Article
Mathematical & Computational Biology
Christopher Schoelzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Summary: Reuse of mathematical models is increasingly important in systems biology, but many models currently face challenges in being easily reusable. Software engineering can address these issues, and the use of appropriate languages can facilitate model reusability.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Tina. M. M. Olsson, Knut Sundell
Summary: Publication and related biases pose significant threats to the validity of research synthesis, potentially leading to misleading results. This study examined the presence of positive outcome bias, time-lag bias, and place-of-publication bias in published research on psychological, social, and behavioral interventions. The results, based on 527 Swedish outcome trials from 1990 to 2019, showed no difference in the number of studies reporting significant versus non-significant findings or strong effect sizes. There was also no evidence of time-lag bias or place-of-publication bias. The average reported effect size and proportion of studies reporting significant effects remained consistent over time.
Article
Biotechnology & Applied Microbiology
Daehee Choi, Jaeho Lee, Jinyoung Jung
Summary: This study improved the cultivation rate of ANAMMOX microorganisms in the PN/ANAM-MOX reactor using mathematical representations accounting for reaction kinetics, and proposed control strategies to improve reactor performance and cope with fluctuations in raw reject water properties. The results provide important references for scale-up or design of the ANAMMOX process.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
History & Philosophy Of Science
Mikkel Willum Johansen, Josefine Lomholt Pallavicini
Summary: There have been considerable variations in the frequency and types of diagrams used in mathematical publications over the last century. Diagrams were relatively common at the beginning of the period, but were almost completely unused for about four decades before reappearing in the 1950s in a different type. This change in publication practice indicates a shift in mathematicians' choice of representations and suggests more fundamental changes during the period under consideration.
Article
Environmental Sciences
Wei Xu, Zhulin Liu
Summary: In 2017, China initiated comprehensive control measures for rural water pollution, with the aim of completing the purification of rural domestic sewage by 2030. Short-term goals focused on ensuring safe drinking water, while medium and long-term goals aimed to eliminate all sources of pollution. Mathematical models were used to assess progress in rural sewage treatment, the efficiency of treatment facilities, and the current state of water pollution in China. Results indicate that the short-term goals have been largely achieved, with a 98% rural tap water penetration rate and approximately 95% of water meeting drinking standards. However, implementing medium and long-term goals has been challenging due to weak rural economy, scattered residences, and high sewage treatment costs. The treatment rate for agricultural non-point source sewage and domestic sewage remains low, and surface water in rural areas is generally classified as Class IV or V. The study identified insufficient economic support as a key factor hindering effective sewage treatment, suggesting that the government should increase investment in rural sewage treatment facilities.
Editorial Material
Chemistry, Physical
William E. Acree, Evonne R. Huang, Kelly Kim
Summary: The author presents a polemic regarding the goodness-of-fit values of the predictive expressions used to describe the solubility data of stearic acid. By averaging relative deviations, positive and negative deviations cancel in the van't Hoff model, while the absolute values of deviations are averaged in the modified Apelblat model.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Mechanics
Guofa Ji, Shaoqi Chen, Tong Zhou, Zhiwen Huang, Fengxia Li
Summary: This paper introduces a new method of calculating network fracture conductivity based on electrical similitude principle and experimental data. The accuracy of this method is verified through comparison of experimental and prediction data, providing a reference for the optimization of fracture network conductivity in shale reservoir multi-staged fracturing.
Review
Psychiatry
Abraham Nunes, Selena Singh, Jared Allman, Suzanna Becker, Abigail Ortiz, Thomas Trappenberg, Martin Alda
Summary: This paper provides a critical review of dynamical systems models of bipolar disorder (BD) and introduces the validity appraisal guide for computational models (VAG-CM) for evaluating these models. The review identified data-driven models with face validity, theory-driven models with predictive validity, and theory-driven models lacking all forms of validity. Future studies should adopt a hybrid approach that combines empirical data and generative models to operationalize BD features and should be conducted alongside long-term prospective cohort studies.
