Multicomponent dynamical systems: SRB measures and phase transitions

We discuss a notion of phase transitions in multicomponent systems and clarify relations between deterministic chaotic and stochastic models of this type of systems. Connections between various definitions of SRB measures are considered as well.Comment: 13 pages, LaTeX 2

OBIS-USA: A Data-Sharing Legacy of the Census of Marine Life

This is the publisher's version, also available electronically from http://www.tos.org/oceanography.The United States Geological Survey's Biological Informatics Program hosts OBIS-USA, the US node of the Ocean Biogeographic Information System (OBIS). OBIS-USA gathers, coordinates, applies standard formats to, and makes widely available data on biological collections in marine waters of the United States and other areas where US investigators have collected data and, in some instances, specimens. OBIS-USA delivers its data to OBIS international, which then delivers its data to the Global Biodiversity Information Facility (GBIF) and other Web portals for marine biodiversity data. OBIS-USA currently has 145 data sets from 36 participants, representing over 6.5 million occurrence records of over 83,000 taxa from more than 888,000 locations. OBIS-USA, a legacy of the decade-long (2001–2010) international collaborative Census of Marine Life enterprise, continues to add data, including those from ongoing Census projects. Among the many challenges in creating OBIS, including OBIS-USA, were developing a community of trust and shared value among data providers, and demonstrating to providers the value of making their data accessible to others. Challenges also posed by the diversity of data sets relevant to marine biodiversity stored on thousands of computers, in a variety of formats, not all widely accessible, have been met in OBIS-USA by implementing a uniform standard and publishing platform that is easily accessible to a broad range of users

Emulation and History Matching using the hmer Package

Modelling complex real-world situations such as infectious diseases, geological phenomena, and biological processes can present a dilemma: the computer model (referred to as a simulator) needs to be complex enough to capture the dynamics of the system, but each increase in complexity increases the evaluation time of such a simulation, making it difficult to obtain an informative description of parameter choices that would be consistent with observed reality. While methods for identifying acceptable matches to real-world observations exist, for example optimisation or Markov chain Monte Carlo methods, they may result in non-robust inferences or may be infeasible for computationally intensive simulators. The techniques of emulation and history matching can make such determinations feasible, efficiently identifying regions of parameter space that produce acceptable matches to data while also providing valuable information about the simulator's structure, but the mathematical considerations required to perform emulation can present a barrier for makers and users of such simulators compared to other methods. The hmer package provides an accessible framework for using history matching and emulation on simulator data, leveraging the computational efficiency of the approach while enabling users to easily match to, visualise, and robustly predict from their complex simulators.Comment: 40 pages, 11 figures; submitted to Journal of Statistical Software: author order correcte

Designing an automated clinical decision support system to match clinical practice guidelines for opioid therapy for chronic pain

Abstract Background Opioid prescribing for chronic pain is common and controversial, but recommended clinical practices are followed inconsistently in many clinical settings. Strategies for increasing adherence to clinical practice guideline recommendations are needed to increase effectiveness and reduce negative consequences of opioid prescribing in chronic pain patients. Methods Here we describe the process and outcomes of a project to operationalize the 2003 VA/DOD Clinical Practice Guideline for Opioid Therapy for Chronic Non-Cancer Pain into a computerized decision support system (DSS) to encourage good opioid prescribing practices during primary care visits. We based the DSS on the existing ATHENA-DSS. We used an iterative process of design, testing, and revision of the DSS by a diverse team including guideline authors, medical informatics experts, clinical content experts, and end-users to convert the written clinical practice guideline into a computable algorithm to generate patient-specific recommendations for care based upon existing information in the electronic medical record (EMR), and a set of clinical tools. Results The iterative revision process identified numerous and varied problems with the initially designed system despite diverse expert participation in the design process. The process of operationalizing the guideline identified areas in which the guideline was vague, left decisions to clinical judgment, or required clarification of detail to insure safe clinical implementation. The revisions led to workable solutions to problems, defined the limits of the DSS and its utility in clinical practice, improved integration into clinical workflow, and improved the clarity and accuracy of system recommendations and tools. Conclusions Use of this iterative process led to development of a multifunctional DSS that met the approval of the clinical practice guideline authors, content experts, and clinicians involved in testing. The process and experiences described provide a model for development of other DSSs that translate written guidelines into actionable, real-time clinical recommendations.http://deepblue.lib.umich.edu/bitstream/2027.42/78267/1/1748-5908-5-26.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/2/1748-5908-5-26.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/3/1748-5908-5-26-S3.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/4/1748-5908-5-26-S2.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/5/1748-5908-5-26-S1.TIFFPeer Reviewe

