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arXiv 2024年

作者： Emons, Martin Gunz, Samuel Crowell, Helena L. Mallona, Izaskun Furrer, Reinhard Robinson, Mark D. Department of Molecular Life Sciences SIB Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Barcelona Spain Department of Mathematical Modeling and Machine Learning University of Zurich Zurich Switzerland

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can give rise to very different data modalities. The characteristics of the two data types are well known in adjacent fields such as spatial statistics as point patterns and lattice data, and there is a wide range of tools available. This paper discusses the application of spatial statistics to spatially-resolved omics data and in particular, discusses various advantages, challenges, and nuances. This work is accompanied by a vignette, pasta, that showcases the usefulness of spatial statistics in biology using several R packages. © 2024, CC BY.

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InterCriteria Analysis of the Financial System in the EU Countries 10

InterCriteria Analysis of the Financial System in the EU Cou...

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10th IEEE International Conference on Intelligent Systems, IS 2020

作者： Danailova-Veleva, Slaviiana Doukovska, Lyubka Atanassova, Vassia IICT-BAS Intelligent Systems Department Sofia Bulgaria IBBE-BAS Bioinformatics and Mathematical Modeling Department Sofia Bulgaria

ISBN: (纸本)9781728154565

The paper presents an analysis of the financial systems of the EU member states which is an actual problem. The paper showcases a new method of analyzing and grading of the connection between the criteria defining the state of the financial systems. The presented multicriteria decision making method is based on two fundamental concepts: Intuitionistic Fuzzy Sets (IFSs) and Index Matrices (IMs). We have named it 'InterCriteria' decision making approach. The data for the financial systems of the EU member states is sourced from the World Economic Forum's Global Competitiveness Reports for 2019. The assessment was made using 12 main drivers, so called Pillars. The main goal is to assess the competitiveness of each EU country. © 2020 IEEE.

关键词： Intelligent systems

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Kinetic modules are sources of concentration robustness in biochemical networks

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Science Advances 2025年第22期11卷 eads7269页

作者： Langary, Damoun Küken, Anika Nikoloski, Zoran Systems Biology and Mathematical Modeling Max Planck Institute of Molecular Plant Physiology Potsdam14476 Germany Bioinformatics Department Institute of Biochemistry and Biology University of Potsdam Potsdam14476 Germany

Modules represent fundamental building blocks of cellular networks and are thought to facilitate robustness of phenotypes against perturbations. While reaction kinetic shapes the concentration of components and reaction rates, its use in identification of modules entails knowledge of parameter values. Here, we demonstrate that kinetic modules can be efficiently identified on the basis of steady-state reaction rate couplings in large-scale biochemical networks endowed with mass action kinetics without knowledge of parameter values. We then link the kinetic modules of metabolic networks with robustness of metabolite concentrations to perturbations. Analyzing 34 metabolic network models of 26 organisms, we demonstrate that the ordered binding enzyme mechanism leads to increased concentration robustness compared to random binding. Our findings pave the way for usage of modules in synthetic biology and biotechnological applications. Copyright © 2025 The Authors, some rights reserved

关键词： Rate constants

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The theory of prioritized Muirhead mean operators under the presence of Complex Single-Valued Neutrosophic values

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Decision Analytics Journal 2023年 7卷

作者： Imran, Raiha Ullah, Kifayat Ali, Zeeshan Akram, Maria Senapati, Tapan Department of Mathematics Riphah Institute of Computing & Applied Sciences (RICAS) Riphah International University (Lahore Campus) Lahore 54000 Pakistan Department of Mathematics & Statistics International Islamic University Islamabad Islamabad 44000 Pakistan KERMIT Department of Mathematical Modeling Statistics and Bioinformatics Coupure Links 653 Ghent University Ghent Belgium School of Mathematics and Statistics Southwest University Chongqing Beibei 400715 China

The Muirhead mean (MM) operator is effective and feasible and is used for aggregating the finite collection of attributes into a singleton set, where the averaging and geometric aggregation operators are the special cases of the MM operator. Furthermore, the Complex Single-Valued Neutrosophic (CSVN) set theory is more reliable than the intuitionistic fuzzy set theory because it can easily handle awkward and unreliable information with the triplet, such as yes, abstinence, and no. In this manuscript, we present the theory of MM operators under the presence of CSVN values, such as the CSVN prioritized MM (CSVNPMM) operator and the CSVN prioritized dual MM (CSVNPDMM) operator. Some important and dominant properties are examined in the derived theory. Additionally, to verify the above information with the help of some appropriate examples, we demonstrate a Multi-Attribute Decision-Making (MADM) method for the proposed operators under the consideration of CSVN information. Finally, we compare the derived operators with some prevailing information to state the practicality and validity of the proposed method. © 2023 The Author(s)

关键词： Complex single-valued neutrosophic sets Decision support Dual Muirhead mean operators Multi-attribute decision-making Prioritized Muirhead

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InterCriteria Analysis of the Financial System in the EU Countries

InterCriteria Analysis of the Financial System in the EU Cou...

