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arXiv 2022年

作者： Alser, Mohammed Waymost, Sharon Ayyala, Ram Lawlor, Brendan Abdill, Richard J. Rajkumar, Neha LaPierre, Nathan Brito, Jaqueline Ribeiro-Dos-Santos, André M. Firtina, Can Almadhoun, Nour Sarwal, Varuni Eskin, Eleazar Hu, Qiyang Strong, Derek Kim, Byoung-Do Abedalthagafi, Malak S. Mutlu, Onur Mangul, Serghei Department of Information Technology and Electrical Engineering ETH Zürich Zürich8092 Switzerland Department of Computer Science UCLA Los AngelesCA90095 United States Department of Translational Biomedical Informatics University of Southern California Los AngelesCA90089 United States Department of Clinical Pharmacy University of Southern California Los AngelesCA90089 United States Department of Computer Science Munster Technological University CorkT12 P928 Ireland Department of Genetics Cell Biology and Development University of Minnesota MinneapolisMN55417 United States Department of Bioengineering UCLA Los AngelesCA90095 United States Institute for Systems Genetics NYU Grossman School of Medicine New YorkNY10016 United States Department of Computational Medicine University of California Los AngelesCA90095 United States Department of Human Genetics University of California Los AngelesCA90095 United States Office of Advanced Research Computing UCLA Los AngelesCA90095 United States Center for Advanced Research Computing University of Southern California Los AngelesCA90089 United States Genomics Research Department Saudi Human Genome Project King Fahad Medical City King Abdulaziz City for Science and Technology Riyadh Saudi Arabia King Salman Center for Disability Research Riyadh12512 Saudi Arabia Riyadh Saudi Arabia

Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to install and use. Here, we systematically review practices across prominent packaging, virtualization, and containerization platforms. We outline the challenges, advantages, and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers, and system administrators. We also propose principles to make packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research. © 2022, CC BY.

关键词： Containers

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Improved Fitness Dependent Optimizer for Solving Economic Load Dispatch Problem

arXiv

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arXiv 2022年

作者： Tahir, Barzan Hussein Rashid, Tarik A. Rauf, Hafiz Tayyab Bacanin, Nebojsa Chhabra, Amit Vimal, S. Yaseen, Zaher Mundher Department of Computer Science and Engineering University of Kurdistan Helwer Erbil Iraq Centre for Smart Systems AI and Cybersecurity Staffordshire University Stoke-on-Trent United Kingdom Singidunum University Danijelova 32 Belgrade11000 Serbia Department of Computer Engineering and Technology Guru Nanak Dev University Amritsar India Department of Artificial Intelligence and Data Science Ramco Institute of Technology North Venganallur Village Virudhunagar District Tamilnadu Rajapalayam626 117 India Department of Earth Sciences and Environment Faculty of Science and Technology Universiti Kebangsaan Malaysia Selangor Bangi43600 Malaysia USQ's Advanced Data Analytics Research Group School of Mathematics Physics and Computing University of Southern Queensland QLD4350 Australia New era and Development in Civil Engineering Research Group Scientific Research Center Al-Ayen University Thi-Qar64001 Iraq