The actin-binding protein Hip1R associates with clathrin during early stages of endocytosis and promotes clathrin assembly in vitro

Huntingtin-interacting protein 1 related (Hip1R) is a novel component of clathrin-coated pits and vesicles and is a mammalian homologue of Sla2p, an actin-binding protein important for both actin organization and endocytosis in yeast. Here, we demonstrate that Hip1R binds via its putative central coiled-coil domain to clathrin, and provide evidence that Hip1R and clathrin are associated in vivo at sites of endocytosis. First, real-time analysis of Hip1R–YFP and DsRed–clathrin light chain (LC) in live cells revealed that these proteins show almost identical temporal and spatial regulation at the cell cortex. Second, at the ultrastructure level, immunogold labeling of ‘unroofed’ cells showed that Hip1R localizes to clathrin-coated pits. Third, overexpression of Hip1R affected the subcellular distribution of clathrin LC. Consistent with a functional role for Hip1R in endocytosis, we also demonstrated that it promotes clathrin cage assembly in vitro. Finally, we showed that Hip1R is a rod-shaped apparent dimer with globular heads at either end, and that it can assemble clathrin-coated vesicles and F-actin into higher order structures. In total, Hip1R's properties suggest an early endocytic function at the interface between clathrin, F-actin, and lipids

The Hartree limit of Born's ensemble for the ground state of a bosonic atom or ion

The non-relativistic bosonic ground state is studied for quantum N-body systems with Coulomb interactions, modeling atoms or ions made of N "bosonic point electrons" bound to an atomic point nucleus of Z "electron" charges, treated in Born--Oppenheimer approximation. It is shown that the (negative) ground state energy E(Z,N) yields the monotonically growing function (E(l N,N) over N cubed). By adapting an argument of Hogreve, it is shown that its limit as N to infinity for l > l* is governed by Hartree theory, with the rescaled bosonic ground state wave function factoring into an infinite product of identical one-body wave functions determined by the Hartree equation. The proof resembles the construction of the thermodynamic mean-field limit of the classical ensembles with thermodynamically unstable interactions, except that here the ensemble is Born's, with the absolute square of the ground state wave function as ensemble probability density function, with the Fisher information functional in the variational principle for Born's ensemble playing the role of the negative of the Gibbs entropy functional in the free-energy variational principle for the classical petit-canonical configurational ensemble.Comment: Corrected version. Accepted for publication in Journal of Mathematical Physic

Stability analysis of polarized domains

Polarized ferrofluids, lipid monolayers and magnetic bubbles form domains with deformable boundaries. Stability analysis of these domains depends on a family of nontrivial integrals. We present a closed form evaluation of these integrals as a combination of Legendre functions. This result allows exact and explicit formulae for stability thresholds and growth rates of individual modes. We also evaluate asymptotic behavior in several interesting limits.Comment: 12 pages, 3 figures, Late

Attracting Manifold for a Viscous Topology Transition

An analytical method is developed describing the approach to a finite-time singularity associated with collapse of a narrow fluid layer in an unstable Hele-Shaw flow. Under the separation of time scales near a bifurcation point, a long-wavelength mode entrains higher-frequency modes, as described by a version of Hill's equation. In the slaved dynamics, the initial-value problem is solved explicitly, yielding the time and analytical structure of a singularity which is associated with the motion of zeroes in the complex plane. This suggests a general mechanism of singularity formation in this system.Comment: 4 pages, RevTeX, 3 ps figs included with text in uuencoded file, accepted in Phys. Rev. Let