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LC-MS analysis: Mini review frequently used open source softwares 6

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LC-MS analysis: Mini review frequently used open source soft...

6th International Conference on Information Technology, computer and Electrical Engineering, ICITACEE 2019

作者： Binanto, Iwan Warnars, Harco Leslie Hendric Spits Sianipar, Nesti Fronika Abbas, Bahtiar Saleh Sanata Dharma University Informatics Department Yogyakarta Indonesia Bina Nusantara University BINUS Graduate Program Doctor Computer Science Computer Science Department Jakarta11480 Indonesia Research Interest Group Biotechnology Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781728126890

This paper provides information about open source softwares that most often used as a tool to analyze data generated from the Liquid chromatography-mass spectrometer (LC-MS) instrument and including a little discussion about how LC-MS works. LC-MS consists of Liquid Chromatography and Mass Spectrometer analytical instruments. This device extensively used in Metabolomics, because it provides more comprehensive information about the metabolites. It also shows the breadth of the diversity of chemical compounds in metabolites that make difficult and time-consuming to identification of metabolite's structures. This is an obstacle in efficient and accurate identification. So, many open source softwares developed to simplify and speed up the analysis and interpretation of LC-MS result. There are popular open source softwares. We compiling mini review of this open source softwares. The conclusion is open source softwares quite helpful in terms of data analysis and interpretation of compounds contained, but no one has provided a single interpretation, still need experts for reliable interpretation. © 2019 IEEE.

关键词： Liquid chromatography

Question-Answering System Extracts Information on Injection Drug Use from Clinical Notes

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arXiv 2023年

作者： Mahbub, Maria Goethert, Ian Danciu, Ioana Knight, Kathryn Srinivasan, Sudarshan Tamang, Suzanne Rozenberg-Ben-Dror, Karine Solares, Hugo Martins, Susana Trafton, Jodie Begoli, Edmon Peterson, Gregory D. Cyber Resilience and Intelligence Division Oak Ridge National Laboratory Oak RidgeTN United States Information Technology Services Division Oak Ridge National Laboratory Oak RidgeTN United States Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN United States Department of Biomedical Informatics Vanderbilt University NashvilleTN United States Program Evaluation and Resource Center Office of Mental Health and Suicide Prevention Department of Veterans Affairs United States Department of Medicine Stanford University School of Medicine StanfordCA United States Veterans Affairs Great Lakes Health Care System WestchesterIL United States Department of Electrical Engineering and Computer Science University of Tennessee Knoxville KnoxvilleTN United States

Background: Injection drug use (IDU) is a dangerous health behavior that increases mortality and morbidity. Identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no International Classification of Disease (ICD) code and the only place IDU information can be indicated is unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods: To address this gap in clinical information, we design and demonstrate a question-answering (QA) framework to extract information on IDU from clinical notes. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We utilize 2323 clinical notes of 1145 patients sourced from the VA Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information on temporally out-of-distribution data. Results: Here we show that for a strict match between gold-standard and predicted answers, the QA model achieves 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions: Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care. © 2023, CC BY-NC-ND.

关键词： Data warehouses

Comprehensive investigation of proteoglycan gene expression in breast cancer: Discovery of a unique proteoglycan gene signature linked to the malignant phenotype

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Proteoglycan research

Proteoglycan research 2025年第1期3卷 e70014页

作者： Simone Buraschi Gabriel Pascal Federico Liberatore Renato V Iozzo Department of Pathology and Genomic Medicine and the Translational Cellular Oncology Program Sidney Kimmel Cancer Center Sidney Kimmel Medical College at Thomas Jefferson University Philadelphia PA 19107 USA. School of Computer Science and Informatics Cardiff University Cardiff CF24 4AG UK.

