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Impact of statins on the survival of patients with cancer: a nationwide population-based cohort study in South Korea

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Cancer Communications 2022年第2期42卷 184-187页

作者： Juhee Ahn Sungho Won Sanghun Lee Department of Public Health Science Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Interdisciplinary Program of Bioinformatics Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Institute of Health and Environment Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Department of Bioconvergence&Engineering Dankook UniversityYongin-siGyeonggi-do 16890Republic of Korea Channing Division of Network Medicine Brigham and Women’s HospitalBostonMassachusetts 02115the United States of America

Dear Editor For over 30 years,3-hydroxy-3-methylglutaryl-coenzyme A(HMG-CoA)reductase inhibitors,statins,have been recommended worldwide as cost-effective lipid-lowering drugs for cardiovascular disease[1].Cheng et *** that lipid synthesis inhibitors are a promising anti-cancer treatment in preclinical studies and early phases of clinical trials[2].However,the association between statin use and cancer incidence or survival remains controversial[3,4].

关键词： cancer clinical drugs

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

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Scientific Reports 2023年第1期13卷 1-10页

作者： Kuo, Tzu-Yun Wang, Jen-Hung Huang, Yung-Wen Sung, Ting-Yi Chen, Ching-Tai Department of Biochemical Science and Technology National Taiwan University Taipei 10617 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Statistical Science Academia Sinica Taipei 11529 Taiwan Institute of Information Science Academia Sinica Taipei 11529 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 11221 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan Department of Bioinformatics and Biomedical Engineering Asia University Taichung 41354 Taiwan Center for Precision Health Research Asia University Taichung 41354 Taiwan

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms;its executable files, user manual, and sample data sets are freely available at https://***/comics/Software_*** . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline. © 2023, Springer Nature Limited.

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DIRECTED SCATTERING FOR KNOWLEDGE GRAPH-BASED CELLULAR SIGNALING ANALYSIS

arXiv

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arXiv 2023年

作者： Venkat, Aarthi Chew, Joyce Rodriguez, Ferran Cardoso Tape, Christopher J. Perlmutter, Michael Krishnaswamy, Smita Program for Computational Biology and Bioinformatics Yale University United States Department of Mathematics University of California Los Angeles United States Department of Oncology University College London Cancer Institute United Kingdom Department of Mathematics Boise State University United States Department of Genetics and Computer Science Yale University United States

Directed graphs are a natural model for many phenomena, in particular scientific knowledge graphs such as molecular interaction or chemical reaction networks that define cellular signaling relationships. In these situations, source nodes typically have distinct biophysical properties from sinks. Due to their ordered and unidirectional relationships, many such networks also have hierarchical and multiscale structure. However, the majority of methods performing node- and edge-level tasks in machine learning do not take these properties into account, and thus have not been leveraged effectively for scientific tasks such as cellular signaling network inference. We propose a new framework called Directed Scattering Autoencoder (DSAE) which uses a directed version of a geometric scattering transform, combined with the non-linear dimensionality reduction properties of an autoencoder and the geometric properties of the hyperbolic space to learn latent hierarchies. We show this method outperforms numerous others on tasks such as embedding directed graphs and learning cellular signaling networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Directed graphs

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The need for integrated systems biology approaches for biotechnological applications

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Biotechnology Notes 2021年 2卷 39-43页

作者： Selvarajoo, Kumar Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR) Biopolis Singapore Singapore Institute of Food and Biotechnology Innovation (SIFBI) Agency for Science Technology and Research (A*STAR) Biopolis Singapore Synthetic Biology Translational Research Program & SynCTI Yong Loo Lin School of Medicine National University of Singapore (NUS) Kent Ridge Singapore

Biotechnology applications have contributed significantly to “factory in a lab” research. Although the largely adopted Design–Build–Test–Learn cycle has considerably improved synthetic biology and metabolic engineering capabilities, we are still far from achieving industrial efficiency. As we are now faced with the challenge of exponential population growth and drastic climatic changes affecting the traditional agriculture, there is an imminent need to optimize biotechnology applications, especially for the alternative food source initiative, which has received immense attention recently. Here, I highlight the importance of multi-disciplinary research, and the need to develop integrated systems biology methods, using high-throughput omics data, dynamic modelling and machine learning techniques, to further enhance the lab-based production process. Moving forward in this direction will likely reduce the overall cost and increase the output for the longer term future. © 2021 The Authors

