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Dynamic linear model

Delphine Ropers, Aline Métris
Qualitative modeling approaches allow to provide a coarse-grained description of the functioning of cellular networks when experimental data are scarce and heterogeneous. We translate the primary literature data on the response of Escherichia coli to hyperosmotic stress caused by NaCl addition into a piecewise linear (PL) model. We provide a data file of the qualitative model, which can be used for simulation of changes of protein concentrations and of DNA coiling during the physiological response of the bacterium to the stress...
December 2016: Data in Brief
Paul R Territo, Jill A Meyer, Jonathan S Peters, Amanda A Riley, Brian P McCarthy, Mingzhang Gao, Min Wang, Mark A Green, Qi-Huang Zheng, Gary D Hutchins
BACKGROUND: The P2X7 receptor represents a novel molecular target for imaging neuroinflammation via PET. GSK1482160, a potent P2X7 receptor antagonist, has high receptor affinity, blood-brain barrier penetration, and has been recently radiolabel ((11)C-GSK1482160). Therefore, we report the initial physical and biological characterization of this novel ligand. METHODS: (11)C-GSK1482160 synthesis was according to published methods. Cell density studies were performed in human embryonic kidney cell lines expressing human P2X7 receptors (HEK293-hP2X7R) and analyzed by western blot analysis, immuno-fluorescence assay (IFA), and radiologic-immunohistochemistry (RIHC) using P2X7R polyclonal antibodies...
October 20, 2016: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
Marta R Pereira, Cristian S Dambros, Charles E Zartman
PREMISE OF THE STUDY: Resource allocation is difficult to characterize in plants because of the challenges of quantifying gametes and propagules. We surveyed six sympatric, unisexual species in the family Calymperaceae (Bryophyta) to test for trade-offs in prezygotic sexual and asexual expression and density-dependent survivorship of female gametangia. METHODS: We tallied gametangial and asexual propagule output for 1820 shoots from 17 populations of six species at monthly intervals during one year (2010-2011) in a central Amazonian forest...
October 7, 2016: American Journal of Botany
Lijun Liu, Yongfeng Yin, Zenghu Zhang, Yashwant K Malaiya
Modern infrastructure networks are often coupled together and thus could be modeled as interdependent networks. Overload and interdependent effect make interdependent networks more fragile when suffering from attacks. Existing research has primarily concentrated on the cascading failure process of interdependent networks without load, or the robustness of isolated network with load. Only limited research has been done on the cascading failure process caused by overload in interdependent networks. Redundant design is a primary approach to enhance the reliability and robustness of the system...
2016: PloS One
Samuel A Neymotin, Benjamin A Suter, Salvador Dura-Bernal, Gordon M G Shepherd, Michele Migliore, William W Lytton
Corticospinal neurons (SPI), thick-tufted pyramidal neurons in motor cortex layer 5B that project caudally via the medullary pyramids, display distinct class-specific electrophysiological properties in vitro: strong sag with hyperpolarization, lack of adaptation, and a nearly linear frequency-current (FI) relationship. We used our electrophysiological data to produce a pair of large archives of SPI neuron computer models in two model classes: 1. Detailed models with full reconstruction; 2. Simplified models with 6 compartments...
October 19, 2016: Journal of Neurophysiology
Hongshi Huang, Noël Keijsers, Herwin Horemans, Qinwei Guo, Yuanyuan Yu, Henk Stam, Stephan Praet, Yingfang Ao
OBJECTIVES: Anterior Cruciate Ligament (ACL) deficiency may result in abnormal lower limb loading with increased foot pronation. This study evaluated spatiotemporal parameters and plantar pressure distribution during walking in participants with and without an ACL rupture. DESIGN: Cross-sectional. METHODS: Plantar pressure was measured in 42 unilateral ACL deficient (ACLD) participants and 32 healthy controls while walking barefoot. Spatiotemporal parameters, pressure distribution and center of pressure (CoP) during foot roll off were determined...
