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What makes a reaction network "chemical"?

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arXiv 2022年

作者： Müller, Stefan Flamm, Christoph Stadler, Peter F. Faculty of Mathematics University of Vienna Oskar-Morgenstern-Platz 1 WienA-1090 Austria Department of Theoretical Chemistry University of Vienna Währinger Straße 17 WienA-1090 Austria Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases University Leipzig LeipzigD-04107 Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Faculdad de Ciencias Universidad Nacional de Colombia Sede Bogotá Ciudad Universitaria DC BogotáCOL-111321 Colombia Santa Fe Institute 1399 Hyde Park Road Santa FeNM87501 United States

Background: Reaction networks (RNs) comprise a set X of species and a set R of reactions Y → Y′, each converting a multiset of educts Y ⊆ X into a multiset Y′ ⊆ X of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix S ∈ X×R have been discussed extensively in the chemical literature. Here, we provide sufficient conditions for S that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively. Results: Chemically plausible RNs allow neither a perpetuum mobile, i.e., a "futile cycle" of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of the stoichiometric matrix S. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and – in a stricter sense – futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. Furthermore, it is sufficient for the existence of a realization in terms of sum formulas, obeying conservation of "atoms". In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless S implies that they are "obligatory isomers". In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved. In particular, for every conservative RN, there exists a Lewis realization, in which any two compounds are realized by pairwisely distinct mu

关键词： Energy conservation

Electrocardiographic Deep Learning for Predicting Post-Procedural Mortality

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arXiv 2022年

作者： Ouyang, David Theurer, John Stein, Nathan R. Hughes, J. Weston Elias, Pierre He, Bryan Yuan, Neal Duffy, Grant Sandhu, Roopinder K. Ebinger, Joseph Botting, Patrick Jujjavarapu, Melvin Claggett, Brian Tooley, James E. Poterucha, Tim Chen, Jonathan H. Nurok, Michael Perez, Marco Perotte, Adler Zou, James Y. Cook, Nancy R. Chugh, Sumeet S. Cheng, Susan Albert, Christine M. Department of Cardiology Smidt Heart Institute Cedars-Sinai Medical Center United States Division of Artificial Intelligence in Medicine Department of Medicine Cedars-Sinai Medical Center United States Department of Computer Science Stanford University United States Milstein Division of Cardiology Department of Medicine Columbia University Irving Medical Center United States Department of Biomedical Informatics Columbia University Irving Medical Center United States Division of Cardiovascular Medicine Department of Medicine Brigham and Women's Hospital United States Division of Cardiology Department of Medicine Stanford University United States Division of Bioinformatics Research Department of Medicine Stanford University United States Division of Anesthesia Department of Surgery Cedars-Sinai Medical Center United States Department of Biomedical Data Science Stanford University United States Division of Preventive Medicine Department of Medicine Brigham and Women's Hospital United States

Background. Pre-operative risk assessments used in clinical practice are limited in their ability to identify risk for post-operative mortality. We hypothesize that electrocardiograms contain hidden risk markers that can help prognosticate post-operative mortality. Methods. In a derivation cohort of 45,969 pre-operative patients (age 59±19 years, 55% women), a deep learning algorithm was developed to leverage waveform signals from pre-operative ECGs to discriminate post-operative mortality. Model performance was assessed in a holdout internal test dataset and in two external hospital cohorts and compared with the Revised Cardiac Risk Index (RCRI) score. Results. In the derivation cohort, there were 1,452 deaths. The algorithm discriminates mortality with an AUC of 0.83 (95% CI 0.79-0.87) surpassing the discrimination of the RCRI score with an AUC of 0.67 (CI 0.61-0.72) in the held out test cohort. Patients determined to be high risk by the deep learning model's risk prediction had an unadjusted odds ratio (OR) of 8.83 (5.57- 13.20) for post-operative mortality as compared to an unadjusted OR of 2.08 (CI 0.77-3.50) for postoperative mortality for RCRI >2. The deep learning algorithm performed similarly for patients undergoing cardiac surgery with an AUC of 0.85 (CI 0.77 - 0.92), non-cardiac surgery with an AUC of 0.83 (0.79 - 0.88), and catherization/endoscopy suite procedures with an AUC of 0.76 (0.72 - 0.81). The algorithm similarly discriminated risk for mortality in two separate external validation cohorts from independent healthcare systems with AUCs of 0.79 (0.75-0.83) and 0.75 (0.74-0.76) respectively. Conclusion. The findings demonstrate how a novel deep learning algorithm, applied to preoperative ECGs, can improve discrimination of post-operative mortality. Copyright © 2022, The Authors. All rights reserved.

