1
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Huo X, Liu P. An agent-based model on antimicrobial de-escalation in intensive care units: Implications on clinical trial design. PLoS One 2024; 19:e0301944. [PMID: 38626111 PMCID: PMC11020418 DOI: 10.1371/journal.pone.0301944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 03/21/2024] [Indexed: 04/18/2024] Open
Abstract
Antimicrobial de-escalation refers to reducing the spectrum of antibiotics used in treating bacterial infections. This strategy is widely recommended in many antimicrobial stewardship programs and is believed to reduce patients' exposure to broad-spectrum antibiotics and prevent resistance. However, the ecological benefits of de-escalation have not been universally observed in clinical studies. This paper conducts computer simulations to assess the ecological effects of de-escalation on the resistance prevalence of Pseudomonas aeruginosa-a frequent pathogen causing nosocomial infections. Synthetic data produced by the models are then used to estimate the sample size and study period needed to observe the predicted effects in clinical trials. Our results show that de-escalation can reduce colonization and infections caused by bacterial strains resistant to the empiric antibiotic, limit the use of broad-spectrum antibiotics, and avoid inappropriate empiric therapies. Further, we show that de-escalation could reduce the overall super-infection incidence, and this benefit becomes more evident under good compliance with hand hygiene protocols among health care workers. Finally, we find that any clinical study aiming to observe the essential effects of de-escalation should involve at least ten arms and last for four years-a size never attained in prior studies. This study explains the controversial findings of de-escalation in previous clinical studies and illustrates how mathematical models can inform outcome expectations and guide the design of clinical studies.
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Affiliation(s)
- Xi Huo
- Department of Mathematics, University of Miami, Coral Gables, FL, United States of Ameica
| | - Ping Liu
- LinkedIn Corporation, Mountain View, CA, United States of Ameica
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2
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Tung HR, Lawley SD. Understanding and Quantifying Network Robustness to Stochastic Inputs. Bull Math Biol 2024; 86:55. [PMID: 38607457 DOI: 10.1007/s11538-024-01283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
A variety of biomedical systems are modeled by networks of deterministic differential equations with stochastic inputs. In some cases, the network output is remarkably constant despite a randomly fluctuating input. In the context of biochemistry and cell biology, chemical reaction networks and multistage processes with this property are called robust. Similarly, the notion of a forgiving drug in pharmacology is a medication that maintains therapeutic effect despite lapses in patient adherence to the prescribed regimen. What makes a network robust to stochastic noise? This question is challenging due to the many network parameters (size, topology, rate constants) and many types of noisy inputs. In this paper, we propose a summary statistic to describe the robustness of a network of linear differential equations (i.e. a first-order mass-action system). This statistic is the variance of a certain random walk passage time on the network. This statistic can be quickly computed on a modern computer, even for complex networks with thousands of nodes. Furthermore, we use this statistic to prove theorems about how certain network motifs increase robustness. Importantly, our analysis provides intuition for why a network is or is not robust to noise. We illustrate our results on thousands of randomly generated networks with a variety of stochastic inputs.
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Affiliation(s)
- Hwai-Ray Tung
- Department of Mathematics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Sean D Lawley
- Department of Mathematics, University of Utah, Salt Lake City, UT, 84112, USA.
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3
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Ciupe SM, Dahari H, Ploss A. Mathematical Models of Early Hepatitis B Virus Dynamics in Humanized Mice. Bull Math Biol 2024; 86:53. [PMID: 38594319 PMCID: PMC11003933 DOI: 10.1007/s11538-024-01284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Analyzing the impact of the adaptive immune response during acute hepatitis B virus (HBV) infection is essential for understanding disease progression and control. Here we developed mathematical models of HBV infection which either lack terms for adaptive immune responses, or assume adaptive immune responses in the form of cytolytic immune killing, non-cytolytic immune cure, or non-cytolytic-mediated block of viral production. We validated the model that does not include immune responses against temporal serum hepatitis B DNA (sHBV) and temporal serum hepatitis B surface-antigen (HBsAg) experimental data from mice engrafted with human hepatocytes (HEP). Moreover, we validated the immune models against sHBV and HBsAg experimental data from mice engrafted with HEP and human immune system (HEP/HIS). As expected, the model that does not include adaptive immune responses matches the observed high sHBV and HBsAg concentrations in all HEP mice. By contrast, while all immune response models predict reduction in sHBV and HBsAg concentrations in HEP/HIS mice, the Akaike Information Criterion cannot discriminate between non-cytolytic cure (resulting in a class of cells refractory to reinfection) and antiviral block functions (of up to 99 % viral production 1-3 weeks following peak viral load). We can, however, reject cytolytic killing, as it can only match the sHBV and HBsAg data when we predict unrealistic levels of hepatocyte loss.
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Affiliation(s)
- Stanca M Ciupe
- Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| | - Harel Dahari
- Division of Hepatology, Department of Medicine, Loyola University, Chicago, IL, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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4
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Chen J, Guo X, Charbonneau D, Azizi A, Fewell J, Kang Y. Dynamics of Information Flow and Task Allocation of Social Insect Colonies: Impacts of Spatial Interactions and Task Switching. Bull Math Biol 2024; 86:50. [PMID: 38581473 DOI: 10.1007/s11538-024-01280-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/03/2024] [Indexed: 04/08/2024]
Abstract
Models of social interaction dynamics have been powerful tools for understanding the efficiency of information spread and the robustness of task allocation in social insect colonies. How workers spatially distribute within the colony, or spatial heterogeneity degree (SHD), plays a vital role in contact dynamics, influencing information spread and task allocation. We used agent-based models to explore factors affecting spatial heterogeneity and information flow, including the number of task groups, variation in spatial arrangements, and levels of task switching, to study: (1) the impact of multiple task groups on SHD, contact dynamics, and information spread, and (2) the impact of task switching on SHD and contact dynamics. Both models show a strong linear relationship between the dynamics of SHD and contact dynamics, which exists for different initial conditions. The multiple-task-group model without task switching reveals the impacts of the number and spatial arrangements of task locations on information transmission. The task-switching model allows task-switching with a probability through contact between individuals. The model indicates that the task-switching mechanism enables a dynamical state of task-related spatial fidelity at the individual level. This spatial fidelity can assist the colony in redistributing their workforce, with consequent effects on the dynamics of spatial heterogeneity degree. The spatial fidelity of a task group is the proportion of workers who perform that task and have preferential walking styles toward their task location. Our analysis shows that the task switching rate between two tasks is an exponentially decreasing function of the spatial fidelity and contact rate. Higher spatial fidelity leads to more agents aggregating to task location, reducing contact between groups, thus making task switching more difficult. Our results provide important insights into the mechanisms that generate spatial heterogeneity and deepen our understanding of how spatial heterogeneity impacts task allocation, social interaction, and information spread.
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Affiliation(s)
- Jun Chen
- Simon A. Levin Mathematical and Computational Modeling Sciences Center, Arizona State University, 1031 Palm Walk, Tempe, AZ, 85281, USA
| | - Xiaohui Guo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | | | - Asma Azizi
- Department of Mathematics, Kennesaw State University, Marrieta, GA, 30060, USA
| | - Jennifer Fewell
- School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Yun Kang
- Sciences and Mathematics Faculty, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA.
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5
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Saghafi S, Rumbell T, Gurev V, Kozloski J, Tamagnini F, Wedgwood KCA, Diekman CO. Inferring Parameters of Pyramidal Neuron Excitability in Mouse Models of Alzheimer's Disease Using Biophysical Modeling and Deep Learning. Bull Math Biol 2024; 86:46. [PMID: 38528167 PMCID: PMC10963524 DOI: 10.1007/s11538-024-01273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
Abstract
Alzheimer's disease (AD) is believed to occur when abnormal amounts of the proteins amyloid beta and tau aggregate in the brain, resulting in a progressive loss of neuronal function. Hippocampal neurons in transgenic mice with amyloidopathy or tauopathy exhibit altered intrinsic excitability properties. We used deep hybrid modeling (DeepHM), a recently developed parameter inference technique that combines deep learning with biophysical modeling, to map experimental data recorded from hippocampal CA1 neurons in transgenic AD mice and age-matched wildtype littermate controls to the parameter space of a conductance-based CA1 model. Although mechanistic modeling and machine learning methods are by themselves powerful tools for approximating biological systems and making accurate predictions from data, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. DeepHM addresses these shortcomings by using conditional generative adversarial networks to provide an inverse mapping of data to mechanistic models that identifies the distributions of mechanistic modeling parameters coherent to the data. Here, we demonstrated that DeepHM accurately infers parameter distributions of the conductance-based model on several test cases using synthetic data generated with complex underlying parameter structures. We then used DeepHM to estimate parameter distributions corresponding to the experimental data and infer which ion channels are altered in the Alzheimer's mouse models compared to their wildtype controls at 12 and 24 months. We found that the conductances most disrupted by tauopathy, amyloidopathy, and aging are delayed rectifier potassium, transient sodium, and hyperpolarization-activated potassium, respectively.
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Affiliation(s)
- Soheil Saghafi
- Department of Mathematical Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, 07102, USA
- Department of Biomedical Informatics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Timothy Rumbell
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | - James Kozloski
- IBM T.J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | | | - Casey O Diekman
- Department of Mathematical Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, 07102, USA.
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6
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Abstract
In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function enjoys a more benign landscape than its Euclidean counterpart and Bayesian optimization is employed for computation. Numerical experiments show improved accuracy and efficiency over existing algorithms on the alignment of real protein molecules. In the context of aligning heterogeneous pairs, we illustrate a potential need for new distance functions.
