Article
Computer Science, Information Systems
Dimitris Tsaras, George Trimponias, Lefteris Ntaflos, Dimitris Papadias
Summary: The paper introduces an Awareness-to-Influence model for maximizing collective influence of multiple competing products and proposes a game-theoretic GCW framework for computing seed sets. The research shows that the proposed methods are effective and scalable in large social networks.
PROCEEDINGS OF THE VLDB ENDOWMENT
(2021)
Article
Meteorology & Atmospheric Sciences
Jian-Guo Li
Summary: The study discretizes shallow water equations on a regional spherical multiple-cell grid and successfully simulates a filling experiment in the Mediterranean Sea grid. Results show that the model can accurately predict the filling process and the generation of tsunami waves, with the orientation of initial disturbance playing a significant role in subsequent wave propagation.
Article
Engineering, Environmental
Yuechao Zhang, Qinqin Hao, Oumei Wang, Xiao-Hua Zhang, Fanghua Liu
Summary: Microbial iron reduction plays a crucial role in marine ecosystems, contributing to element cycling and supporting biological activities. Fermentative iron reduction exhibits a pH-buffering effect and improves glucose consumption, bacterial growth, and metabolite production.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2023)
Article
Food Science & Technology
Mingtang Tan, Zhaoyang Ding, Yuanming Chu, Jing Xie
Summary: This study examined the potential use of three Good's buffers (MES, MOPS, and HEPES) in inhibiting acidity-induced denaturation of myofibrillar protein (MFP). The highest acidity variation was observed in the center and bottom of large bottles due to freeze-concentration effect. Good's buffers tend to become alkaline during freezing, preventing crystallization of sodium phosphate (NaP) buffer. Acidification from freezing Na-P disrupted the natural conformation of MFP and induced the formation of large protein aggregates. Adding 15 mM MES, 20 mM MOPS, and 30 mM HEPES neutralized strong acidity drop induced by freezing 20 mM Na-P, significantly improving the stability of MFP conformation (P < 0.05). This research is crucial for meeting the growing protein demand and groundbreaking for expanding the applicability of Good's buffers in the food industry.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Chemistry, Medicinal
Lisa Samuelsen, Rene Holm, Christian Schonbeck
Summary: The study investigated the effects of 11 buffers and ionic strength on the binding between bile salt taurochenodeoxycholate and ionic sulfobutylether-I3-cyclodextrin. It was found that both ionic strength and competitive binding influenced the stability constant of the complexes. Different buffers had varied impacts on the stability constant of the complexes, with carboxylic acid buffers decreasing the stability constant relative to changes in ionic strength.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Chemistry, Physical
Horacio Serna, Ariel G. Meyra, Eva G. Noya, Wojciech T. Gozdz
Summary: Systems with short-range attraction and long-range repulsion can form ordered microphases under bulk and confinement conditions. In this study, a model colloidal system with competing interactions under confinement in narrow spherical shells was investigated using Grand Canonical Monte Carlo (GCMC) simulations. Three parent ordered structures were observed, consisting of toroidal clusters and two spherical clusters (Type I), toroidal clusters and one spherical cluster (Type II), and toroidal clusters alone (Type III). These structures can often coexist with related structures derived from them by a simple transformation. A general method to characterize and predict the structures obtained under confinement in spherical shells was proposed. The deformation of spherical shells into ellipsoidal ones affects the system's structure, favoring helical structures with prolate ellipsoids and toroidal structures with oblate ellipsoids.
Review
Chemistry, Multidisciplinary
Anna L. Neuer, Inge K. Herrmann, Alexander Gogos
Summary: The field of nanomedicine is rapidly advancing with a focus on inorganic and inorganic-organic composite nanomaterials. However, challenges remain in using these materials in clinical trials due to their complex chemistry and potential degradation. This review discusses recent advances in understanding the biochemical transformations of these materials, provides a refined terminology for primary reaction mechanisms, and highlights suitable analytical techniques. The review also highlights opportunities for diagnostic and therapeutic purposes, as well as current challenges and research priorities.
Article
Multidisciplinary Sciences
Sarah P. Hammarlund, Tomas Gedeon, Ross P. Carlson, William R. Harcombe
Summary: The study shows that in a bacterial community, mutualists can promote coexistence among competitors by providing them with different limiting resources, as demonstrated through mathematical modeling.
