Article
Biology
Amanda Albright, Brendan C. Fry, Alice Verticchio, Brent Siesky, Alon Harris, Julia Arciero
Summary: The study expands a hybrid model of the retinal microvascular network to include the effects of local blood flow regulation on oxygenation. The model predicts that impaired blood flow regulation, as well as increased intraocular pressure, can cause decreased tissue oxygenation. The heterogeneity of the vascular network highlights localized defects in tissue oxygenation that may be involved in ocular diseases.
MATHEMATICAL BIOSCIENCES
(2023)
Article
Multidisciplinary Sciences
Hyeygjeon Chang
Summary: This paper discusses a quantitative method for evaluating the chance of drug-resistant virus emergence in HIV/AIDS drug treatments. Mathematical models and analysis methods are used to study the iGDR and STI therapies, explaining why STI therapy often fails and concluding the advantages of iGDR in reducing the threat of drug-resistant virus emergence.
Article
Plant Sciences
Anastasia Kitashova, Vladimir Brodsky, Palak Chaturvedi, Iro Pierides, Arindam Ghatak, Wolfram Weckwerth, Thomas Naegele
Summary: A plant's genome encodes the proteins necessary for metabolism, and its interactions with the environment affect its growth, development, and adaptation to adverse conditions. Despite advances in genome sequencing technologies, predicting metabolic phenotypes from genotype x environment interactions remains incomplete. Understanding the dependence and expression of molecular organization levels in growth conditions is a current challenge.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Biology
Raquel Nunes Palmeira, Marco Colnaghi, Stuart A. Harrison, Andrew Pomiankowski, Nick Lane
Summary: This study reveals that the universal core of metabolism could have emerged from thermodynamically favored prebiotic pathways at the origin of life. Mathematical simulations show that nucleotide catalysis can promote protocell growth, but only when nucleotides directly catalyze CO2 fixation. These findings offer a new framework for the emergence of greater metabolic complexity.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Engineering, Chemical
Ryszard Myhan, Marek Markowski
Summary: Convective cereal grain drying is an energy-intensive process that can be optimized using mathematical models. The developed mathematical model considers all stages of the drying process and has been validated for both batch and continuous flow drying of different types of grains. Simulation results show that the proposed models accurately depict process flow in both types of dryers.
Article
Biochemistry & Molecular Biology
Antonia Elizabeth Yuko, Vagner Oliveira Carvalho Rigaud, Justin Kurian, Ji H. Lee, Nicole Kasatkin, Michael Behanan, Tao Wang, Anna Maria Luchesse, Sadia Mohsin, Walter J. Koch, Hong Wang, Mohsin Khan
Summary: By promoting LIN28a induced metabolic flexibility, it enhances the survival and proliferation of cardiac tissue derived stem like cells, contributing to the repair of the heart after injury.
Article
Thermodynamics
Arkadiusz Szczesniak, Jaroslaw Milewski, Olaf Dybinski, Kamil Futyma, Jakub Skibinski, Aliaksandr Martsinchyk
Summary: The aim of this paper is to compare the performance of multi-tank storage with a moving thermocline against single tank storage. The results highlight the benefits of multi-tank storage in reducing heat loss through the thermocline. It also presents a dynamic model of the system and examines the thickness of the thermal insulation.
Article
Engineering, Multidisciplinary
Muhammad Sajid Iqbal, Nauman Ahmed, Ali Akgul, Ammad Mehmood Satti, Zafar Iqbal, Ali Raza, Muhammad Rafiq, Rukhshanda Anjum, Mohammed Zakarya, Choonkil Park
Summary: This article investigates the transmission of polio-virus disease in the human population. The classical model is converted into the fractal fractional epidemic model and the existence of the solution is ensured using fixed point theory. Equilibria points are determined and the role of the basic reproduction number in disease communication and model stability is examined. Simulated graphs are presented to support the preliminary results and claims. The findings of the study are finally presented.
ALEXANDRIA ENGINEERING JOURNAL
(2023)
Review
Biotechnology & Applied Microbiology
Vinoj Chamilka Liyanaarachchi, Gannoru Kankanamalage Sanuji Hasara Nishshanka, P. H. Viraj Nimarshana, Jo-Shu Chang, Thilini U. U. Ariyadasa, Dillirani Nagarajan
Summary: This review comprehensively discusses existing mathematical modeling techniques that simulate the bioaccumulation of natural astaxanthin in diverse organisms, as well as associated challenges, solutions, and future perspectives.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Takashi Amemiya, Kenichi Shibata, Tomohiko Yamaguchi
Summary: Cancer cells exhibit different metabolic phenotypes in tumor tissues. Glycolytic phenotype, characterized by oscillations in metabolite concentrations, is a crucial feature of malignant cancers. Higher frequencies of oscillations in glycolytic cancer cells indicate higher glycolytic enzyme activities, and glycolytic oscillations can serve as a medical indicator to evaluate cancer malignancy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cardiac & Cardiovascular Systems
Nikolaus Berndt, Johannes Eckstein, Iwona Wallach, Sarah Nordmeyer, Marcus Kelm, Marieluise Kirchner, Leonid Goubergrits, Marie Schafstedde, Anja Hennemuth, Milena Kraus, Tilman Grune, Philipp Mertins, Titus Kuehne, Hermann-Georg Holzhuetter
Summary: The study utilized a comprehensive kinetic model of cardiac energy metabolism to assess the energy status of the left ventricles in healthy participants and patients with aortic stenosis and mitral valve insufficiency. The results indicated that patients had increased MVATP[rest] and decreased MVATP[max], leading to a decreased myocardial ATP production reserve, despite having preserved ejection fraction. The energy status was closely associated with mechanical energy demand.