TRANSLATIONAL PSYCHIATRY
(2022)
Article
Multidisciplinary Sciences
Brydon Eastman, Michelle Przedborski, Mohammad Kohandel
Summary: The study shows that chemotherapeutic dosing strategies learned through reinforcement learning methods are more resilient to perturbations in patient-specific parameter values. By training an agent on mean-value parameters and allowing periodic access to a more easily measurable metric, relative bone marrow density, drug dosing schedules that outperform classical optimal control methods can be developed.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Artificial Intelligence
Jipeng Qiang, Xindong Wu
Summary: Recent approaches in Text Simplification have focused on learning simplification rewrites from parallel corpora, but the lack of such corpora has been a challenge. This paper tackles unsupervised Text Simplification without parallel sentences, introducing a phrase-based machine translation system that outperforms some supervised baselines on benchmark datasets.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2021)
Article
Engineering, Biomedical
Yoojin Seo, Seokyoung Bang, Jeongtae Son, Dongsup Kim, Yong Jeong, Pilnam Kim, Jihun Yang, Joon-Ho Eom, Nakwon Choi, Hong Nam Kim
Summary: In the past few decades, the prediction of adverse reactions to drugs mainly relied on 2D in vitro models and animal models. However, with advancements in computational power, in silico models have emerged as a time-efficient and cost-effective alternative. The concept of the physiome has bridged experimental datasets with computational models, leading to the development of 3D in vitro brain models to overcome limitations in experimental data collection from traditional models.
BIOACTIVE MATERIALS
(2022)
Article
Physiology
Yuda Munarko, Dewan M. Sarwar, Anand Rampadarath, Koray Atalag, John H. Gennari, Maxwell L. Neal, David P. Nickerson
Summary: Semantic annotation is crucial for the reusability and reproducibility of biosimulation models, with the recommended use of RDF and the proposed interface NLIMED to convert natural language queries into SPARQL. NLIMED's approach for chunking and annotating queries has been shown to be more effective than the NCBO Annotator.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Dillon W. P. Tay, Naythan Z. X. Yeo, Krishnan Adaikkappan, Yee Hwee Lim, Shi Jun Ang
Summary: Natural products are a rich source of bioactive compounds for various applications. A database containing 67,064,204 natural product-like molecules was generated using a recurrent neural network, greatly expanding the library size compared to known natural products. This study demonstrates the potential of using deep generative models for high throughput in silico discovery of novel natural product chemical space.
Article
Computer Science, Interdisciplinary Applications
Can Jin, Wuxing Zhang, Pengfei Liu, Xu Yang, Markus Oeser
Summary: A method for simplifying the geometry of asphalt mixtures microstructures was proposed and evaluated for accuracy, showing stress and strain curves of simplified models were very close to original models with significantly reduced computational time. This approach allows for reliable and efficient simulation of asphalt mixtures using the FE method.
COMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING
(2021)
Article
Computer Science, Information Systems
Ivan A. Konovalenko, Anna A. Smagina, Dmitry P. Nikolaev, Petr P. Nikolaev
Summary: The construction of perceptually uniform color space is crucial for color theory, as many image processing applications require color difference to mimic human perception. It is difficult to approximate perceptual difference using Euclidean distance within linear color coordinate systems. ProLab, a new color coordinate system, performs far better than widely used CIELAB system in terms of perceptual uniformity.
Editorial Material
Biochemical Research Methods
Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David Nickerson, Anand Rampadarath
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Physiology
Megan E. Guidry, David P. Nickerson, Edmund J. Crampin, Martyn P. Nash, Denis S. Loiselle, Kenneth Tran
FRONTIERS IN PHYSIOLOGY
(2020)
Article
Biochemical Research Methods
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran, Edmund J. Crampin, David P. Nickerson
Summary: Simulating complex biological and physiological systems and predicting their behaviors remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, aiding in model development and simulation. A general methodology for composing models can improve model composition and ensure physical plausibility, as demonstrated through automated model composition using a human arterial circulation model.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Physiology
Mahyar Osanlouy, Anita Bandrowski, Bernard de Bono, David Brooks, Antonino M. Cassara, Richard Christie, Nazanin Ebrahimi, Tom Gillespie, Jeffrey S. Grethe, Leonardo A. Guercio, Maci Heal, Mabelle Lin, Niels Kuster, Maryann E. Martone, Esra Neufeld, David P. Nickerson, Elias G. Soltani, Susan Tappan, Joost B. Wagenaar, Katie Zhuang, Peter J. Hunter
Summary: The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Physiology
Nima Afshar, Soroush Safaei, David P. Nickerson, Peter J. Hunter, Vinod Suresh
Summary: The study investigated the absorption of non-isotonic glucose by small intestinal epithelial cells using a computational model. It found that apical GLUT2 uptake is sensitive to factors such as high luminal glucose levels, blood flow rates, and low inlet blood glucose concentrations. Translocation of GLUT2 to the apical membrane increases glucose uptake into the cell, but reducing efflux capacity results in decreased net absorption.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Frohlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry Jakubowski, Ryann Jordan, Matus Kalas, Matthias Koenig, Wolfram Liebermeister, Rahuman S. Malik Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Mueller, Chris J. Myers, Aurelien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loic Pauleve, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Joern Starruss, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
