Correction to: Predicting Radiotherapy Patient Outcomes with Real-Time Clinical Data Using Mathematical Modelling
Bull Math Biol. 2024 Feb 28;86(4):35. doi: 10.1007/s11538-024-01268-2.NO ABSTRACTPMID:38416252 | DOI:10.1007/s11538-024-01268-2 (Source: Bulletin of Mathematical Biology)
Source: Bulletin of Mathematical Biology - February 28, 2024 Category: Bioinformatics Authors: Alexander P Browning Thomas D Lewin Ruth E Baker Philip K Maini Eduardo G Moros Jimmy Caudell Helen M Byrne Heiko Enderling Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
First Passage Times of Long Transient Dynamics in Ecology
Bull Math Biol. 2024 Feb 23;86(4):34. doi: 10.1007/s11538-024-01259-3.ABSTRACTLong transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attract...
Source: Bulletin of Mathematical Biology - February 23, 2024 Category: Bioinformatics Authors: Grant R Poulsen Claire E Plunkett Jody R Reimer Source Type: research
3D Genome Reconstruction from Partially Phased Hi-C Data
Bull Math Biol. 2024 Feb 22;86(4):33. doi: 10.1007/s11538-024-01263-7.ABSTRACTThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruct...
Source: Bulletin of Mathematical Biology - February 22, 2024 Category: Bioinformatics Authors: Diego Cifuentes Jan Draisma Oskar Henriksson Annachiara Korchmaros Kaie Kubjas Source Type: research
3D Genome Reconstruction from Partially Phased Hi-C Data
Bull Math Biol. 2024 Feb 22;86(4):33. doi: 10.1007/s11538-024-01263-7.ABSTRACTThe 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruct...
Source: Bulletin of Mathematical Biology - February 22, 2024 Category: Bioinformatics Authors: Diego Cifuentes Jan Draisma Oskar Henriksson Annachiara Korchmaros Kaie Kubjas Source Type: research
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Bull Math Biol. 2024 Feb 16;86(3):32. doi: 10.1007/s11538-024-01257-5.ABSTRACTIn some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commuta...
Source: Bulletin of Mathematical Biology - February 16, 2024 Category: Bioinformatics Authors: Yue Wang Blerta Shtylla Tom Chou Source Type: research
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Bull Math Biol. 2024 Feb 16;86(3):32. doi: 10.1007/s11538-024-01257-5.ABSTRACTIn some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commuta...
Source: Bulletin of Mathematical Biology - February 16, 2024 Category: Bioinformatics Authors: Yue Wang Blerta Shtylla Tom Chou Source Type: research
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Bull Math Biol. 2024 Feb 16;86(3):32. doi: 10.1007/s11538-024-01257-5.ABSTRACTIn some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commuta...
Source: Bulletin of Mathematical Biology - February 16, 2024 Category: Bioinformatics Authors: Yue Wang Blerta Shtylla Tom Chou Source Type: research
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Bull Math Biol. 2024 Feb 16;86(3):32. doi: 10.1007/s11538-024-01257-5.ABSTRACTIn some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commuta...
Source: Bulletin of Mathematical Biology - February 16, 2024 Category: Bioinformatics Authors: Yue Wang Blerta Shtylla Tom Chou Source Type: research
Order-of-Mutation Effects on Cancer Progression: Models for Myeloproliferative Neoplasm
Bull Math Biol. 2024 Feb 16;86(3):32. doi: 10.1007/s11538-024-01257-5.ABSTRACTIn some patients with myeloproliferative neoplasms (MPN), two genetic mutations are often found: JAK2 V617F and one in the TET2 gene. Whether one mutation is present influences how the other subsequent mutation will affect the regulation of gene expression. In other words, when a patient carries both mutations, the order of when they first arose has been shown to influence disease progression and prognosis. We propose a nonlinear ordinary differential equation, the Moran process, and Markov chain models to explain the non-additive and non-commuta...
Source: Bulletin of Mathematical Biology - February 16, 2024 Category: Bioinformatics Authors: Yue Wang Blerta Shtylla Tom Chou Source Type: research
Impacts of Vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 Variants Alpha and Delta on Coronavirus Disease 2019 Transmission Dynamics in Four Metropolitan Areas of the United States
Bull Math Biol. 2024 Feb 14;86(3):31. doi: 10.1007/s11538-024-01258-4.ABSTRACTTo characterize Coronavirus Disease 2019 (COVID-19) transmission dynamics in each of the metropolitan statistical areas (MSAs) surrounding Dallas, Houston, New York City, and Phoenix in 2020 and 2021, we extended a previously reported compartmental model accounting for effects of multiple distinct periods of non-pharmaceutical interventions by adding consideration of vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants Alpha (lineage B.1.1.7) and Delta (lineage B.1.617.2). For each MSA, we found region-specific pa...
Source: Bulletin of Mathematical Biology - February 14, 2024 Category: Bioinformatics Authors: Abhishek Mallela Ye Chen Yen Ting Lin Ely F Miller Jacob Neumann Zhili He Kathryn E Nelson Richard G Posner William S Hlavacek Source Type: research
Impacts of Vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 Variants Alpha and Delta on Coronavirus Disease 2019 Transmission Dynamics in Four Metropolitan Areas of the United States
Bull Math Biol. 2024 Feb 14;86(3):31. doi: 10.1007/s11538-024-01258-4.ABSTRACTTo characterize Coronavirus Disease 2019 (COVID-19) transmission dynamics in each of the metropolitan statistical areas (MSAs) surrounding Dallas, Houston, New York City, and Phoenix in 2020 and 2021, we extended a previously reported compartmental model accounting for effects of multiple distinct periods of non-pharmaceutical interventions by adding consideration of vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants Alpha (lineage B.1.1.7) and Delta (lineage B.1.617.2). For each MSA, we found region-specific pa...
Source: Bulletin of Mathematical Biology - February 14, 2024 Category: Bioinformatics Authors: Abhishek Mallela Ye Chen Yen Ting Lin Ely F Miller Jacob Neumann Zhili He Kathryn E Nelson Richard G Posner William S Hlavacek Source Type: research
Optimal Control with RdCVFL for Degenerating Photoreceptors
Bull Math Biol. 2024 Feb 12;86(3):29. doi: 10.1007/s11538-024-01256-6.ABSTRACTBoth the rod and cone photoreceptors, along with the retinal pigment epithelium have been experimentally and mathematically shown to work interdependently to maintain vision. Further, the theoredoxin-like rod-derived cone viability factor (RdCVF) and its long form (RdCVFL) have proven to increase photoreceptor survival in experimental results. Aerobic glycolysis is the primary source of energy production for photoreceptors and RdCVF accelerates the intake of glucose into the cones. RdCVFL helps mitigate the negative effects of reactive oxidative ...
Source: Bulletin of Mathematical Biology - February 12, 2024 Category: Bioinformatics Authors: Kathryn Wifvat Erika T Camacho Matthias Kawski Thierry L éveillard Stephen Wirkus Source Type: research