September 30, 2016: Journal of Science and Medicine in Sport
Kari E Veblen, Lauren M Porensky, Corinna Riginos, Truman P Young
The widespread replacement of wild ungulate herbivores by domestic livestock in African savannas is composed of two interrelated phenomena: (1) loss or reduction in numbers of individual wildlife species or guilds and (2) addition of livestock to the system. Each can have important implications for plant community dynamics. Yet very few studies have experimentally addressed the individual, combined, and potentially interactive effects of wild vs. domestic herbivore species on herbaceous plant communities within a single system...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Richard W Hass
Divergent thinking has often been used as a proxy measure of creative thinking, but this practice lacks a foundation in modern cognitive psychological theory. This article addresses several issues with the classic divergent-thinking methodology and presents a new theoretical and methodological framework for cognitive divergent-thinking studies. A secondary analysis of a large dataset of divergent-thinking responses is presented. Latent semantic analysis was used to examine the potential changes in semantic distance between responses and the concept represented by the divergent-thinking prompt across successive response iterations...
October 17, 2016: Memory & Cognition
Maurice Filo, Fadi Karameh, Mariette Awad
The cochlea is an indispensable preliminary processing stage in auditory perception that employs mechanical frequency-tuning and electrical transduction of incoming sound waves. Cochlear mechanical responses are shown to exhibit active nonlinear spatiotemporal response dynamics (e.g., otoacoustic emission). To model such phenomena, it is often necessary to incorporate cochlear fluid-membrane interactions. This results in both excessively high-order model formulations and computationally intensive solutions that limit their practical use in simulating the model and analyzing its response even for simple single-tone inputs...
October 17, 2016: Biological Cybernetics
Richard A Gray, Pras Pathmanathan
Elucidating the underlying mechanisms of fatal cardiac arrhythmias requires a tight integration of electrophysiological experiments, models, and theory. Existing models of transmembrane action potential (AP) are complex (resulting in over parameterization) and varied (leading to dissimilar predictions). Thus, simpler models are needed to elucidate the "minimal physiological requirements" to reproduce significant observable phenomena using as few parameters as possible. Moreover, models have been derived from experimental studies from a variety of species under a range of environmental conditions (for example, all existing rabbit AP models incorporate a formulation of the rapid sodium current, INa, based on 30 year old data from chick embryo cell aggregates)...
October 2016: PLoS Computational Biology
Kyaw Hpone Myint, Jonathan R Brown, Anne R Shim, Barbara E Wyslouzil, Lisa Michelle Hall
The formation of block copolymer micelles with and without hydrophobic nanoparticles is simulated using dissipative particle dynamics. We use the model developed by Spaeth et al. [J. Chem. Phys. 134, 164902 (2011)], and drive micelle formation by adjusting the interaction parameters linearly over time to represent a rapid change from organic solvent to water. For different concentrations of added nanoparticles, we determine characteristic times for micelle formation and coagulation, and characterize micelles with respect to size, polydispersity, and nanoparticle loading...
October 17, 2016: Journal of Physical Chemistry. B
Jelena Obradović, Jenna E Finch
This study employed piecewise growth curve modeling to examine how children's executive function (EF) skills relate to different components of children's physiological response trajectory - initial arousal, reactivity, and recovery. The sample included 102 ethnically diverse kindergarteners, whose EF skills were measured using standard tasks and observer ratings. Physiological response was measured via changes in respiratory sinus arrhythmia (RSA) in response to a laboratory socio-cognitive challenge. Children's cool and hot EF skills were differentially related to both linear and quadratic components of RSA response during the challenge...
October 16, 2016: Developmental Science
Robert D Gregg, Anne E Martin
Recent work has extended the control method of virtual constraints, originally developed for autonomous walking robots, to powered prosthetic legs for lower-limb amputees. Virtual constraints define desired joint patterns as functions of a mechanical phasing variable, which are typically enforced by torque control laws that linearize the output dynamics associated with the virtual constraints. However, the output dynamics of a powered prosthetic leg generally depend on the human interaction forces, which must be measured and canceled by the feedback linearizing control law...
