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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

四川生理科学杂志 2022年第7期44卷 1299-1299页

作者： Jonathan E Pekar Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA Department of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA 92037 USA Department of Computer Science and Engineering University of California San Diego La Jolla CA 92093 USA Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ 85721 USA W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health Baltimore MD 21205 USA New York City Public Health Laboratory New York City Department of Health and Mental Hygiene New York NY 11101 USA Department of Microbiology Institute for Viral Diseases Biosafety Center College of Medicine Korea University Seoul South Korea BK21 Graduate Program Department of Biomedical Sciences Korea University College of Medicine Seoul 02841 Republic of Korea National Public Health Laboratory National Centre for Infectious Diseases Singapore Malaysia Genome and Vaccine Institute Jalan Bangi 43000 Kajang Selangor Malaysia Department of Medicine University of California San Diego La Jolla CA 92093 USA Department of Microbiology and Immunology School of Medicine Tulane University New Orleans LA 70112 USA Zalgen Labs Frederick MD 21703 USA Global Virus Network (GVN) Baltimore MD 21201 USA Sydney Institute for Infectious Diseases School of Life and Environmental Sciences and School of Medical Sciences The University of Sydney Sydney NSW 2006 Australia Institute of Evolutionary Biology University of Edinburgh King’s Buildings Edinburgh EH9 3FL UK Department of Biomathematics David Geffen School of Medicine Un

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event.

关键词： epidemiology likely acute

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Real-time optimization using gradient adaptive selection and classification from infrared sensors measurement for esterification oleic acid with glycerol

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International Journal of Intelligent Computing and Cybernetics 2017年第2期10卷 130-144页

作者： Iwan Aang Soenandi Taufik Djatna Ani Suryani Irzaman Post Graduate Program of Agro-industrial Technology Bogor Agricultural UniversityBogorIndonesia and Faculty of Engineering and Computer ScienceKrida Wacana Christian UniversityJakartaIndonesia Post Graduate Program of Agro-industrial Technology Bogor Agricultural UniversityBogorIndonesia Department of Physics Faculty of Mathematics and Natural SciencesBogor Agricultural UniversityBogorIndonesia

Purpose-The production of glycerol derivatives by the esterification process is subject to many constraints related to the yield of the production target and the lack of process *** accurate monitoring and controlling of the process can improve production yield and *** purpose of this paper is to propose a real-time optimization(RTO)using gradient adaptive selection and classification from infrared sensor measurement to cover various disturbances and uncertainties in the ***/methodology/approach-The integration of the esterification process optimization using self-optimization(SO)was developed with classification process was combined with necessary condition optimum(NCO)as gradient adaptive selection,supported with laboratory scaled medium wavelength infrared(mid-IR)sensors,and measured the proposed optimization system indicator in the batch *** Process Modeling and Notation(BPMN 2.0)was built to describe the tasks of SO workflow in collaboration with NCO as an abstraction for the conceptual ***,Stateflow modeling was deployed to simulate the three states of gradient-based adaptive control combined with support vector machine(SVM)classification and Arduino microcontroller for ***-This new method shows that the real-time optimization responsiveness of control increased product yield up to 13 percent,lower error measurement with percentage error 1.11 percent,reduced the process duration up to 22 minutes,with an effective range of stirrer rotation set between 300 and 400 rpm and final temperature between 200 and 210℃ which was more efficient,as it consumed less *** limitations/implications-In this research the authors just have an experiment for the esterification process using glycerol,but as a development concept of RTO,it would be possible to apply for another chemical reaction or *** implications-This research introduces new development of an RTO approach to optimal con

关键词： Gradient technique Infrared sensor Real-time optimization Simulation and modelling Support vector machine

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Commuting planar polynomial vector fields for conservative Newton systems

arXiv

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arXiv 2018年

作者： Nagloo, Joel Ovchinnikov, Alexey Thompson, Peter Cuny Bronx Community College Department of Mathematics and Computer Science 2155 University Avenue BronxNY10453 United States Cuny Queens College Department of Mathematics 65-30 Kissena Blvd QueensNY11367 United States Cuny Graduate Center PH.D. Programs in Mathematics and Computer Science 365 Fifth Avenue New YorkNY10016 United States Cuny Graduate Center PH.D. Program in Mathematics 365 Fifth Avenue New YorkNY10016 United States

