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Correction: Real-world effectiveness and safety of trastuzumab-deruxtecan in Japanese patients with HER2-positive advanced gastric cancer (EN-DEAVOR study)

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Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 2025年第1期28卷 62页

作者： Hisato Kawakami Koki Nakanishi Akitaka Makiyama Hirotaka Konishi Satoshi Morita Yukiya Narita Naotoshi Sugimoto Keiko Minashi Motohiro Imano Rin Inamoto Yasuhiro Kodera Hiroki Kume Keita Yamaguchi Wataru Hashimoto Kei Muro Department of Medical Oncology Kindai University Faculty of Medicine Osakasayama Japan. kawakami_h@med.kindai.ac.jp. Department of Gastroenterological Surgery Nagoya University Graduate School of Medicine Nagoya Japan. Cancer Center Gifu University Hospital Gifu Japan. Division of Digestive Surgery Kyoto Prefectural University of Medicine Kyoto Japan. Department of Biomedical Statistics and Bioinformatics Kyoto University Graduate School of Medicine Kyoto Japan. Department of Clinical Oncology Aichi Cancer Center Hospital Nagoya Japan. Department of Genetic Oncology Osaka International Cancer Institute Osaka Japan. Division of Gastroenterology Chiba Cancer Center Chiba Japan. Department of Surgery Kindai University Faculty of Medicine Osakasayama Japan. Department of Gastroenterology Saitama Cancer Center Saitama Japan. Oncology Medical Science Department I Daiichi Sankyo Co. Ltd. Tokyo Japan. Data Intelligence Department Daiichi Sankyo Co. Ltd. Tokyo Japan.

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A Design of Deep Learning Experimentation for Fruit Freshness Detection

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

作者： Febrian Valentino Tjeng Wawan Cenggoro Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480

Indonesia is a country with a tropical climate so that fruit and vegetable plants can grow easily in *** have many good nutrients such as vitamins, proteins and others. But the fruit also has a period where the fruit is said to be fresh *** this time there are still many fruit supplier companies that send fruit unfit for consumption due to lack of accuracy in the process of sorting the fruit when the fruit is taken from the plantation and the entry of other fruit into an improper packaging. Thus, it makes detecting food spoilage from the production stage to consumption is very important. We propose a design of computer vision-based technique usingdeep learning with the Convolutional Neural Network (CNN) model to detect fruit freshness. The specially designed CNN model is then evaluated with public datasets of fruits fresh and rotten for classification derived from Kaggle.

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

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Journal of proteome research 2023年第4期22卷 1024-1042页

作者： Gilbert S Omenn Lydie Lane Christopher M Overall Charles Pineau Nicolle H Packer Ileana M Cristea Cecilia Lindskog Susan T Weintraub Sandra Orchard Michael H A Roehrl Edouard Nice Siqi Liu Nuno Bandeira Yu-Ju Chen Tiannan Guo Ruedi Aebersold Robert L Moritz Eric W Deutsch University of Michigan Ann Arbor Michigan48109 United States. Institute for Systems Biology Seattle Washington98109 United States. CALIPHO Group SIB Swiss Institute of Bioinformatics and University of Geneva 1015Lausanne Switzerland. University of British Columbia Vancouver British ColumbiaV6T 1Z4 Canada. French Institute of Health and Medical Research 35042RENNESCedexFrance. Macquarie University Sydney New South Wales2109 Australia. Griffith University's Institute for Glycomics Sydney New South Wales2109 Australia. Princeton University Princeton New Jersey08544 United States. Uppsala University 752 36Uppsala Sweden. University of Texas Health Science Center-San Antonio San Antonio Texas78229-3900 United States. EMBL-EBI Hinxton CambridgeshireCB10 1SD United Kingdom. Memorial Sloan Kettering Cancer Center New York New York10065 United States. Monash University ClaytonVictoria3800 Australia. BGI Group Shenzhen518083 P. R. China. University of California San Diego La Jolla California92093 United States. National Taiwan University Academia Sinica Nankang Taipei11529 Taiwan. Westlake University Guomics Laboratory of Big Proteomic Data Hangzhou310024 ZhejiangProvinceP. R. China. Institute of Molecular Systems Biology in ETH Zurich 8092Zurich Switzerland.

