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Functional annotation of chemical libraries across diverse biological processes (vol 13, pg 982, 2017)

NATURE CHEMICAL BIOLOGY 2017年第12期13卷 1286-1286页

作者： Piotrowski, Jeff S. Li, Sheena C. Deshpande, Raamesh Simpkins, Scott W. Nelson, Justin Yashiroda, Yoko Barber, Jacqueline M. Safizadeh, Hamid Wilson, Erin Okada, Hiroki Gebre, Abraham A. Kubo, Karen Torres, Nikko P. LeBlanc, Marissa A. Andrusiak, Kerry Okamoto, Reika Yoshimura, Mami DeRango-Adem, Eva van Leeuwen, Jolanda Shirahige, Katsuhiko Baryshnikova, Anastasia Brown, Grant W. Hirano, Hiroyuki Costanzo, Michael Andrews, Brenda Ohya, Yoshikazu Osada, Hiroyuki Yoshida, Minoru Myers, Chad L. Boone, Charles RIKEN Center for Sustainable Resource Science Wako Saitama Japan Department of Computer Science and Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Electrical and Computer Engineering University of Minnesota-Twin Cities Minneapolis Minnesota USA Department of Integrated Biosciences Graduate School of Frontier Sciences University of Tokyo Kashiwa Chiba Japan Donnelly Centre University of Toronto Toronto Ontario Canada Institute of Molecular and Cellular Biosciences Center for Epigenetic Disease University of Tokyo Bunkyo-ku Tokyo Japan Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton New Jersey USA Department of Biochemistry University of Toronto Toronto Ontario Canada.

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound’s mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

关键词： Chemical genetics High-throughput screening Networks and systems biology Target identification

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Assessing Media’s Representation of Frustration Towards Venezuelan Migrants in Colombia 16th

Assessing Media’s Representation of Frustration Towards Ven...

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16th International Conference on Social Computing, Behavioral-Cultural modeling and Prediction and Behavior Representation in modeling and Simulation, SBP-BRiMS 2023

作者： Llinas, Brian Huseynli, Guljannat Frydenlund, Erika Palacio, Katherine Llinas, Humberto Padilla, Jose J. Computer Science Department Old Dominion University NorfolkVA United States Graduate Program of International Studies Old Dominion University NorfolkVA United States Virginia Modeling Analysis and Simulation Center Old Dominion University SuffolkVA United States Universidad del Norte Kilómetro 5 Vía Atlántico Puerto Colombia Colombia

ISBN: (纸本)9783031431289

This research utilizes statistical path modeling to examine the relationship between the number of Venezuelans migrating to Colombia due to economic collapse and the media's coverage of specific topics. We focus on media coverage expressing frustration regarding migration, infrastructure, government, and geopolitics. Our approach combines quantitative analysis of code frequencies from qualitative content analysis of 1,360 regional newspaper articles on migration-related issues. Our findings indicate that an increase in the Venezuelan population in Colombia leads to more negative media coverage of infrastructure impacts, such as hospitals and schools. This negative coverage, referred to as "frustration," indirectly contributes to increased coverage of infrastructure frustration. This suggests an opportunity for intervention by balancing media coverage to reduce the excessive use of negative language and stereotypes, potentially mitigating anti-migrant sentiment fueled by frustration towards infrastructure. Furthermore, we observe that as migration increases, coverage of frustration towards geopolitics decreases, while frustration towards the Colombian government rises. This shift may reflect a transition from contemplating the causes of migration to focusing on the humanitarian response (or lack thereof) by the host government in accommodating the new arrivals. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Artificial intelligence

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Data Logging and Non-invasive IoMT Approach for Rats Monitoring in Laboratory Experiments 37th

Data Logging and Non-invasive IoMT Approach for Rats Monit...

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37th International Conference on Advanced Information Networking and Applications, AINA 2023

作者： Barbosa, Bryan C. M. Garan, Steven A. Quintela, Barbara Melo Dantas, Mario R. Universidade Federal de Juiz de Fora Juiz de Fora Brazil Center for Research and Education in Aging University of California Berkeley and Lawrence Berkeley National Laboratory BerkeleyCA United States Computational Physiology and High Performance Computing Laboratory and Computer Science Department at Universidade Federal de Juiz de Fora Juiz de Fora Brazil Computer Science Graduate Program at Universidade Federal de Juiz de Fora Juiz de Fora Brazil

ISBN: (纸本)9783031290558

It is being observed that the use of Internet of Medical Things (IoMT) in health sciences research grows as the technology and miniaturization of devices occur. Those devices often times suffer from several issues such as: being invasive, lacking the ability to collect many signals concurrently and communication. The present work proposes an approach to the use of an ultra-small IoMT device to fulfill the functions of a bio-signals data collector, a mathematical models processor, a data transmitter-receptor through the network, and a mechanical actuators controller. Our test environment was conceived to be used in animal models. This is an ongoing project from which partial results indicate that, when functioning, the device will use real-time data for monitoring bio-signals and helping with decision-making as it interacts with the organism. The data collection is going to be made through low-cost non-invasive sensors. Therefore, it can favor installation, maintenance, access, and promote a better quality of life for the user. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Decision making