关键词： Learning algorithms

data for Genomics in Healthcare: The Potential of Next-Generation Sequencing in Developing Precision Medicine

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IOP Conference Series: Earth and Environmental science 2021年第1期794卷

作者： Dafa Dwi Antara Michael Yahezkiel Lie Muhammad Darisza Nicola Kertapati Ivan Valentino Bharuno Mahesworo Ika Nurlaila Haryono Soeparno Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480

Recent advances in genomics on healthcare technology have opened the path towards more precise treatments by analysing patients' genome using a high throughput DNA sequencing technology called Next Generation Sequencing (NGS). The information obtained is further used to determine a more effective treatment path for patients based on their genetic profiles. It can also be employed to predict the risk of patients developing certain diseases. Despite particular difficulties it might create in the first phase of settling the integrative frameworks down, a successful combination of NGS and Big data technology would offer a huge improvement in terms of the effectiveness of treatments and medicine administration for the patients. This paper elucidates a general overview of how NGS-based DNA sequencing makes precision medicine possible and describes the use of Big data for genomics in healthcare-wise.

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Smart IoT CPO Storage Tank

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： Rengga Arnalis Renjani Hermantoro Prima Okta Adi Nugraha Kartika Purwandari Teddy Suparyanto Bens Pardamean Department of Agricultural Engineering Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Indonesia's crude palm oil (CPO) production from year to year continues to increase, at the end of 2020 it reached 17.35 million tons, up 3.6% from the previous year. Increasing production will result in more CPO stock and require good storage. The storage process that occurs is to maintain the temperature of the CPO so that the quality is not damaged. This temperature regulation is still done manually and raises the risk of work accidents. The purpose of this research is to create a temperature control system and automatic volume measurement that can be monitored from a smartphone. The manufacture of a control system used ESP8266 NodeMCu microcontroller, temperature sensor, proximity sensor, and 1000-Watt heater. Programming used the Arduino IDE and C++. The result of this study was an IoT CPO Storage Tank design equipped with sensors and microcontrollers. The temperature was measured with the DS18B20 sensor had a data accuracy of 99.19% while the volume measured with the HC-SR04 sensor had an accuracy of 99.78%. data obtained from the sensor could be seen through the Thingspeak application from a computer or smartphone.

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Application for sugarcane plantation: Manpower and transportation planning

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AIP Conference Proceedings 2023年第1期2594卷

作者： H. G. Mawandha D. Sudigyo T. Suparyanto B. Pardamean Department of Agrotechnology Institute of Agriculture STIPER Yogyakarta Indonesia 55281 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Sugarcane plantations in Indonesia are still managed in a labor-intensive manner, especially plantation-owned by farmers. Labor intensive means that every stage of work in sugarcane plantation management still uses manpower. One of the jobs in sugarcane plantations that requires a lot of labor is sugar cane harvesting. Trend changing in the workforce gender would affect the quantity and quality of jobs, which is determined by the workforce's capacity and the workload of the work performed. The result of this research was a sugarcane agricultural calculator that made it simple for farmers to measure manpower and transportation requirements in estimating harvest costs. Manpower and transportation of harvested sugarcane commodities were estimated through the workload approach, namely, crop production and manpower's ability to carry a load. These two components helped sugarcane farmers to determine manpower and transportation during the harvest. The final yield produced by the projected harvest labor cost would be known immediately.

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Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

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arXiv 2020年

作者： Schaller, David Geiß, Manuela Stadler, Peter F. Hellmuth, Marc Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Bioinformatics Group Department of Computer Science & Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Software Competence Center Hagenberg GmbH Softwarepark 21 HagenbergA-4232 Austria Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine at Leipzig University Universität Leipzig Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States School of Computing University of Leeds EC Stoner Building LeedsLS2 9JT United Kingdom

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the Reciprocal Best Match Graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the Best Match Graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique "augmented tree" that explains the BMG and identifies all u-fp edges in terms of overlapping sets of species in certain subtrees. The augmented tree can be constructed as a refinement of the unique least resolved tree of the BMG in polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology *** Codes 92-08, MSC 92D15, MSC 68R01 Copyright © 2020, The Authors. All rights reserved.

