies to overcome capsular contracture. Secondly, we introduced that the main research approaches are to inhibit fibrosis with anti-inflammatory drugs or antibiotics, to control the topography of the surface of silicone implants, and to administer plasma treatment. Each study examined aspects of the various mechanisms by which capsular contracture could occur, and addressed the effects of inhibiting fibrosis. Conclusion: This review introduces various silicone surface modification methods to date and examines their limitations. This review will help identify new directions in inhibiting the fibrosis of silicone implants. © 2018 The Author(s).

关键词： Capsular contracture Fibrosis Foreign body reaction Inflammation Modification Silicone implant

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Connecting distant entities with induction through conditional random fields for named entity recognition: Precursor-induced CRF

arXiv

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arXiv 2018年

作者： Lee, Wangjin Choi, Jinwook Interdisciplinary Program for Bioengineering Seoul National University Korea Republic of Department of Biomedical Engineering College of Medicine Seoul National University Korea Republic of Institute of Medical and Biological Engineering Medical Research Center Seoul National University Korea Republic of

This paper presents a method of designing specific high-order dependency factor on the linear chain conditional random fields (CRFs) for named entity recognition (NER). Named entities tend to be separated from each other by multiple outside tokens in a text, and thus the first-order CRF as well as the second-order CRF may innately lose transition information between distant named entities. The proposed design uses outside label in NER as a transmission medium of precedent entity information on the CRF. Then, empirical results apparently demonstrate that it is possible to exploit long-distance label dependency in the original first-order linear chain CRF structure upon NER while reducing computational loss rather than in the second-order CRF. Copyright © 2018, The Authors. All rights reserved.

关键词： Random processes

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Proteomic Data and Drug Implications for Cerebral Microvascular Endothelial Cells Under Varying Oxygen Levels

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Scientific data 2025年第1期12卷 989页

作者： Sarah Barakat Fan Yang Hayriye Ecem Yelkenci Kıvanç Kök Giovanni E Mann Emrah Eroğlu Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. sarah.barakat1@medipol.edu.tr. King's British Heart Foundation Centre of Research Excellence School of Cardiovascular and Metabolic Medicine & Sciences Faculty of Life Sciences & Medicine King's College London 150 Stamford Street London SE1 9NH UK. Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. guvanch@medipol.edu.tr. Department of Biostatistics and Medical Informatics International School of Medicine Istanbul Medipol University Istanbul 34810 Turkey. guvanch@medipol.edu.tr. Molecular Biology Genetics and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Istanbul 34956 Turkey.

Hyperoxia in standard cell cultures (18 kPa O) imposes cellular oxidative stress, potentially skewing research and drug screening outcomes. Cerebral microvascular endothelial cells (hCMEC/D3) experience no more than 7 kPa O in vivo. In this study, hCMEC/D3 cells were adapted to 5 kPa O for 5 days to optimize an in vitro physiological cell culture model. Using a SYNAPT G2-Si mass spectrometer, we compared the proteomic profiles of cells cultured under 5 kPa versus 18 kPa O. A substantial proteomic shift under hyperoxia highlighted the strong impact of oxygen levels on protein expression. We further investigated the effect of oxygen levels on drug screening using sulforaphane (SFN), an inducer of NRF2-regulated antioxidant defense genes. SFN induced more pronounced changes in proteomic profiles under 18 kPa O compared to 5 kPa, indicating oxygen-dependent cellular drug responses. This dataset offers a valuable resource for analyzing oxygen-sensitive proteomic changes. Comparative studies using different drugs or cell types could further elucidate oxygen-dependent signaling and inform the development of therapies aligned with physiological oxygen levels.

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AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets

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Immunoinformatics (Amsterdam, Netherlands) 2023年 10卷 100025页

作者： William D Lees Scott Christley Ayelet Peres Justin T Kos Brian Corrie Duncan Ralph Felix Breden Lindsay G Cowell Gur Yaari Martin Corcoran Gunilla B Karlsson Hedestam Mats Ohlin Andrew M Collins Corey T Watson Christian E Busse Institute of Structural and Molecular Biology Birkbeck College London England. Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal. Peter O'Donnell Jr. School of Public Health UT Southwestern Medical Center Dallas TX USA. Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel. Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville KY USA. Department of Biological Sciences Simon Fraser University Burnaby BC Canada. Fred Hutchinson Cancer Research Center Seattle WA USA. Peter O'Donnell Jr. School of Public Health Department of Immunology School of Biomedical Sciences UT Southwestern Medical Center Dallas TX USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Swede. Department of Immunotechnology and SciLifeLab Lund University Lund Sweden. School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia. Division of B Cell Immunology German Cancer Research Center Heidelberg Germany.

Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.

关键词： AIRR-seq Immune receptor Immune receptor germline Immune receptor repertoire Rep-seq

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Virtual reality sound localization testing in cochlear implant users 8

Virtual reality sound localization testing in cochlear impla...

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8th International IEEE EMBS Conference on Neural engineering, NER 2017

作者： Sechler, Stephen D. Lopez Valdes, Alejandro Waechter, Saskia M. Simoes-Franklin, Cristina Viani, Laura Reilly, Richard B. Trinity Centre for Bioengineering School of Engineering Trinity College University of Dublin Dublin 2 Ireland National Cochlear Implant Program Beaumont Hospital Dublin 9 Ireland

ISBN: (纸本)9781538619162

Localizing sounds in our environment is a fundamental perceptual ability. However, methods to assess sound localization ability are often cumbersome, requiring large speaker array systems. In adults with sensorineural hearing loss who are fitted with cochlear implant (CIs), sound localization is known to improve when bilateral CIs are used compared to a single CI. This study proposes a portable virtual reality (VR) tool for measuring sound localization in bilateral cochlear implant (CI) users. Head related transfer functions (HRTFs) were used to replicate 3-dimensional sounds delivered to the users via headphones or a direct connect (DC) CI audio cable. Users wearing the VR headset were then instructed to turn and face these sound sources. From measurements of head position and velocity, objective measures of accuracy were derived. Pilot testing of the device was conducted with 4 bilateral CI participants and 12 normal hearing (NH) participants. Results showed that NH listeners performed better than CI users in all metrics. Bilateral CI users performed above chance level when presented with sounds to their first implanted ear only or to both implants simultaneously. Compared to previously reported localization studies, NH listeners demonstrated lower performance using this VR system. This study provides a foundation for objective sound localization testing in bilateral CI users in a clinical setting. © 2017 IEEE.

关键词： Cochlear implants

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Corrigendum to "Nitric oxide biosensor uncovers diminished ferrous iron-dependency of cultured cells adapted to physiological oxygen levels" [Redox Biol. 53 (2022) 102319]

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Redox biology 2022年 54卷 102364页

作者： Gulsah Sevimli Matthew J Smith Tuba Akgul Caglar Şükriye Bilir Melike Secilmis Hamza Y Altun Esra N Yigit Fan Yang Thomas P Keeley Roland Malli Gürkan Öztürk Giovanni E Mann Emrah Eroglu Molecular Biology Genetics and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey. King's British Heart Foundation Centre of Research Excellence School of Cardiovascular and Metabolic Medicine & Sciences Faculty of Life Sciences & Medicine King's College London 150 Stamford Street London SE1 9NH UK. Molecular Biology Genetics and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul Turkey. Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul Turkey Department of Biotechnology Gebze Technical University Kocaeli Turkey. Target Discovery Institute University of Oxford Oxford OX3 7FZ UK. Molecular Biology and Biochemistry Gottfried Schatz Research Center Medical University of Graz 8010 Graz Austria BioTechMed Graz Mozartgasse 12/II 8010 Graz Austria. Physiology Department International School of Medicine Istanbul Medipol University Istanbul Turkey. King's British Heart Foundation Centre of Research Excellence School of Cardiovascular and Metabolic Medicine & Sciences Faculty of Life Sciences & Medicine King's College London 150 Stamford Street London SE1 9NH UK. Electronic address: giovanni.mann@kcl.ac.uk. Molecular Biology and Biochemistry Gottfried Schatz Research Center Medical University of Graz 8010 Graz Austria. Electronic address: emrah.eroglu@sabanciuniv.edu.

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The control of brain network dynamics across diverse scales of space and time

arXiv

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arXiv 2019年

作者： Tang, Evelyn Baum, Graham L. Roalf, David R. Satterthwaite, Theodore D. Pasqualetti, Fabio Bassett, Danielle S. Department of Bioengineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Max Planck Institute for Dynamics and Self-Organization Göttingen37079 Germany Neuroscience Graduate Program Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Psychiatry Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Mechanical Engineering University of California Riverside RiversideCA92521 United States Department of Physics & Astronomy College of Arts & Sciences University of Pennsylvania PA19104 United States Department of Electrical & Systems Engineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Department of Neurology Perelman School of Medicine University of Pennsylvania PA19104 United States

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community based sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow time scales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast time scales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure. Copyright © 2019, The Authors. All rights reserved.