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Affiliation(s)
- Amit Singer
- Department of Mathematics, Princeton University, Princeton, NJ, USA
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Ruiyi Yang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
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7
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Ritwika VPS, Gopinathan A, Yeakel JD. Beyond the kill: The allometry of predation behaviours among large carnivores. J Anim Ecol 2024. [PMID: 38459609 DOI: 10.1111/1365-2656.14070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
The costs of foraging can be high while also carrying significant risks, especially for consumers feeding at the top of the food chain. To mitigate these risks, many predators supplement active hunting with scavenging and kleptoparasitic behaviours, in some cases specializing in these alternative modes of predation. The factors that drive differential utilization of these tactics from species to species are not well understood. Here, we use an energetics approach to investigate the survival advantages of hunting, scavenging and kleptoparasitism as a function of predator, prey and potential competitor body sizes for terrestrial mammalian carnivores. The results of our framework reveal that predator tactics become more diverse closer to starvation, while the deployment of scavenging and kleptoparasitism is strongly constrained by the ratio of predator to prey body size. Our model accurately predicts a behavioural transition away from hunting towards alternative modes of predation with increasing prey size for predators spanning an order of magnitude in body size, closely matching observational data across a range of species. We then show that this behavioural boundary follows an allometric power-law scaling relationship where the predator size scales with an exponent nearing 3/4 with prey size, meaning that this behavioural switch occurs at relatively larger threshold prey body size for larger carnivores. We suggest that our approach may provide a holistic framework for guiding future observational efforts exploring the diverse array of predator foraging behaviours.
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Affiliation(s)
- V P S Ritwika
- Department of Physics, UC Merced, Merced, California, USA
- Department of Communication, UCLA, Los Angeles, California, USA
- Life and Environmental Sciences, UC Merced, Merced, California, USA
| | | | - Justin D Yeakel
- Life and Environmental Sciences, UC Merced, Merced, California, USA
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8
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Xia J, Phan HV, Vistain L, Chen M, Khan AA, Tay S. Computational prediction of protein interactions in single cells by proximity sequencing. PLoS Comput Biol 2024; 20:e1011915. [PMID: 38483861 PMCID: PMC10939233 DOI: 10.1371/journal.pcbi.1011915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Proximity sequencing (Prox-seq) simultaneously measures gene expression, protein expression and protein complexes on single cells. Using information from dual-antibody binding events, Prox-seq infers surface protein dimers at the single-cell level. Prox-seq provides multi-dimensional phenotyping of single cells in high throughput, and was recently used to track the formation of receptor complexes during cell signaling and discovered a novel interaction between CD9 and CD8 in naïve T cells. The distribution of protein abundance can affect identification of protein complexes in a complicated manner in dual-binding assays like Prox-seq. These effects are difficult to explore with experiments, yet important for accurate quantification of protein complexes. Here, we introduce a physical model of Prox-seq and computationally evaluate several different methods for reducing background noise when quantifying protein complexes. Furthermore, we developed an improved method for analysis of Prox-seq data, which resulted in more accurate and robust quantification of protein complexes. Finally, our Prox-seq model offers a simple way to investigate the behavior of Prox-seq data under various biological conditions and guide users toward selecting the best analysis method for their data.
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Affiliation(s)
- Junjie Xia
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Department Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Aly A. Khan
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
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9
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Huang H, Zeng P, Yang Q. Phase transition and higher order analysis of Lq regularization under dependence. Inf inference 2024; 13:iaae005. [PMID: 38384283 PMCID: PMC10878746 DOI: 10.1093/imaiai/iaae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 11/08/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
We study the problem of estimating a [Formula: see text]-sparse signal [Formula: see text] from a set of noisy observations [Formula: see text] under the model [Formula: see text], where [Formula: see text] is the measurement matrix the row of which is drawn from distribution [Formula: see text]. We consider the class of [Formula: see text]-regularized least squares (LQLS) given by the formulation [Formula: see text], where [Formula: see text] [Formula: see text] denotes the [Formula: see text]-norm. In the setting [Formula: see text] with fixed [Formula: see text] and [Formula: see text], we derive the asymptotic risk of [Formula: see text] for arbitrary covariance matrix [Formula: see text] that generalizes the existing results for standard Gaussian design, i.e. [Formula: see text]. The results were derived from the non-rigorous replica method. We perform a higher-order analysis for LQLS in the small-error regime in which the first dominant term can be used to determine the phase transition behavior of LQLS. Our results show that the first dominant term does not depend on the covariance structure of [Formula: see text] in the cases [Formula: see text] and [Formula: see text] which indicates that the correlations among predictors only affect the phase transition curve in the case [Formula: see text] a.k.a. LASSO. To study the influence of the covariance structure of [Formula: see text] on the performance of LQLS in the cases [Formula: see text] and [Formula: see text], we derive the explicit formulas for the second dominant term in the expansion of the asymptotic risk in terms of small error. Extensive computational experiments confirm that our analytical predictions are consistent with numerical results.
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Affiliation(s)
- Hanwen Huang
- Department of Biostatistics, Data Science and Epidemiology, Medical College of Georgia, Augusta University, Augusta, 30912 GA, USA
| | - Peng Zeng
- Department of Mathematics & Statistics, Auburn University, Auburn, 36849 AL, USA
| | - Qinglong Yang
- School of Statistics and Mathematics, Zhongnan University of Economics and Law, Wuhan 430073, Hubei, P. R. China
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10
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Gu Y. Going Deep in Diagnostic Modeling: Deep Cognitive Diagnostic Models (DeepCDMs). Psychometrika 2024; 89:118-150. [PMID: 38079062 DOI: 10.1007/s11336-023-09941-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/15/2023] [Indexed: 05/02/2024]
Abstract
Cognitive diagnostic models (CDMs) are discrete latent variable models popular in educational and psychological measurement. In this work, motivated by the advantages of deep generative modeling and by identifiability considerations, we propose a new family of DeepCDMs, to hunt for deep discrete diagnostic information. The new class of models enjoys nice properties of identifiability, parsimony, and interpretability. Mathematically, DeepCDMs are entirely identifiable, including even fully exploratory settings and allowing to uniquely identify the parameters and discrete loading structures (the " Q -matrices") at all different depths in the generative model. Statistically, DeepCDMs are parsimonious, because they can use a relatively small number of parameters to expressively model data thanks to the depth. Practically, DeepCDMs are interpretable, because the shrinking-ladder-shaped deep architecture can capture cognitive concepts and provide multi-granularity skill diagnoses from coarse to fine grained and from high level to detailed. For identifiability, we establish transparent identifiability conditions for various DeepCDMs. Our conditions impose intuitive constraints on the structures of the multiple Q -matrices and inspire a generative graph with increasingly smaller latent layers when going deeper. For estimation and computation, we focus on the confirmatory setting with known Q -matrices and develop Bayesian formulations and efficient Gibbs sampling algorithms. Simulation studies and an application to the TIMSS 2019 math assessment data demonstrate the usefulness of the proposed methodology.
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Affiliation(s)
- Yuqi Gu
- Department of Statistics, Columbia University, Room 928 SSW, 1255 Amsterdam Avenue, New York, NY, 10027, USA.
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11
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Joshi B, Nguyen TD. Bifunctional enzyme provides absolute concentration robustness in multisite covalent modification networks. J Math Biol 2024; 88:36. [PMID: 38429564 DOI: 10.1007/s00285-024-02060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 03/03/2024]
Abstract
Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions required for a network of this type to have a species with absolute concentration robustness. We find that the robustness in a substrate is endowed by its interaction with a bifunctional enzyme, which is an enzyme that has different roles when isolated versus when bound as a substrate-enzyme complex. When isolated, the bifunctional enzyme promotes production of more molecules of the robust species while when bound, the same enzyme facilitates degradation of the robust species. These dual actions produce robustness in the large class of covalent modification networks. For each network of this type, we find the network conditions for the presence of robustness, the species that has robustness, and its robustness value. The unified approach of simultaneously analyzing a large class of networks for a single property, i.e. absolute concentration robustness, reveals the underlying mechanism of the action of bifunctional enzyme while simultaneously providing a precise mathematical description of bifunctionality.
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Affiliation(s)
- Badal Joshi
- Department of Mathematics, California State University San Marcos, San Marcos, USA
| | - Tung D Nguyen
- Department of Mathematics, Texas A &M University, College Station, USA.
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12
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Zhang A, Mickelin O, Kileel J, Verbeke EJ, Marshall NF, Gilles MA, Singer A. Moment-based metrics for molecules computable from cryogenic electron microscopy images. Biol Imaging 2024; 4:e3. [PMID: 38516630 PMCID: PMC10951804 DOI: 10.1017/s2633903x24000023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 03/23/2024]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution three-dimensional (3D) structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3D reconstruction, known as Kam's method, relies on the moments of the two-dimensional (2D) images. Inspired by Kam's method, we introduce a rotationally invariant metric between two molecular structures, which does not require 3D alignment. Further, we introduce a metric between a stack of projection images and a molecular structure, which is invariant to rotations and reflections and does not require performing 3D reconstruction. Additionally, the latter metric does not assume a uniform distribution of viewing angles. We demonstrate the uses of the new metrics on synthetic and experimental datasets, highlighting their ability to measure structural similarity.
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Affiliation(s)
- Andy Zhang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Oscar Mickelin
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Joe Kileel
- Department of Mathematics and Oden Institute, University of Texas at Austin, Austin, TX, USA
| | - Eric J. Verbeke
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | | | - Marc Aurèle Gilles
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Amit Singer
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
- Department of Mathematics, Princeton University, Princeton, NJ, USA
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13
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Chen L, Gu Y. A Spectral Method for Identifiable Grade of Membership Analysis with Binary Responses. Psychometrika 2024:10.1007/s11336-024-09951-y. [PMID: 38360980 DOI: 10.1007/s11336-024-09951-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/30/2023] [Indexed: 02/17/2024]
Abstract
Grade of membership (GoM) models are popular individual-level mixture models for multivariate categorical data. GoM allows each subject to have mixed memberships in multiple extreme latent profiles. Therefore, GoM models have a richer modeling capacity than latent class models that restrict each subject to belong to a single profile. The flexibility of GoM comes at the cost of more challenging identifiability and estimation problems. In this work, we propose a singular value decomposition (SVD)-based spectral approach to GoM analysis with multivariate binary responses. Our approach hinges on the observation that the expectation of the data matrix has a low-rank decomposition under a GoM model. For identifiability, we develop sufficient and almost necessary conditions for a notion of expectation identifiability. For estimation, we extract only a few leading singular vectors of the observed data matrix and exploit the simplex geometry of these vectors to estimate the mixed membership scores and other parameters. We also establish the consistency of our estimator in the double-asymptotic regime where both the number of subjects and the number of items grow to infinity. Our spectral method has a huge computational advantage over Bayesian or likelihood-based methods and is scalable to large-scale and high-dimensional data. Extensive simulation studies demonstrate the superior efficiency and accuracy of our method. We also illustrate our method by applying it to a personality test dataset.