The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

关键词： Biology and Disease-HPP (B/D-HPP) Grand Challenge Project Human Protein Atlas Human Proteome Project (HPP) Mass Spectrometry Interactive Virtual Environment (MassIVE) PeptideAtlas Ribo-Seq chromosome-centric HPP (C-HPP) missing proteins (MP) neXtProt protein existence (PE metrics) non-MS PE1 proteins small open reading frames (smORFs) uncharacterized protein existence 1 (uPE1)

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data Engineering Pipeline to Analyse Jakarta's Air Quality during COVID-19-Caused Lockdown Periods

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

作者： Reza Rahutomo Bens Pardamean Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Jakarta lifted up lockdown after passing more than 50 days of large-scale social activity restriction and initiated phase opening to new normal. To analyse Jakarta's air quality after passing lockdown, a pipeline of data engineering is needed. By acquiring time series data from ***, a time-series database system is developed with Python programming language and its fundamental libraries namely Pandas, NumPy, SQLite. After PM 2.5 data are pre-processed into average per-hour and grouped by applicable periods (pre-lockdown, lockdown, and phase opening), a pattern of PM 2.5 in South Jakarta is revealed by using data visualization library Matplotlib. The apex of PM 2.5 occurs earlier during lockdown (04:00) and phase opening (02:00) rather than when it was normal or pre-lockdown (08:00) even though the nadir of PM2.5 still occurs at the same time (16:00 – 17:00).

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Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

arXiv

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arXiv 2020年

作者： Schaller, David Geiß, Manuela Stadler, Peter F. Hellmuth, Marc Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Bioinformatics Group Department of Computer Science & Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Software Competence Center Hagenberg GmbH Softwarepark 21 HagenbergA-4232 Austria Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine at Leipzig University Universität Leipzig Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States School of Computing University of Leeds EC Stoner Building LeedsLS2 9JT United Kingdom

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the Reciprocal Best Match Graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the Best Match Graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique "augmented tree" that explains the BMG and identifies all u-fp edges in terms of overlapping sets of species in certain subtrees. The augmented tree can be constructed as a refinement of the unique least resolved tree of the BMG in polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology *** Codes 92-08, MSC 92D15, MSC 68R01 Copyright © 2020, The Authors. All rights reserved.

关键词： Forestry

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Prognostic factors and treatment response in HER2-positive gastric cancer patients receiving trastuzumab deruxtecan: secondary analysis of the EN-DEAVOR study

ESMO Gastrointestinal Oncology

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ESMO Gastrointestinal Oncology 2025年 8卷

作者： K. Nakanishi N. Sugimoto Y. Kodera H. Kawakami A. Makiyama H. Konishi S. Morita Y. Narita K. Minashi M. Imano R. Inamoto T. Nishina T. Kawakami M. Hagiwara H. Kume K. Yamaguchi W. Hashimoto K. Muro Department of Gastroenterological Surgery Nagoya University Graduate School of Medicine Nagoya Japan Department of Genetic Oncology Osaka International Cancer Institute Chuo-ku Osaka Japan NHO Nagoya Medical Center Nagoya Aichi Japan Department of Medical Oncology Kindai University Faculty of Medicine Osakasayama City Osaka Japan Department of Clinical Oncology Tohoku University Graduate School of Medicine Sendai Miyagi Japan Cancer Center Gifu University Hospital Gifu Japan Department of Surgery Kyoto Prefectural University of Medicine Kyoto Japan Department of Biomedical Statistics and Bioinformatics Kyoto University Graduate School of Medicine Yoshidakonoecho Kyoto Japan Department of Clinical Oncology Aichi Cancer Center Hospital Nagoya Aichi Japan Clinical Trial Promotion Department and Department of Gastroenterology Chiba Cancer Center Chiba Japan Department of Surgery Kindai University Faculty of Medicine Osakasayama Osaka Japan Department of Gastroenterology Saitama Cancer Center Saitama Japan Department of Gastrointestinal Medical Oncology NHO Shikoku Cancer Center Minamiumemotomachi Matsuyama Ehime Japan Division of Gastrointestinal Oncology Shizuoka Cancer Center Sunto-gun Shizuoka Japan Department of Surgery Nihonkai General Hospital Sakata Yamagata Japan Oncology Medical Science Department I Daiichi Sankyo Co. Ltd. Chuo City Tokyo Japan Data Intelligence Department Daiichi Sankyo Co. Ltd. Chuo City Tokyo Japan