We study the problem of characterizing polynomial vector fields that commute with a given polynomial vector field on a plane. It is a classical result that one can write down solution formulas for an ODE that corresponds to a planar vector field that possesses a linearly independent commuting vector field. This problemis also central to the question of linearizability of vector fields. Let f ϵ K[x], where K is a field of characteristic zero, and d the derivation that corresponds to the differential equation x = f (x) in a standard way. Let also H be the Hamiltonian polynomial for d, that is H = 1 2 y2-R f (x)dx. It is known that the set of all polynomial derivations that commute with d forms a K[H]-module Md . In this paper, we show that, for every such d, the module Md is of rank 1 if and only if deg f ≥ 2. For example, the classical elliptic equation x = 6x2+a, where a ϵ ℂ, falls into this category.37J30, 13N10, 70H07 Copyright © 2018, The Authors. All rights reserved.

关键词： Hamiltonians

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Derivative-free superiorization: Principle and algorithm

arXiv

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arXiv 2019年

作者： Censor, Yair Garduño, Edgar Helou, Elias S. Herman, Gabor T. Department of Mathematics University of Haifa Mt. Carmel Haifa3498838 Israel Departamento de Ciencias de la Computación Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Universidad Nacional Autónoma de México Cd. Universitaria Mexico CityC.P. 04510 Mexico Department of Applied Mathematics and Statistics University of São Paulo São Carlos São Paulo13566-590 Brazil Computer Science Ph.D. Program Graduate Center City University of New York New YorkNY10016 United States

The superiorization methodology is intended to work with input data of constrained minimization problems, that is, a target function and a set of constraints. However, it is based on an antipodal way of thinking to what leads to constrained minimization methods. Instead of adapting unconstrained minimization algorithms to handling constraints, it adapts feasibility-seeking algorithms to reduce (not necessarily minimize) target function values. This is done by inserting target-function-reducing perturbations into a feasibility-seeking algorithm while retaining its feasibility-seeking ability and without paying a high computational price. A superiorized algorithm that employs component-wise target function reduction steps is presented. This enables derivative-free superiorization (DFS), meaning that superiorization can be applied to target functions that have no calculable partial derivatives or subgradients. The numerical behavior of our derivative-free superiorization algorithm is illustrated on a data set generated by simulating a problem of image reconstruction from projections. The plots of proximity-target curves of our experiments demonstrate the advantage of the proposed derivative-free superiorization algorithm. Copyright © 2019, The Authors. All rights reserved.

关键词： Constrained optimization

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Inventory control systems with safety stock and reorder point approach 1

Inventory control systems with safety stock and reorder poin...

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1st International Conference on Information and Communications Technology, ICOIACT 2018

作者： Efrilianda, Devi Ajeng Mustafid Isnanto, R. Rizal Master Program of Information Systems School of Post Graduate Studies Diponegoro University Semarang Indonesia Department of Statistics Faculty of Science and Mathematics Diponegoro University Semarang Central Java Indonesia Department of Computer Systems Faculty of Engineering Diponegoro University Semarang Indonesia

ISBN: (纸本)9781538609545

The inventory control systems has an important role to monitor the condition of the goods at the supply chain stage of goods distribution from the central warehouse to retail in accordance with consumer demand. The research aims to develop inventory control systems on the supply chain distribution of goods from suppliers to retail through the central warehouse with minimal supply chain costs. Minimization of supply chain cost using martingale model of forecast evaluation, and the result as the basis for calculation of safety stock and reorder point. The results of research are the system that can be used to control inventory and renewal of goods in the central warehouse by calculating the minimization of supply chain cost based on consumer demand. Case studies were conducted on the supply chain distribution of goods from the central warehouse to the retail in Semarang. The observation data derived from the goods distribution from central warehouse to retail for certain products over 4 time periods. Through such inventory control system, can minimize supply chain cost, and product inventory level can be maintained in time and amount of inventory that must be fulfilled. © 2018 IEEE.

关键词： Supply chains

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Classifying Attitudes of Thai Business Organizations Toward the Perceived Benefit of Customer Predictive Analytics

Classifying Attitudes of Thai Business Organizations Toward ...