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A fuzzy transformation approach to enhance active learning for heart disease prediction

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Journal of Intelligent and Fuzzy Systems 2024年第4期46卷 9957-9973页

作者： de Oliveira, Heveraldo R. Vieira, Antônio Wilson Santos, Laércio Ives Osório Camargos Filho, Murilo César Ya. Ekel, Petr Dangelo, Marcos Flávio S.V. Department of Computer Science UNIMONTES MG Montes Claros Brazil Graduate Program in Computer Modeling and Systems UNIMONTES Montes Claros Brazil Department of Exact Sciences UNIMONTES MG MG Montes Claros Brazil Instituto Federal do Norte de Minas Gerais – IFNMG MG Montes Claros Brazil Graduate Program in Health Sciences UNIMONTES MG Montes Claros Brazil Graduate Program in Informatics Pontifical Catholic University of Minas Gerais MG Belo Horizonte Brazil

When providing patient care, healthcare professionals often rely on interpreting laboratory and clinical test results. However, their analysis is constrained by human capacity, leading to uncertainties in diagnoses. Machine learning has the potential to evaluate a larger amount of data and identify patterns and relationships that may otherwise go unnoticed. However, popular machine learning algorithms typically require abundant and labeled data, which is not always available. To address this challenge, the adoption of active learning allows for the selection of the most relevant instances for training, reducing the need for extensive labeling. Additionally, fuzzy logic offers the ability to handle uncertainties. This paper proposes a novel approach that utilizes fuzzy membership functions to transform data as a pre-processing step for active learning. The objective is to approximate similar instances, specifically for the purpose of prediction, thereby minimizing the workload of human experts in labeling data for model training. The results of this study demonstrate the effectiveness of this approach in predicting heart disease and highlight the potential of using membership functions to enhance machine learning models in the analysis of medical information. By incorporating fuzzy logic and active learning, healthcare professionals can benefit from improved accuracy and efficiency in diagnosing and predicting pacients’ health conditions. © 2024 – IOS Press.

关键词： Fuzzy logic

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Comparative Analysis between Three-Leg Interleaved and Conventional Bidirectional Converters Applied in Battery of Wind Power-Battery Unit Supplying an Islanded Microgrid

Comparative Analysis between Three-Leg Interleaved and Conve...

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IEEE General Meeting Power& Energy Society

作者： André C. Do Nascimento Giusep M. S. Ribeiro Lindemberg R. de Lima Pedro A. de Alcântara Luana C. S. Soares Luciano S. Barros Camila M. V. Barros Electrical Engineering Graduate Program Federal Institute of Pará Belém Brazil Electrical Engineering Graduate Program Federal University of Paraíba João Pessoa Brazil Mathematics and Computational Modeling Graduate Program Federal University of Paraíba João Pessoa Brazil Computer Systems Department Federal University of Paraíba João Pessoa Brazil

ISBN: (数字)9798350381832

ISBN: (纸本)9798350381849

Battery energy storage systems (BESS) are crucial for microgrids, enhancing dynamic performance and mitigating uncertainties inherent to isolated environments characterized by intermittent power generation. When microgrid is supplied by wind power in connection with BESS, the bidirectional DC-DC converter associated with BESS assumes a critical responsibility—ensuring the control of a wind power supplied DC-link. This permits the Voltage Source Inverter (VSI) to synthesize consistent voltages for the connected AC load. However, challenges emerge, particularly in arduous stress on switches of the bidirectional converter attributed to elevated current ripple. This stress does not only prejudice the overall system’s functioning but can also potentially leading it to shutdown in case of switch failure. Traditionally, the conventional buck-boost converter topology has been the go-to choice for this application, nevertheless, exploring novel converter topologies, such as interleaved bidirectional DC-DC converter (IBDC) has garnered attention, promising enhanced performance. This paper’s goal is to conduct a comparative analysis of the operation of these converters in an islanded microgrid supplied by a single Permanent Magnet Synchronous Generators (PMSG) small-scale wind turbine with a BESS system. Load variation with Maximum Power Point Tracking (MPPT) operation of the PMSG is performed during MATLAB/Simulink environment simulations. The results suggest significant advantages for the interleaved three-phase converter, such as reduced battery charging current ripple, switch disturbance, and voltage ripple in the DC-link.