关键词： Brain

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Early Assessment of Acute Renal Rejection Post-transplantation: A Combined Imaging and Clinical Biomarkers Protocol

Early Assessment of Acute Renal Rejection Post-transplantati...

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2018 IEEE International Symposium on Signal Processing and Information Technology, ISSPIT 2018

作者： Shehata, Mohamed Taher, Fatma Ghazal, Mohammed Mahmoud, Ali Beache, Garth El-Ghar, Mohamed Abou Dwyer, Amy C. Elmaghraby, Adel El-Baz, Ayman BioImaging Lab Bioengineering Department University of Louisville LouisvilleKY United States College of Technological Innovation Zayed University Dubai United Arab Emirates Electrical and Computer Engineering Department Abu Dhabi University Abu Dhabi United Arab Emirates Radiology Department University of Louisville LouisvilleKY United States Radiology Department Urology and Nephrology Center Mansoura University Mansoura Egypt Kidney Disease Program University of Louisville LouisvilleKY United States Computer Engineering and Computer Science Department University of Louisville LouisvilleKY United States

ISBN: (纸本)9781538675687

Non-invasive evaluation of renal transplant function is crucial. Hence, a computer-assisted diagnostic (CAD) system is introduced in this paper to evaluate kidney function post-transplantation. The developed CAD system integrates clinical-based with diffusion weighted (DW) MR image-based biomarkers. The latter are derived from 3D DW-MRIs at multiple strengths and duration of the magnetic field (i.e. b-values). These DW-MRI scans were acquired at multiple geographical areas (Egypt and USA) using different scanner types (GE and Philips). The developed CAD system first segments kidneys using level-sets method and then estimates the DW-MRI image-markers, known as apparent diffusion coefficients (ADCs), from the segmented kidney. Then, the clinical biomarkers (serum creatinine and creatinine clearance) are integrated with the DW-MR image-markers (ADCs) resulted in new integrated markers known as integrated ADCs (IADCs). These IADCs are then used to construct cumulative distribution functions (CDFs) at multiple b-values. Finally, these markers (i.e. CDFs of the IADCs) are used to assess renal transplant status using different classifiers. Our CAD system demonstrates an almost consistent accuracy of 93%, sensitivity of 93%, and specificity of 92% in distinguishing acute rejection (AR) from non-rejection (NR) renal transplants, making the proposed diagnostic platform independent from the geographical area, scanner type, and classifier. These promising preliminary results are of high diagnostic accuracy and suggest that the developed CAD system might be noninvasively able to diagnose renal allograft status. © 2018 IEEE.

关键词： Creatinine

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

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Genome biology 2025年第1期26卷 31页

作者： Jacob Matthew Schreiber Carles A Boix Jin Wook Lee Hongyang Li Yuanfang Guan Chun-Chieh Chang Jen-Chien Chang Alex Hawkins-Hooker Bernhard Schölkopf Gabriele Schweikert Mateo Rojas Carulla Arif Canakoglu Francesco Guzzo Luca Nanni Marco Masseroli Mark James Carman Pietro Pinoli Chenyang Hong Kevin Y Yip Jefrey P Spence Sanjit Singh Batra Yun S Song Shaun Mahony Zheng Zhang Wuwei Tan Yang Shen Yuanfei Sun Minyi Shi Jessika Adrian Richard S Sandstrom Nina P Farrell Jessica M Halow Kristen Lee Lixia Jiang Xinqiong Yang Charles B Epstein J Seth Strattan Bradley E Bernstein Michael P Snyder Manolis Kellis William S Noble Anshul Bharat Kundaje Department of Genetics Stanford University Stanford CA USA. jmschreiber91@***. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Department of Genetics Stanford University Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Research and Development DeepSeq.AI San Francisco CA USA. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department of Empirical Inference Max Planck Institute for Intelligent Systems Stuttgart Germany. School of Life Sciences University of Dundee Dundee UK. Department of Electronics Information and Bioengineering Politecnico Di Milano Milan Italy. Department of Computational Biology University of Lausanne Lausanne Switzerland. Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong. Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Statistics University of California Berkeley Berkeley CA USA. Department of Biochemistry & Molecular Biology Center for Eukaryotic Gene Regulation Pennsylvania State University University Park PA USA. Department of Statistics Pennsylvania State University University Park PA USA. Department of Electrical and Computer Engineering Texas A&M University College Station TX USA. Altius Institute Seattle WA USA. Epigenomics Program The Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Computer Science Stanford University Stanford CA USA.

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