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View article: Partially-functional exhausted CD8+ T cells can contribute to short-term viral suppression: a computational prediction for children with perinatal HIV
Partially-functional exhausted CD8+ T cells can contribute to short-term viral suppression: a computational prediction for children with perinatal HIV Open
We and others have reported evidence of T cell exhaustion in children with perinatal HIV with increased expression of inhibitory receptors PD-1, CD160, and TIM-3, but there is limited data on the virologic functional consequences of this i…
View article: Rules of Life at the Interface of Calcium Signaling and Mechanobiology
Rules of Life at the Interface of Calcium Signaling and Mechanobiology Open
Living systems process a broad range of internal and external stimuli, respond to environmental constraints, and adapt to various conditions. The functional interactions between components and mechanisms operating at each scale - from mole…
View article: Timing matters in macrophage/CD4+ T cell interactions: an agent-based model comparing <i>Mycobacterium tuberculosis</i> host-pathogen interactions between latently infected and naïve individuals
Timing matters in macrophage/CD4+ T cell interactions: an agent-based model comparing <i>Mycobacterium tuberculosis</i> host-pathogen interactions between latently infected and naïve individuals Open
Tuberculosis (TB), caused by Mycobacterium tuberculosis ( Mtb ), remains a significant health challenge. Clinical manifestations of TB exist across a spectrum with a majority of infected individuals remaining asymptomatic, commonly referre…
View article: Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms
Local traveling waves of cytosolic calcium elicited by defense signals or wounding are propagated by distinct mechanisms Open
Cytosolic Ca 2+ signatures with specific spatiotemporal patterns play crucial roles in plant responses to biotic and abiotic stresses. Perception of microbe- or damage-associated molecular patterns (MAMPs or DAMPs) initiates signaling casc…
View article: Scaffolded team-based computational modeling and simulation projects for promoting representational competence and regulatory skills
Scaffolded team-based computational modeling and simulation projects for promoting representational competence and regulatory skills Open
Background This study posits that scaffolded team-based computational modeling and simulation projects can support model-based learning that can result in evidence of representational competence and regulatory skills. The study involved 11…
View article: Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma Open
Tuberculosis (TB) remains a global public health threat. Understanding the dynamics of host-pathogen interactions within TB granulomas will assist in identifying what leads to the successful elimination of infection. In vitro TB models pro…
View article: In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models
In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models Open
In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool for examining host-pathogen interactions and screening drugs. With the development of more complex in vitro models, there is a need for tools to help analyze…
View article: Evaluation of fendiline treatment in VP40 system with nucleation-elongation process: a computational model of Ebola virus matrix protein assembly
Evaluation of fendiline treatment in VP40 system with nucleation-elongation process: a computational model of Ebola virus matrix protein assembly Open
Ebola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 laboratories hinder experimental work to advance our understanding of EBOV an…
View article: Biomedical and Agricultural Engineering Undergraduate Students Programming Self-Beliefs and Changes Resulting from Computational Pedagogy
Biomedical and Agricultural Engineering Undergraduate Students Programming Self-Beliefs and Changes Resulting from Computational Pedagogy Open
Background: The growing demand for computing skills in all science and engineering-related fields begs the question of how college graduates in science and engineering can be best equipped with computational thinking and computer programmi…
View article: Microglial roles in Alzheimer's disease: An <scp>agent‐based</scp> model to elucidate microglial spatiotemporal response to <scp>beta‐amyloid</scp>
Microglial roles in Alzheimer's disease: An <span>agent‐based</span> model to elucidate microglial spatiotemporal response to <span>beta‐amyloid</span> Open
Alzheimer's disease (AD) is characterized by beta‐amyloid (Aβ) plaques in the brain and widespread neuronal damage. Because of the high drug attrition rates in AD, there is increased interest in characterizing neuroimmune responses to Aβ p…
View article: Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly"
Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly" Open
This is the original simulation data sets for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly".
View article: Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly"
Simulation data for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly" Open
This is the original simulation data sets for paper "Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly".