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International Symposium on Soft Computing and Intelligent Systems (SCIS)

作者： Santisook Limpeeticharoenchot Nagul Cooharojananone Thira Chavarnakul Kanokwan Atchariyachanvanich Technopreneurship and Innovation Management Program Graduate School Chulalongkorn University Bangkok Thailand Department of Mathematics and Computer Science Faculty of Science Chulalongkorn University Bangkok Thailand Department of Commerce Chulalongkorn University Bangkok Thailand Faculty of Information Technology King Mongkut’s Institute of Technology Ladkrabang Bangkok Thailand

ISBN: (纸本)9781538626344;9781538626337

In this paper, we applied K-means++, Agglomerative and Decision Tree techniques to classify characteristics of Thai business organizations toward the perceived benefit of predictive analytics. We believe that different characteristics of business organizations require different solution approaches to overcome challenges and gain business value. In the exploratory survey, we collected 84 respondents, who are data analysts, business analysts, business owners, management, and IT managers. The respondents' size of organization varies from small firms to large firms. The result from three techniques of classification shows that Thai business organizations perceiving the benefit of predictive analytics could be divided into two groups. We further confirmed that with the analysis of variance technique to identify the difference of means in each parameter. We also found that the most important descriptive profile is led by customer-related factors such as a change in the percentage of customers, the number of direct customers, and number of sales and marketing staff. These are followed by technology factors, which are the number of external and internal data sources and number of analytics and technologies currently used for data analytics.

关键词： Organizations Data analysis Clustering algorithms Big Data Organizational aspects Decision trees

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Ten quick tips for deep learning in biology

arXiv

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arXiv 2021年

作者： Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others. © 2021, CC BY.

关键词： Learning algorithms

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Validation of MRI-VLFF for the non-invasive measurement of steatosis in children

GastroHep

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GastroHep 2020年第4期2卷

作者： Miriam B. Vos Eduardo Castillo-Leon Jack Knight-Scott Rebecca Cleeton Alvin Jay Freeman Jennifer K. Frediani Albert Hernandez Stephen F. Simoneaux Jun Kong Alton Brad Farris Michael J House Tim St. Pierre Division of Gastroenterology Hepatology and Nutrition Department of Pediatrics Emory University Atlanta GA USA Children's Healthcare of Atlanta Atlanta GA USA Nutrition and Health Sciences Program Laney Graduate School Emory University Atlanta GA USA Department of Radiology Children's Healthcare of Atlanta Atlanta GA USA Department of Computer Science and Biomedical Informatics Emory University Atlanta GA USA Department of Mathematics and Statistics and Computer Science Georgia State University Atlanta GA USA Department of Pathology and Laboratory Medicine Emory University Atlanta GA USA School of Physics Mathematics and Computing The University of Western Australia Crawley WA Australia Resonance Health Ltd Claremont WA Australia

Background & Aims Magnetic resonance-based steatosis measurement of the liver has become the non-invasive gold standard; however very few diagnostic thresholds have been independently validated and none in children. This study was designed to validate diagnostic thresholds, assess repeatability and the relationship to histology of a proprietary MRI volumetric liver fat fraction (VLFF) method (HepaFat-Scan ® ) and magnetic resonance spectroscopy (MRS) proton density fat fraction (PDFF) method. Methods This cross-sectional study assesses the diagnostic accuracy of MRI-VLFF and MRS-PDFF of 50 children who had a clinically indicated liver biopsy. Twenty-five children were randomly selected for intra-examination repeatability. The positive pixel count (PPC) algorithm was used to quantify the area of fat vesicles in the histology. The area under the receiver operating characteristic curve (AUROC) was used to assess the diagnostic accuracy. Bland-Altman plots were used to compare the methods and examine the repeatability. Results The MRI-VLFF ranged from 0.3% to 35.4% and the MRS-PDFF ranged from 0.5% to 36.9%. Based on histopathological analysis, the diagnostic accuracy of MRI-VLFF for steatosis detection (grade 0 vs 1-3) showed an AUROC of 0.95 (95% confidence interval [CI]: 0.89-1.00), whereas MRI-PDFF classified grade 0 vs 1-3 showed an AUROC of 0.96 (95% CI: 0.91-1.00). The repeatability coefficients were 1.8 (±0.5) % for MRI-VLFF and 2.1 (±0.6) % for MRS-PDFF. There was no bias between MRI-VLFF and PPC steatosis. To allow direct comparison, MRS-PDFF was converted to MRS-VLFF. Small, but significant biases were measured between PPC steatosis and MRS-VLFF (−1.38%) and between MRI-VLFF and MRS-VLFF (−1.39%). Conclusions Both MRI-VLFF and MRS-PDFF accurately estimated hepatic steatosis in children with excellent agreement with the histological assessment.

