Design of Hamiltonian Monte Carlo for perfect simulation of general continuous distributions

Hamiltonian Monte Carlo (HMC) is an efficient method of simulating smooth distributions and has motivated the widely used No-U-turn Sampler (NUTS) and software Stan. We build on NUTS and the technique of “unbiased sampling” to design HMC algorithms that produce perfect simulation of general continuous distributions that are amenable to HMC. Our methods enable separation of Markov chain Monte Carlo convergence error from experimental error, and thereby provide much more powerful MCMC convergence diagnostics than current state-of-the-art summary statistics which confound these two errors. Objective comparison of different MCMC algorithms is provided by the number of derivative evaluations per perfect sample point. We demonstrate the methodology with applications to normal, t and normal mixture distributions up to 100 dimensions, and a 12-dimensional Bayesian Lasso regression. HMC runs effectively with a goal of 20 to 30 points per trajectory. Numbers of derivative evaluations per perfect sample point range from 390 for a univariate normal distribution to 12,000 for a 100-dimensional mixture of two normal distributions with modes separated by six standard deviations, and 22,000 for a 100-dimensional t-distribution with four degrees of freedom

The impact of a walking intervention in older adults: examining factors related to physical activity, cognitive functioning, and quality of life

With increasing life expectancies, being physically and mentally fit is important, especially in later years of life. The purpose of this study was to investigate factors related to a walking intervention in older adults. Eighteen older adults (ages 65 to 79) were recruited to complete a six-month walking intervention while tracking changes in cognition and quality of life (QoL) with bi-monthly questionnaires. Subjects also identified an informant to provide information regarding cognition and QoL at the same time intervals. An informal interview was completed with subjects at post-testing. Physical activity was recorded in a daily logbook, and an activity tracker was used for three one-week periods over the duration of the study. Three questions were explored. First, what effects does a walking intervention have on elderly individuals’ cognition and QoL? Second, are objective or subjective methods of recording activity more feasible for older adults? Finally, are both subject and informant measures reliable ways of capturing data? Results indicated that both informant and subject measures were highly correlated, indicating both provide similar information. It was found that objective methods of tracking physical activity were more effective and feasible with older adults. Finally, by maintaining a sufficient level of physical activity, participants experienced an overall increase in cognition and QoL

High resolution mapping of Puget Sound shorelines

In an effort to collect high-resolution baseline coastal topographic data of beaches and bluffs around the Puget Sound and Strait of Juan de Fuca, the Washington State Department of Ecology Coastal Monitoring & Analysis Program (CMAP) conducted a series of boat-based lidar surveys in October 2013, May through September 2015, and May 2016 at a total of 16 sites spanning 220 km of shoreline and over two dozen drift cells. The drift cells were selected based on a rigorous and systematic geospatial analysis of bluff-backed beaches for their potential for significant bluff sediment supply to intact shorelines identified as having a relative abundance of habitat for forage fish, eelgrass, herring, shellfish, and geoduck, as well as having previous investments in beach restoration projects, and potential for future shoreline armoring and habitat loss based on population growth scenarios. As such, the surveyed drift cells are top candidates for implementing drift cell-scale protection and restoration strategies. The boat-based lidar and GPS topography data were used to produce 0.5-m digital elevation models (DEMs) for the beaches and bluffs at each of the survey sites. These DEMs provide the opportunity to inventory and characterize the shoreline landscape that affects nearshore ecosystem services such as feeder bluff activity, beach slope and width, and the position, length, and elevation of armoring relative to the backshore. Boat-based lidar provides an advantageous point of view of the bluff face, resulting in high resolution data which is needed to gain insight into bluff failure and erosion mechanisms and corresponding sediment transport processes. In addition, it successfully collects data under overhanging vegetation and overwater structures. Repeat surveys in the future would enable change analyses for quantifying bluff sediment supply, changes in marine riparian vegetation, and a better understanding of the linkages between physical and ecological processes

PREDICTORS OF DRINKING BEHAVIOUR AMONG ADOLESCENTS AND YOUNG ADULTS: A NEW PSYCHOSOCIAL CONTROL PERSPECTIVE

This find is registered at Portable Antiquities of the Netherlands with number PAN-0002525

Evaluating methods to obtain high resolution nearshore bathymetry and coastal topography for Puget Sound

The Washington State Department of Ecology Coastal Monitoring & Analysis Program performed a coastal topographic and bathymetric survey of Port Gamble Bay between March 9 and March 28, 2014. Boat-based topographic lidar was collected along the shoreline of the bay and multibeam bathymetric sonar was collected throughout the bay to obtain a seamless topographic-bathymetric surface with complete coverage of Port Gamble Bay. The survey was performed with a R2Sonic 2022 multibeam echosounder, an Optech ILRIS-HD-ER mobile laser scanner, and an Applanix POS MV 320 v5 receiving real-time kinematic positioning corrections. The Joint Airborne Lidar Bathymetry Technical Center of Expertise (JALBTCX) performed a topographic and bathymetric lidar survey of Port Gamble Bay on September 4, 2014. The Coastal Zone Mapping and Imaging Lidar (CZMIL) system was used to obtain seamless coastal topographic-bathymetric coastal intertidal and nearshore coverage of Port Gamble Bay. The bathymetric depth coverage is limited to laser extinction, which is determined by water clarity. The availability of these two datasets provides the unique opportunity to compare data between high-resolution boat-based lidar and multibeam systems and the state-of-the-art airborne topo-bathy lidar system and also assess detection and resolution of specific features throughout a range of water depths across the nearshore important to habitat and restoration efforts. This effort provides a detailed comparison of coverage and resolution of nearshore features and will help clarify differences between these capabilities to aid in planning complementary efforts in coastal zone mapping and monitoring