Economic Load Dispatch depicts a fundamental role in the operation of power systems, as it decreases the environmental load, minimizes the operating cost, and preserves energy resources. The optimal solution to Economic Load Dispatch problems and various constraints can be obtained by evolving several evolutionary and swarm-based algorithms. The major drawback to swarm-based algorithms is premature convergence towards an optimal solution. Fitness Dependent Optimizer is a novel optimization algorithm stimulated by the decision-making and reproductive process of bee swarming. Fitness Dependent Optimizer (FDO) examines the search spaces based on the searching approach of Particle Swarm Optimization. To calculate the pace, the fitness function is utilized to generate weights that direct the search agents in the phases of exploitation and exploration. In this research, the authors have carried out Fitness Dependent Optimizer to solve the Economic Load Dispatch problem by reducing fuel cost, emission allocation, and transmission loss. Moreover, the authors have enhanced a novel variant of Fitness Dependent Optimizer, which incorporates novel population initialization techniques and dynamically employed sine maps to select the weight factor for Fitness Dependent Optimizer. The enhanced population initialization approach incorporates a quasi-random Sabol sequence to generate the initial solution in the multi-dimensional search space. A standard 24-unit system is employed for experimental evaluation with different power demands. Empirical results obtained using the enhanced variant of the Fitness Dependent Optimizer demonstrate superior performance in terms of low transmission loss, low fuel cost, and low emission allocation compared to the conventional Fitness Dependent Optimizer. The experimental study obtained 7.94E-12, the lowest transmission loss using the enhanced Fitness Dependent Optimizer. Correspondingly, various standard estimations are used to prove the stability

关键词： Decision making

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Comprehending the risk of foodborne and waterborne disease outbreaks: Current situation and control measures with Special reference to the Indian Scenario

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Heliyon 2024年第16期10卷 e36344页

作者： Albert, Venencia Ramamurthy, Thandavarayan Das, Samaresh G Dolma, Karma Majumdar, Tapan Baruah, Pranjal Jyoti Chaliha Hazarika, Suranjana Apum, Basumoti Das, Madhuchhanda Indian Council of Medical Research Ansari Nagar East New Delhi 110029 India ICMR-National Institute for Research in Bacterial Infections (NIRBI) West Bengal Kolkata 700010 India Center for Development of Advanced Computing (CDAC) West Bengal Kolkata 700 091 India Department of Microbiology Sikkim Manipal Institute of Medical Sciences (SMIMS) Sikkim Manipal University Sikkim Gangtok 737102 India Department of Microbiology Agartala Government Medical College Tripura Agartala 799006 India ICMR Regional Medical Research Centre (RMRC) Assam Dibrugarh 786001 India Department of Microbiology Gauhati Medical College and Hospital Assam Guwahati 781032 India Department of Microbiology Bankin Pertin General Hospital & Research Institute Arunachal Pradesh Pasighat 791102 India Division of Development Research Indian Council of Medical Research Department of Health Research (Ministry of Health & Family Welfare) P.O. Box No. 4911 Ansari Nagar East New Delhi 110029 India

Background: Foodborne and waterborne diseases and outbreaks are a neglected public health issue worldwide. In developing countries, diarrheal disease caused by foodborne and waterborne infections is a major cause of ill health. There is a lack of information on foodborne pathogens, their transmission routes, outbreaks, and related mortalities, due to the absence of a robust disease surveillance system and adequately equipped laboratories. Although hygiene practices are much better in Western countries, the widespread use of preserved and raw food items is a cause of concern. Consequently, the occurrence of foodborne diseases is not rare in these countries either. WHO has recently released the ‘Global Strategy for Food Safety 2022–2030’, addressing the emerging challenges, new technologies, and innovative approaches to strengthen food safety systems and enhance laboratory capacity for foodborne disease surveillance. Foodborne outbreaks are a huge challenge in India. Malnutrition, anemia, hookworm and enteric infections, are the predominant cryptic health conditions among children in rural and tribal areas, leading to severe consequences, including death, and posing a substantial threat to public health. Combating such events with adequate food safety and hygiene practices is achievable. Systematic collection of data can help to develop food safety policies that could reduce the burden of foodborne diseases. Objective: This review aims to examine the current situation of foodborne and waterborne diseases, identification of the factors contributing to their occurrence and outbreaks, and defining the gaps in control measures, challenges, and potential solutions in improving the public health system. Methods: Strengths, weaknesses, opportunities, and threats (SWOT) analysis was made based on the literature review of foodborne and waterborne infections to assess the current situation and to identify knowledge gaps. Finding: SWOT analysis showed the strength and gaps in th