Solid tumors present a formidable challenge in oncology, necessitating innovative approaches to improve therapeutic outcomes. Proteoglycans, multifaceted molecules within the tumor microenvironment, have garnered attention due to their diverse roles in cancer progression. Their unique ability to interact with specific membrane receptors, growth factors, and cytokines provides a promising avenue for the development of recombinant proteoglycan-based therapies that could enhance the precision and efficacy of cancer treatment. In this study, we performed a comprehensive analysis of the proteoglycan gene landscape in human breast carcinomas. Leveraging the available wealth of genomic and clinical data regarding gene expression in breast carcinoma and using a machine learning model, we identified a unique gene expression signature composed of five proteoglycans differentially modulated in the tumor tissue: Syndecan-1 and asporin (upregulated) and decorin, PRELP and podocan (downregulated). Additional query of the breast carcinoma data revealed that serglycin, previously shown to be increased in breast carcinoma patients and mouse models and to correlate with a poor prognosis, was indeed decreased in the vast majority of breast cancer patients and its levels inversely correlated with tumor progression and invasion. This proteoglycan gene signature could provide novel diagnostic capabilities in breast cancer biology and highlights the need for further utilization of publicly available datasets for the clinical validation of preclinical experimental results.

关键词： PRELP Proteoglycan gene signature asporin decorin podocan syndecan-1

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

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arXiv 2023年

作者： Lekadir, Karim Feragen, Aasa Fofanah, Abdul Joseph Frangi, Alejandro F. Buyx, Alena Emelie, Anais Lara, Andrea Porras, Antonio R. Chan, An-Wen Navarro, Arcadi Glocker, Ben Botwe, Benard O. Khanal, Bishesh Beger, Brigit Wu, Carol C. Cintas, Celia Langlotz, Curtis P. Rueckert, Daniel Mzurikwao, Deogratias Fotiadis, Dimitrios I. Zhussupov, Doszhan Ferrante, Enzo Meijering, Erik Weicken, Eva González, Fabio A. Asselbergs, Folkert W. Prior, Fred Krestin, Gabriel P. Collins, Gary S. Tegenaw, Geletaw S. Kaissis, Georgios Misuraca, Gianluca Tsakou, Gianna Dwivedi, Girish Kondylakis, Haridimos Jayakody, Harsha Woodruf, Henry C. Mayer, Horst Joachim Aerts, Hugo JWL Walsh, Ian Chouvarda, Ioanna Buvat, Irène Tributsch, Isabell Rekik, Islem Duncan, James Kalpathy-Cramer, Jayashree Zahir, Jihad Park, Jinah Mongan, John Gichoya, Judy W. Schnabel, Julia A. Kushibar, Kaisar Riklund, Katrine Mori, Kensaku Marias, Kostas Amugongo, Lameck M. Fromont, Lauren A. Maier-Hein, Lena Alberich, Leonor Cerdá Rittner, Leticia Phiri, Lighton Marrakchi-Kacem, Linda Donoso-Bach, Lluís Martí-Bonmatí, Luis Cardoso, M. Jorge Bobowicz, Maciej Shabani, Mahsa Tsiknakis, Manolis Zuluaga, Maria A. Bielikova, Maria Fritzsche, Marie-Christine Camacho, Marina Linguraru, Marius George Wenzel, Markus De Bruijne, Marleen Tolsgaard, Martin G. Ghassemi, Marzyeh Ashrafuzzaman, Md Goisauf, Melanie Yaqub, Mohammad Abadía, Mónica Cano Mahmoud, Mukhtar M.E. Elattar, Mustafa Rieke, Nicola Papanikolaou, Nikolaos Lazrak, Noussair Díaz, Oliver Salvado, Olivier Pujol, Oriol Sall, Ousmane Guevara, Pamela Gordebeke, Peter Lambin, Philippe Brown, Pieta Abolmaesumi, Purang Dou, Qi Lu, Qinghua Osuala, Richard Nakasi, Rose Zhou, S. Kevin Napel, Sandy Colantonio, Sara Albarqouni, Shadi Joshi, Smriti Carter, Stacy Klein, Stefan Petersen, Steffen E. Aussó, Susanna Awate, Suyash Raviv, Tammy Riklin Cook, Tessa Mutsvangwa, Tinashe E.M. Rogers, Wendy A. Niessen, Wiro J. Puig-Bosch, Xènia Zeng, Yi Mohammed, Yunusa G. Aquino, Yves Saint James Salahuddin, Zohaib Starmans, Martijn P.A. Department de Matemàtiques i Informàtica Universitat de Barcelona Barcelona Spain Barcelona Spain DTU Compute Technical University of Denmark Kgs Lyngby Denmark Department of Mathematics and Computer Science Faculty of Science and Technology Milton Margai Technical University Freetown Sierra Leone Center for Computational Imaging & Simulation Technologies in Biomedicine Schools of Computing and Medicine University of Leeds Leeds United Kingdom Cardiovascular Science and Electronic Engineering Departments KU Leuven Leuven Belgium Institute of History and Ethics in Medicine Technical University of Munich Munich Germany Faculty of Engineering of Systems Informatics and Sciences of Computing Galileo University Guatemala City Guatemala Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Anschutz Medical Campus AuroraCO United States Department of Medicine Women’s College Research Institute University of Toronto Toronto Canada Universitat Pompeu Fabra BarcelonaBeta Brain Research Center Barcelona Spain Department of Computing Imperial College London London United Kingdom School of Biomedical & Allied Health Sciences University of Ghana Accra Ghana Department of Midwifery & Radiography School of Health & Psychological Sciences City University of London United Kingdom Kathmandu Nepal European Heart Network Brussels Belgium Department of Thoracic Imaging University of Texas MD Anderson Cancer Center Houston United States IBM Research Africa Nairobi Kenya Departments of Radiology Medicine and Biomedical Data Science Stanford University School of Medicine Stanford United States Institute for AI and Informatics in Medicine Klinikum rechts der Isar Technical University Munich Munich Germany Department of Computing Imperial College London London United Kingdom Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania United Republic of Ioannina Greece Almaty AI Lab Almaty Kazakhstan