Diffuse X-ray emission in spiral galaxies

We compare the soft diffuse X-ray emission from Chandra images of 12 nearby intermediate inclination spiral galaxies to the morphology seen in Halpha, molecular gas, and mid-infrared emission. We find that diffuse X-ray emission is often located along spiral arms in the outer parts of spiral galaxies but tends to be distributed in a rounder morphology in the center. The X-ray morphology in the spiral arms matches that seen in the mid-infrared or Halpha and so implies that the X-ray emission is associated with recent active star formation. We see no strong evidence for X-ray emission trailing the location of high mass star formation in spiral arms. However, population synthesis models predict a high mechanical energy output rate from supernovae for a time period that is about 10 times longer than the lifetime of massive ionizing stars, conflicting with the narrow appearance of the arms in X-rays. The fraction of supernova energy that goes into heating the ISM must depend on environment and is probably higher near sites of active star formation. The X-ray estimated emission measures suggest that the volume filling factors and scale heights are high in the galaxy centers but low in the outer parts of these galaxies. The differences between the X-ray properties and morphology in the centers and outer parts of these galaxies suggest that galactic fountains operate in outer galaxy disks but that winds are primarily driven from galaxy centers.Comment: 28 pages, 4 figures, to be submitted to Ap

PDE8 controls CD4(+) T cell motility through the PDE8A-Raf-1 kinase signaling complex

The levels of cAMP are regulated by phosphodiesterase enzymes (PDEs), which are targets for the treatment of inflammatory disorders. We have previously shown that PDE8 regulates T cell motility. Here, for the first time, we report that PDE8A exerts part of its control of T cell function through the V-raf-1 murine leukemia viral oncogene homolog 1 (Raf-1) kinase signaling pathway. To examine T cell motility under physiologic conditions, we analyzed T cell interactions with endothelial cells and ligands in flow assays. The highly PDE8-selective enzymatic inhibitor PF-04957325 suppresses adhesion of in vivo myelin oligodendrocyte glycoprotein (MOG) activated inflammatory CD4(+) T effector (Teff) cells to brain endothelial cells under shear stress. Recently, PDE8A was shown to associate with Raf-1 creating a compartment of low cAMP levels around Raf-1 thereby protecting it from protein kinase A (PKA) mediated inhibitory phosphorylation. To test the function of this complex in Teff cells, we used a cell permeable peptide that selectively disrupts the PDE8A-Raf-1 interaction. The disruptor peptide inhibits the Teff-endothelial cell interaction more potently than the enzymatic inhibitor. Furthermore, the LFA-1/ICAM-1 interaction was identified as a target of disruptor peptide mediated reduction of adhesion, spreading and locomotion of Teff cells under flow. Mechanistically, we observed that disruption of the PDE8A-Raf-1 complex profoundly alters Raf-1 signaling in Teff cells. Collectively, our studies demonstrate that PDE8A inhibition by enzymatic inhibitors or PDE8A-Raf-1 kinase complex disruptors decreases Teff cell adhesion and migration under flow, and represents a novel approach to target T cells in inflammation

Perfect simulation from unbiased simulation

We show that any application of the technique of unbiased simulation becomes perfect simulation when coalescence of the two coupled Markov chains can be practically assured in advance. This happens when a fixed number of iterations is high enough that the probability of needing any more to achieve coalescence is negligible; we suggest a value of $10^{-20}$. This finding enormously increases the range of problems for which perfect simulation, which exactly follows the target distribution, can be implemented. We design a new algorithm to make practical use of the high number of iterations by producing extra perfect sample points with little extra computational effort, at a cost of a small, controllable amount of serial correlation within sample sets of about 20 points. Different sample sets remain completely independent. The algorithm includes maximal coupling for continuous processes, to bring together chains that are already close. We illustrate the methodology on a simple, two-state Markov chain and on standard normal distributions up to 20 dimensions. Our technical formulation involves a nonzero probability, which can be made arbitrarily small, that a single perfect sample point may have its place taken by a "string" of many points which are assigned weights, each equal to $\pm 1$, that sum to~$1$. A point with a weight of $-1$ is a "hole", which is an object that can be cancelled by an equivalent point that has the same value but opposite weight $+1$.Comment: 17 pages, 4 figures; for associated R scripts, see https://github.com/George-Leigh/PerfectSimulatio