关键词： Foodborne diseases Hygiene practices Outbreaks Public health Surveillance

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The Effect of Epoxidized Natural Rubber as A Compatibilizer on the Properties of Standard Malaysian Rubber/Ethylene Propylene Diene Monomer Blends

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Journal of Physics: Conference Series 2018年第1期1019卷

作者： A M Alakrach R Hamzah N Z Noriman Omar S Dahham Z Shayfull S Z Syed Idrus S Sudin Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Faculty of Engineering Technology (FETech) Universiti Malaysia Perlis (UniMAP) Level 1 Block S2 UniCITI Alam Campus Sungai Chucuh Padang Besar 02100 Perlis Malaysia School of Manufacturing Engineering Universiti Malaysia Perlis Arau 02600 Malaysia Green Design and Manufacture Research Group Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Universiti Malaysia Perlis Kangar 0100 Malaysia School of Human Development and Techno-communication (iKOM) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP School of Computer and Communication Engineering (SCCE) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP

In this study, the effects of epoxidized natural rubber (ENR-50) as compatibilizer on the properties of Standard Malaysian Rubber/Ethylene Propylene Diene Monomer (SMR L/EPDM) blend were investigated. Standard Malaysian Rubber/Ethylene Propylene Diene Monomer / Epoxidized Natural Rubber (SMR L/EPDM / ENR-50) blends were prepared by two-roll mill with five different compositions (i.e., 80/20/0, 80/20/1, 80/20/3, 80/20/5, 80/20/7 and 80/20/10), which the (SMR L/EPDM) content fixed at 80/20 which is the optimum ratio for (SMR L/EPDM) depending on our previous study. Cure characteristics, mechanical properties studies were performed to determine the compatibility of SMR L/EPDM blends in the presence of ENR-50 as a compatibilizer. The optimum cure characteristics showed by SMR L/EPDM blends with the presence of ENR-50, which lower scorch time t2 and cure time t90 and increase the cure rate index CRI. In addition, SMR L/EPDM blends with the presence of ENR-50 have improved the physical properties such as swelling test, crosslink density and hardness test.

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Recycled Natural Rubber Latex Gloves Filled Chloroprene Rubber: Effects of Compatibilizers

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Journal of Physics: Conference Series 2018年第1期1019卷 012067-012067页

作者： Alakrach, A M Hamzah, R Noriman, N Z Dahham, Omar S Shayfull, Z Syed Idrus, S Z Sudin, S Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Faculty of Engineering Technology (FETech) Universiti Malaysia Perlis (UniMAP) Level 1 Block S2 UniCITI Alam Campus Sungai Chucuh Padang Besar 02100 Perlis Malaysia School of Manufacturing Engineering Universiti Malaysia Perlis Arau 02600 Malaysia Green Design and Manufacture Research Group Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Universiti Malaysia Perlis Kangar 0100 Malaysia School of Human Development and Techno-communication (iKOM) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP School of Computer and Communication Engineering (SCCE) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP

In this study, the effects of the compatibilizers; trans-polyoctylene (TOR) and epoxidized natural rubber (ENR-50), on the cure characteristics and tensile properties of recycled natural rubber latex gloves (rNR-G) filled chloroprene rubber (CR) were investigated. Blends consisting of rNR-G in a weight ratio 20 phr in CR and The compatibilizers TOR and ENR-50 at different concentrations, i.e. 2, 4, 6, 8 and 10 phr, were prepared using a two roll mill. Incorporation of TOR resulted in a reducing of the cure characteristics, meanwhile ENR-50 increased them. On the other hand, both of TOR and ENR-50 were improved tensile properties. These effects are attributed to the enhanced interfacial adhesion between rNR-G and phases through the compatibilizing effect induced by TOR and ENR-50, and the good dispersion of the rNR-G phase in the CR matrix. The results confirmed that TOR and ENR-50 could potentially be used as compatibilizers for the recycled natural rubber latex gloves filled chloroprene rubber.

