Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments

Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state changes, e.g., changes induced by dynamic micro-environments, photobleaching, and other heterogeneity inherent in biological processes. This study focuses on techniques for analyzing Single Particle Tracking (SPT) data experiencing abrupt state changes. We demonstrate the approach on GFP tagged chromatids experiencing metaphase in yeast cells and probe the effective forces resulting from dynamic interactions that reflect the sum of a number of physical phenomena. State changes are induced by factors such as microtubule dynamics exerting force through the centromere, thermal polymer fluctuations, etc. Simulations are used to demonstrate the relevance of the approach in more general SPT data analyses. Refined force estimates are obtained by adopting and modifying a nonparametric Bayesian modeling technique, the Hierarchical Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT applications. The HDP-SLDS method shows promise in systematically identifying dynamical regime changes induced by unobserved state changes when the number of underlying states is unknown in advance (a common problem in SPT applications). We expand on the relevance of the HDP-SLDS approach, review the relevant background of Hierarchical Dirichlet Processes, show how to map discrete time HDP-SLDS models to classic SPT models, and discuss limitations of the approach. In addition, we demonstrate new computational techniques for tuning hyperparameters and for checking the statistical consistency of model assumptions directly against individual experimental trajectories; the techniques circumvent the need for "ground-truth" and subjective information.Comment: 25 pages, 6 figures. Differs only typographically from PLoS One publication available freely as an open-access article at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.013763

Resonance expansions in quantum mechanics

The goal of this contribution is to discuss various resonance expansions that have been proposed in the literature.Comment: 10 pages and 1 figure; presented at the Istanbul workshop on pseudo-Hermitian Hamiltonian

Double Exchange Models: Self Consistent Renormalisation

We propose a scheme for constructing classical spin Hamiltonians from Hunds coupled spin-fermion models in the limit J_H/t \to \infinity. The strong coupling between fermions and the core spins requires self-consistent calculation of the effective exchange in the model, either in the presence of inhomogeneities or with changing temperature. In this paper we establish the formalism and discuss results mainly on the ``clean'' double exchange model, with self consistently renormalised couplings, and compare our results with exact simulations. Our method allows access to system sizes much beyond the reach of exact simulations, and we can study transport and optical properties of the model without artificial broadening. The method discussed here forms the foundation of our papers Phys. Rev. Lett. 91, 246602 (2003), and Phys. Rev. Lett. 92, 126602 (2004).Comment: 11 pages revtex. Final version, to appear in EPJ

CP Violation in \tau ->\nu\pi K_S and D->\pi K_S: The Importance of K_S-K_L Interference

The $B$-factories have measured CP asymmetries in the $\tau\to\pi K_S\nu$ and $D\to K_S\pi$ modes. The $K_S$ state is identified by its decay to two pions at a time that is close to the $K_S$ lifetime. Within the Standard Model and many of its extensions, the asymmetries in these modes come from CP violation in $K^0-\bar{K}^0$ mixing. We emphasize that the interference between the amplitudes of intermediate $K_S$ and $K_L$ is as important as the pure $K_S$ amplitude. Consequently, the measured asymmetries depend on the times over which the relevant decay rates are integrated and on features of the experiment.Comment: 4 pages, 4 figure

Comparative Analysis of Asthma Incidence Between Breastfed and Bottle-fed Children (Aged 3-7 Years Old)

This study primarily aimed to compare the incidence of asthma between breastfed and bottle-fed children. And to determine if the demographic characteristics such as age, sex, ordinal position in the family and familial history of asthma affect the incidence of asthma as well. This study used Comparative-Survey Design through self-structured questionnaire given to the parents of the respondents who were the 3-7 year-old asthmatic children, selected through purposive sampling technique. The data gathered were thentabulated and analyzed using Chi-Square Method of Association. It was found out that most of the asthmatic respondents were between 5-7 years old which showed a high association between the age and the incidence of asthma. It implies that as the age increases, the incidence of asthma also increases. Results also showed that males are more likely to have high incidence of asthma than females. The incidence of asthma is likewise higher in eldest respondents than the middle or youngest. Moreover, there is a significant relationship between the familial history of asthma and its incidence. And finally, the feeding status of the respondents whether breastfed or bottle-fed during the first 6 months of life affects the incidence of asthma as the incidence is higher in bottle-fed than in breastfed respondent

Reporter\u27s Occupation and Source of Adverse Device Event Reports Contained in the FDA\u27s MAUDE Database