关键词： Food biotechnology Machine learning Metabolic engineering Omics Synthetic biology Systems biology

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Lockdown strategy worth lives: The SEIRD modelling in COVID-19 outbreak in Indonesia 2

Lockdown strategy worth lives: The SEIRD modelling in COVID-...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Nurlaila, I. Hidayat, A.A. Pardamean, B. Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Lockdowns, despite their conflicting restrictions and consequences they might offer when enforced as a national strategy, are deemed to be suggestive for a prompt conquer to the Coronavirus Disease-19 (COVID-19) outbreak. There have been some success stories such as in China, South Korea and our ASEAN member fellow, Vietnam, which exhibited extremely fallen numbers of COVID-19 cases post the enforcement of lockdown. Indonesia, however, remains in the crux of dispute whether or not the lockdown is opted to force COVID-19 transmission down under control. We, in this respect, employ the most popular model which has been broadly applied in the field of epidemiology, referred to as SEIRD (Susceptible, Exposed, Infectious, Recovered, and Death), the extension form of an age-structured SEIR, where the Death (D) is included to provide more factual situation. We modify the I (Infectious) fraction as symp-tomatic (Is) and asymptomatic (Ia) infectives. There are three lockdown scenarios simulated in our modified SEIRD with the starting date are 26 April 2020 when the immediate lockdown was enacted-and a-week and two-week-gaps, respectively. We figured out that by stipulating the lockdown without delay (26 April 2020), the new cases could be kept below 10,000. A week delay escalates case number to 5,000 and delay for one more week results in beyond 20,000 new cases. Furthermore, when the intervention is delayed following the delayed lockdown, normalization would demand a longer period within which dealing with more critical and dying patients is unavoidable and should be more anticipated. © Published under licence by IOP Publishing Ltd.

关键词： Coronavirus

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Continuous Spatiotemporal Transformers

arXiv

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arXiv 2023年

作者： de Oliveira Fonseca, Antonio Henrique Zappala, Emanuele Caro, Josue Ortega van Dijk, David Interdepartmental Neuroscience Program Yale University New HavenCT United States Department of Computer Science Yale University New HavenCT United States Department of Neuroscience Yale University New HavenCT United States Wu Tsai Institute Yale University New HavenCT United States Yale University New HavenCT United States Interdepartmental Program in Computational Biology & Bioinformatics Yale University New HavenCT United States

Modeling spatiotemporal dynamical systems is a fundamental challenge in machine learning. Transformer models have been very successful in NLP and computer vision where they provide interpretable representations of data. However, a limitation of transformers in modeling continuous dynamical systems is that they are fundamentally discrete time and space models and thus have no guarantees regarding continuous sampling. To address this challenge, we present the Continuous Spatiotemporal Transformer (CST), a new transformer architecture that is designed for modeling of continuous systems. This new framework guarantees a continuous and smooth output via optimization in Sobolev space. We benchmark CST against traditional transformers as well as other spatiotemporal dynamics modeling methods and achieve superior performance in a number of tasks on synthetic and real systems, including learning brain dynamics from calcium imaging data. © 2023, CC BY-NC-SA.

关键词： Sobolev spaces

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Clinically and orally compatible formulation-manufactured DDX5 (p68)-targeting molecular glue FL118 products exhibit low toxicity but high efficacy against human cancer

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Journal of Pharmaceutical Analysis 2024年第11期14卷 1717-1720页

作者： Xiang Ling Wenjie Wu Li Yan Leslie Curtin Melanie M.Farrauto Sandra Sexton Anmbreen Jamroze Changjun Yu Christos Fountzilas Dean G.Tang Fengzhi Li Department of Pharmacology&Therapeutics Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA Canget BioTekpharma LLC BuffaloNew York14203USA Department of Biostatistics&Bioinformatics Roswell Park Comprehensive Cancer Center BuffaloNew York14263USA Comparative Oncology Shared Resources Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA California Institute of Technology PasadenaCA91125USA Department of Medicine Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA Developmental Therapeutics(DT)Program Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA Pancreatic Cancer Research Center Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA Genitourinary(GU)Oncology Research Center Roswell Park Comprehensive Cancer CenterBuffaloNew York14263USA