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International IEEE Conference on Intelligent Systems, IS

作者： Slaviiana Danailova-Veleva Lyubka Doukovska Vassia Atanassova Intelligent Systems Department IICT-BAS Sofia Bulgaria Bioinformatics and Mathematical Modeling Department IBBE-BAS Sofia Bulgaria

ISBN: (数字)9781728154565

ISBN: (纸本)9781728154572

The paper presents an analysis of the financial systems of the EU member states which is an actual problem. The paper showcases a new method of analyzing and grading of the connection between the criteria defining the state of the financial systems. The presented multicriteria decision making method is based on two fundamental concepts: Intuitionistic Fuzzy Sets (IFSs) and Index Matrices (IMs). We have named it `InterCriteria' decision making approach. The data for the financial systems of the EU member states is sourced from the World Economic Forum's Global Competitiveness Reports for 2019. The assessment was made using 12 main drivers, so called Pillars. The main goal is to assess the competitiveness of each EU country.

关键词： Indexes Economic indicators Decision making Fuzzy sets Correlation Venture capital

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Improvement of effluent quality and cost saving at a 750,000pe WRRF using an extensively validated CFD model 91

Improvement of effluent quality and cost saving at a 750,000...

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91st Annual Water Environment Federation Technical Exhibition and Conference, WEFTEC 2018

作者： Rehman, U. Audenaert, W. Bellandi, G. Flameling, T. Weijers, S. Nopens, I. BIOMATH Department of Mathematical Modeling Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent9000 Belgium AM-TEAM Advanced modelling for process optimisation Hulstbaan 63 Sint-Niklaas9112 Belgium Waterboard De Dommel PO Box 10.001 DA Boxtel5280 Netherlands Department of Civil and Environmental Engineering University of Florence via di S. Marta 3 Florence50139 Italy

ISBN: (纸本)9781510877474

Besides trial-and-error approaches, conventional flowsheet modelling (such as tanks-in-series (TIS)) is widely used to optimize the performance of Water Resource Recovery Facilities (WRRFs). However, this modelling approach lacks the ability to consider design parameters such as propellers and aerator configurations. Trial-and-error based optimisation of such parameters is in many cases highly risky or even impossible. By appropriate use of computational fluid dynamics (CFD), one can accurately and efficiently evaluate different design changes prior to actual implementation, while severely extending system understanding. The current study shows the practical application of CFD for full-scale bioreactor optimization in terms of performance (lower effluent nitrate) and cost. The CFD model was unprecedentedly validated using a construction crane for dissolved oxygen profiling. Also flow velocities were measured. Different new propeller settings and aerator configurations were tested. Unwanted oxygen near the inlet of the anoxic zone could be reduced up to 20%. One of the promising scenarios was implemented in practice and the impact on effluent quality is currently being evaluated. The operational change will have a potential operational cost saving of minimum 500,000 EUR/y. Copyright © 2018 Water Environment Federation

关键词： Bioreactors

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Generalized net model of surface emg data processing for control of active elbow orthosis device

Generalized net model of surface emg data processing for con...

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Advances in Neural Networks and Applications 2018, ANNA 2018

作者： Ribagin, Simeon Pencheva, Tania Shannon, Anthony Department of Bioinformatics and Mathematical Modelling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Sofia Bulgaria Department of Health and Social Care Medical College University "Prof. D-r Asen Zlatarov" Burgas Bulgaria Department of QSAR and Molecular Modeling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Sofia Bulgaria Warrane College University of New South Wales KensingtonNSW2033 Australia

ISBN: (纸本)9783800747566

Surface Electromyography (sEMG) signals have been increasingly used in many applications, including biomedical, neuroprosthetic limbs, orthotic or rehabilitation devices, human machine interactions etc. In order to use such signals for the control purposes, a certain processing algorithm has to be performed. This paper presents a novel approach for sEMG data processing with the usage of generalized nets theory. We propose an abstract model representing the sEMG data processing, which can be used in the control frameworks of active elbow orthosis devices. © 2018 VDE VERLAG GMBH Berlin Offenbach

关键词： Data handling

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Generalized Net Model of Surface EMG Data Processing for Control of Active Elbow Orthosis Device

Generalized Net Model of Surface EMG Data Processing for Con...

