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Stratifying vascular disease patients into homogeneous subgroups using machine learning and FLAIR MRI biomarkers

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Npj imaging

Npj imaging 2024年第1期2卷 56页

作者： Karissa Chan Corinne Fischer Pejman Jabehdar Maralani Sandra E Black Alan R Moody April Khademi Department of Electrical Computer and Biomedical Engineering Toronto Metropolitan University Toronto ON Canada. Institute for Biomedical Engineering Science Tech (iBEST) a Partnership between St. Michael's Hospital and Toronto Metropolitan University Toronto ON Canada. Keenan Research Center for Biomedical Science St. Michael's Hospital Unity Health Network Toronto ON Canada. Department of Medical Imaging University of Toronto Toronto ON Canada. Institute of Medical Science University of Toronto Toronto ON Canada. Horvitz Brain Sciences Research Program Sunnybrook Research Institute Toronto ON Canada. Division of Neurology Department of Medicine Sunnybrook Health Sciences Centre Toronto ON Canada. L.C. Campbell Cognitive Neurology Research Unit Sunnybrook Health Sciences Centre Toronto ON Canada. Vector Institute for Artificial Intelligence Toronto ON Canada.

This study proposes a framework to stratify vascular disease patients based on brain health and cerebrovascular disease (CVD) risk using regional FLAIR biomarkers. Intensity and texture biomarkers were extracted from FLAIR volumes of 379 atherosclerosis patients. K-Means clustering identified five homogeneous subgroups. The 15 most important biomarkers for subgroup differentiation, identified via Random Forest classification, were used to generate biomarker profiles. ANOVA tests showed age and white matter lesion volume were significantly ( < 0.05) different across subgroups, while Fisher's tests revealed significant ( < 0.05) differences in the prevalence of several vascular risk factors across subgroup. Based on biomarker and clinical profiles, Subgroup 4 was characterized with neurodegeneration unrelated to CVD, Subgroup 3 identified patients with high CVD risk requiring aggressive intervention, and Subgroups 1, 2, and 5 identified patients with varying levels of moderate risk, suitable for long-term lifestyle interventions. This study supports personalized treatment and risk stratification based on FLAIR biomarkers.

关键词： Brain imaging Image processing

Secure state estimation and control for cyber security of AC microgirds

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arXiv 2019年

作者： Fooladivanda, Dariush Hu, Qie Chang, Young Hwan Sauer, Peter W. Department of Mechanical and Aerospace Engineering University of California San Diego United States Department of Electrical Engineering and Computer Sciences University of California Berkeley United States Department of Biomedical Engineering and Computational Biology Program Oregon Health and Science University United States Department of Electrical and Computer Engineering University of Illinois Urbana-Champaign United States

A timely, accurate, and secure dynamic state estimation is needed for reliable monitoring and efficient control of microgrids. The synchrophasor technology enables us to obtain synchronized measurements in real-time and to develop dynamic state estimators for real-time monitoring and control of microgrids. In this study, we consider an AC microgrid comprising several synchronous generators and inverter-interface power supplies, and focus on securely estimating the dynamic states of the microgrid from a set of corrupted data. We propose a dynamic state estimator which enables the microgrid operator to reconstruct the dynamic states of the microgrid from a set of corrupted data. Finally, we consider an AC microgrid with the same topology as the IEEE 33-bus distribution system, and numerically show that the proposed secure estimation algorithm can accurately reconstruct the attack signals. Copyright © 2019, The Authors. All rights reserved.

关键词： State estimation

Epigenetic factor competition reshapes the EMT landscape

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arXiv 2022年

作者： Ali Al-Radhawi, M. Tripathi, Shubham Zhang, Yun Sontag, Eduardo D. Levine, Herbert Department of Electrical and Computer Engineering Northeastern University BostonMA02115 United States Center for Theoretical Biological Physics Northeastern University BostonMA02115 United States PhD Program in Systems Synthetic and Physical Biology Rice University HoustonTX77005 United States Whitehead Institute for Biomedical Research CambridgeMA02142 United States Department of Bioengineering Northeastern University BostonMA02115 United States Department of Physics Northeastern University BostonMA02115 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States State Key Laboratory of Molecular Oncology National Cancer Center National Clinical Research Center for Cancer Cancer Hospital Chinese Academy of Medical Sciences Peking Union Medical College Beijing100021 China

The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions. © 2022, CC BY-NC-ND.