Background: Despite major advances in artificial intelligence (AI) research for healthcare, the deployment and adoption of AI technologies remain limited in clinical practice. In recent years, concerns have been raised about the clinical, technical, ethical and legal risks associated with healthcare AI. To increase adoption in the real world, it is essential that AI technologies are trusted and accepted by patients, clinicians, health organisations and authorities. This paper describes the FUTURE-AI framework as the first international consensus guideline for trustworthy AI in healthcare. Methods: The FUTURE-AI consortium was founded in 2021 and now comprises 117 interdisciplinary experts from 50 countries representing all continents, including AI scientists, clinical researchers, biomedical ethicists, and social scientists. Over a two-year period, the consortium established guiding principles and best practices for trustworthy and deployable AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. Findings: The FUTURE-AI framework was established based on six guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 30 best practices were defined, addressing technical, clinical, socio-ethical and legal dimensions of trustworthy AI. The recommendations cover the entire lifecycle of healthcare AI, from design, development and validation to regulation, deployment, and monitoring. Interpretation: FUTURE-AI is a structured, risk-informed framework which provides guidance for constructing healthcare AI tools that will be trusted, deployed and adopted in real-world clinical practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of healthcare AI. Copyright © 2023, The Authors. All rights

关键词： Clinical research

Literature Review of Religion Video Game

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Literature Review of Religion Video Game

2019 International Congress on Applied Information Technology, AIT 2019

作者： Wibawa, Setya Chendra Rahayu, Yuni Sri Wrahatnolo, Tri Vindy, V. Warnars, Harco Leslie Hendric Spits Hashimoto, Kiyota Universitas Negeri Surabaya Jawa Timur Informatics Department 60213 Indonesia Universitas Negeri Surabaya Jawa Timur Biology Department 60213 Indonesia Universitas Negeri Surabaya Jawa Timur Electrical Engineering Department 60213 Indonesia Game Application Technology Program School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Faculty of Technology and Environment Prince Songkla University Thailand

ISBN: (纸本)9781728158624

In this current digital era, the video game is favorite especially among young people. Besides widely known as a form of entertainment, some messages or lessons can be learned from a video game that may affect the players. Conscious or unconscious, games have influenced many sectors of life, and it has been recognized as a serious game and no exception to religion. Human as a living creature, like or dislike or even as an atheist should believe with something out there, and religion is as a medium which connects human with something out there. The game as a representation of entertaining, intelligent application will represent joy and happiness in human life's activities, and inevitably games will influence human religion. In the end, religion game will help the human to increase their faith in those their belief based on their religion. Similar to Information Technology which is implemented in business to increase revenue, the game as an entertaining intelligent application will increase human's faith. One kind of video game that provides it is religion video games which are the result of the incorporation between religion and video games. In this paper, we do a literature review about religion video games. We try to summarize how religious elements can be incorporated into a video game which can be seen from the parts, components, and approaches of the religion video game itself. We also try to summarize the positive side and controversies in religion video games. © 2019 IEEE.