Our recent breakthrough discovery demonstrated that the anticancer drug FL118 tightly binds to and then dephosphorylates and degrades the oncogenic protein DEAD-box helicase 5(DDX5),leading to the inhibition of DDX5 downstream targets(e.g.,survivin,myeloid cell leukemia 1(Mcl-1),X-linked inhibitor of apoptosis(XIAP),c-Myc,mutant Kras,etc.)[1].FL118 is a molecular glue(MG)that can alter the interactomes of two or more non-interacting proteins[2].Thus,FL118 exhibits high efficacy against colorectal and pancreatic cancer xenograft tumors[1,3].However,moving FL118 into clinical trials requires a clinically compatible FL118 drug product(DP)that possesses high antitumor efficacy and low toxicity via oral(ideal)or intravenous(iv)***,we report the development and characterization of a clinically and orally compatible FL118 *** show that(1)FL118 drug substances(DS)exhibit high chemical stability under various test conditions;(2)a clinically and orally compatible FL118 DP can be manufactured through the formulation of FL118 DS with 2-hydroxypropyl-bcyclodextrin(HPbCD)using mixed solvents of glacial acetic acid(GAA)with ethanol through microfluidizer-mediated spray dried dispersion(M-SDD).

关键词： DDX5 formulation breakthrough

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South jakarta's air quality using PM 2.5 data at the beginning of COVID-19 Restriction 6

South jakarta's air quality using PM 2.5 data at the beginni...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Rahutomo, Reza Purwandari, Kartika Hidayat, Alam Ahmad Pardamean, Bens Bina Nusantara University School of Information Systems Information System Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

As soon as the lockdown was established in Jakarta, Indonesia, people experienced a change in Jakarta's air quality. This research was conducted to answer several challenges such as: where to find Indonesia's air quality open data platforms, how to handle the acquired data with SQL technology, and how to validate whether the air quality of Jakarta was significantly changed from a period to another or not. With particulate matter 2.5 (PM 2.5) data acquired by The United States Diplomatic Post in South Jakarta, a data visualization was generated to describe the fluctuation of PM 2.5 from February 29th to June 29th. By conducting a two-sample t-test, a significant change in South Jakarta's air quality was revealed. The test concluded that South Jakarta's air quality got worse even after a lockdown was established. © 2021 IEEE.

关键词： COVID-19

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Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

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Nano Energy 2024年 125卷

作者： Cheng, Yu-Ying Ganguly, Anindita Cheng, Yi-Yun Ortiz, Christopher Llynard D. Pal, Arnab Shah, Pramod Kaswan, Kuldeep Yang, Lee-Wei Lin, Zong-Hong Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Internet of Senses Research Center National Tsing Hua University Hsinchu30013 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300044 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu300044 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu300044 Taiwan Biomedical Artificial Intelligence PhD Program National Tsing Hua University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei Taiwan

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available. © 2024 Elsevier Ltd

关键词： Nanosensors

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Double negative T cells,a potential biomarker for systemic lupus erythematosus

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Precision Clinical Medicine 2020年第1期3卷 34-43页

作者： Jessy J.Alexander Alexander Jacob Anthony Chang Richard J.Quigg James N.Jarvis Department of Pathology University of ChicagoChicagoIL 60637USA Departments of Medicine PediatricsJacobs School of Medicine and Biomedical Sciences and GeneticsGenomics&Bioinformatics ProgramUniversity at BuffaloBuffaloNY 14203USA

Systemic lupus erythematosus(SLE)is an autoimmune disease that is a challenge to diagnose and *** is an urgent need for biomarkers to help define organ involvement,and more effective therapies.A unique population of T cells,the CD3^(+)CD4^(−)CD8^(−)(DNeg)cells,is significantly increased in lupus *** cases(53%)of pediatric SLE patients had elevated DNeg cells in their peripheral blood,which correlated with kidney function(R^(2)=0.54).Significant infiltration of DNeg cells was observed in both adult and pediatric lupus kidneys by *** the first time,this study provides direct evidence that DNeg cells facilitate kidney injury in preclinical 8-week-old MRL/lpr lupus *** lupus mice,the increase in DNeg cells tracked with worsening disease and correlated with kidney function(R^(2)=0.85).Our results show that DNeg cells per se can cause kidney dysfunction,increase in number with increase in disease pathology,and could serve as a potential biomarker.

关键词： CD3^(+)CD4^(−)CD8^(−)T cells glomerulonephritis inflammation lupus

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