Article
Multidisciplinary Sciences
Shrey Dutta, Kartik K. Iyer, Sampsa Vanhatalo, Michael Breakspear, James A. Roberts
Summary: Disruption to the brain's oxygen supply triggers pathological dynamics and brain injuries. Here, the authors develop a model of coupled metabolic-neuronal activity that generates burst suppression patterns similar to those of infants after birth asphyxia.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Shrey Dutta, Kartik K. Iyer, Sampsa Vanhatalo, Michael Breakspear, James A. Roberts
Summary: This article presents research on the relationship between brain activity and oxygen supply. The researchers used computational modeling to explore the mechanisms by which oxygen depletion generates pathological brain activity and found that restricting oxygen supply leads to transitions from normal to pathological activity patterns. Trajectories through parameter space track key features of clinical electrophysiology recordings and reveal differences in parameter values between infants with good recovery outcomes and those with poor outcomes.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Gaoyang Li, Li Liu, Wei Du, Huansheng Cao
Summary: The authors develop a method called Decrem, which integrates locally coupled reactions and global transcriptional regulation of metabolism, to reconstruct genome-scale metabolic networks. Decrem achieves accurate predictions of phenotypes and has broad applications in bioengineering, synthetic biology, and microbial pathology.
NATURE COMMUNICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Juan M. Duran
Summary: In this article, the author focuses on the role of computer simulations as exploratory strategies. The non-theory-driven nature of simulations is established, referring to their ability to characterize phenomena without relying on a predefined conceptual framework. Three exploratory strategies for computer simulations are presented: (1) starting points and continuation of scientific inquiry, (2) varying the parameters, and (3) scientific prototyping.
MINDS AND MACHINES
(2023)
Article
Chemistry, Physical
Paul L. Chariou, Karin L. Lee, Jonathan K. Pokorski, Gerald M. Saidel, Nicole F. Steinmetz
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Article
Biochemical Research Methods
Joydeep Sarkar, Alka A. Potdar, Gerald M. Saidel
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Endocrinology & Metabolism
Yanjun Li, Thomas P. J. Solomon, Jacob M. Haus, Gerald M. Saidel, Marco E. Cabrera, John P. Kirwan
AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM
(2010)
Article
Physiology
Jessica Spires, L. Bruce Gladden, Bruno Grassi, Gerald M. Saidel, Nicola Lai
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
(2012)
Article
Physiology
Jessica Spires, L. Bruce Gladden, Bruno Grassi, Matthew L. Goodwin, Gerald M. Saidel, Nicola Lai
AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY
(2013)
Article
Engineering, Biomedical
Andrew S. Fu, Thimma R. Thatiparti, Gerald M. Saidel, Horst A. von Recum
ANNALS OF BIOMEDICAL ENGINEERING
(2011)
Article
Biochemistry & Molecular Biology
Peng Yao, Alka A. Potdar, Abul Arif, Partho Sarothi Ray, Rupak Mukhopadhyay, Belinda Willard, Yichi Xu, Jun Yan, Gerald M. Saidel, Paul L. Fox
Article
Cell & Tissue Engineering
David T. Chang, Gerald M. Saidel, James M. Anderson
CELLULAR AND MOLECULAR BIOENGINEERING
(2009)
Article
Cell & Tissue Engineering
Jaeyeon Kim, Gerald M. Saidel, Satish C. Kalhan
CELLULAR AND MOLECULAR BIOENGINEERING
(2011)
Article
Cell & Tissue Engineering
Yanjun Li, Nicola Lai, John P. Kirwan, Gerald M. Saidel
CELLULAR AND MOLECULAR BIOENGINEERING
(2012)
Article
Biophysics
Xin Chen, Gerald M. Saidel
JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME
(2010)
Article
Cell & Tissue Engineering
Andrew S. Fu, Loran D. Solorio, Eben Alsberg, Gerald M. Saidel
JOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE
(2017)
Article
Computer Science, Interdisciplinary Applications
Christopher M. Heylman, Sharon Santoso, Melissa D. Krebs, Gerald M. Saidel, Eben Alsberg, George F. Muschler
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2014)
Article
Biochemical Research Methods
Shannon R. Moore, Gerald M. Saidel, Ulf Knothe, Melissa L. Knothe Tate
PLOS COMPUTATIONAL BIOLOGY
(2014)
Article
Physiology
China M. Kummitha, Satish C. Kalhan, Gerald M. Saidel, Nicola Lai
PHYSIOLOGICAL REPORTS
(2014)