NATURE COMMUNICATIONS
(2021)
Article
Oceanography
Fang Hou, Zhiyi Gao, Jianguo Li, Fujiang Yu
Summary: This paper presents an efficient algorithm for generating a spherical multiple-cell grid, which adopts a recursive loop structure and provides two refinement methods: arbitrary area refinement and nearshore refinement. Numerical experiments demonstrate that this algorithm is more flexible and operable compared to existing grid generation algorithms.
ACTA OCEANOLOGICA SINICA
(2022)
Article
Polymer Science
Lucie Nova, Filip Uhlik
Summary: This study investigates the response mechanism of star-like micelles formed by triblock copolymers to variations in ionic strength and salt counterion valency. The results show that the morphological type of the micelles can be controlled by changing the salt counterion valency.
Article
Chemistry, Physical
Thomas Nevolianis, Raja A. Ahmed, Arnim Hellweg, Michael Diedenhofen, Kai Leonhard
Summary: Accurately predicting partition coefficients is crucial for drug design, but the performance of existing methods is unclear. In this study, the COSMO-RS approach is used to predict the toluene/water partition coefficients for 16 molecules in the SAMPL9 challenge. Both submissions achieve high R2 values, but there are deviations compared to previous challenges.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Pharmacology & Pharmacy
Harrison B. Rose, Madison M. Wilber, Andreas S. Bommarius
Summary: Determining the equilibrium pH in complex aqueous solutions has become increasingly important across various fields, and linearization methods enable easier modeling of equilibrium and reactor dynamics. This study demonstrates detailed modeling of enthalpic changes in isothermal titration calorimetry through calculations, and compares the acid dissociation constants of three furancarboxylic acids.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Computer Science, Theory & Methods
Jian-Guo Li
Summary: The Spherical Multiple-Cell (SMC) grid is an unstructured grid that supports flexible domain shapes and multi-resolutions. It has been implemented and extended in the WAVEWATCH III (WW3) wave model to improve parallelization performance and computational efficiency.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
(2022)
Article
Chemistry, Analytical
Lea Gundorff Nielsen, Thomas Just Sorensen
Summary: The photophysical properties of a europium(III) complex were studied in different buffer systems and pH values. The buffers had no effect on the europium luminescence, but a lower emission intensity was observed in one of the buffers due to quenching. The effect of pH on the complex's photophysics was minimal, but it did influence the intensity ratio between fluorescence and luminescence.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2023)
Article
Pharmacology & Pharmacy
Lukas Vesely, Behera Susrisweta, Dominik Heger
Summary: The study found that Good's buffers tend to alkalize during the freezing process, especially at lower pH values, with MES showing the most significant acidity changes. Additionally, Good's buffers are able to alleviate the strong acidification in sodium phosphate buffer, and can be adjusted in different concentrations to balance their impact on the solution's acidity.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Mathematics
Daniela Calvetti, Alexander P. Hoover, Johnie Rose, Erkki Somersalo
Summary: Understanding the dynamics of COVID-19 spread between connected communities is crucial for planning mitigation measures. A novel metapopulation network model is proposed and analyzed for this purpose, utilizing optimal transport theory to describe population redistribution due to traffic and SEIR compartment models to account for infection dynamics in individual communities. Model simulations reveal densely populated regions as potential amplifiers of infection for surrounding less densely populated areas, in line with observed infection patterns during the pandemic, and can be used to test various mitigation strategies.
Article
Mathematics, Applied
D. Calvetti, A. Hoover, J. Rose, E. Somersalo
Summary: This article presents a dynamic model for the spread of epidemics, especially COVID-19, and discusses the inverse problem of estimating unknown states and model parameters based on noisy observations. The Bayesian particle filtering algorithm is used to estimate the state and model parameters, providing insights into the size of unaccounted asymptomatic individuals and uncertainty quantification. The algorithm is shown to be viable through computed examples using simulated and real data, with results consistent with CDC suggestions.
Article
Radiology, Nuclear Medicine & Medical Imaging
A. Bocchinfuso, D. Calvetti, E. Somersalo
Summary: The transport of gases across cell membranes is crucial for various cell functions, and mathematical models are essential for understanding and testing hypotheses regarding gas transport. Recent studies suggest that the presence of a liquid-membrane pH sensitive electrode on the cell surface may disturb the pH locally and cause a systematic bias in measured values. This work proposes a computationally lightweight numerical algorithm to simulate surface pH data and investigates the effect of different model parameters on the output through numerical experiments.
