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Dynamic ¹³C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin (vol 23, 100855, 2020)

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ISCIENCE 2020年第12期23卷 100855页

作者： Quek, Lake-Ee Krycer, James R. Ohno, Satoshi Yugi, Katsuyuki Fazakerley, Daniel J. Scalzo, Richard Elkington, Sarah D. Dai, Ziwei Hirayama, Akiyoshi Ikeda, Satsuki Shoji, Futaba Suzuki, Kumi Locasale, Jason W. Soga, Tomoyoshi James, David E. Kuroda, Shinya Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia School of Mathematics and Statistics The University of Sydney Sydney NSW 2006 Australia Sydney Medical School The University of Sydney Sydney NSW 2006 Australia Department of Biological Sciences Graduate School of Science University of Tokyo Hongo 7-3-1 Bunkyo-ku Tokyo 113-0033 Japan School of Life and Environmental Sciences The University of Sydney Sydney NSW 2006 Australia Institute for Advanced Biosciences Keio University Tsuruoka Yamagata 997-0052 Japan YCI Laboratory for Trans-Omics Young Chief Investigator Program RIKEN Center for Integrative Medical Sciences 1-7-22 Suehiro-cho Tsurumi-ku Yokohama Kanagawa 230-0045 Japan Faculty of Engineering and Information Technologies The University of Sydney Sydney NSW 2006 Australia Department of Pharmacology and Cancer Biology Duke University School of Medicine Duke University Durham NC 27710 USA AMED-CREST AMED 1-7-1 Otemachi Chiyoda-Ku Tokyo 100-0004 Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8562 Japan CREST Japan Science and Technology Agency Bunkyo-ku Tokyo 113-0033 Japan

Cellular metabolism is dynamic, but quantifying non-steady metabolic fluxes by stable isotope tracers presents unique computational challenges. Here, we developed an efficient 13 C-tracer dynamic metabolic flux analysis (13C-DMFA) framework for modeling central carbon fluxes that vary over time. We used B-splines to generalize the flux parameterization system and to improve the stability of the optimization algorithm. As proof of concept, we investigated how 3T3-L1 cultured adipocytes acutely metabolize glucose in response to insulin. Insulin rapidly stimulates glucose uptake, but intracellular pathways responded with differing speeds and magnitudes. Fluxes in lower glycolysis increased faster than those in upper glycolysis. Glycolysis fluxes rose disproportionally larger and faster than the tricarboxylic acid cycle, with lactate a primary glucose end product. The uncovered array of flux dynamics suggests that glucose catabolism is additionally regulated beyond uptake to help shunt glucose into appropriate pathways. This work demonstrates the value of using dynamic intracellular fluxes to understand metabolic function and pathway regulation.

关键词： Biological Sciences Flux Data Metabolomics Metabolic Flux Analysis

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Sensitivity Analysis with AHP Method: Selection of Foundation Design on Bridge Sei Muara Bulan Anak 2

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Journal of Physics: Conference Series 2018年第1期1028卷

作者： Hendrik Sulistio Mega Waty Muhammad Ikhsan Setiawan Nuning Kurniasih Ansari Saleh Ahmar Department of Civil Engineering Doctoral Program Tarumanagara University Jakarta 11440 Indonesia Department of Civil Engineering Narotama University Surabaya Jawa Timur 60117 Indonesia Faculty of Communication Science Library & Information Science Universitas Padjadjaran Bandung Jawa Barat 45363 Indonesia Department of Statistics Universitas Negeri Makassar Indonesia

The selection of the bridge is fundamental thing to Sei Anak Muara Bulan 2 Bridge Planning. After knowing the results of capacity analysis of land and pile support capacity, ease of implementation, determine the selection of foundation planning decisions. The results of AHP implementation indicate that the aspects of land and pile carrying capacity are the main priority criteria with the amount 61.7% as the reason to determine the choice of bridge foundation and the result of alternative is the foundation of equal to 42,2%

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Steady Rayleigh-BénardRayleigh-Bénard convection between stress-free boundaries

arXiv

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arXiv 2020年

作者： Wen, Baole Goluskin, David LeDuc, Matthew Chini, Gregory P. Doering, Charles R. Department of Mathematics University of Michigan Ann ArborMI48109-1043 United States Department of Mathematics & Statistics University of Victoria VictoriaBCV8P 5C2 Canada Department of Physics University of Michigan Ann ArborMI48109-1040 United States Program in Integrated Applied Mathematics University of New Hampshire DurhamNH03824 United States Department of Mechanical Engineering University of New Hampshire DurhamNH03824 United States Center for the Study of Complex Systems University of Michigan Ann ArborMI48109-1042 United States