July 2016: Proceedings of the ... American Control Conference
Ruofei Bu, Hillel Price, Sorin Mitran, Carlton Zdanski, Amy L Oldenburg
Quantitative endoscopic imaging is at the vanguard of novel techniques in the assessment upper airway obstruction. Anatomic optical coherence tomography (aOCT) has the potential to provide the geometry of the airway lumen with high-resolution and in 4 dimensions. By coupling aOCT with measurements of pressure, optical coherence elastography (OCE) can be performed to characterize airway wall stiffness. This can aid in identifying regions of dynamic collapse as well as informing computational fluid dynamics modeling to aid in surgical decision-making...
2016: Proceedings of SPIE
Sourabh Boruah, Damien L Subit, Glenn R Paskoff, Barry S Shender, Jeff R Crandall, Robert S Salzar
The strength and compliance of the dense cortical layers of the human skull have been examined since the beginning of the 20th century with the wide range in the observed mechanical properties attributed to natural biological variance. Since this variance may be explained by the difference in structural arrangement of bone tissue, micro-computed tomography (µCT) was used in conjunction with mechanical testing to study the relationship between the microstructure of human skull cortical coupons and their mechanical response...
October 1, 2016: Journal of the Mechanical Behavior of Biomedical Materials
Shuo Wang, Sujin Kim, Kelly P Cosgrove, Evan D Morris
The "linear parametric neurotransmitter PET" (lp-ntPET) model was introduced to capture the time course of transient endogenous neurotransmitter response to drug stimulus from dynamic PET data. We previously used this novel analysis tool to probe the short-lived dopamine (DA) response induced by cigarette smoking in the PET scanner. It allowed us to find a sex difference in the DA signature of cigarette smoking. To make best use of this tool to characterize neurotransmitter response to drug stimulus, the sensitivity of lp-ntPET to detect such responses must be maximized...
October 12, 2016: NeuroImage
Juyoung Park, Muna Aryal, Natalia Vykhodtseva, Yong-Zhi Zhang, Nathan McDannold
Drug delivery in brain tumors is challenging because of the presence of blood-brain barrier (BBB) and the blood-tumor barrier (BTB). Focused ultrasound (FUS) combined with microbubbles can enhance the permeability of the BTB in brain tumors, as well as disrupting the BBB in the surrounding tissue. In this study, dynamic contrast-enhanced Magnetic Resonance Imaging (DCE-MRI) was used to characterize FUS-induced permeability changes in a rat glioma model and in the normal brain and to investigate the relationship between these changes and the resulting concentration of the chemotherapy agent doxorubicin (DOX)...
October 11, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia, Paraskevi Gkeka
Ligand-functionalized nanoparticles (NPs) are a promising platform for imaging and drug delivery applications. A number of recent molecular simulation and theoretical studies explored how these NPs interact with model lipid membranes. However, interactions between ligand-coated NPs leading to possible cooperative effects and association have not been investigated. In this coarse-grained molecular dynamics study, we focus on a specific case of several anionic, ligand-coated NPs embedded in a lipid membrane. Several new effects are observed...
October 14, 2016: Nanoscale
Mohammad Farazmand, Themistoklis P Sapsis
Drawing upon the bursting mechanism in slow-fast systems, we propose indicators for the prediction of such rare extreme events which do not require a priori known slow and fast coordinates. The indicators are associated with functionals defined in terms of optimally time-dependent (OTD) modes. One such functional has the form of the largest eigenvalue of the symmetric part of the linearized dynamics reduced to these modes. In contrast to other choices of subspaces, the proposed modes are flow invariant and therefore a projection onto them is dynamically meaningful...
September 2016: Physical Review. E
Itay Grinberg, Oleg V Gendelman
We explore the dynamics of strongly localized periodic solutions (discrete solitons or discrete breathers) in a finite one-dimensional chain of oscillators. Localization patterns with both single and multiple localization sites (breathers and multibreathers) are considered. The model involves parabolic on-site potential with rigid constraints (the displacement domain of each particle is finite) and a linear nearest-neighbor coupling. When the particle approaches the constraint, it undergoes an inelastic impact according to Newton's impact model...
September 2016: Physical Review. E
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