BIOMEDICAL PHYSICS & ENGINEERING EXPRESS
(2022)
Article
Urology & Nephrology
Seong-Ki Lee, Rossana Occhipinti, Fraser J. Moss, Mark D. Parker, Irina I. Grichtchenko, Walter F. Boron
Summary: This study aims to differentiate the movements of HCO3 2, CO35, and H1 across membranes. Through electrophysiology and heterologous expression in Xenopus oocytes, the researchers investigated the transport of bicarbonate (HCO32) by SLC4 family members. The results showed that the Cl-HCO3 exchanger AE1 (SLC4A1) can transport HCO32, while the electrogenic Na/HCO3 cotransporter NBCe1 (SLC4A4) and the electroneutral Na1-driven Cl-HCO3 exchanger NDCBE (SLC4A8) cannot. Mathematical simulations further supported CO35 transport as the mechanism for NBCe1.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Mathematics, Applied
N. Waniorek, D. Calvetti, E. Somersalo
Summary: Dictionary learning has been widely used in various applications, such as image denoising, face recognition, remote sensing, medical imaging, and feature extraction, to represent a signal using dictionary atoms. Sparse dictionary learning is particularly interesting when the signal can be represented by a few vectors in a given basis. This paper proposes using hierarchical Bayesian models for sparse dictionary learning, which can capture features of the underlying signals, such as sparse representation and nonnegativity. The framework can also be used for dimensionality reduction of an annotated dictionary through feature extraction, reducing the computational complexity of the learning task.
Article
Clinical Neurology
Rabeah Bayazid, Christina Orru', Rabail Aslam, Yvonne Cohen, Amelia Silva-Rohwer, Seong-Ki Lee, Rossana Occhipinti, Qingzhong Kong, Shashirekha Shetty, Mark L. Cohen, Byron Caughey, Lawrence B. Schonberger, Brian S. Appleby, Ignazio Cali
Summary: Two distinct PrP plaque phenotypes can affect sCJDMM genotype in sCJD patients, with slightly different clinical features, histopathology, and molecular properties.
ACTA NEUROPATHOLOGICA
(2023)
Article
Astronomy & Astrophysics
Nathaniel Starkman, Jo Bovy, Jeremy J. Webb, Daniela Calvetti, Erkki Somersalo
Summary: Researchers used self-organizing maps and Kalman filters to reconstruct the path of a stellar stream, taking into account measurement errors and data sparsity. This method allows for comparison with simulations and analysis of multiple stellar stream tracks.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2023)
Meeting Abstract
Physiology
Rossana Occhipinti, Matthew Makowski, Heath Gasier, Walter Boron
Article
Mathematics, Applied
A. Bocchinfuso, D. Calvetti, E. Somersalo
Summary: Bayesian particle filters (PFs) are a useful alternative for estimating model parameters and uncertainties in dynamical systems with time series data. PFs are particularly valuable in high-dimensional state spaces where numerical solutions are time-consuming. The PF solution can also provide insights into the sensitivity of unknown parameters to different temporal segments of the data, guiding more efficient data collection procedures. This article applies the PF method to estimate cell membrane permeability to gases using pH measurements, addressing challenges of high dimensionality and micro-environment effects.
Article
Biology
Gideon Idumah, Erkki Somersalo, Daniela Calvetti
Summary: The roles of neurons and astrocytes in supplying energy for their tasks during neuronal activation are influenced by their active roles and associated metabolism. The comprehensive mathematical model of brain metabolism presented in this article accounts for biochemical processes, neuron-astrocyte interaction, and metabolite diffusion. The model assumes diffusion in the extracellular space and astrocyte compartment, with the diffusion across the syncytium network implemented based on gap junction strength. The diffusion process is numerically implemented using a finite element method, and computational experiments show the effects on brain energy metabolism.
JOURNAL OF THEORETICAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Seong-Ki Lee, Walter F. Boron, Rossana Occhipinti
Summary: Carbonic anhydrases (CAs) are essential for physiological processes due to their role in catalyzing the conversion of CO2 and water to bicarbonate and protons, impacting pH levels. In the kidneys, CAs and HCO3- transporters, specifically the NCBTs and AEs, play significant roles in urinary acid secretion, particularly HCO3- reabsorption. Recent findings suggest that NCBTs transport CO32- instead of HCO3-, suggesting a revised understanding of their function. This review examines the role of CAs and HCO3- transporters in renal acid-base physiology and discusses the implications of novel findings on HCO3- reabsorption.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Meeting Abstract
Physiology
W. F. Boron, S. -K. Lee, R. Occhipinti, F. J. Moss
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)