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Affiliation(s)
- Ling Chen
- Department of Statistics, Columbia University, New York, NY, 10027, USA
| | - Yuqi Gu
- Department of Statistics, Columbia University, New York, NY, 10027, USA.
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14
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Cronin JT, Goddard Ii J, Muthunayake A, Quiroa J, Shivaji R. Predator-induced prey dispersal can cause hump-shaped density-area relationships in prey populations. J Math Biol 2024; 88:20. [PMID: 38270669 DOI: 10.1007/s00285-023-02040-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 09/29/2023] [Accepted: 11/28/2023] [Indexed: 01/26/2024]
Abstract
Predation can both reduce prey abundance directly (through density-dependent effects) and indirectly through prey trait-mediated effects. Over the years, many studies have focused on describing the density-area relationship (DAR). However, the mechanisms responsible for the DAR are not well understood. Loss and fragmentation of habitats, owing to human activities, creates landscape-level spatial heterogeneity wherein patches of varying size, isolation and quality are separated by a human-modified "matrix" of varying degrees of hostility and has been a primary driver of species extinctions and declining biodiversity. How matrix hostility in combination with trait-mediated effects influence DAR, minimum patch size, and species coexistence remains an open question. In this paper, we employ a theoretical spatially explicit predator-prey population model built upon the reaction-diffusion framework to explore effects of predator-induced emigration (trait-mediated emigration) and matrix hostility on DAR, minimum patch size, and species coexistence. Our results show that when trait-mediated response strength is sufficiently strong, ranges of patch size emerge where a nonlinear hump-shaped prey DAR is predicted and other ranges where coexistence is not possible. In a conservation perspective, DAR is crucial not only in deciding whether we should have one large habitat patch or several-small (SLOSS), but for understanding the minimum patch size that can support a viable population. Our study lends more credence to the possibility that predators can alter prey DAR through predator-induced prey dispersal.
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Affiliation(s)
- James T Cronin
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jerome Goddard Ii
- Department of Mathematics, Auburn University Montgomery, Montgomery, AL, 36124, USA.
| | - Amila Muthunayake
- Department of Mathematics, Weber State University, Ogden, UT, 84408, USA
| | - Juan Quiroa
- Department of Mathematics, North Carolina State University, Raleigh, NC, 27607, USA
| | - Ratnasingham Shivaji
- Department of Mathematics and Statistics, University of North Carolina Greensboro, Greensboro, NC, 27412, USA
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15
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Huang J, Tataru D. Local Well-Posedness of the Skew Mean Curvature Flow for Small Data in d≧2 Dimensions. Arch Ration Mech Anal 2024; 248:10. [PMID: 38283828 PMCID: PMC10811054 DOI: 10.1007/s00205-023-01952-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
The skew mean curvature flow is an evolution equation for d dimensional manifolds embedded in R d + 2 (or more generally, in a Riemannian manifold). It can be viewed as a Schrödinger analogue of the mean curvature flow, or alternatively as a quasilinear version of the Schrödinger Map equation. In an earlier paper, the authors introduced a harmonic/Coulomb gauge formulation of the problem, and used it to prove small data local well-posedness in dimensions d ≧ 4 . In this article, we prove small data local well-posedness in low-regularity Sobolev spaces for the skew mean curvature flow in dimension d ≧ 2 . This is achieved by introducing a new, heat gauge formulation of the equations, which turns out to be more robust in low dimensions.
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Affiliation(s)
- Jiaxi Huang
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing, 100081 People’s Republic of China
| | - Daniel Tataru
- Department of Mathematics, University of California, Berkeley, Berkeley, CA 94720 USA
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16
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Li Z, Schlick T. Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics. Nucleic Acids Res 2024; 52:583-599. [PMID: 38015443 PMCID: PMC10810283 DOI: 10.1093/nar/gkad1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
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Affiliation(s)
- Zilong Li
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York University, New York, NY 10003, USA
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17
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Sudakow I, Reinitz J, Vakulenko SA, Grigoriev D. Evolution of biological cooperation: an algorithmic approach. Sci Rep 2024; 14:1468. [PMID: 38233462 PMCID: PMC10794236 DOI: 10.1038/s41598-024-52028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024] Open
Abstract
This manuscript presents an algorithmic approach to cooperation in biological systems, drawing on fundamental ideas from statistical mechanics and probability theory. Fisher's geometric model of adaptation suggests that the evolution of organisms well adapted to multiple constraints comes at a significant complexity cost. By utilizing combinatorial models of fitness, we demonstrate that the probability of adapting to all constraints decreases exponentially with the number of constraints, thereby generalizing Fisher's result. Our main focus is understanding how cooperation can overcome this adaptivity barrier. Through these combinatorial models, we demonstrate that when an organism needs to adapt to a multitude of environmental variables, division of labor emerges as the only viable evolutionary strategy.
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Affiliation(s)
- Ivan Sudakow
- School of Mathematics and Statistics, The Open University, Milton Keynes, MK7 6AA, UK.
| | - John Reinitz
- Departments of Statistics, Ecology and Evolution, Molecular Genetics and Cell Biology, University of Chicago, Chicago, 10587, IL, USA
| | - Sergey A Vakulenko
- Institute for Problems in Mechanical Engineering, Russian Academy of Sciences, Saint Petersburg, 199178, Russia
- Saint Petersburg Electrotechnical University, Saint Petersburg, 197022, Russia
| | - Dima Grigoriev
- CNRS, Mathématiques, Université de Lille, Villeneuve d'Ascq, Lille, 59655, France
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18
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Alaifari R, Bartolucci F, Steinerberger S, Wellershoff M. On the connection between uniqueness from samples and stability in Gabor phase retrieval. Sampl Theory Signal Process Data Anal 2024; 22:6. [PMID: 38261858 PMCID: PMC10794308 DOI: 10.1007/s43670-023-00079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 11/18/2023] [Indexed: 01/25/2024]
Abstract
Gabor phase retrieval is the problem of reconstructing a signal from only the magnitudes of its Gabor transform. Previous findings suggest a possible link between unique solvability of the discrete problem (recovery from measurements on a lattice) and stability of the continuous problem (recovery from measurements on an open subset of R 2 ). In this paper, we close this gap by proving that such a link cannot be made. More precisely, we establish the existence of functions which break uniqueness from samples without affecting stability of the continuous problem. Furthermore, we prove the novel result that counterexamples to unique recovery from samples are dense in L 2 ( R ) . Finally, we develop an intuitive argument on the connection between directions of instability in phase retrieval and certain Laplacian eigenfunctions associated to small eigenvalues.
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Affiliation(s)
- Rima Alaifari
- Department of Mathematics, Seminar for Applied Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland
| | - Francesca Bartolucci
- Institute of Applied Mathematics, TU Delft, Mekelweg 4, 2628 CD Delft, The Netherlands
| | - Stefan Steinerberger
- Department of Mathematics, University of Washington, C-138 Padelford, Seattle, WA 98195-4350 USA
| | - Matthias Wellershoff
- Department of Mathematics, University of Maryland, 4176 Campus Drive, College Park, MD 20742 USA
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19
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Díaz I, Hoffman KL, Hejazi NS. Causal survival analysis under competing risks using longitudinal modified treatment policies. Lifetime Data Anal 2024; 30:213-236. [PMID: 37620504 DOI: 10.1007/s10985-023-09606-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/17/2023] [Indexed: 08/26/2023]
Abstract
Longitudinal modified treatment policies (LMTP) have been recently developed as a novel method to define and estimate causal parameters that depend on the natural value of treatment. LMTPs represent an important advancement in causal inference for longitudinal studies as they allow the non-parametric definition and estimation of the joint effect of multiple categorical, ordinal, or continuous treatments measured at several time points. We extend the LMTP methodology to problems in which the outcome is a time-to-event variable subject to a competing event that precludes observation of the event of interest. We present identification results and non-parametric locally efficient estimators that use flexible data-adaptive regression techniques to alleviate model misspecification bias, while retaining important asymptotic properties such as [Formula: see text]-consistency. We present an application to the estimation of the effect of the time-to-intubation on acute kidney injury amongst COVID-19 hospitalized patients, where death by other causes is taken to be the competing event.
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Affiliation(s)
- Iván Díaz
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, NY, 10016, USA.
| | - Katherine L Hoffman
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Nima S Hejazi
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
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20
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Anderson HG, Takacs GP, Harris DC, Kuang Y, Harrison JK, Stepien TL. Global stability and parameter analysis reinforce therapeutic targets of PD-L1-PD-1 and MDSCs for glioblastoma. J Math Biol 2023; 88:10. [PMID: 38099947 PMCID: PMC10724342 DOI: 10.1007/s00285-023-02027-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/30/2023] [Accepted: 11/05/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma (GBM) is an aggressive primary brain cancer that currently has minimally effective treatments. Like other cancers, immunosuppression by the PD-L1-PD-1 immune checkpoint complex is a prominent axis by which glioma cells evade the immune system. Myeloid-derived suppressor cells (MDSCs), which are recruited to the glioma microenviroment, also contribute to the immunosuppressed GBM microenvironment by suppressing T cell functions. In this paper, we propose a GBM-specific tumor-immune ordinary differential equations model of glioma cells, T cells, and MDSCs to provide theoretical insights into the interactions between these cells. Equilibrium and stability analysis indicates that there are unique tumorous and tumor-free equilibria which are locally stable under certain conditions. Further, the tumor-free equilibrium is globally stable when T cell activation and the tumor kill rate by T cells overcome tumor growth, T cell inhibition by PD-L1-PD-1 and MDSCs, and the T cell death rate. Bifurcation analysis suggests that a treatment plan that includes surgical resection and therapeutics targeting immune suppression caused by the PD-L1-PD1 complex and MDSCs results in the system tending to the tumor-free equilibrium. Using a set of preclinical experimental data, we implement the approximate Bayesian computation (ABC) rejection method to construct probability density distributions that estimate model parameters. These distributions inform an appropriate search curve for global sensitivity analysis using the extended fourier amplitude sensitivity test. Sensitivity results combined with the ABC method suggest that parameter interaction is occurring between the drivers of tumor burden, which are the tumor growth rate and carrying capacity as well as the tumor kill rate by T cells, and the two modeled forms of immunosuppression, PD-L1-PD-1 immune checkpoint and MDSC suppression of T cells. Thus, treatment with an immune checkpoint inhibitor in combination with a therapeutic targeting the inhibitory mechanisms of MDSCs should be explored.