关键词： Transcription factors

Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

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SSRN

SSRN 2024年

作者： Saad Menezes, Maria Clara Hoffman, Alexander F. Tan, Amelia L.M. Nalbandyan, Mariné Omenn, Gilbert S. Mazzotti, Diego R. Hernández-Arango, Alejandro Visweswaran, Shyam Venkatesh, Shruthi Mandl, Kenneth D. Bourgeois, Florence T. Lee, James W.K. Makmur, Andrew Hanauer, David A. Semanik, Michael G. Kerivan, Lauren T. Hill, Terra Forero, Julian Restrepo Castro, Carlos Andrés C.R. Vigna, Matteo Ceriana, Piero Abu-El-rub, Noor Avillach, Paul Bellazzi, Riccardo Callaci, Thomas Gutiérrez-Sacristán, Alba Malovini, Alberto Mathew, Jomol P. Morris, Michele Murthy, Venkatesh Parimbelli, Enea Patel, Lav P. Sáez, Carlos Samayamuthu, Malarkodi Jebathilagam Thompson, Jeffrey A. Tibollo, Valentina Xia, Zongqi Kohane, Isaac S. Harvard Medical School Department of Biomedical Informatics 10 Shattuck Street BostonMA02115 United States School of Medicine and Public Health University of Wisconsin-Madison Office of Informatics and Information Technology 750 Highland Ave MadisonWI53705 United States University of Michigan Department of Computational Medicine & Bioinformatics Internal Medicine Human Genetics Environmental Health 100 Washtenaw Avenue Ann ArborMI48109 United States University of Kansas Medical Center Division of Medical Informatics Division of Pulmonary Critical Care and Sleep Medicine Department of Internal Medicine 3901 Rainbow Blvd Kansas CityKS66160 United States University of Antioquia Hospital Alma Máter de Antioquia Department of Internal Medicine Calle 64 N°51 D - 154 Medellín Colombia University of Pittsburgh Department of Biomedical Informatics 5607 Baum Blvd PittsburghPA15206 United States University of Pittsburgh Department of Neurology 3501 5th Avenue PittsburghPA15206 United States Boston Children's Hospital Computational Health Informatics Program 300 Longwood Avenue BostonMA02115 United States Boston Children's Hospital Department of Pediatrics 300 Longwood Avenue BostonMA02115 United States National University Health System Department of Surgery 1E Kent Ridge Rd Singapore119228 Singapore National University Health System Department of Diagnostic Imaging 1E Kent Ridge Rd Singapore119228 Singapore University of Michigan Department of Learning Health Sciences NCRC 100 2800 Plymouth Road Ann ArborMI48109 United States University of Kansas Medical Center Department of Surgery 3901 Rainbow Blvd Kansas CityKS66160 United States Istituti Clinici Scientifici Maugeri IRCCS Respiratory rehabilitation unit Via Maugeri 10 Pavia27100 Italy University of Kansas Medical Center 3901 Rainbow Blvd Kansas CityKS66160 United States University of Pavia Department of Electrical Computer and Biomedical Engineering via Ferrata 5 Pavia2710

Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the United States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati

关键词： Medical computing

Bright high-purity quantum emitters in aluminium nitride integrated photonics

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arXiv 2020年

作者： Lu, Tsung-Ju Lienhard, Benjamin Jeong, Kwang-Yong Moon, Hyowon Iranmanesh, Ava Grosso, Gabriele Englund, Dirk Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Photonics Initiative Advanced Science Research Center and Physics Program Graduate Center City University of New York New YorkNY10031 United States Department of Physics Korea University Seoul02841 Korea Republic of

Solid-state quantum emitters (QEs) are fundamental in photonic-based quantum information processing. There is strong interest to develop high-quality QEs in III-nitride semiconductors because of their sophisticated manufacturing driven by large and growing applications in optoelectronics, high voltage power transistors, and microwave amplifiers. Here, we report the generation and direct integration of QEs in an aluminium nitride-based photonic integrated circuit platform. For individual waveguide-integrated QEs, we measure an off-chip count rate exceeding 6 × 104 counts per second (cps) (saturation rate > 8.6 × 104 cps). In an unpatterned thin-film sample, we measure antibunching with g(2)(0) ~ 0.05 and photon count rates exceeding 8 × 105 cps (saturation rate > 1 × 106 cps). Although spin and detailed optical linewidth measurements are left for future work, these results already show the potential for high-quality QEs monolithically integrated in a wide range of III-nitride device technologies that would enable new quantum device opportunities and industrial scalability. Copyright © 2020, The Authors. All rights reserved.