关键词： Maximum power point trackers Magnetic separation Microgrids DC-DC power converters Wind power generation Permanent magnets Batteries Topology Wind turbines Stress

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Homogenisation for the monodomain model in the presence of microscopic fibrotic structures

arXiv

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arXiv 2020年

作者： Lawson, Brodie A.J. dos Santos, Rodrigo Weber Turner, Ian W. Bueno-Orovio, Alfonso Burrage, Pamela Burrage, Kevin Centre for Data Science Queensland University of Technology QLD Australia ARC Centre of Excellence for Mathematical and Statistical Frontiers Queensland University of Technology QLD Australia Graduate Program on Computational Modeling Universidade de Juiz de Fora Minas Gerais Brazil Department of Computer Science University of Oxford Oxfordshire United Kingdom

MSC Codes 35B27computational models in cardiac electrophysiology are notorious for long runtimes, restricting the numbers of nodes and mesh elements in the numerical discretisations used for their solution. This makes it particularly challenging to incorporate structural heterogeneities on small spatial scales, preventing a full understanding of the critical arrhythmogenic effects of conditions such as cardiac fibrosis. In this work, we explore the technique of homogenisation by volume averaging for the inclusion of non-conductive micro-structures into larger-scale cardiac meshes with minor computational overhead. Importantly, our approach is not restricted to periodic patterns, enabling homogenised models to represent, for example, the intricate patterns of collagen deposition present in different types of fibrosis. We first highlight the importance of appropriate boundary condition choice for the closure problems that define the parameters of homogenised models. Then, we demonstrate the technique’s ability to correctly upscale the effects of fibrotic patterns with a spatial resolution of 10 µm into much larger numerical mesh sizes of 100-250 µm. The homogenised models using these coarser meshes correctly predict critical pro-arrhythmic effects of fibrosis, including slowed conduction, source/sink mismatch, and stabilisation of re-entrant activation patterns. As such, this approach to homogenisation represents a significant step towards whole organ simulations that unravel the effects of microscopic cardiac tissue heterogeneities. © 2020, CC BY.

关键词： Heart

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SRAMM: Short read alignment mapping metrics

arXiv

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arXiv 2021年

作者： Chon, Alvin Huang, Xiaoqiu Bioinformatics and Computational Biology Graduate Program Iowa State University AmesIA50010 United States Department of Computer Science Iowa State University AmesIA50010 United States

Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering process of aligned short reads for various downstream applications. SRAMM is compatible with Python 2.6+ and Python 3.6+ on all operating systems. It works with any short read aligner that generates SAM/BAM/CRAM file outputs and reports 'AS' tags. It is freely available under the MIT license at http://***/achon/sramm. © 2021, CC BY.

关键词： Mapping

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Agile parallel bioinformatics workflow management using Pwrake

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BMC Research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

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Biclustering Method to Capture the Spatial Pattern and to Identify the Causes of Social Vulnerability in Indonesia: A New Recommendation for Disaster Mitigation Policy

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Procedia computer science 2019年 157卷 31-37页

作者： Puspita Anggraini Kaban Robert Kurniawan Rezzy Eko Caraka Bens Pardamean Budi Yuniarto Sukim Computational Statistics Department Polytechnic of Statistics - STIS Jakarta 13330 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Indonesia College of Informatics Chaoyang University of Technology Taichung City 41349 Taiwan (R.O.C.) Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Geographically, Indonesia is a meeting point of three continental plates. Scilicet, the Eurasian Plate, the Indo-Australian Plate, and the Pacific Plate. Therefore, Indonesia is part of the infamous volcanic zone called the ”Ring of Fire” and one of the areas prone to natural disasters such as volcanic eruptions, earthquakes, tsunamis, floods, and landslides. This study aims to capture the spatial pattern and identify the causes of social vulnerability in the districts/cities in Indonesia using the biclustering method. The data is extracted from the Indonesian National Socio-Economic Survey (SUSENAS) by BPS-Statistics in 2014. The biclustering result indicates that each district/city has its own social vulnerability characteristics and shows that the vulnerable aspects of each district/city are different. The adjacent observations tend to have social vulenrability characteristics. The results of this study can be used as a reference for national disaster mitigation policy in Indonesia.

关键词： biclustering disaster mitigation social vulnerability SoVI spatial pattern

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Investigating measures for applying statistical process control in software organizations

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Journal of Software Engineering Research and Development 2018年第1期6卷 1-31页

作者： Daisy Ferreira Brito Monalessa Perini Barcellos Gleison Santos Ontology and Conceptual Modeling Research Group (NEMO) Department of Computer Science Federal University of Espírito Santo Vitória Brazil Graduate Program on Information Systems - Federal University of the State of Rio de Janeiro UNIRIO Rio de Janeiro Brazil

The growing interest in improving software processes has led organizations to aim for high maturity, where statistical process control (SPC) is required. SPC makes it possible to analyze process behavior, predict process performance in future projects and monitor process performance against established goals. The selection of measures for SPC can be a challenging task. Although the literature suggests measures for SPC, information is fragmented. With an aim towards providing a consolidated set of measures for SPC, as well as processes and goals related to these measures, we investigated the literature through a systematic mapping. Following that, we applied a questionnaire to three professionals from Brazilian organizations to check whether the measures they have used in SPC initiatives could also be found in literature. In this paper we discuss our main findings related to the 47 goals, 15 processes and 84 measures identified considering the systematic mapping and the questionnaire results.

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