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Affiliation(s)
- Hannah G Anderson
- Department of Mathematics, University of Florida, Gainesville, FL, USA
| | - Gregory P Takacs
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Duane C Harris
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA
| | - Jeffrey K Harrison
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Tracy L Stepien
- Department of Mathematics, University of Florida, Gainesville, FL, USA.
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21
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Fawole E, Ristenpart WD. High-Voltage Electrodes in Moist Air Accumulate Charge That is Retained after Removing the Electric Field. Langmuir 2023; 39:17745-17755. [PMID: 38033188 PMCID: PMC10720467 DOI: 10.1021/acs.langmuir.3c02390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
Applying a high voltage to a metal electrode that is disconnected from a circuit rapidly induces a capacitive charge, which quickly relaxes after removal of the applied voltage. Here, we report that if the electrode is placed in air at a sufficiently high relative humidity and provided the connection between the high-voltage supply and the electrode is composed of two different metals, the expected capacitive charge is followed by a gradual increase in charge. Surprisingly, this extra charge persists after the removal of the applied voltage and even after physically removing the electrode from the Faraday cup used to measure the charge. We report the median charge, average charge rate, and residual charge for different applied voltages, different metal-metal connections, and varied humidity. We interpret the results in terms of a proposed water ionization mechanism and discuss the implications of the findings for high-voltage fluidic systems.
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Affiliation(s)
| | - William D. Ristenpart
- Dept. of Chemical Engineering, University of California at Davis, Davis, California 95616, United States
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22
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Molstad AJ, Motwani K. Multiresolution categorical regression for interpretable cell-type annotation. Biometrics 2023; 79:3485-3496. [PMID: 37798600 DOI: 10.1111/biom.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/07/2023] [Indexed: 10/07/2023]
Abstract
In many categorical response regression applications, the response categories admit a multiresolution structure. That is, subsets of the response categories may naturally be combined into coarser response categories. In such applications, practitioners are often interested in estimating the resolution at which a predictor affects the response category probabilities. In this paper, we propose a method for fitting the multinomial logistic regression model in high dimensions that addresses this problem in a unified and data-driven way. Our method allows practitioners to identify which predictors distinguish between coarse categories but not fine categories, which predictors distinguish between fine categories, and which predictors are irrelevant. For model fitting, we propose a scalable algorithm that can be applied when the coarse categories are defined by either overlapping or nonoverlapping sets of fine categories. Statistical properties of our method reveal that it can take advantage of this multiresolution structure in a way existing estimators cannot. We use our method to model cell-type probabilities as a function of a cell's gene expression profile (i.e., cell-type annotation). Our fitted model provides novel biological insights which may be useful for future automated and manual cell-type annotation methodology.
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Affiliation(s)
- Aaron J Molstad
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Keshav Motwani
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
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23
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Patterson D, Levin S, Staver AC, Touboul J. Pattern Formation in Mesic Savannas. Bull Math Biol 2023; 86:3. [PMID: 38010440 PMCID: PMC10682166 DOI: 10.1007/s11538-023-01231-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
We analyze a spatially extended version of a well-known model of forest-savanna dynamics, which presents as a system of nonlinear partial integro-differential equations, and study necessary conditions for pattern-forming bifurcations. Homogeneous solutions dominate the dynamics of the standard forest-savanna model, regardless of the length scales of the various spatial processes considered. However, several different pattern-forming scenarios are possible upon including spatial resource limitation, such as competition for water, soil nutrients, or herbivory effects. Using numerical simulations and continuation, we study the nature of the resulting patterns as a function of system parameters and length scales, uncovering subcritical pattern-forming bifurcations and observing significant regions of multistability for realistic parameter regimes. Finally, we discuss our results in the context of extant savanna-forest modeling efforts and highlight ongoing challenges in building a unifying mathematical model for savannas across different rainfall levels.
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Affiliation(s)
- Denis Patterson
- High Meadows Environmental Institute, Princeton University, Princeton, NJ, 08544, USA.
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.
- Department of Mathematical Sciences, Durham University, Durham, UK.
| | - Simon Levin
- High Meadows Environmental Institute, Princeton University, Princeton, NJ, 08544, USA
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Ann Carla Staver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Touboul
- Department of Mathematics, Brandeis University, Waltham, MA, 02453, USA
- Volen National Center for Complex Systems, Brandeis University, Waltham, MA, 02453, USA
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24
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Silver M, Phelps W, Masarik K, Burke K, Zhang C, Schwartz A, Wang M, Nitka AL, Schutz J, Trainor T, Washington JW, Rheineck BD. Prevalence and Source Tracing of PFAS in Shallow Groundwater Used for Drinking Water in Wisconsin, USA. Environ Sci Technol 2023; 57:17415-17426. [PMID: 37916814 PMCID: PMC10653221 DOI: 10.1021/acs.est.3c02826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
Samples from 450 homes with shallow private wells throughout the state of Wisconsin (USA) were collected and analyzed for 44 individual per- and polyfluoroalkyl substances (PFAS), general water quality parameters, and indicators of human waste as well as agricultural influence. At least one PFAS was detected in 71% of the study samples, and 22 of the 44 PFAS analytes were detected in one or more samples. Levels of PFOA and/or PFOS exceeded the proposed Maximum Contaminant Levels of 4 ng/L, put forward by the U.S. Environmental Protection Agency (EPA) in March 2023, in 17 of the 450 samples, with two additional samples containing PFHxS ≳ 9 ng/L (the EPA-proposed hazard index reference value). Those samples above the referenced PFAS levels tend to be associated with developed land and human waste indicators (artificial sweeteners and pharmaceuticals), which can be released to groundwater via septic systems. For a few samples with levels of PFOA, PFOS, and/or PFHxS > 40 ng/L, application of wastes to agricultural land is a possible source. Overall, the study suggests that human waste sources, septic systems in particular, are important sources of perfluoroalkyl acids, especially ones with ≤8 perfluorinated carbons, in shallow groundwater.
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Affiliation(s)
- Matthew Silver
- Bureau
of Drinking Water and Groundwater—Groundwater Section, Wisconsin Department of Natural Resources, Madison, Wisconsin 53707, United States
| | - William Phelps
- Bureau
of Drinking Water and Groundwater—Groundwater Section, Wisconsin Department of Natural Resources, Madison, Wisconsin 53707, United States
| | - Kevin Masarik
- Center
for Watershed Science and Education, College of Natural Resources, University of Wisconsin—Stevens Point, Stevens Point, Wisconsin 54481, United States
| | - Kyle Burke
- Environmental
Health Division—Organics, Wisconsin
State Laboratory of Hygiene, Madison, Wisconsin 53707, United States
| | - Chen Zhang
- Environmental
Health Division—Organics, Wisconsin
State Laboratory of Hygiene, Madison, Wisconsin 53707, United States
| | - Alex Schwartz
- Environmental
Health Division—Organics, Wisconsin
State Laboratory of Hygiene, Madison, Wisconsin 53707, United States
| | - Miaoyan Wang
- Department
of Statistics, University of Wisconsin—Madison, Madison, Wisconsin 53707, United States
| | - Amy L. Nitka
- Center
for Watershed Science and Education, College of Natural Resources, University of Wisconsin—Stevens Point, Stevens Point, Wisconsin 54481, United States
| | - Jordan Schutz
- Bureau
of Drinking Water and Groundwater—Groundwater Section, Wisconsin Department of Natural Resources, Madison, Wisconsin 53707, United States
| | - Tom Trainor
- Bureau
of Environmental Analysis and Sustainability − Laboratory Certification, Wisconsin Department of Natural Resources, Green Bay, Wisconsin 54313, United States
| | - John W. Washington
- Center
for
Environmental Measurement and Modeling, U.S. Environmental Protection Agency, Athens, Georgia 30605, United States
| | - Bruce D. Rheineck
- Bureau
of Drinking Water and Groundwater—Groundwater Section, Wisconsin Department of Natural Resources, Madison, Wisconsin 53707, United States
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25
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Krishnan N, Sarpangala N, Gamez M, Gopinathan A, Ross JL. Effects of cytoskeletal network mesh size on cargo transport. Eur Phys J E Soft Matter 2023; 46:109. [PMID: 37947921 DOI: 10.1140/epje/s10189-023-00358-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023]
Abstract
Intracellular transport of cargoes in the cell is essential for the organization and functioning cells, especially those that are large and elongated. The cytoskeletal networks inside large cells can be highly complex, and this cytoskeletal organization can have impacts on the distance and trajectories of travel. Here, we experimentally created microtubule networks with varying mesh sizes and examined the ability of kinesin-driven quantum dot cargoes to traverse the network. Using the experimental data, we deduced parameters for cargo detachment at intersections and away from intersections, allowing us to create an analytical theory for the run length as a function of mesh size. We also used these parameters to perform simulations of cargoes along paths extracted from the experimental networks. We find excellent agreement between the trends in run length, displacement, and trajectory persistence length comparing the experimental and simulated trajectories.