关键词： III-V semiconductors

Two-dimensional pentagonal material Penta-PdPSe: A first-principle study

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arXiv 2021年

作者： Bafekry, Asadolah Fadlallah, M.M. Faraji, M. Shafique, A. Jappor, H.R. Abdolhoseini Sarsari, I. Ang, Yee Sin Ghergherehchi, M. Department of Radiation Application Shahid Beheshti University Tehran*** Iran Department of Physics Faculty of Science Benha University Benha13518 Egypt Micro and Nanotechnology Graduate Program TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu Ankara06560 Turkey Department of Physics Lahore University of Management Sciences Lahore Pakistan Department of Physics College of Education for Pure Sciences University of Babylon Hilla Iraq Department of Physics Isfahan University of Technology Isfahan84156-83111 Iran Cluster Singapore University of Technology and Design Singapore487372 Singapore Department of Electrical and Computer Engineering Sungkyunkwan University Suwon16419 Korea Republic of

Low-symmetry Penta-PdPSe with intrinsic in-plane anisotropy synthesized successfully [P. Li et al., Adv. Mater., 2102541 (2021)]. Motivated by this experimental discovery, we investigate the structural, mechanical, electronic, optical and thermoelectric properties of PdPSe monolayer via density functional theory calculations. The phonon dispersion, molecular dynamics simulation, the cohesive energy mechanical properties of the penta-PdPSe monolayer is verified to confirm its stability. The phonon spectrum represents a striking gap between the high-frequency and the low-frequency optical branches and an out-of-plane flexure mode with a quadratic dispersion in the long-wavelength limit. The Poisson’s ratio indicates that penta-PdPSe is a brittle monolayer. The pendaPdPSe monolayer is an indirect semiconductor with bandgap of 1.40 (2.07) eV using PBE (HSE06) functional. Optical properties simulation suggests that PdPSe is capable of absorbing a substantial range of visible to ultraviolet light. Band alignment analysis also reveals the compatibility of PdPSe for water splitting photocatalysis application. By combining the electrical and thermal transport properties of PdPSe, we show that a high PF is achievable at room temperature, thus making PdPSe a candidate material for thermoelectric application. Our findings reveal the strong potential of penta-PdPSe monolayer for a wide array of applications, including optoelectronic, water splitting and thermoelectric device applications. © 2021, CC BY.

关键词： Monolayers

Consensus Recommendations for Hyperpolarized [1‐13C]pyruvate MRI Multi-center Human Studies