Background EN-DEAVOR was a multi-institutional retrospective study evaluating the effectiveness and safety of trastuzumab deruxtecan (T-DXd) in gastric cancer patients. This secondary analysis investigated prognostic factors for real-world progression-free survival (rwPFS) and objective response rate (ORR) for T-DXd as third- or later-line treatment. Patients and methods Patients aged ≥20 years with histopathologically confirmed human epidermal growth factor receptor 2 (HER2)-positive unresectable advanced or recurrent gastric or gastroesophageal junction adenocarcinoma, who had worsened after chemotherapy, were included. Patients received T-DXd as third- or later-line therapy between September 2020 and September 2021. Univariate and multivariate analyses identified prognostic factors for rwPFS and ORR. Results Of the 307 patients, 75.6% were male and 69.1% were aged ≥65 years. The median duration of prior trastuzumab treatment was 6.5 months (range 0-81.5 months). Multivariate analysis showed HER2 immunohistochemistry (IHC) 3+ [hazard ratio (HR) 0.65, 95% confidence interval (CI) 0.49-0.86], intestinal type lesions (HR 0.59, 95% CI 0.43-0.79), modified Glasgow Prognostic Score (mGPS) 0 and 1 (HR 0.71, 95% CI 0.53-0.95), and longer duration of prior trastuzumab treatment (≥ median) (HR 0.75, 95% CI 0.58-0.97) as positive prognostic factors for rwPFS. Longer prior trastuzumab treatment was also a positive prognostic factor for ORR (odds ratio 2.02, 95% CI 1.13-3.63). Conclusions Patients with clinical benefits from prolonged trastuzumab treatment are likely to benefit from T-DXd. Similarly, HER2 IHC 3+, intestinal type lesions, and better mGPS (0 or 1) are associated with longer rwPFS. However, T-DXd should not be withheld even in patients without these factors, as a median PFS of 3.42 months was observed in those with the shortest prior trastuzumab exposure.

关键词： EN-DEAVOR gastric or gastroesophageal junction cancer HER2 positive prognostic factors trastuzumab deruxtecan modified Glasgow Prognostic Score

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Weeds e-Catalog as a Tool for Identification of Weeds in Plantation

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

作者： Hangger Gahara Mawandha Teddy Suparyanto Bens Pardamean Agrotechnology Department Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Agricultural Engineering Department Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Universitas Bina Nusantara Jakarta Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta

Weeds are one of the organisms that interfere with plant growth. Information about the identity of weeds becomes very important on plantations. Although weeds data digitization has been done a lot, currently there is still not much weeds data information system can be accessed online. Weeds management is often dealt with weeds herbarium or weeds photographs. In an effort to provide a good information system for farmers, this research aims to create a database of various types of weeds and an information system that can be accessed online. The methodology for developing a weed catalog information system uses the Software Development Life Cycle (SDLC). Weed samples in database were collected through systematic random sampling in the form of images and text. The result of this study is a Weeds Electronic Catalog or Weeds e-Catalog that can facilitate the information of weeds identity such as names, classifications, morphology, life cycles, and habitats of various types of weeds that grow on plantation land. Weeds e-Catalog can be used by plantation practitioners and farmers to make decisions in controlling weeds.

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Maternal human papillomavirus infection and the risk of congenital malformations: A nationwide population-based cohort study

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Journal of Medical Virology 2024年第4期96卷 e29549-e29549页