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Affiliation(s)
- Nimisha Krishnan
- Physics Department, Syracuse University, Crouse Drive, Syracuse, NY, 13104, USA
| | - Niranjan Sarpangala
- Department of Physics, University of California, Merced, 5200 North Lake Rd, Merced, CA, 95343, USA
| | - Maria Gamez
- Department of Physics, University of California, Merced, 5200 North Lake Rd, Merced, CA, 95343, USA
| | - Ajay Gopinathan
- Department of Physics, University of California, Merced, 5200 North Lake Rd, Merced, CA, 95343, USA
| | - Jennifer L Ross
- Physics Department, Syracuse University, Crouse Drive, Syracuse, NY, 13104, USA.
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26
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Eissa TL, Kilpatrick ZP. Learning efficient representations of environmental priors in working memory. PLoS Comput Biol 2023; 19:e1011622. [PMID: 37943956 PMCID: PMC10662764 DOI: 10.1371/journal.pcbi.1011622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/21/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Experience shapes our expectations and helps us learn the structure of the environment. Inference models render such learning as a gradual refinement of the observer's estimate of the environmental prior. For instance, when retaining an estimate of an object's features in working memory, learned priors may bias the estimate in the direction of common feature values. Humans display such biases when retaining color estimates on short time intervals. We propose that these systematic biases emerge from modulation of synaptic connectivity in a neural circuit based on the experienced stimulus history, shaping the persistent and collective neural activity that encodes the stimulus estimate. Resulting neural activity attractors are aligned to common stimulus values. Using recently published human response data from a delayed-estimation task in which stimuli (colors) were drawn from a heterogeneous distribution that did not necessarily correspond with reported population biases, we confirm that most subjects' response distributions are better described by experience-dependent learning models than by models with fixed biases. This work suggests systematic limitations in working memory reflect efficient representations of inferred environmental structure, providing new insights into how humans integrate environmental knowledge into their cognitive strategies.
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Affiliation(s)
- Tahra L. Eissa
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Zachary P. Kilpatrick
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, Colorado, United States of America
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, Colorado, United States of America
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27
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Howerton E, Dahlin K, Edholm CJ, Fox L, Reynolds M, Hollingsworth B, Lytle G, Walker M, Blackwood J, Lenhart S. The effect of governance structures on optimal control of two-patch epidemic models. J Math Biol 2023; 87:74. [PMID: 37861753 PMCID: PMC10589198 DOI: 10.1007/s00285-023-02001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
Infectious diseases continue to pose a significant threat to the health of humans globally. While the spread of pathogens transcends geographical boundaries, the management of infectious diseases typically occurs within distinct spatial units, determined by geopolitical boundaries. The allocation of management resources within and across regions (the "governance structure") can affect epidemiological outcomes considerably, and policy-makers are often confronted with a choice between applying control measures uniformly or differentially across regions. Here, we investigate the extent to which uniform and non-uniform governance structures affect the costs of an infectious disease outbreak in two-patch systems using an optimal control framework. A uniform policy implements control measures with the same time varying rate functions across both patches, while these measures are allowed to differ between the patches in a non-uniform policy. We compare results from two systems of differential equations representing transmission of cholera and Ebola, respectively, to understand the interplay between transmission mode, governance structure and the optimal control of outbreaks. In our case studies, the governance structure has a meaningful impact on the allocation of resources and burden of cases, although the difference in total costs is minimal. Understanding how governance structure affects both the optimal control functions and epidemiological outcomes is crucial for the effective management of infectious diseases going forward.
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Affiliation(s)
- Emily Howerton
- Department of Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Kyle Dahlin
- Center for the Ecology of Infectious Diseases, Odum School of Ecology, University of Georgia, Athens, GA, USA.
| | | | - Lindsey Fox
- Mathematics Discipline, Eckerd College, Saint Petersburg, FL, USA
| | - Margaret Reynolds
- Department of Mathematical Sciences, United States Military Academy, West Point, NY, USA
| | | | - George Lytle
- Department of Biology, Chemistry, Mathematics, and Computer Science, University of Montevallo, Montevallo, AL, USA
| | - Melody Walker
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Julie Blackwood
- Department of Mathematics and Statistics, Williams College, Williamstown, MA, USA
| | - Suzanne Lenhart
- Department of Mathematics, University of Tennessee, Knoxville, TN, USA
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28
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Daniels BC, Wang Y, Page RE, Amdam GV. Identifying a developmental transition in honey bees using gene expression data. PLoS Comput Biol 2023; 19:e1010704. [PMID: 37733808 PMCID: PMC10547183 DOI: 10.1371/journal.pcbi.1010704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 10/03/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Abstract
In many organisms, interactions among genes lead to multiple functional states, and changes to interactions can lead to transitions into new states. These transitions can be related to bifurcations (or critical points) in dynamical systems theory. Characterizing these collective transitions is a major challenge for systems biology. Here, we develop a statistical method for identifying bistability near a continuous transition directly from high-dimensional gene expression data. We apply the method to data from honey bees, where a known developmental transition occurs between bees performing tasks in the nest and leaving the nest to forage. Our method, which makes use of the expected shape of the distribution of gene expression levels near a transition, successfully identifies the emergence of bistability and links it to genes that are known to be involved in the behavioral transition. This proof of concept demonstrates that going beyond correlative analysis to infer the shape of gene expression distributions might be used more generally to identify collective transitions from gene expression data.
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Affiliation(s)
- Bryan C. Daniels
- School of Complex Adaptive Systems, Arizona State University, Tempe, Arizona, United States of America
| | - Ying Wang
- Banner Health Corporation, Phoenix, Arizona, United States of America
| | - Robert E. Page
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Entomology and Nematology, University of California Davis, Davis, California, United States of America
| | - Gro V. Amdam
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Aas, Norway
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29
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Huang Q, Kim J, Wang K, Vecchioni S, Ohayon YP, Seeman NC, Jonoska N, Sha R. Environmentally Controlled Oscillator with Triplex Guided Displacement of DNA Duplexes. Nano Lett 2023; 23:7593-7598. [PMID: 37561947 PMCID: PMC10450806 DOI: 10.1021/acs.nanolett.3c02176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The use of DNA triplex association is advantageous for the reconfiguration of dynamic DNA nanostructures through pH alteration and can provide environmental control for both structural changes and molecular signaling. The combination of pH-induced triplex-forming oligonucleotide (TFOs) binding with toehold-mediated strand displacement has recently garnered significant attention in the field of structural DNA nanotechnology. While most previous studies use single-stranded DNA to displace or replace TFOs within the triplex, here we demonstrate that pH alteration allows a DNA duplex, with a toehold assistance, to displace TFOs from the components of another DNA duplex. We examined the dependence of this process on toehold length and show that the pH changes allow for cyclic oscillations between two molecular formations. We implemented the duplex/triplex design onto the surface of 2D DNA origami in the form outlining binary digits 0 or 1 and verified the oscillatory conformational changes between the two formations with atomic force microscopy.
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Affiliation(s)
- Qiuyan Huang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Jiyeon Kim
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Kun Wang
- Department
of Physics, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P. Ohayon
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C. Seeman
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Nataša Jonoska
- Department
of Mathematics and Statistics, University
of South Florida, Tampa, Florida 33620, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
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30
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Morgan J, Lindsay AE. Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics. PLoS Comput Biol 2023; 19:e1011216. [PMID: 37647345 PMCID: PMC10497171 DOI: 10.1371/journal.pcbi.1011216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/12/2023] [Accepted: 08/05/2023] [Indexed: 09/01/2023] Open
Abstract
T cells form transient cell-to-cell contacts with antigen presenting cells (APCs) to facilitate surface interrogation by membrane bound T cell receptors (TCRs). Upon recognition of molecular signatures (antigen) of pathogen, T cells may initiate an adaptive immune response. The duration of the T cell/APC contact is observed to vary widely, yet it is unclear what constructive role, if any, such variations might play in immune signaling. Modeling efforts describing antigen discrimination often focus on steady-state approximations and do not account for the transient nature of cellular contacts. Within the framework of a kinetic proofreading (KP) mechanism, we develop a stochastic First Receptor Activation Model (FRAM) describing the likelihood that a productive immune signal is produced before the expiry of the contact. Through the use of extreme statistics, we characterize the probability that the first TCR triggering is induced by a rare agonist antigen and not by that of an abundant self-antigen. We show that defining positive immune outcomes as resilience to extreme statistics and sensitivity to rare events mitigates classic tradeoffs associated with KP. By choosing a sufficient number of KP steps, our model is able to yield single agonist sensitivity whilst remaining non-reactive to large populations of self antigen, even when self and agonist antigen are similar in dissociation rate to the TCR but differ largely in expression. Additionally, our model achieves high levels of accuracy even when agonist positive APCs encounters are rare. Finally, we discuss potential biological costs associated with high classification accuracy, particularly in challenging T cell environments.
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Affiliation(s)
- Jonathan Morgan
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, South Bend, Indiana, United States of America
- Biophysics Graduate Program, University of Notre Dame, South Bend, Indiana, United States of America
| | - Alan E. Lindsay
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, South Bend, Indiana, United States of America
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31
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Rene L, Linero AR, Slate E. Causal mediation and sensitivity analysis for mixed-scale data. Stat Methods Med Res 2023; 32:1249-1266. [PMID: 37194551 PMCID: PMC10500957 DOI: 10.1177/09622802231173491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The goal of causal mediation analysis, often described within the potential outcomes framework, is to decompose the effect of an exposure on an outcome of interest along different causal pathways. Using the assumption of sequential ignorability to attain non-parametric identification, Imai et al. (2010) proposed a flexible approach to measuring mediation effects, focusing on parametric and semiparametric normal/Bernoulli models for the outcome and mediator. Less attention has been paid to the case where the outcome and/or mediator model are mixed-scale, ordinal, or otherwise fall outside the normal/Bernoulli setting. We develop a simple, but flexible, parametric modeling framework to accommodate the common situation where the responses are mixed continuous and binary, and, apply it to a zero-one inflated beta model for the outcome and mediator. Applying our proposed methods to the publicly-available JOBS II dataset, we (i) argue for the need for non-normal models, (ii) show how to estimate both average and quantile mediation effects for boundary-censored data, and (iii) show how to conduct a meaningful sensitivity analysis by introducing unidentified, scientifically meaningful, sensitivity parameters.