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Deep Learning-Based Automatic Multi-Level Airway Collapse Monitoring on Obstructive Sleep Apnea Patients

arXiv

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arXiv 2024年

作者： Hsu, Ying-Chieh Liu, Stanley Yung-Chuan Huang, Chao-Jung Wu, Chi-Wei Cheng, Ren-Kai Hsu, Jane Yung-Jen Huang, Shang-Ran Cheng, Yuan-Ren Hsu, Fu-Shun Department of Biomedical Engineering National Taiwan University Taipei Taiwan Department of Otolaryngology Head and Neck Surgery Taipei Tzu Chi Hospital Buddhist Tzu Chi Medical Foundation Taipei Taiwan Tzu Chi University School of Medicine Hualien Taiwan Department of Oral & Maxillofacial Surgery Nova Southeastern University College of Dental Medicine College of Allopathic Medicine Florida United States All Vista Healthcare Center Center for AI and Advanced Robotics National Taiwan University Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Artificial Intelligence Chang Gung University College of Intelligent Computing Taoyuan Taiwan Heroic Faith Medical Science Co. Ltd. New Taipei Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan Department of Internal Medicine Chung Shan Medical University Taichung Taiwan Hospital Development Affairs Office Chung Shan Medical University Hospital Taichung Taiwan

This study investigated the use of deep learning to identify multi-level upper airway collapses in obstructive sleep apnea (OSA) patients based on snoring sounds. We fi-ne-tuned ResNet-50 and Audio Spectrogram Transformer (AST) models using snoring recordings from 37 subjects undergoing drug-induced sleep endoscopy (DISE) between 2020 and 2021. Snoring sounds were labeled according to the VOTE (Velum, Orophar-ynx, Tongue Base, Epiglottis) classification, resulting in 259 V, 403 O, 77 T, 13 E, 1016 VO, 46 VT, 140 OT, 39 OE, 30 VOT, and 3150 non-snoring (N) 0.5-second clips. The models were trained for two multi-label classification tasks: identifying obstructions at V, O, T, and E levels, and identifying retropalatal (RP) and retroglossal (RG) obstruc-tions. Results showed AST slightly outperformed ResNet-50, demonstrating good abil-ity to identify V (F1-score: 0.71, MCC: 0.61, AUC: 0.89), O (F1-score: 0.80, MCC: 0.72, AUC: 0.94), and RP obstructions (F1-score: 0.86, MCC: 0.77, AUC: 0.97). However, both models struggled with T, E, and RG classifications due to limited data. Retrospective analysis of a full-night recording showed the potential to profile airway obstruction dynamics. We expect this information, combined with polysomnography and other clinical parameters, can aid clinical triage and treatment planning for OSA patients. © 2024, CC BY-SA.

关键词： Endoscopy

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New Slow Release Fertilizer from ENR-50/RH/Urea Composites: Effect of Sodium Chloride Concentration

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Journal of Physics: Conference Series 2018年第1期1019卷

作者： Marwa N Al-Samarrai R Hamzah S T Sam N Z Noriman Omar S Dahham S Z Syed Idrus S Sudin Center of Excellence Geopolymer and Green Technology (CEGeoGTech) Faculty of Engineering Technology (FETech) Universiti Malaysia Perlis (UniMAP) Level 1 Block S2 UniCITI Alam Campus Sungai Chucuh Padang Besar 02100 Perlis Malaysia. School of Bioprocess Engineering Universiti Malaysia Perlis (UniMAP) Kompleks Pengajian Jejawi 3 02600 Arau Perlis Malaysia. School of Human Development and Techno-communication (iKOM) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP School of Computer and Communication Engineering (SCCE) Green Advanced Computing and Technology (GREAT) Research Group – CEGeoGTech Universiti Malaysia Perlis (UniMAP