关键词： Serious games

Explanation by progressive exaggeration

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arXiv 2019年

作者： Singla, Sumedha Pollack, Brian Chen, Junxiang Batmanghelich, Kayhan Department of Computer Science University of Pittsburgh Department of Biomedical Informatics University of Pittsburgh Department of Biomedical Informatics Department of Computer Science Intelligent Systems Program University of Pittsburgh

As machine learning methods see greater adoption and implementation in high stakes applications such as medical image diagnosis, the need for model interpretability and explanation has become more critical. Classical approaches that assess feature importance (e.g., saliency maps) do not explain how and why a particular region of an image is relevant to the prediction. We propose a method that explains the outcome of a classification black-box by gradually exaggerating the semantic effect of a given class. Given a query input to a classifier, our method produces a progressive set of plausible variations of that query, which gradually change the posterior probability from its original class to its negation. These counter-factually generated samples preserve features unrelated to the classification decision, such that a user can employ our method as a "tuning knob" to traverse a data manifold while crossing the decision boundary. Our method is model agnostic and only requires the output value and gradient of the predictor with respect to its input. Copyright © 2019, The Authors. All rights reserved.

关键词： Semantics

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

Ramadhan short-term electric load: A hybrid model of cycle spinning wavelet and group method data handling (CSW-GMDH)

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IAENG International Journal of Computer Science

IAENG International Journal of computer science 2019年第4期46卷 670页

作者： Caraka, Rezzy Eko Chen, Rung Ching Toharudin, Toni Pardamean, Bens Bakar, Sakhinah Abu Yasin, Hasbi College of Informatics Chaoyang University of Technology Taichung City41349 Taiwan Department of Statistics Padjadjaran University Bandung Indonesia College of Informatics Chaoyang University of Technology Taichung City41349 Indonesia Bioinformatics Data Science Research Center Bina Nusantara University Indonesia BINUS Graduate Program-Master of Computer Science Bina Nusantara University. Indonesia School of Mathematical Sciences FST The National University of Malaysia Malaysia Department of Statistics Diponegoro University Semarang Indonesia

In general, performing a nonlinearity time series analysis in the modeling of data can reach a robust and increase the quality of the results. Wavelet methods have successfully been applied in a great variety of applications for modeling also forecasting. Wavelet Transform divided into two categories. There is continuous wavelet (CWT) and a discrete wavelet transform (DWT). Cycle spinning unlike the discrete wavelet transform (DWT), is highly redundant, non-orthogonal, also defined naturally for all sample sizes. There is a Group Method of Data Handling (GMDH) algorithm, which is a multivariate analysis method can be used in modeling and identifying uncertainty on linear also nonlinearity systems. In this paper, we aim to explain the combination of A-Trous wavelet transforms applied on cycle spinning and group method of data handling (GMDH) in data of short-term electric load holy month of Ramadhan from 2014 to 2015. © 2019, International Association of Engineers.

关键词： Discrete wavelet transforms

D-SRGAN: DEM Super-Resolution with Generative Adversarial Networks

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arXiv 2020年

作者： Demiray, Bekir Z. Sit, Muhammed Demir, Ibrahim Department of Computer Science University of Iowa Iowa City United States Graduate Program in Informatics University of Iowa Iowa City United States Department of Civil & Environmental Engineering University of Iowa Iowa City United States

—LIDAR (light detection and ranging) is an optical remote-sensing technique that measures the distance between sensor and object, and the reflected energy from the object. Over the years, LIDAR data has been used as the primary source of Digital Elevation Models (DEMs). DEMs have been used in a variety of applications like road extraction, hydrological modeling, flood mapping, and surface analysis. A number of studies in flooding suggest the usage of high- resolution DEMs as inputs in the applications improve the overall reliability and accuracy. Despite the importance of high-resolution DEM, many areas in the United States and the world do not have access to high-resolution DEM due to technological limitations or the cost of the data collection. With recent development in Graphical Processing Units (GPU) and novel algorithms, deep learning techniques have become attractive to researchers for their performance in learning features from high-resolution datasets. Numerous new methods have been proposed such as Generative Adversarial Networks (GANs) to create intelligent models that correct and augment large-scale datasets. In this paper, a GAN based model is developed and evaluated, inspired by single image super-resolution methods, to increase the spatial resolution of a given DEM dataset up to 4 times without additional information related to data. Copyright © 2020, The Authors. All rights reserved.

关键词： Generative adversarial networks