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Affiliation(s)
- Lexi Rene
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Antonio R Linero
- Department of Statistics and Data Sciences, University of Texas at Austin, Austin, TX, USA
| | - Elizabeth Slate
- Department of Statistics, Florida State University, Tallahassee, FL, USA
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32
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Chen J, Rincon JOR, DeGrandi-Hoffman G, Fewell J, Harrison J, Kang Y. Impacts of seasonality and parasitism on honey bee population dynamics. J Math Biol 2023; 87:19. [PMID: 37389742 DOI: 10.1007/s00285-023-01952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 05/11/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023]
Abstract
The honeybee plays an extremely important role in ecosystem stability and diversity and in the production of bee pollinated crops. Honey bees and other pollinators are under threat from the combined effects of nutritional stress, parasitism, pesticides, and climate change that impact the timing, duration, and variability of seasonal events. To understand how parasitism and seasonality influence honey bee colonies separately and interactively, we developed a non-autonomous nonlinear honeybee-parasite interaction differential equation model that incorporates seasonality into the egg-laying rate of the queen. Our theoretical results show that parasitism negatively impacts the honey bee population either by decreasing colony size or destabilizing population dynamics through supercritical or subcritical Hopf-bifurcations depending on conditions. Our bifurcation analysis and simulations suggest that seasonality alone may have positive or negative impacts on the survival of honey bee colonies. More specifically, our study indicates that (1) the timing of the maximum egg-laying rate seems to determine when seasonality has positive or negative impacts; and (2) when the period of seasonality is large it can lead to the colony collapsing. Our study further suggests that the synergistic influences of parasitism and seasonality can lead to complicated dynamics that may positively and negatively impact the honey bee colony's survival. Our work partially uncovers the intrinsic effects of climate change and parasites, which potentially provide essential insights into how best to maintain or improve a honey bee colony's health.
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Affiliation(s)
- Jun Chen
- Simon A. Levin Mathematical and Computational Modeling Sciences Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Jordy O Rodriguez Rincon
- Simon A. Levin Mathematical and Computational Modeling Sciences Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Gloria DeGrandi-Hoffman
- Carl Hayden Bee Research Center, United States Department of Agriculture-Agricultural Research Service, Tucson, AZ, 85719, USA
| | - Jennifer Fewell
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Jon Harrison
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yun Kang
- Sciences and Mathematics Faculty, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, 85212, USA.
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33
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Khodaei M, Owen M, Beerli P. Geodesics to characterize the phylogenetic landscape. PLoS One 2023; 18:e0287350. [PMID: 37352194 PMCID: PMC10289362 DOI: 10.1371/journal.pone.0287350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/04/2023] [Indexed: 06/25/2023] Open
Abstract
Phylogenetic trees are fundamental for understanding evolutionary history. However, finding maximum likelihood trees is challenging due to the complexity of the likelihood landscape and the size of tree space. Based on the Billera-Holmes-Vogtmann (BHV) distance between trees, we describe a method to generate intermediate trees on the shortest path between two trees, called pathtrees. These pathtrees give a structured way to generate and visualize part of treespace. They allow investigating intermediate regions between trees of interest, exploring locally optimal trees in topological clusters of treespace, and potentially finding trees of high likelihood unexplored by tree search algorithms. We compared our approach against other tree search tools (Paup*, RAxML, and RevBayes) using the highest likelihood trees and number of new topologies found, and validated the accuracy of the generated treespace. We assess our method using two datasets. The first consists of 23 primate species (CytB, 1141 bp), leading to well-resolved relationships. The second is a dataset of 182 milksnakes (CytB, 1117 bp), containing many similar sequences and complex relationships among individuals. Our method visualizes the treespace using log likelihood as a fitness function. It finds similarly optimal trees as heuristic methods and presents the likelihood landscape at different scales. It found relevant trees that were not found with MCMC methods. The validation measures indicated that our method performed well mapping treespace into lower dimensions. Our method complements heuristic search analyses, and the visualization allows the inspection of likelihood terraces and exploration of treespace areas not visited by heuristic searches.
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Affiliation(s)
- Marzieh Khodaei
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States of America
| | - Megan Owen
- Department of Mathematics, Lehman College and Graduate Center, CUNY, NY, NY, United States of America
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States of America
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34
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Nguyen K, Rutter EM, Flores KB. Estimation of Parameter Distributions for Reaction-Diffusion Equations with Competition using Aggregate Spatiotemporal Data. Bull Math Biol 2023; 85:62. [PMID: 37268762 DOI: 10.1007/s11538-023-01162-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Reaction-diffusion equations have been used to model a wide range of biological phenomenon related to population spread and proliferation from ecology to cancer. It is commonly assumed that individuals in a population have homogeneous diffusion and growth rates; however, this assumption can be inaccurate when the population is intrinsically divided into many distinct subpopulations that compete with each other. In previous work, the task of inferring the degree of phenotypic heterogeneity between subpopulations from total population density has been performed within a framework that combines parameter distribution estimation with reaction-diffusion models. Here, we extend this approach so that it is compatible with reaction-diffusion models that include competition between subpopulations. We use a reaction-diffusion model of glioblastoma multiforme, an aggressive type of brain cancer, to test our approach on simulated data that are similar to measurements that could be collected in practice. We use Prokhorov metric framework and convert the reaction-diffusion model to a random differential equation model to estimate joint distributions of diffusion and growth rates among heterogeneous subpopulations. We then compare the new random differential equation model performance against other partial differential equation models' performance. We find that the random differential equation is more capable at predicting the cell density compared to other models while being more time efficient. Finally, we use k-means clustering to predict the number of subpopulations based on the recovered distributions.
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Affiliation(s)
- Kyle Nguyen
- Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, USA
- Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA
| | - Erica M Rutter
- Department of Applied Mathematics, University of California, Merced, Merced, CA, USA
| | - Kevin B Flores
- Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC, USA.
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA.
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35
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Abstract
Biological events are often initiated when a random "searcher" finds a "target," which is called a first passage time (FPT). In some biological systems involving multiple searchers, an important timescale is the time it takes the slowest searcher(s) to find a target. For example, of the hundreds of thousands of primordial follicles in a woman's ovarian reserve, it is the slowest to leave that trigger the onset of menopause. Such slowest FPTs may also contribute to the reliability of cell signaling pathways and influence the ability of a cell to locate an external stimulus. In this paper, we use extreme value theory and asymptotic analysis to obtain rigorous approximations to the full probability distribution and moments of slowest FPTs. Though the results are proven in the limit of many searchers, numerical simulations reveal that the approximations are accurate for any number of searchers in typical scenarios of interest. We apply these general mathematical results to models of ovarian aging and menopause timing, which reveals the role of slowest FPTs for understanding redundancy in biological systems. We also apply the theory to several popular models of stochastic search, including search by diffusive, subdiffusive, and mortal searchers.
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Affiliation(s)
- Sean D Lawley
- Department of Mathematics, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Joshua Johnson
- Division of Reproductive Sciences, Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
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36
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Drucker B, Goldwyn JH. Structure and dynamics that specialize neurons for high-frequency coincidence detection in the barn owl nucleus laminaris. Biol Cybern 2023; 117:143-162. [PMID: 37129628 DOI: 10.1007/s00422-023-00962-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/14/2023] [Indexed: 05/03/2023]
Abstract
A principal cue for sound source localization is the difference in arrival times of sounds at an animal's two ears (interaural time difference, ITD). Neurons that process ITDs are specialized to compare the timing of inputs with submillisecond precision. In the barn owl, ITD processing begins in the nucleus laminaris (NL) region of the auditory brain stem. Remarkably, NL neurons are sensitive to ITDs in high-frequency sounds (kilohertz-range). This contrasts with ITD-based sound localization in analogous regions in mammals where ITD sensitivity is typically restricted to lower-frequency sounds. Guided by previous experiments and modeling studies of tone-evoked responses of NL neurons, we propose NL neurons achieve high-frequency ITD sensitivity if they respond selectively to the small-amplitude, high-frequency oscillations in their inputs, and remain relatively non-responsive to mean input level. We use a biophysically based model to study the effects of soma-axon coupling on dynamics and function in NL neurons. First, we show that electrical separation of the soma from the axon region in the neuron enhances high-frequency ITD sensitivity. This soma-axon coupling configuration promotes linear subthreshold dynamics and rapid spike initiation, making the model more responsive to input oscillations, rather than mean input level. Second, we provide new evidence for the essential role of phasic dynamics for high-frequency neural coincidence detection. Transforming our model to the phasic firing mode further tunes the model to respond selectively to the oscillating inputs that carry ITD information. Similar structural and dynamical mechanisms specialize mammalian auditory brain stem neurons for ITD sensitivity, and thus, our work identifies common principles of ITD processing and neural coincidence detection across species and for sounds at widely different frequencies.
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Affiliation(s)
- Ben Drucker
- Department of Mathematics and Statistics, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081, USA
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA, 10587, USA
| | - Joshua H Goldwyn
- Department of Mathematics and Statistics, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081, USA.