View article: Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma Open
Tuberculosis (TB) remains a global public health threat with increasing prevalence. Understanding the dynamics of host-pathogen interactions within TB granulomas will assist in identifying what leads to successful elimination of infection.…
View article: Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load
Mathematical modeling indicates that regulatory inhibition of CD8+ T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load Open
Immunotherapeutic cytokines can activate immune cells against cancers and chronic infections. N-803 is an IL-15 superagonist that expands CD8 + T cells and increases their cytotoxicity. N-803 also temporarily reduced viral load in a limite…
View article: Impact of Ebola virus nucleoprotein on VP40 virus-like particle production: a computational approach
Impact of Ebola virus nucleoprotein on VP40 virus-like particle production: a computational approach Open
Ebola virus (EBOV) protein VP40 can assemble and bud in the form of virus-like particles (VLPs) when expressed in the absence of other EBOV proteins in mammalian cells. When nucleoprotein (NP) is co-expressed, VLPs will contain inclusion-b…
View article: Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly
Evaluation of Fendiline Treatment in VP40 System with Nucleation-Elongation Process: A Computational Model of Ebola Virus Matrix Protein Assembly Open
Ebola virus (EBOV) infection is threatening human health, especially in Central and West Africa. Limited clinical trials and the requirement of biosafety level-4 (BSL-4) laboratories hinders experimental work to advance our understanding o…
View article: <i>In silico</i>agent-based modeling approach to characterize multiple<i>in vitro</i>tuberculosis infection models
<i>In silico</i>agent-based modeling approach to characterize multiple<i>in vitro</i>tuberculosis infection models Open
In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool to examine host-pathogen interactions and screen drugs. With the development of more complex in vitro models, there is a need for tools to help analyze and i…
View article: Mathematical modeling indicates that regulatory inhibition of CD8<sup>+</sup>T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load
Mathematical modeling indicates that regulatory inhibition of CD8<sup>+</sup>T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load Open
Immunotherapeutic cytokines can activate immune cells against cancers and chronic infections. N-803 is an IL-15 superagonist that expands CD8 + T cells and increases their cytotoxicity. N-803 also temporarily reduced viral load in a limite…
View article: Systems biology approaches to investigate the role of granulomas in TB-HIV coinfection
Systems biology approaches to investigate the role of granulomas in TB-HIV coinfection Open
The risk of active tuberculosis disease is 15-21 times higher in those coinfected with human immunodeficiency virus-1 (HIV) compared to tuberculosis alone, and tuberculosis is the leading cause of death in HIV+ individuals. Mechanisms driv…
View article: Chemokine Signaling Caused by<i>Mycobacterium avium</i>Biofilms in the Lung Airway Increases Bacterial Loads by Spatially Diverting Macrophages
Chemokine Signaling Caused by<i>Mycobacterium avium</i>Biofilms in the Lung Airway Increases Bacterial Loads by Spatially Diverting Macrophages Open
Mycobacterium avium Complex (MAC) are ubiquitous environmental biofilm-forming microbes that can colonize and infect patient lungs. Incidence and prevalence of MAC infections are increasing globally, and reinfection is common. Thus, MAC in…
View article: Phosphatidylserine clustering by the Ebola virus matrix protein is a critical step in viral budding
Phosphatidylserine clustering by the Ebola virus matrix protein is a critical step in viral budding Open
Phosphatidylserine (PS) is a critical lipid factor in the assembly and spread of numerous lipid-enveloped viruses. Here, we describe the ability of the Ebola virus (EBOV) matrix protein eVP40 to induce clustering of PS and promote viral bu…
View article: Mechanisms of phosphatidylserine influence on viral production: A computational model of Ebola virus matrix protein assembly
Mechanisms of phosphatidylserine influence on viral production: A computational model of Ebola virus matrix protein assembly Open
Ebola virus (EBOV) infections continue to pose a global public health threat, with high mortality rates and sporadic outbreaks in Central and Western Africa. A quantitative understanding of the key processes driving EBOV assembly and buddi…
View article: Mechanisms of phosphatidylserine influence on viral production: a computational model of Ebola virus matrix protein assembly -- Software in Matlab
Mechanisms of phosphatidylserine influence on viral production: a computational model of Ebola virus matrix protein assembly -- Software in Matlab Open
This is the code for paper "Mechanisms of phosphatidylserine influence on viral production: a computational model of Ebola virus matrix protein assembly" as part of supporting information.
View article: Mathematical modeling of N-803 treatment in SIV-infected non-human primates
Mathematical modeling of N-803 treatment in SIV-infected non-human primates Open
Immunomodulatory drugs could contribute to a functional cure for Human Immunodeficiency Virus (HIV). Interleukin-15 (IL-15) promotes expansion and activation of CD8 + T cell and natural killer (NK) cell populations. In one study, an IL-15 …
View article: The Role of Biofilms, Bacterial Phenotypes, and Innate Immune Response in <i>Mycobacterium avium</i> Colonization to Infection
The Role of Biofilms, Bacterial Phenotypes, and Innate Immune Response in <i>Mycobacterium avium</i> Colonization to Infection Open
Mycobacterium avium complex (MAC), is known for colonizing and infecting humans following inhalation of the bacteria. MAC pulmonary disease is notoriously difficult to treat and prone to recurrence. Both the incidence and prevalence MAC pu…