A green and renewable slow release material (SRM) was developed using combination of urea, epoxidized natural rubber (ENR-50), NaCl and rice husk (RH). The RH was used as a support to store urea within its fibrous structure after chemical modification with 7% sodium hydroxide (NaOH). ENR-50/NaCl was used as a coating material for RH/urea beads. Two different content of salt (5% and 10% NaCl) was used to study the effect of pore formation on the composites. FTIR spectroscopy reveals that urea was successfully absorbed into RH and the recorded peaks were overlapped with the main components of RH such as cellulose, hemicellulose and lignin. UV-Vis reveals that at 10% salt loading releases urea higher than 5% salt loading. This is due to the formation of many pores in this ENR-50 composite.

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Placental Vessel Segmentation and Registration in Fetoscopy: Literature Review and MICCAI FetReg2021 Challenge Findings

arXiv

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arXiv 2022年

作者： Bano, Sophia Casella, Alessandro Vasconcelos, Francisco Qayyum, Abdul Benzinou, Abdesslam Mazher, Moona Meriaudeau, Fabrice Lena, Chiara Cintorrino, Ilaria Anita De Paolis, Gaia Romana Biagioli, Jessica Grechishnikova, Daria Jiao, Jing Bai, Bizhe Qiao, Yanyan Bhattarai, Binod Gaire, Rebati Raman Subedi, Ronast Vazquez, Eduard Plotka, Szymon Lisowska, Aneta Sitek, Arkadiusz Attilakos, George Wimalasundera, Ruwan David, Anna L. Paladini, Dario Deprest, Jan De Momi, Elena Mattos, Leonardo S. Moccia, Sara Stoyanov, Danail Department of Computer Science University College London United Kingdom Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Italy The BioRobotics Institute Department of Excellence in Robotics and AI Scuola Superiore Sant'Anna Italy Fetal Medicine Unit Elizabeth Garrett Anderson Wing University College London Hospital United Kingdom EGA Institute for Women's Health Faculty of Population Health Sciences University College London United Kingdom Department of Development and Regeneration University Hospital Leuven Belgium Department of Fetal and Perinatal Medicine Istituto Giannina Gaslini Italy ENIB UMR CNRS 6285 LabSTICC 29238 France Department of Computer Engineering and Mathematics University Rovira i Virgili Spain ImViA Laboratory University of Bourgogne Franche-Comté France Physics Department Lomonosov Moscow State University Russia Fudan University China Medical Computer Vision and Robotics Group Department of Mathematical and Computational Sciences University of Toronto Canada Co. Ltd China NepAL Applied Mathematics and Informatics Institute for Research Nepal Redev Technology United Kingdom Sano Center for Computational Medicine Poland Quantitative Healthcare Analysis Group Informatics Institute University of Amsterdam Amsterdam Netherlands Center for Advanced Medical Computing and Simulation Massachusetts General Hospital Harvard Medical School BostonMA United States

Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to restore a physiological blood exchange among twins. The procedure is particularly challenging, from the surgeon's side, due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to amniotic fluid turbidity, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation of pathological anastomoses, resulting in persistent TTTS. Computer-assisted intervention (CAI) can provide TTTS surgeons with decision support and context awareness by identifying key structures in the scene and expanding the fetoscopic field of view through video mosaicking. Research in this domain has been hampered by the lack of high-quality data to design, develop and test CAI algorithms. Through the Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge, which was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge, we released the first large-scale multi-center TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms with a focus on creating drift-free mosaics from long duration fetoscopy videos. For this challenge, we released a dataset of 2060 images, pixel-annotated for vessels, tool, fetus and background classes, from 18 in-vivo TTTS fetoscopy procedures and 18 short video clips of an average length of 411 frames for developing placental scene segmentation and frame registration for mosaicking techniques. Seven teams participated in this challenge and their model performance was assessed on an unseen test dataset of 658 pixel-annotated images from 6 fetoscopic procedures and 6 short clips. The challenge provided an opportunity for creating generalized solutions for fetoscopic scene understanding and mosaicking. In this paper,

关键词： Pixels

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Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs)

Efficient targeted gene disruption in Xenopus embryos using ...