Steady two-dimensional Rayleigh-Bénard convection between stress-free isothermal boundaries is studied via numerical computations. We explore properties of steady convective rolls with aspect ratios π/5 ⩽ Γ ⩽ 4π, where Γ is the width-to-height ratio for a pair of counter-rotating rolls, over eight orders of magnitude in the Rayleigh number, 103 ⩽ Ra ⩽ 1011, and four orders of magnitude in the Prandtl number, 10−2 ⩽ Pr ⩽ 102. At large Ra where steady rolls are dynamically unstable, the computed rolls display Ra → ∞ asymptotic scaling. In this regime, the Nusselt number Nu that measures heat transport scales as Ra1/3 uniformly in Pr. The prefactor of this scaling depends on Γ and is largest at Γ ≈ 1.9. The Reynolds number Re for large-Ra rolls scales as Pr−1Ra2/3 with a prefactor that is largest at Γ ≈ 4.5. All of these large-Ra features agree quantitatively with the semi-analytical asymptotic solutions constructed by Chini & Cox (2009). Convergence of Nu and Re to their asymptotic scalings occurs more slowly when Pr is larger and when Γ is smaller. Copyright © 2020, The Authors. All rights reserved.

关键词： Prandtl number

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Direct Comparison of RT-ddPCR and Targeted Amplicon Sequencing for SARS-CoV-2 Mutation Monitoring in Wastewater

SSRN

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SSRN 2022年

作者： Lou, Esther G. Sapoval, Nicolae McCall, Camille Bauhs, Lauren Carlson-Stadler, Russell Kalvapalle, Prashant Lai, Yanlai Palmer, Kyle Penn, Ryker Rich, Whitney Wolken, Madeline Ensor, Katherine B. Hopkins, Loren Treangen, Todd J. Stadler, Lauren B. Department of Civil and Environmental Engineering Rice University 6100 Main Street MS 519 HoustonTX77005 United States Department of Computer Science Rice University 6100 Main Street HoustonTX77005 United States Systems Synthetic and Physical Biology Graduate Program Rice University 6100 Main Street HoustonTX77005 United States Houston Health Department 8000 N. Stadium Dr. HoustonTX77054 United States Department of Statistics Rice University 6100 Main Street MS 138 HoustonTX77005 United States

Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3;hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing. © 2022, The Authors. All rights reserved.

关键词： SARS

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Ten simple rules for reproducible research in jupyter notebooks

arXiv

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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Comparison of the Effectiveness of Machine Learning Techniques for the Number of Road Traffic Injuries

Comparison of the Effectiveness of Machine Learning Techniqu...

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International ECTI Northern Section Conference on Electrical, Electronics, Computer and Telecommunications engineering (ECTI-NCON)

作者： Wirawan Puttamat Wikanda Phaphan Anuchit Jitpattanakul Chainarong Pianpailoon Sakorn Mekruksavanich Department of Mathematics Faculty of Education Chaiyaphum Rajabhat University Chaiyaphum Thailand Department of Applied Statistics Faculty of Applied Science King Mongkut’s University of Technology North Bangkok Bangkok Thailand Research Group in Statistical Learning and Inference Department of Mathematics Faculty of Applied Science King Mongkut’s University of Technology North Bangkok Bangkok Thailand Intelligent and Nonlinear Dynamic Innovations Research Center Curriculum and Teaching Program (Mathematics) Faculty of Education Sakon Nakhon Rajabhat University Sakon Nakhon Thailand Department of Computer Engineering School of Information and Communication University of Phayao Phayao Thailand

This article aims to compare forecasting techniques with machine learning techniques for predicting the number of people injured in road accidents using data from the Injury Information Collaboration Center, Department of Disease Control, Ministry of Public Health Outpatient Files (OPD) spanning the years 2018 to 2022. The four machine-learning techniques examined in this study include Decision Tree Regression, Random Forest Regression, Support Vector Regression, and Multiple Linear Regression. The data analysis was performed using the R programming language. The results revealed that the Decision Tree Regression technique yielded the most accurate predictions for the number of road traffic injuries, as evidenced by its lowest values of MAE, MSE, and RMSE.