关键词： Forestry

Chemical transformation motifs - Modelling pathways as integer hyperflows

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arXiv 2017年

作者： Andersen, Jakob L. Flamm, Christoph Merkle, Daniel Stadler, Peter F. Earth-Life Science Institute Tokyo Institute of Technology Tokyo 152-8550 Japan Department of Mathematics and Computer Science University of Southern Denmark Odense M DK-5230 Denmark Research group Bioinformatics and Computational Biology Faculty of Computer Science University of Vienna Vienna 1090 Austria Institute for Theoretical Chemistry University of Vienna Wien 1090 Austria Halle-Jena-Leipzig and Competence Center for Scalable Data Services Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases University of Leipzig Leipzig D-04107 Germany Max Planck Institute for Mathematics in the Sciences Leipzig D-04103 Germany Fraunhofer Institute for Cell Therapy and Immunology Leipzig D-04103 Germany Center for non-coding RNA in Technology and Health University of Copenhagen Frederiksberg C DK-1870 Denmark Santa Fe Institute 1399 Hyde Park Rd Santa Fe NM 87501 United States Research Network Chemistry Meets Microbiology University of Vienna Wien A-1090 Austria

We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions. Pathways are modelled as integer hyperflows and we expand the network model by detailed routing constraints. In contrast to the more traditional approaches like Flux Balance Analysis or Elementary Mode analysis we insist on integer-valued flows. While this choice makes it necessary to solve possibly hard integer linear programs, it has the advantage that more detailed mechanistic questions can be formulated. It is thus possible to query networks for general transformation motifs, and to automatically enumerate optimal and near-optimal pathways. Similarities and differences between our work and traditional approaches in metabolic network analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest. Copyright © 2017, The Authors. All rights reserved.

关键词： Integer programming

Relative Timing Information and Orthology in Evolutionary Scenarios

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arXiv 2022年

作者： Schaller, David Hartmann, Tom Lafond, Manuel Wieseke, Nicolas Stadler, Peter F. Hellmuth, Marc Bioinformatics Group Department of Computer Science Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Department of Computer Science Université de Sherbrooke 2500 boul. de l’Université SherbrookeQCJ1K 2R1 Canada Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine Leipzig University Universität Leipzig Germany Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States Swarm Intelligence and Complex Systems Group Department of Computer Science Leipzig University Augustusplatz 10 LeipzigD-04109 Germany Department of Mathematics Faculty of Science Stockholm University StockholmSE - 106 91 Sweden

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs. © 2022, CC BY.

关键词： Genes

Deep Learning with Greedy Layer-Wise Compound Scaling for Temperature and Humidity Prediction in Solar Dryer Dome

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SSRN

SSRN 2022年

作者： Cenggoro, Tjeng Wawan Elwirehardja, Gregorius Natanael Dominic, Nicholas Setiawan, Karli Eka Rahutomo, Reza Djuana, Endang Gunawan, Fergyanto E. Budiman, Arief S. Romeli, Sugiarto Pardamean, Bens Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia Electrical Engineering Department Faculty of Industrial Technology Universitas Trisakti Jakarta11440 Indonesia Industrial Engineering Department BINUS Graduate Program Master of Industrial Engineering Bina Nusantara University Jakarta11480 Indonesia Department of Manufacturing and Mechanical Engineering and Technology Oregon Institute of Technology Klamath FallsOR97601 United States PT. Impack Pratama Industri Jakarta Indonesia

Drying has been an eco-friendly and cost-efficient method to reduce post-harvest losses of agricultural crops. In various countries, the technique has been widely utilized in the form of Solar Dryer Dome (SDD) buildings. Accurate indoor microclimate forecasting is very important to implement smart control systems in SDDs that can maintain the ideal conditions, as the availability of solar energy is limited only at daytimes and the temperature may drop significantly during nighttimes in remote areas. The microclimate variables that play an important role in maintaining ideal environmental conditions include temperature and relative humidity. © 2022, The Authors. All rights reserved.

关键词： Forecasting