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STRING-AVERAGING ALGORITHMS FOR CONVEX FEASIBILITY WITH INFINITELY MANY SETS

arXiv

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arXiv 2018年

作者： Kong, T. Yung Pajoohesh, Homeira Herman, Gabor T. Computer Science Department Queens College City University of New York FlushingNY11367 United States Mathematics Department Medgar Evers College City University of New York BrooklynNY11225 United States Computer Science Ph.D. Program The Graduate Center City University of New York New YorkNY10016 United States

Algorithms for convex feasibility find or approximate a point in the intersection of given closed convex sets. Typically there are only finitely many convex sets, but the case of infinitely many convex sets also has some applications. In this context, a string is a finite sequence of points each of which is obtained from the previous point by considering one of the convex sets. In a string-averaging algorithm, an iterative step from a first point to a second point computes a number of strings, all starting with the first point, and then calculates a (weighted) average of those strings’ end-points: This average is that iterative step’s second point, which is used as the first point for the next iterative step. For string-averaging algorithms based on strings in which each point either is the projection of the previous point on one of the convex sets or is equal to the previous point, we present theorems that provide answers to the following question: "How can the iterative steps be specified so that the string-averaging algorithm generates a convergent sequence whose limit lies in the intersection of the sets of a given convex feasibility problem?" This paper focuses on the case where the given collection of convex sets is infinite, whereas prior work on the same question that we are aware of has assumed the collection of convex sets is finite (or has been applicable only to a small subset of the algorithms we consider). The string-averaging algorithms that are shown to generate a convergent sequence whose limit lies in the intersection are also shown to be perturbation resilient, so they can be superiorized to generate sequences that also converge to a point of the intersection but in a manner that is superior with respect to some application-dependent criterion.46N10 46N40 47H09 47H10 47J25 47N10 65F10 65J99 65K10 90C25 90C30 Copyright © 2018, The Authors. All rights reserved.

关键词： Iterative methods

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Designing the Application of Security Text Messages into Audio Files Using Data Encryption Standard (DES) Algorithms Using the End of File (EOF) Method 1

Designing the Application of Security Text Messages into Aud...

引用

1st Workshop on Environmental science, Society, and Technology, WESTECH 2018

作者： Pardede, A.M.H. Pramana, Anggi Zarlis, Muhammad Iskandar, Akbar Manurung, Rosida Tiurma Sriadhi, S. Kurniawan, Citra Hasibuan, Abdurrozzaq Siregar, Nurintan Asyiah Sari, Ayu Esteka Mulyaningsih, Indrya Iskandar Alam, Teguh Hidayat Ibrahim Listyorini, Tri Winarno, Edy Tulus STMIK Kaputama Binjai Sumatera Utara Indonesia Department of Computer Science Universitas Sumatera Utara Medan Indonesia Department of Informatics STMIK AKBA Makassar Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Department of Electrical Engineering Sekolah Tinggi Teknik Malang Indonesia Faculty of Engineering Universitas Islam Sumatera Utara Medan Indonesia Department of Management STIE Labuhanbatu Sumatera Utara Indonesia Department of Management STIE Sakti Alam Kerinci Jambi Indonesia Department of Indonesian Language Teaching Institut Agama Islam Negeri Syekh Nurjati Cirebon Indonesia Department of Informatics Engineering Universitas Muhammadiyah Sorong Sorong Indonesia Department of English Education Universitas Muhammadiyah Sorong Sorong Indonesia Department of Informatics Universitas Muria Kudus Indonesia Faculty of Information Technology Universitas Stikubank Semarang Indonesia Department of Mathematics Universitas Sumatera Utara Medan Indonesia

There are several ways to deal with security issues of confidential data sent via the internet, including using cryptographic techniques and steganography. Steganography is the science and art of concealing information / messages in a media in such a way that its existence is not detected by other parties who are not entitled to the information. Instead, cryptography disguises the meaning of a message, but does not hide that there is a message because the file looks suspicious. The Steganography technique used here was End Of File (EOF). The EOF technique described how to add data or files at the end of the image file. For this technique, the size of data or files that will be hidden could be larger than the size of the image file. The hidden data will be inserted at the end of the file so that it will not affect the image. This steganography application is also equipped with a cryptographic function Data Encryption Standard (DES) at the time of insertion of data that functions as a generator code and encrypts data, so that the security of a data in the file is more protected and protected from those who are not entitled to know the data. © Published under licence by IOP Publishing Ltd.

关键词： Steganography

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