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2012全国发育生物学大会

作者： Yong Lei Hui Zhao Xiaogang Guo Yun Liu Yang Cao Yi Deng Xiongfeng Chen Hon Ki Christopher Cheng Igor B.Dawid Yonglong Chen Shenzhen Research Institute The Chinese University of Hong Kong Shenzhen 518057 P.R.China Key Laboratory of Regenerative Biology Guangzhou Institutes of Biomedicine and HealthChinese Academy of Sciences Guangzhou 510530 P.R.China Department of Biology South University of Science and Technology of China Shenzhen 518055 P.R.China Advanced Biomedical Computing Center National Cancer Institute National Institutes of Health Frederick MD 21702 USA Program in Genomics of Differentiation The Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD 20892 USA School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Shatin New TerritoriesHong Kong P.R.China School of Biomedical Sciences Faculty of Medicine The Chinese University of Hong Kong Shatin New TerritoriesHong Kong P.R.China

Transcription activator-like effector nucleases (TALENs) are a novel approach for directed gene disruption and have been proved to be effective in various animal *** we report that TALENs can induce somatic mutations in Xenopus embryos with reliably high efficiency and that such mutations are heritable through germline *** modified the Golden Gate method for TALEN assembly to make the product suitable for RNA transcription and microinjection into Xenopus embryos.

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An integrated cyberGIS and machine learning framework for fine-scale prediction of Urban Heat Island using satellite remote sensing and urban sensor network data

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Urban informatics 2022年第1期1卷 6页

作者： Fangzheng Lyu Shaohua Wang Su Yeon Han Charlie Catlett Shaowen Wang cyberGIS Center for Advanced Digital and Spatial Studies University of Illinois at Urbana-Champaign Urbana IL USA. Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign Urbana IL USA. Key Laboratory of Digital Earth Science Aerospace Information Research Institute Chinese Academy of Sciences Beijing 100094 China. International Research Center of Big Data for Sustainable Development Goals Beijing 100094 China. Computing Environment and Life Sciences Argonne National Laboratory Chicago IL USA.

Due to climate change and rapid urbanization, Urban Heat Island (UHI), featuring significantly higher temperature in metropolitan areas than surrounding areas, has caused negative impacts on urban communities. Temporal granularity is often limited in UHI studies based on satellite remote sensing data that typically has multi-day frequency coverage of a particular urban area. This low temporal frequency has restricted the development of models for predicting UHI. To resolve this limitation, this study has developed a cyber-based geographic information science and systems (cyberGIS) framework encompassing multiple machine learning models for predicting UHI with high-frequency urban sensor network data combined with remote sensing data focused on Chicago, Illinois, from 2018 to 2020. Enabled by rapid advances in urban sensor network technologies and high-performance computing, this framework is designed to predict UHI in Chicago with fine spatiotemporal granularity based on environmental data collected with the Array of Things (AoT) urban sensor network and Landsat-8 remote sensing imagery. Our computational experiments revealed that a random forest regression (RFR) model outperforms other models with the prediction accuracy of 0.45 degree Celsius in 2020 and 0.8 degree Celsius in 2018 and 2019 with mean absolute error as the evaluation metric. Humidity, distance to geographic center, and PM concentration are identified as important factors contributing to the model performance. Furthermore, we estimate UHI in Chicago with 10-min temporal frequency and 1-km spatial resolution on the hottest day in 2018. It is demonstrated that the RFR model can accurately predict UHI at fine spatiotemporal scales with high-frequency urban sensor network data integrated with satellite remote sensing data.

关键词： Machine learning Remote sensing Urban Heat Island Urban sensor network cyberGIS

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