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arXiv 2025年

作者： Punwani, Shonit Larson, Peder E.Z. Laustsen, Christoffer VanderMeulen, Jan Ardenkjær-Larsen, Jan Henrik Autry, Adam W. Bankson, James A. Bernard, Jenna Bok, Robert Bertelsen, Lotte Bonde Che, Jenny Chen, Albert P. Chowdhury, Rafat Comment, Arnaud Cunningham, Charles H. Dang, Duy Gallagher, Ferdia A. Gaunt, Adam Gong, Yangcan Gordon, Jeremy W. Grimmer, Ashley Grist, James Hansen, Esben Søvsø Szocska Lerche, Mathilde Hauge Hesketh, Richard L. Hoevener, Jan-Bernd Hsieh, Ching-Yi Keshari, Kayvan R. Kozerke, Sebastian Lanz, Titus Mayer, Dirk McLean, Mary Park, Jae Mo Slater, Jim Tyler, Damian Vanderheyden, Jean-Luc von Morze, Cornelius Zaccagna, Fulvio Zaha, Vlad Xu, Duan Vigneron, Daniel Department of Radiology University College London Hospital NHS Foundation Trust London United Kingdom Centre for Medical Imaging University College London London United Kingdom Department of Radiology and Biomedical Imaging University of California San FranciscoCA94143 United States The MR Research Center Department of Clinical Medicine Aarhus University Aarhus Denmark Department of Health Services Research & Policy London School of Hygiene & Tropical Medicine London United Kingdom Department of Imaging Physics The University of Texas MD Anderson Cancer Center HoustonTX United States GE Healthcare TorontoON Canada GE HealthCare Pollards Wood Nightingales Lane Chalfont St Giles BuckinghamshireHP8 4SP United Kingdom Physical Sciences Sunnybrook Research Institute TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Department of Radiology University of Cambridge Cambridge University Hospitals NHS Foundation Trust Cambridge United Kingdom GE Healthcare San FranciscoCA United States Oxford Centre for Clinical Magnetic Resonance Research University of Oxford Oxford United Kingdom Department of Health Technology Technical University of Denmark Kgs. Lyngby2800 Denmark Cancer Research UK Cambridge Institute University of Cambridge Cambridge United Kingdom Section Biomedical Imaging University Hospital Schleswig-Holstein Kiel University Campus Kiel Germany Research Center for Radiation Medicine Chang Gung University Taoyuan Taiwan Department of Medical Imaging and Intervention Chang Gung Memorial Hospital at Linkou Taoyuan Taiwan Department of Radiology Memorial Sloan Kettering Cancer Center New YorkNY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New YorkNY United States Institute for Biomedical Engineering University and ETH Zurich Zurich Switzerland RAPID Biomedical GmbH Rimpar97222 Germany Department of Diagnostic Radiology and Nuclear Medicine University of Mary

Magnetic resonance imaging of hyperpolarized (HP) [1-13C]pyruvate allows in-vivo assessment of metabolism and has translated into human studies across diseases at 15 centers worldwide. Consensus on best practice for multi-center studies is required to develop clinical applications. This paper presents the results of a 2-round formal consensus building exercise carried out by experts with HP [1-13C]pyruvate human study experience. Twenty-nine participants from 13 sites brought together expertise in pharmacy methods, MR physics, translational imaging, and data-analysis;with the goal of providing recommendations and best practice statements on conduct of multi-center human studies of HP [1-13C]pyruvate MRI. Overall, the group reached consensus on approximately two-thirds of 246 statements in the questionnaire, covering ‘HP 13C-Pyruvate Preparation’, ‘MRI System Setup, Calibration, and Phantoms’, ‘Acquisition and Reconstruction’, and ‘Data Analysis and Quantification’. Consensus was present across categories, examples include that: (i) different HP pyruvate preparation methods could be used in human studies, but that the same release criteria have to be followed;(ii) site qualification and quality assurance must be performed with phantoms and that the same field strength must be used, but that the rest of the system setup and calibration methods could be determined by individual sites;(iii) the same pulse sequence and reconstruction methods were preferable, but the exact choice should be governed by the anatomical target;(iv) normalized metabolite area-under-curve (AUC) values and metabolite AUC were the preferred metabolism metrics. The work confirmed areas of consensus for multi-center study conduct and identified where further research is required to ascertain best practice. © 2025, CC BY.

关键词： Redundancy

Implementation of Augmented Reality in Pretend Play Therapy for Children with Autism Spectrum Disorder 3

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Implementation of Augmented Reality in Pretend Play Therapy ...

3rd International Conference on Computing and Applied Informatics 2018, ICCAI 2018

作者： Syahputra, M.F. Angkasih, A.P. Purnamawati, S. Andayani, U. Abdullah, D. Sriadhi, S. Iskandar, A. Rosida, T.M. Fitriany, J. Sari, I.N. Utama, M.D. Nanuru, R.F. Department of Information Technology Faculty of Computer Science and Information Technology Universitas Sumatera Utara Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Utara Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Informatics Engineering STMIK AKBA Makassar Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Pediatric Universitas Malikussaleh Aceh Utara Indonesia Departement of Social Science Education Program Post Graduate Program Universitas Kanjuruhan Malang Malang Indonesia Faculty of Social and Political Science Universitas Kristen Indonesia Maluku Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia

Autism Spectrum Disorder is a pervasive developmental disorder that will affect children in terms of interpersonal communication, social interaction, and imaginative levels in play. Many therapies to help the motor neuron performance is one of them Pretend Play. Pretend Play is a therapy that invites children in playing to demonstrate something else and tell how to use objects that are considered in the child's imagination. However, in the era of highly developed technology, many fields have used the Augmented Reality method as a visualization of various aspects. With this method researchers will present the therapeutic visualization of the block to 3D transportation tool that is useful for strengthening motor nerves and visual strength of the child. The system can run well during marker detection, marker movement, and 3D object display with the accuracy of precision angle and distance between virtual world with real world reach 100% with angle 0 at distance 31 cm and the maximum distance from the marker is 46 cm and the maximum angle is 30. © 2019 Published under licence by IOP Publishing Ltd.

关键词： Augmented reality

Short-Term Effects of a Therapeutic Diet on Biochemical Parameters in Hemodialysis Patients: A Randomized Crossover Trial

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Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation 2023年第6期33卷 731-739页

作者： Wan-Chuan Tsai Shih-Ping Hsu Yen-Ling Chiu Hon-Yen Wu Chia-Chin Luan Ju-Yeh Yang Mei-Fen Pai Cheng-Jui Lin Wan-Yu Lin Wen-Huei Sun Yu-Sen Peng Division of Nephrology Department of Internal Medicine Far Eastern Memorial Hospital New Taipei City Taiwan Center for General Education Lee-Ming Institute of Technology New Taipei City Taiwan. School of Life Science National Taiwan Normal University Taipei City Taiwan. Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan. Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei City Taiwan Faculty of Medicine School of Medicine National Yang-Ming University Taipei City Taiwan. Dietary Department Far Eastern Memorial Hospital New Taipei City Taiwan. Division of Nephrology Department of Internal Medicine Far Eastern Memorial Hospital New Taipei City Taiwan. Division of Nephrology Department of Internal Medicine Mackay Memorial Hospital Taipei City Taiwan Department of Medicine Mackay Medical College Taipei City Taiwan Mackay Junior College of Medicine Nursing and Management Taipei City Taiwan. Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei City Taiwan. Dietary Department Far Eastern Memorial Hospital New Taipei City Taiwan. Electronic address: 830636231@mail.femh.org.tw. Department of Applied Cosmetology Lee-Ming Institute of Technology New Taipei City Taiwan Department of Electrical Engineering Yuan Ze University Taoyuan City Taiwan. Electronic address: taan70@***.

OBJECTIVE:Although unhealthy diets exacerbate nutritional and metabolic derangements in patients with end-stage kidney disease (ESKD), how therapeutic diets that possess a variety of different dietary strategies acutely modify diverse biochemical parameters related to cardiovascular disease remains underexplored. METHODS:Thirty-three adults with end-stage kidney disease undergoing thrice-weekly hemodialysis participated in a randomized crossover trial comparing a therapeutic diet with their usual diets for 7 days, separated by a 4-week washout period. The therapeutic diet was characterized by adequate calorie and protein amounts, natural food ingredients with a low phosphorus-to-protein ratio, higher portions of plant-based food, and high fiber content. The primary outcome measure was the mean difference in the change-from-baseline intact fibroblast growth factor 23 (FGF23) level between the 2 diets. The other outcomes of interest included changes in mineral parameters, uremic toxins, and high-sensitivity C-reactive protein (hs-CRP) levels. RESULTS:Compared with the usual diet, the therapeutic diet lowered intact FGF23 levels (P = .001), decreased serum phosphate levels (P < .001), reduced intact parathyroid hormone (PTH) levels (P = .003), lowered C-terminal FGF23 levels (P = .03), increased serum calcium levels (P = .01), and tended to lower total indoxyl sulfate levels (P = .07) but had no significant effect on hs-CRP levels. Among these changes, reduction in serum phosphate level achieved in 2 days, modifications of intact PTH and calcium levels in 5 days, and reductions in intact and C-terminal FGF23 levels in 7 days of therapeutic diet intervention. CONCLUSION:Within the 1-week intervention period, the dialysis-specific therapeutic diet rapidly reversed mineral abnormalities and tended to decrease total indoxyl sulfate levels in patients undergoing hemodialysis but had no effect on inflammation. Future studies to assess the long-term effects of such therapeuti

关键词： FGF23 dialysis inflammation therapeutic diet uremic toxin