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37
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Karaaslanli A, Saha S, Maiti T, Aviyente S. Kernelized multiview signed graph learning for single-cell RNA sequencing data. BMC Bioinformatics 2023; 24:127. [PMID: 37016281 PMCID: PMC10071725 DOI: 10.1186/s12859-023-05250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/22/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Characterizing the topology of gene regulatory networks (GRNs) is a fundamental problem in systems biology. The advent of single cell technologies has made it possible to construct GRNs at finer resolutions than bulk and microarray datasets. However, cellular heterogeneity and sparsity of the single cell datasets render void the application of regular Gaussian assumptions for constructing GRNs. Additionally, most GRN reconstruction approaches estimate a single network for the entire data. This could cause potential loss of information when single cell datasets are generated from multiple treatment conditions/disease states. RESULTS To better characterize single cell GRNs under different but related conditions, we propose the joint estimation of multiple networks using multiple signed graph learning (scMSGL). The proposed method is based on recently developed graph signal processing (GSP) based graph learning, where GRNs and gene expressions are modeled as signed graphs and graph signals, respectively. scMSGL learns multiple GRNs by optimizing the total variation of gene expressions with respect to GRNs while ensuring that the learned GRNs are similar to each other through regularization with respect to a learned signed consensus graph. We further kernelize scMSGL with the kernel selected to suit the structure of single cell data. CONCLUSIONS scMSGL is shown to have superior performance over existing state of the art methods in GRN recovery on simulated datasets. Furthermore, scMSGL successfully identifies well-established regulators in a mouse embryonic stem cell differentiation study and a cancer clinical study of medulloblastoma.
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Affiliation(s)
- Abdullah Karaaslanli
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA.
| | - Satabdi Saha
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tapabrata Maiti
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
| | - Selin Aviyente
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA
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38
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KhudaBukhsh WR, Khalsa SK, Kenah E, Rempała GA, Tien JH. COVID-19 dynamics in an Ohio prison. Front Public Health 2023; 11:1087698. [PMID: 37064663 PMCID: PMC10098107 DOI: 10.3389/fpubh.2023.1087698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
Incarcerated individuals are a highly vulnerable population for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the transmission of respiratory infections within prisons and between prisons and surrounding communities is a crucial component of pandemic preparedness and response. Here, we use mathematical and statistical models to analyze publicly available data on the spread of SARS-CoV-2 reported by the Ohio Department of Rehabilitation and Corrections (ODRC). Results from mass testing conducted on April 16, 2020 were analyzed together with time of first reported SARS-CoV-2 infection among Marion Correctional Institution (MCI) inmates. Extremely rapid, widespread infection of MCI inmates was reported, with nearly 80% of inmates infected within 3 weeks of the first reported inmate case. The dynamical survival analysis (DSA) framework that we use allows the derivation of explicit likelihoods based on mathematical models of transmission. We find that these data are consistent with three non-exclusive possibilities: (i) a basic reproduction number >14 with a single initially infected inmate, (ii) an initial superspreading event resulting in several hundred initially infected inmates with a reproduction number of approximately three, or (iii) earlier undetected circulation of virus among inmates prior to April. All three scenarios attest to the vulnerabilities of prisoners to COVID-19, and the inability to distinguish among these possibilities highlights the need for improved infection surveillance and reporting in prisons.
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Affiliation(s)
- Wasiur R. KhudaBukhsh
- School of Mathematical Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Sat Kartar Khalsa
- Wexner Medical Center, The Ohio State University, Columbus, OH, United States
| | - Eben Kenah
- Division of Biostatistics, The Ohio State University, Columbus, OH, United States
| | - Gregorz A. Rempała
- Division of Biostatistics, Department of Mathematics, The Ohio State University, Columbus, OH, United States
| | - Joseph H. Tien
- Division of Epidemiology, Department of Mathematics, The Ohio State University, Columbus, OH, United States
- *Correspondence: Joseph H. Tien
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39
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Colunga AL, Colebank MJ, Olufsen MS. Parameter inference in a computational model of haemodynamics in pulmonary hypertension. J R Soc Interface 2023; 20:20220735. [PMID: 36854380 PMCID: PMC9974303 DOI: 10.1098/rsif.2022.0735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
Pulmonary hypertension (PH), defined by a mean pulmonary arterial pressure (mPAP) greater than 20 mmHg, is characterized by increased pulmonary vascular resistance and decreased pulmonary arterial compliance. There are few measurable biomarkers of PH progression, but a conclusive diagnosis of the disease requires invasive right heart catheterization (RHC). Patient-specific cardiovascular systems-level computational models provide a potential non-invasive tool for determining additional indicators of disease severity. Using computational modelling, this study quantifies physiological parameters indicative of disease severity in nine PH patients. The model includes all four heart chambers, the pulmonary and systemic circulations. We consider two sets of calibration data: static (systolic and diastolic values) RHC data and a combination of static and continuous, time-series waveform data. We determine a subset of identifiable parameters for model calibration using sensitivity analyses and multi-start inference and perform posterior uncertainty quantification. Results show that additional waveform data enables accurate calibration of the right atrial reservoir and pump function across the PH cohort. Model outcomes, including stroke work and pulmonary resistance-compliance relations, reflect typical right heart dynamics in PH phenotypes. Lastly, we show that estimated parameters agree with previous, non-modelling studies, supporting this type of analysis in translational PH research.
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Affiliation(s)
- Amanda L. Colunga
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Mitchel J. Colebank
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA
- University of California, Irvine—Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center, and Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - REU Program
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Mette S. Olufsen
- Department of Mathematics, North Carolina State University, Raleigh, NC, USA
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40
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Wu K, Karmakar S. A model-free approach to do long-term volatility forecasting and its variants. Financ Innov 2023; 9:59. [PMID: 36873387 PMCID: PMC9974404 DOI: 10.1186/s40854-023-00466-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Volatility forecasting is important in financial econometrics and is mainly based on the application of various GARCH-type models. However, it is difficult to choose a specific GARCH model that works uniformly well across datasets, and the traditional methods are unstable when dealing with highly volatile or short-sized datasets. The newly proposed normalizing and variance stabilizing (NoVaS) method is a more robust and accurate prediction technique that can help with such datasets. This model-free method was originally developed by taking advantage of an inverse transformation based on the frame of the ARCH model. In this study, we conduct extensive empirical and simulation analyses to investigate whether it provides higher-quality long-term volatility forecasting than standard GARCH models. Specifically, we found this advantage to be more prominent with short and volatile data. Next, we propose a variant of the NoVaS method that possesses a more complete form and generally outperforms the current state-of-the-art NoVaS method. The uniformly superior performance of NoVaS-type methods encourages their wide application in volatility forecasting. Our analyses also highlight the flexibility of the NoVaS idea that allows the exploration of other model structures to improve existing models or solve specific prediction problems.
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Affiliation(s)
- Kejin Wu
- Department of Mathematics, University of California San Diego, La Jolla, USA
| | - Sayar Karmakar
- Department of Statistics, University of Florida, Gainesville, USA
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41
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Chen G, Han J, Xue Q. Boundedness of Complements for Log Calabi-Yau Threefolds. Peking Math J 2023; 7:1-33. [PMID: 38444737 PMCID: PMC10913441 DOI: 10.1007/s42543-022-00057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/03/2022] [Accepted: 11/17/2022] [Indexed: 03/07/2024]
Abstract
In this paper, we study the theory of complements, introduced by Shokurov, for Calabi-Yau type varieties with the coefficient set [0, 1]. We show that there exists a finite set of positive integers N , such that if a threefold pair ( X / Z ∋ z , B ) has an R -complement which is klt over a neighborhood of z, then it has an n-complement for some n ∈ N . We also show the boundedness of complements for R -complementary surface pairs.
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Affiliation(s)
- Guodu Chen
- Institute for Theoretical Sciences, Westlake University, Hangzhou, 310024 Zhejiang China
| | - Jingjun Han
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200438 China
| | - Qingyuan Xue
- Department of Mathematics, The University of Utah, Salt Lake City, UT 84112 USA
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42
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Perez C, Karmakar S. An NLP-assisted Bayesian time-series analysis for prevalence of Twitter cyberbullying during the COVID-19 pandemic. Soc Netw Anal Min 2023; 13:51. [PMID: 36937491 PMCID: PMC10016178 DOI: 10.1007/s13278-023-01053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023]
Abstract
COVID-19 has brought about many changes in social dynamics. Stay-at-home orders and disruptions in school teaching can influence bullying behavior in-person and online, both of which leading to negative outcomes in victims. To study cyberbullying specifically, 1 million tweets containing keywords associated with abuse were collected from the beginning of 2019 to the end of 2021 with the Twitter API search endpoint. A natural language processing model pre-trained on a Twitter corpus generated probabilities for the tweets being offensive and hateful. To overcome limitations of sampling, data were also collected using the count endpoint. The fraction of tweets from a given daily sample marked as abusive is multiplied to the number reported by the count endpoint. Once these adjusted counts are assembled, a Bayesian autoregressive Poisson model allows one to study the mean trend and lag functions of the data and how they vary over time. The results reveal strong weekly and yearly seasonality in hateful speech but with slight differences across years that may be attributed to COVID-19.
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Affiliation(s)
- Christopher Perez
- Department of Statistics, University of Florida, Gainesville, FL 32601 USA
| | - Sayar Karmakar
- Department of Statistics, University of Florida, Gainesville, FL 32601 USA
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43
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Xu Z, Yue P, Feng JJ. Poroelastic modelling reveals the cooperation between two mechanisms for albuminuria. J R Soc Interface 2023; 20:20220634. [PMID: 36628531 PMCID: PMC9832287 DOI: 10.1098/rsif.2022.0634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Albuminuria occurs when albumin leaks abnormally into the urine. Its mechanism remains unclear. A gel-compression hypothesis attributes the glomerular barrier to compression of the glomerular basement membrane (GBM) as a gel layer. Loss of podocyte foot processes would allow the gel layer to expand circumferentially, enlarge its pores and leak albumin into the urine. To test this hypothesis, we develop a poroelastic model of the GBM. It predicts GBM compression in healthy glomerulus and GBM expansion in the diseased state, essentially confirming the hypothesis. However, by itself, the gel compression and expansion mechanism fails to account for two features of albuminuria: the reduction in filtration flux and the thickening of the GBM. A second mechanism, the constriction of flow area at the slit diaphragm downstream of the GBM, must be included. The cooperation between the two mechanisms produces the amount of increase in GBM porosity expected in vivo in a mutant mouse model, and also captures the two in vivo features of reduced filtration flux and increased GBM thickness. Finally, the model supports the idea that in the healthy glomerulus, gel compression may help maintain a roughly constant filtration flux under varying filtration pressure.