Summary: Computational models have great potential in accelerating bioscience, bioengineering, and medicine. However, reproducing and reusing simulations is still challenging due to the different formats and methods used by different software tools. To address this issue, we developed BioSimulators, a central registry that provides consistent interfaces and recommendations for simulation tools, using standards and validation tools to ensure consistency. We anticipate that BioSimulators will facilitate the exchange, reproduction, and combination of simulations by modelers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Physiology
Yuda Munarko, Dewan M. Sarwar, Anand Rampadarath, Koray Atalag, John H. Gennari, Maxwell L. Neal, David P. Nickerson
Summary: Semantic annotation is crucial for the reusability and reproducibility of biosimulation models, with the recommended use of RDF and the proposed interface NLIMED to convert natural language queries into SPARQL. NLIMED's approach for chunking and annotating queries has been shown to be more effective than the NCBO Annotator.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J. Crampin, David P. Nickerson
Summary: Hierarchical modelling is essential for complex and large-scale models. To address the challenges in integrating biosimulation models, an approach to automatically and confidently compose biosimulation models using bond graphs and semantic annotations is proposed. By coupling a model of the Ras-MAPK cascade and a model of upstream activation of EGFR, this approach aims to provide researchers and modellers with readily accessible comprehensive biological systems models.
Article
Biology
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J. Crampin, David P. Nickerson
Summary: This article introduces a new framework that automatically converts SBML models into bond graphs to assess the physical plausibility and thermodynamic consistency of the models. By converting the models into bond graphs, mergeable and physically plausible coupled models can be obtained.
MATHEMATICAL BIOSCIENCES
(2022)
Article
Physiology
Nari Kim, Julius D. Pronto, David P. Nickerson, Andrew J. Taberner, Peter J. Hunter
Summary: This study investigates the underlying mechanism for the differences between left ventricle (LV) and right ventricle (RV) using a modular modeling approach. The researchers developed a new integrative model by combining validated individual components of existing models and found that the ionic mechanisms play a role in the variation in force production between ventricles.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Leyla Noroozbabaee, Pablo J. Blanco, Soroush Safaei, David P. Nickerson
Summary: We review a collection of published renal epithelial transport models and build a consistent and reusable mathematical model that can reproduce many observations and predictions from the literature. The flexible modular model can be adapted to specific configurations of epithelial transport, and this work focuses on transport in the proximal convoluted tubule of the renal nephron.
Editorial Material
Mathematical & Computational Biology
Matthias Koenig, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Bjorn Sommer, Dagmar Waltemath, Falk Schreiber
Summary: This journal issue presents updated specifications of COMBINE standards in systems and synthetic biology, including updates to CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. It also serves as a reference for the latest specifications of all COMBINE standards. Additionally, the editorial provides an overview of the COMBINE 2022 meeting in Berlin.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2023)
Article
Mathematical & Computational Biology
John H. Gennari, Matthias Koenig, Goksel Misirli, Maxwell L. Neal, David P. Nickerson, Dagmar Waltemath
Summary: The specification provides a technical guideline for encoding standardized annotations in computational biomedical models and their associated files, promoting model reuse and enabling semantic comparisons.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2021)
Article
Mathematical & Computational Biology
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomas Helikar, Jonathan Karr, David Nickerson, Herbert Sauro, Dagmar Waltemath, Matthias Koenig
Summary: SED-ML is a computer-readable format for sharing information about simulation experiments, supporting collaboration among modelers, experimentalists, and engineers. Version 4 of Level 1 significantly expands capabilities to cover additional types of models, model languages, parameter estimations, simulations, analyses, and visualizations.
JOURNAL OF INTEGRATIVE BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru, David P. Nickerson, Herbert M. Sauro
Summary: Although reproducibility is crucial in the scientific method, it is challenging to replicate many results. Researchers have found that only 50% of published simulation results in systems biology can be repeated. By utilizing various resources, investigators can make their research more accessible, executable, and comprehensible to others. Improved reproducibility will accelerate the development of more sophisticated models, benefiting precision medicine and synthetic biology.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2021)