作者： Hsieh, Tina Yi Jin Chen, Thomas Yen Ting Liao, Pei-Lun Huang, Jing-Yang Ma, Kevin Sheng-Kai Hung, Yao-Min Chang, Renin Wei, James Cheng-Chung Department of Obstetrics and Gynecology Beth Israel Deaconess Medical Center Boston MA United States Department of Bioinformatics Harvard Medical School Boston MA United States Department of Otolaryngology-Head and Neck Surgery Kaohsiung Medical University Hospital Kaohsiung Taiwan Institute of Medicine Chung Shan Medical University Taichung Taiwan Center for Health Data Science Department of Medical Research Chung Shan Medical University Hospital Taichung Taiwan Department of Epidemiology Harvard T.H. Chan School of Public Health Boston MA United States Department of Dermatology Massachusetts General Hospital Boston MA United States Division of Pharmacoepidemiology and Pharmacoeconomics Department of Medicine Brigham and Women's Hospital Harvard Medical School Boston MA United States Center for Global Health Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Division of Nephrology Department of Internal Medicine Taipei Veterans General Hospital Taitung Branch Taipei Taiwan Master Program in Biomedicine College of Science and Engineering National Taitung University Taitung Taiwan College of Health and Nursing Meiho University Pingtung Taiwan Department of Medical Education and Research Kaohsiung Veterans General Hospital Kaohsiung Taiwan Department of Emergency Medicine Kaohsiung Veterans General Hospital Kaohsiung Taiwan Department of Recreation and Sports Management Tajen University Pingtung Taiwan Department of Allergy Immunology & Rheumatology Chung Shan Medical University Hospital Taichung Taiwan Department of Nursing Chung Shan Medical University Taichung Taiwan Graduate Institute of Integrated Medicine China Medical University Taichung Taiwan Department of Medical Research Taichung Veterans General Hospital Taichung Taiwan

Previous research has explored theories regarding the vertical transmission of human papillomavirus (HPV) infection and its association with adverse pregnancy and perinatal outcomes. However, the impact of maternal HPV infection on congenital anomalies (CAs) in offspring remains relatively understudied. We conducted a population-based cohort study linking the Taiwan Birth Registry, Taiwan Death Registry, and National Health Insurance Research database, in which newborns born in Taiwan between 2009 and 2015 were included. We established a maternal HPV infection cohort comprising 37 807 newborns and matched them with a comparison group of 151 228 newborns at a 1:4 ratio based on index year, age, and sex. The study examined a composite outcome and subgroups of different types of congenital malformations. Differences in cumulative incidence of CAs were assessed using Kaplan–Meier curves and log-rank tests. Adjusted hazard ratios (aHRs) were estimated using Cox proportional hazard regressions. No significant association was found between HPV infection and the broad spectrum of CAs (aHR: 1.04, 95% confidence interval [CI]: 0.98–1.10;log-rank test p = 0.14). However, we observed a 19% increased risk of musculoskeletal CAs in the maternal HPV infection group (aHR: 1.19;95% CI: 1.05–1.34) compared to those without maternal HPV exposure. Other factors, including the type of HPV (aHR: 0.65;95% CI: 0.16–2.63), the timing of exposure (during or before pregnancy), and maternal age (aHR for <30 years: 1.02, 95% CI: 0.94–1.1;aHR for 30–39 years: 1.05, 95% CI: 0.99–1.11;aHR for ≥40 years: 0.88, 95% CI: 0.67–1.17), did not significantly affect the risk for any CA. In conclusion, gestation detection of HPV infection was associated with musculoskeletal CAs but not other major CAs. Prospective studies are warranted to elucidate the necessity of prenatal screening in populations at risk. © 2024 Wiley Periodicals LLC.

关键词： adverse pregnancy congenital malformations human papillomavirus infection outcomes

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T-ICAHT: grading and prognostic impact of thrombocytopenia after CAR T-cell therapy

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Blood 2025年 blood2025028833页