Introduction: A review of the medical device adverse events submitted to the United States Food & Drug Administration (FDA) Manufacturer and User Facility Device Experience (MAUDE) database was undertaken to determine the major sources of the information. Methods: The reporter’s occupation and source of the medical device report were determined for acquisition dates Jan 1, 1997 to Dec 31, 2018. A total of 7,766,737 adverse event records were analyzed. Results: 96.6% of reports originated with the manufacturer. Patients (patients/family/friend) were the most frequent submitter of reports directly to the FDA, almost five times as often as physicians. Nurses submitted reports directly to the FDA 2.77 times as often as physicians. Only 0.49% of physician reports were submitted directly to the FDA, representing 0.09% of total MAUDE reports. Conclusion: Increasing physician reporting directly to the FDA and MAUDE through the MedWatch reporting system is an imperative. Incorporating information from the perspective of the physician has the potential of increasing the quality of the data and improving the reliability of post-market surveillance

An experimental and theoretical study on the crystal structure and elastic properties of Ta1-xOx coatings

The production of Ta1-xOx coatings has attracted a lot of attention due to their wide variety of industrial applications. Nonetheless, to properly control the functional properties of these coatings, a good understanding of their structural properties must be achieved. Ta1-xOx phases have structural similarities since they are formed by the distortion of the body centered cubic (bcc) Ta structure and, therefore, a clear and unequivocal identification of the crystalline phases is not trivial. In this regard, this work proposes a theoretical and experimental study to understand the evolution of the structural and the elastic properties of Ta-based coatings. The coatings were deposited by magnetron sputtering as a function of oxygen content and characterized by EPMA (electron probe microanalysis), XRD (X-ray diffraction), STEM (scanning transmission electron microscopy) and SAW (surface acoustic waves). The results demonstrate the formation of a bcc alpha-Ta phase in the non-reactive Ta coating, which transitions to a mixture of crystalline tantalum and tantalum oxide phases for low oxygen concentrations while amorphous phases are observed for high oxygen levels. Ab-initio calculations of different Ta-O phases are in good agreement with the experimental results and reveal that the oxygen addition to the metallic Ta phase, leads to a distortion of the Ta crystal structure, causing a decrease in density and an increase of the elastic constants.- This research is sponsored by FEDER funds through the program COMPETE -Programa Operacional Factores de Competitividade and by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UID/FIS/04650/2013, and UID/EMS/00285/2013 and with a PhD fellowship SFRH/BD/98199/2013. The authors also thank the financial support in the framework of ERA-SIINN/0004/2013 and PTDC/CTM-NAN/4242/2014 projects

The first direct measurement of ¹²C (¹²C,n) ²³Mg at stellar energies

Neutrons produced by the carbon fusion reaction ¹²C(¹²C,n)²³Mg play an important role in stellar nucleosynthesis. However, past studies have shown large discrepancies between experimental data and theory, leading to an uncertain cross section extrapolation at astrophysical energies. We present the first direct measurement that extends deep into the astrophysical energy range along with a new and improved extrapolation technique based on experimental data from the mirror reaction ¹²C(¹²C,p)²³Na. The new reaction rate has been determined with a well-defined uncertainty that exceeds the precision required by astrophysics models. Using our constrained rate, we find that ¹²C(¹²C,n)²³Mg is crucial to the production of Na and Al in Pop-III Pair Instability Supernovae. It also plays a non-negligible role in the production of weak s-process elements as well as in the production of the important galacti

On Singularity Formation of a Nonlinear Nonlocal System

We investigate the singularity formation of a nonlinear nonlocal system. This nonlocal system is a simplified one-dimensional system of the 3D model that was recently proposed by Hou and Lei in [13] for axisymmetric 3D incompressible Navier-Stokes equations with swirl. The main difference between the 3D model of Hou and Lei and the reformulated 3D Navier-Stokes equations is that the convection term is neglected in the 3D model. In the nonlocal system we consider in this paper, we replace the Riesz operator in the 3D model by the Hilbert transform. One of the main results of this paper is that we prove rigorously the finite time singularity formation of the nonlocal system for a large class of smooth initial data with finite energy. We also prove the global regularity for a class of smooth initial data. Numerical results will be presented to demonstrate the asymptotically self-similar blow-up of the solution. The blowup rate of the self-similar singularity of the nonlocal system is similar to that of the 3D model.Comment: 28 pages, 9 figure