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Affiliation(s)
- Zelai Xu
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2
| | - Pengtao Yue
- Department of Mathematics, Virginia Tech, Blacksburg, VA 24061, USA
| | - James J. Feng
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2
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44
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Mosheiff N, Ermentrout B, Huang C. Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability. PLoS Comput Biol 2023; 19:e1010843. [PMID: 36626362 PMCID: PMC9870129 DOI: 10.1371/journal.pcbi.1010843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/23/2023] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Neural activity in the cortex is highly variable in response to repeated stimuli. Population recordings across the cortex demonstrate that the variability of neuronal responses is shared among large groups of neurons and concentrates in a low dimensional space. However, the source of the population-wide shared variability is unknown. In this work, we analyzed the dynamical regimes of spatially distributed networks of excitatory and inhibitory neurons. We found chaotic spatiotemporal dynamics in networks with similar excitatory and inhibitory projection widths, an anatomical feature of the cortex. The chaotic solutions contain broadband frequency power in rate variability and have distance-dependent and low-dimensional correlations, in agreement with experimental findings. In addition, rate chaos can be induced by globally correlated noisy inputs. These results suggest that spatiotemporal chaos in cortical networks can explain the shared variability observed in neuronal population responses.
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Affiliation(s)
- Noga Mosheiff
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for the Neural Basis of Cognition, Pittsburgh, Pennsylvania, United States of America
| | - Bard Ermentrout
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chengcheng Huang
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for the Neural Basis of Cognition, Pittsburgh, Pennsylvania, United States of America
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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45
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Polimeno M, Kim C, Blanchette F. Toward a Realistic Model of Diffusion-Limited Aggregation: Rotation, Size-Dependent Diffusivities, and Settling. ACS Omega 2022; 7:40826-40835. [PMID: 36406481 PMCID: PMC9670102 DOI: 10.1021/acsomega.2c03547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In this Brownian dynamics simulation study on the formation of aggregates made of spherical particles, we build on the well-established diffusion-limited cluster aggregation (DLCA) model. We include rotational effects, allow diffusivities to be size-dependent as is physically relevant, and incorporate settling under gravity. We numerically characterize the growth dynamics of aggregates and find that their radius of gyration, R g, grows approximately as R g ∼ t 1.02 for classical DLCA but slows to an approximate growth rate of R g ∼ t 0.71 when diffusivity is size-dependent. We also analyze the fractal structure of the resulting aggregates and find that their fractal dimension, d, decreases from d ≈ 1.8 for classical DLCA to d ≈ 1.7 when size-dependent rotational diffusion is included. The addition of settling effects further reduces the fractal dimension observed to d ≈ 1.6 and appears to result in aggregates with a vertical extent marginally smaller than their horizontal extent.
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46
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Zhang Y, de Souza RS, Chen YC. sconce: a cosmic web finder for spherical and conic geometries. Mon Not R Astron Soc 2022; 517:1197-1217. [PMID: 36246727 PMCID: PMC9553091 DOI: 10.1093/mnras/stac2504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called sconce (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (scms) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard scms method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as sconce-scms and has been made publicly available.
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Affiliation(s)
- Yikun Zhang
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Rafael S de Souza
- Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030, China
| | - Yen-Chi Chen
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
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47
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Elonen A, Natarajan AK, Kawamata I, Oesinghaus L, Mohammed A, Seitsonen J, Suzuki Y, Simmel FC, Kuzyk A, Orponen P. Algorithmic Design of 3D Wireframe RNA Polyhedra. ACS Nano 2022; 16:16608-16616. [PMID: 36178116 PMCID: PMC9620399 DOI: 10.1021/acsnano.2c06035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 06/01/2023]
Abstract
We address the problem of de novo design and synthesis of nucleic acid nanostructures, a challenge that has been considered in the area of DNA nanotechnology since the 1980s and more recently in the area of RNA nanotechnology. Toward this goal, we introduce a general algorithmic design process and software pipeline for rendering 3D wireframe polyhedral nanostructures in single-stranded RNA. To initiate the pipeline, the user creates a model of the desired polyhedron using standard 3D graphic design software. As its output, the pipeline produces an RNA nucleotide sequence whose corresponding RNA primary structure can be transcribed from a DNA template and folded in the laboratory. As case examples, we design and characterize experimentally three 3D RNA nanostructures: a tetrahedron, a triangular bipyramid, and a triangular prism. The design software is openly available and also provides an export of the targeted 3D structure into the oxDNA molecular dynamics simulator for easy simulation and visualization.
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Affiliation(s)
- Antti Elonen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
| | | | - Ibuki Kawamata
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Natural
Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
| | - Lukas Oesinghaus
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Abdulmelik Mohammed
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
- Department
of Biomedical Engineering, San José
State University, San José, California 95192, United States
| | - Jani Seitsonen
- Department
of Applied Physics and Nanomicroscopy Center, Aalto University, 00076 Aalto, Finland
| | - Yuki Suzuki
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8577, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8577, Japan
- Division
of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Friedrich C. Simmel
- Physics
Department E14, Technical University Munich, 85748 Garching, Germany
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, Aalto University, 00076 Aalto, Finland
| | - Pekka Orponen
- Department
of Computer Science, Aalto University, 00076 Aalto, Finland
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48
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McCrea M, Ermentrout B, Rubin JE. A model for the collective synchronization of flashing in Photinus carolinus. J R Soc Interface 2022; 19:20220439. [PMID: 36285439 PMCID: PMC9597172 DOI: 10.1098/rsif.2022.0439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022] Open
Abstract
Recent empirical investigations have characterized the synchronized flashing behaviours of male Photinus carolinus fireflies in their natural habitat in Great Smoky Mountain National Park as well as in controlled environments. We develop a model for the flash dynamics of an individual firefly based on a canonical elliptic burster, a slow-fast dynamical system that produces a repeating pattern of multiple flashes followed by a quiescent period. We show that a small amount of noise renders that oscillation very irregular, but when multiple model fireflies interact through their flashes, the behaviour becomes much more periodic. We show that the aggregate behaviour is qualitatively similar to the experimental findings. We next distribute the fireflies in a two-dimensional spatial domain and vary the interaction range. In addition to synchronization, various spatio-temporal patterns involving propagation of activity emerge spontaneously. Finally, we allow a certain number of fireflies to move and demonstrate how their speed affects the rate and degree of synchronization.
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Affiliation(s)
- Madeline McCrea
- Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bard Ermentrout
- Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan E. Rubin
- Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
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49
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Schwenck J, Punjabi NM, Gaynanova I. bp: Blood pressure analysis in R. PLoS One 2022; 17:e0268934. [PMID: 36083882 PMCID: PMC9462781 DOI: 10.1371/journal.pone.0268934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/19/2022] [Indexed: 11/19/2022] Open
Abstract
Despite the world-wide prevalence of hypertension, there is a lack in open-source software for analyzing blood pressure data. The R package bp fills this gap by providing functionality for blood pressure data processing, visualization, and feature extraction. In addition to the comprehensive functionality, the package includes six sample data sets covering continuous arterial pressure data (AP), home blood pressure monitoring data (HBPM) and ambulatory blood pressure monitoring data (ABPM), making it easier for researchers to get started. The R package bp is publicly available on CRAN and at https://github.com/johnschwenck/bp.
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Affiliation(s)
- John Schwenck
- Department of Statistics, Texas A&M University, College Station, TX, United States of America
- * E-mail:
| | - Naresh M. Punjabi
- Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Irina Gaynanova
- Department of Statistics, Texas A&M University, College Station, TX, United States of America
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50
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Yin F, Butts CT. Highly scalable maximum likelihood and conjugate Bayesian inference for ERGMs on graph sets with equivalent vertices. PLoS One 2022; 17:e0273039. [PMID: 36018834 PMCID: PMC9417041 DOI: 10.1371/journal.pone.0273039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
The exponential family random graph modeling (ERGM) framework provides a highly flexible approach for the statistical analysis of networks (i.e., graphs). As ERGMs with dyadic dependence involve normalizing factors that are extremely costly to compute, practical strategies for ERGMs inference generally employ a variety of approximations or other workarounds. Markov Chain Monte Carlo maximum likelihood (MCMC MLE) provides a powerful tool to approximate the maximum likelihood estimator (MLE) of ERGM parameters, and is generally feasible for typical models on single networks with as many as a few thousand nodes. MCMC-based algorithms for Bayesian analysis are more expensive, and high-quality answers are challenging to obtain on large graphs. For both strategies, extension to the pooled case—in which we observe multiple networks from a common generative process—adds further computational cost, with both time and memory scaling linearly in the number of graphs. This becomes prohibitive for large networks, or cases in which large numbers of graph observations are available. Here, we exploit some basic properties of the discrete exponential families to develop an approach for ERGM inference in the pooled case that (where applicable) allows an arbitrarily large number of graph observations to be fit at no additional computational cost beyond preprocessing the data itself. Moreover, a variant of our approach can also be used to perform Bayesian inference under conjugate priors, again with no additional computational cost in the estimation phase. The latter can be employed either for single graph observations, or for observations from graph sets. As we show, the conjugate prior is easily specified, and is well-suited to applications such as regularization. Simulation studies show that the pooled method leads to estimates with good frequentist properties, and posterior estimates under the conjugate prior are well-behaved. We demonstrate the usefulness of our approach with applications to pooled analysis of brain functional connectivity networks and to replicated x-ray crystal structures of hen egg-white lysozyme.
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Affiliation(s)
- Fan Yin
- Department of Statistics, University of California at Irvine, Irvine, CA, United States of America
| | - Carter T. Butts
- Department of Sociology, Statistics, Computer Science, and EECS and Institute for Mathematical Behavioral Sciences, University of California at Irvine, Irvine, CA, United States of America
- * E-mail:
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