作者： Rejeski, Kai Sanz, Jaime Fei, Teng Nair, Monica S. Hashmi, Hamza Avigdor, Abraham Beyar-Katz, Ofrat Bücklein, Veit L. Curran, Kevin J. Einarsdottir, Sigrun Esensten, Jonathan H. Glaubach, Netta Golan-Accav, Noa Gomez-Llobell, Marina Halamis, Iris Itzhaki, Orit Locke, Frederick L. Mailankody, Sham Marcus, Ronit Maus, Marcela V. Palomba, M. Lia Park, Jae H. Pasquini, Marcelo Raj, Sandeep Rajeeve, Sridevi Salles, Gilles Scordo, Michael Shah, Gunjan L. Shimoni, Avichai Subklewe, Marion Tix, Tobias Usmani, Saad Z. Valid, Ori Valtis, Yannis K. Zuckerman, Tsila Shah, Nirali N. Perales, Miguel-Angel Shouval, Roni Adult Bone Marrow Transplant Service Division of Hematologic Malignancies Memorial Sloan Kettering Cancer Center New York NY United States Cellular Therapy Service Division of Hematologic Malignancies Memorial Sloan Kettering Cancer Center New York NY United States Department of Medicine III Ludwig Maximilian University Hospital Ludwig Maximilian University Munich Munich Germany Departament de Medicina Universitat de Valencia Valencia Spain Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY United States Pediatric Oncology Branch Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD United States Myeloma Service Division of Hematologic Malignancies Memorial Sloan Kettering Cancer Center New York NY United States Division of Hematology and Bone Marrow Transplantation Chaim Sheba Medical Center Faculty of Medicine Tel Aviv University Tel Aviv Israel Department of Hematology and Bone Marrow Transplantation Rambam Health Care Campus Haifa Israel The Ruth and Bruce Rappaport Faculty of Medicine Haifa Technion Israel Department of Pediatrics Memorial Sloan Kettering Cancer Center New York NY United States Advanced Biotherapy Center Sheba Medical Center Ramat Gan Israel Bioinformatics and Big Data Team (Insight) Digital Information Technology Division Rambam Healthcare Campus Haifa Israel Ella Lemelbaum Institute for Immuno-Oncology Sheba Medical Center Ramat Gan Israel Department of Blood and Marrow Transplant and Cellular Immunotherapy Moffitt Cancer Center Tampa FL United States Cellular Immunotherapy Program Cancer Center Massachusetts General Hospital and Harvard Medical School Boston MA United States Lymphoma Service Division of Hematologic Malignancies Memorial Sloan Kettering Cancer Center New York NY United States Department of Medicine Weill Cornell Medical College New York NY United States Medical College of Wisconsin Milwaukee WI United States

Immune effector cell–associated hematotoxicity (ICAHT) was recently introduced as a distinct toxicity category of chimeric antigen receptor (CAR) T-cell (CAR-T) therapy. Although a grading system based solely on neutrophil counts was proposed (hereafter termed N-ICAHT), the prevalence and prognostic impact of thrombocytopenia remain poorly defined. In this multicenter observational study, we systematically examined patterns of thrombocytopenia in 744 patients treated with commercial CD19 CAR-T for B-cell non-Hodgkin lymphoma (B-NHL). We developed a grading system termed T-ICAHT, with thresholds that closely aligned with N-ICAHT, based on depth, duration, and timing of thrombocytopenia. In the core NHL data set, 43% of patients developed any-grade early T-ICAHT (days 0-30), with 23% developing severe (grade ≥3) manifestations. Late T-ICAHT (days 31-100) was observed in 42% (grade ≥3, 13%). Although T-ICAHT and N-ICAHT gradings showed some correlation, considerable discordance was noted. On multivariate analysis, bridging therapy, poor performance status, and high HEMATOTOX scores were associated with increased risk of severe early T-ICAHT. Patients with higher T-ICAHT grades showed increased platelet and red blood cell transfusion burden and more bleeding events. T-ICAHT grades were inversely associated with overall survival (OS), with landmarked 2-year estimates ranging from 67% (grade 0) to 48% (grade 1-2) and 35% (grade ≥3). In multivariable Cox regression analysis, the independent prognostic capacity of T-ICAHT for OS was confirmed. Finally, we validated T-ICAHT's clinical and prognostic utility in 3 external cohorts spanning an additional 599 pediatric and adult patients (NHL, multiple myeloma, and B-cell acute lymphoblastic leukemia), confirming its broad applicability. These findings support integrating T-ICAHT into the ICAHT framework to standardize thrombocytopenia grading in CAR-T recipients. © 2025 American Society of Hematology

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bioinformatics Commons: The Cornerstone of Life and Health Sciences

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Genomics,Proteomics & bioinformatics 2018年第4期16卷 223-225页

作者： Zhang Zhang Yu Xue Fangqing Zhao BIG Data Center and CAS Key Laboratory of Genome Sciences & Information Beijing Institute of Genomics Chinese Academy of Sciences Department of Bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology Beijing Institutes of Life Science Chinese Academy of Sciences

bioinformatics, an interdisciplinary field that combines biology, mathematics, computer science, medicine, and health science, to integrate, analyze, and interpret biological data, is now becoming increasingly data-intensive. To dig out the treasure from big data powered by high-throughput sequencing technologies, it is highly dependent on bioinformatics Commons that involves a variety of fundamental resources, includ-

关键词： bioinformatics Commons The Cornerstone of Life and Health Sciences

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