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The effect of time delay for synchronisation suppression in neuronal networks

arXiv

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arXiv 2022年

作者： Hansen, Matheus Protachevicz, Paulo R. Iarosz, Kelly C. Caldas, Iberê L. Batista, Antonio M. Macau, Elbert E.N. Institute of Science and Technology Federal University of São Paulo - UNIFESP São José dos Campos SP São Paulo Brazil Institute of Physics University of São Paulo SP São Paulo Brazil Faculdade de Telêmaco Borba FATEB Telêmaco Borba Paraná Brazil Graduate Program in Chemical Engineering Federal Technological University of Paraná PR Ponta Grossa Brazil State University of Ponta Grossa PR Ponta Grossa Brazil Mathematics and Statistics Department State University of Ponta Grossa PR Ponta Grossa Brazil

We study the time delay in the synaptic conductance for suppression of spike synchronisation in a random network of Hodgkin Huxley neurons coupled by means of chemical synapses. In the first part, we examine in detail how the time delay acts over the network during the synchronised and desynchronised neuronal activities. We observe a relation between the neuronal dynamics and the syaptic conductance distributions. We find parameter values in which the time delay has high effectiveness in promoting the suppression of spike synchronisation. In the second part, we analyse how the delayed neuronal networks react when pulsed inputs with different profiles (periodic, random, and mixed) are applied on the neurons. We show the main parameters responsible for inducing or not synchronous neuronal oscillations in delayed networks. Copyright © 2022, The Authors. All rights reserved.

关键词： Synchronization

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The determinant of individual smoking consumption in Central Java province

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Journal of Physics: Conference Series 2019年第2期1321卷

作者： S Subanti A R Hakim H S J N Sriwiyanto I M Hakim Department of Statistics Faculty of Mathematics and Natural Science Universitas Sebelas Maret Institute for Research and Social Services Universitas Sebelas Maret Graduate Program in Economics Faculty of Economics and Business Universitas Indonesia Department of Economic Development Faculty of Economics and Business Universitas Sebelas Maret Department of Industrial Engineering Faculty of Engineering Universitas Indonesia

The paper aims to determine the socio-economic factors that significantly affect the individual smoking consumption and to make smoker profile in Central Java Province. This paper uses national economy social survey (Susenas) based on individual analytical units. The estimation technique with ordinary least squares regression. The findings of the paper is the factors that significantly influence the individual smoking consumption are cigarette prices, income, marriage status, urban-rural, education level, poor status, and living condition. This study suggests that to reduce cigarette consumption, the government needs to increase the price of cigarettes. In addition, the government needs to promote anti-smoking campaigns and smoking bans at work.

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Pavement Technology and Airport Infrastructure Expansion Impact

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Journal of Physics: Conference Series 2018年第1期954卷

作者： Sabib M I Setiawan N Kurniasih A S Ahmar C Hasyim Department of Civil Engineering Tarumanagara University Jakarta Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia Faculty of Communication Science Library & Information Science Program Universitas Padjadjaran Bandung Indonesia AHMAR Institute Makassar Indonesia Department of Statistics Universiats Negeri Makassar Indonesia Darul Ulum University Jombang Indonesia

This research aims for analyzing construction and infrastructure development activities potential contribution towards Airport Performance. This research is correlation study with variable research that includes Airport Performance as X variable and construction and infrastructure development activities as Y variable. The population in this research is 148 airports in Indonesia. The sampling technique uses total sampling, which means 148 airports that becomes the population unit then all of it become samples. The results of coefficient correlation (R) test showed that construction and infrastructure development activities variable have a relatively strong relationship with Airport Performance variable, but the value of Adjusted R Square shows that an increase in the construction and infrastructure development activities is influenced by factor other than Airport Performance.

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The Impact of Airport Performance towards Construction and Infrastructure Expansion in Indonesia

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Journal of Physics: Conference Series 2018年第1期954卷

作者： T D Laksono N Kurniasih C Hasyim M I Setiawan A S Ahmar Department of Civil Engineering Universitas Wijayakusuma Purwokerto Indonesia Faculty of Communication Science Library & Information Science Program Universitas Padjadjaran Bandung Indonesia Darul Ulum University Jombang Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia AHMAR Institute Makassar Indonesia Department of Statistics Universiats Negeri Makassar Indonesia

Development that is generated from airport areas includes construction and infrastructure development. This research reviews about how the implementation of material management in certain construction project and the relationship between development especially construction and infrastructure development with Airport Performance. The method that is used in this research is mixed method. The population in this research is 297 airports that are existed in Indonesia. From those 297 airports then it is chosen airports that have the most completed data about construction project and it is obtained 148 airports. Based on the coefficient correlation (R) test it is known that construction and infrastructure development has relatively strong relation with airport performance variable, but there are still other factors that influence construction and infrastructure development become bigger effect.

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