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ANNA '18;Advances in Neural Networks and Applications 2018

作者： Simeon Ribagin Tania Pencheva Anthony Shannon Department of Bioinformatics and Mathematical Modelling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Department of QSAR and Molecular Modeling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Warrane College The University of New South Wales

ISBN: (纸本)9783800747566

关键词： Standing Orders SEMA5B gene Surface Electromyography Automatic data processing data processing Orthotic Devices network model Elbow signals

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Correction to: Meeting report from the fourth meeting of the Computational modeling in Biology Network (COMBINE)

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Standards in genomic sciences 2018年第1期13卷 17页

作者： Dagmar Waltemath Frank T Bergmann Claudine Chaouiya Tobias Czauderna Padraig Gleeson Carole Goble Martin Golebiewski Michael Hucka Nick Juty Olga Krebs Nicolas Le Novère Huaiyu Mi Ion I Moraru Chris J Myers David Nickerson Brett G Olivier Nicolas Rodriguez Falk Schreiber Lucian Smith Fengkai Zhang Eric Bonnet 1Department of Systems Biology and Bioinformatics University of Rostock Rostock Germany. 2Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA. 4Instituto Gulbenkian de Ciência - IGC Rua da Quinta Grande Oeiras Portugal. 3IPK Gatersleben Gatersleben Germany. 5Department of Neuroscience Physiology and Pharmacology University College London London UK. 6School of Computer Science The University of Manchester Manchester UK. 7Heidelberg Institute for Theoretical Studies Heidelberg Germany. 8EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge UK. 14The Babraham Institute Babraham Research Campus Cambridge UK. 9Department of preventive medicine Keck School of Medicine University of Southern California Los Angeles CA USA. 10Center for Cell Analysis and Modeling University of Connecticut Health Center Farmington CT USA. 11Department of Electrical and Computer Engineering University of Utah Salt Lake City USA. 12Auckland Bioengineering Institute University of Auckland Auckland New Zealand. 13Systems Bioinformatics VU University Amsterdam Amsterdam The Netherlands. 15Martin Luther University Halle-Wittenberg Halle Germany. 16Monash University Melbourne Australia. Computational Biology Unit Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases NIH Bethesda MD USA. 18Institut Curie Paris France. INSERM U900 75248 Paris France. 20Mines ParisTech 77300 Fontainebleau Paris France.

[This corrects the article DOI: 10.4056/sigs.5279417.].

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Creation and analysis of biochemical constraint-based models: The COBRA Toolbox v3.0

arXiv

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arXiv 2017年

作者： Heirendt, Laurent Arreckx, Sylvain Pfau, Thomas Mendoza, Sebastián N. Richelle, Anne Heinken, Almut Haraldsdóttir, Hulda S. Wachowiak, Jacek Keating, Sarah M. Vlasov, Vanja Magnusdóttir, Stefania Ng, Chiam Yu Preciat, German Žagare, Alise Chan, Siu H.J. Aurich, Maike K. Clancy, Catherine M. Modamio, Jennifer Sauls, John T. Noronha, Alberto Bordbar, Aarash Cousins, Benjamin El Assal, Diana C. Valcarcel, Luis V. Apaolaza, Iñigo Ghaderi, Susan Ahookhosh, Masoud Guebila, Marouen Ben Kostromins, Andrejs Sompairac, Nicolas Le, Hoai M. Ma, Ding Sun, Yuekai Wang, Lin Yurkovich, James T. Oliveira, Miguel A.P. Vuong, Phan T. El Assal, Lemmer P. Kuperstein, Inna Zinovyev, Andrei Scott Hinton, H. Bryant, William A. Aragón Artacho, Francisco J. Planes, Francisco J. Stalidzans, Egils Maass, Alejandro Vempala, Santosh Hucka, Michael Saunders, Michael A. Maranas, Costas D. Lewis, Nathan E. Sauter, Thomas Palsson, Bernhard Ø. Thiele, Ines Fleming, Ronan M.T. Luxembourg Centre for Systems Biomedicine University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg Life Sciences Research Unit University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg University of Chile Blanco Encalada 2085 Santiago Chile Department of Pediatrics University of California San Diego School of Medicine San DiegoCA92093 United States Hinxton CambridgeCB10 1SD United Kingdom Department of Chemical Engineering Pennsylvania State University University University ParkPA16802 United States Department of Physics University of California San Diego 9500 Gilman Dr. San DiegoCA92093 United States Bioinformatics and Systems Biology Program University of California San Diego San DiegoCA United States Sinopia Biosciences San DiegoCA United States School of Computer Science Algorithms and Randomness Center Georgia Institute of Technology AtlantaGA United States Biomedical Engineering and Sciences Department TECNUN University of Navarra Paseo de Manuel Lardizabal 13 San Sebastian20018 Spain Institute of Microbiology and Biotechnology University of Latvia Jelgavas iela 1 RigaLV-1004 Latvia Department of Management Science and Engineering Stanford University StanfordCA94305-4026 United States Bioengineering Department University of California San Diego San DiegoCA United States Utah State University Research Foundation 1695 North Research Park Way North LoganUT84341 United States Centre for Integrative Systems Biology and Bioinformatics Department of Life Sciences Imperial College London London United Kingdom Department of Mathematics University of Alicante Spain California Institute of Technology Computing and Mathematical Sciences MC 305-16 1200 E. California Blvd. PasadenaCA91125 United States Mathomics Center for Mathematical Modeling University of Chile Beauchef 851 Santiago Chile Novo Nordisk Foundation Center for Biosustainability University of California San Diego San DiegoCA92093 Uni

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Data integration

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