Ecological non-linear state space model selection via adaptive particle Markov chain Monte Carlo (AdPMCMC)

We develop a novel advanced Particle Markov chain Monte Carlo algorithm that is capable of sampling from the posterior distribution of non-linear state space models for both the unobserved latent states and the unknown model parameters. We apply this novel methodology to five population growth models, including models with strong and weak Allee effects, and test if it can efficiently sample from the complex likelihood surface that is often associated with these models. Utilising real and also synthetically generated data sets we examine the extent to which observation noise and process error may frustrate efforts to choose between these models. Our novel algorithm involves an Adaptive Metropolis proposal combined with an SIR Particle MCMC algorithm (AdPMCMC). We show that the AdPMCMC algorithm samples complex, high-dimensional spaces efficiently, and is therefore superior to standard Gibbs or Metropolis Hastings algorithms that are known to converge very slowly when applied to the non-linear state space ecological models considered in this paper. Additionally, we show how the AdPMCMC algorithm can be used to recursively estimate the Bayesian Cram\'er-Rao Lower Bound of Tichavsk\'y (1998). We derive expressions for these Cram\'er-Rao Bounds and estimate them for the models considered. Our results demonstrate a number of important features of common population growth models, most notably their multi-modal posterior surfaces and dependence between the static and dynamic parameters. We conclude by sampling from the posterior distribution of each of the models, and use Bayes factors to highlight how observation noise significantly diminishes our ability to select among some of the models, particularly those that are designed to reproduce an Allee effect

The Grand Tour of the Ruby-East Humboldt Metamorphic Core Complex, Northeastern Nevada: Part 1-Introduction & Road Log

The purpose of this geological excursion is to provide an overview of the multiphase developmental history of the Ruby Mountains and East Humboldt Range, northeastern Nevada. Although these mountain ranges are commonly cited as a classic example of a Cordilleran metamorphic core complex developed through large-magnitude, mid-Tertiary crustal extension, a preceding polyphase Mesozoic contractional history is also well preserved in the ranges. An early phase of this history involved Late Jurassic two-mica granitic magmatism, high-temperature but relatively low-pressure metamorphism, and polyphase deformation in the central Ruby Mountains. In the northern Ruby Mountains and East Humboldt Range, a Late Cretaceous history of crustal shortening, metamorphism, and magmatism is manifested by fold-nappes (involving Archean basement rocks in the northern East Humboldt Range), widespread migmatization, injection of monzogranitic and leucogranitic magmas, all coupled with sillimanite-grade metamorphism. Following Late Cretaceous contraction, a protracted extensional deformation partially overprinted these areas during the Cenozoic. This extensional history may have begun as early as the Late Cretaceous or as late as the mid-Eocene. Late Eocene and Oligocene magmatism occurred at various levels in the crust yielding mafic to felsic orthogneisses in the deep crust, a composite granitic pluton in the upper crust, and volcanic rocks at the surface. Movement along a west-rooted, extensional shear zone in the Oligocene and early Miocene led to core-complex exhumation. The shear zone produced mylonitic rocks about 1 km thick at deep crustal levels, and an overprint of brittle detachment faulting at shallower levels as unroofing proceeded. Megabreccias and other synextensional sedimentary deposits are locally preserved in a tilted, upper Eocene through Miocene stratigraphic sequence. Neogene magmatism included the emplacement of basalt dikes and eruption of rhyolitic rocks. Subsequent Basin and Range normal faulting, as young as Holocene, records continued tectonic extension

Design and operation of automated ice-tethered profilers for real-time seawater observations in the polar oceans

An automated, easily-deployed Ice-Tethered Profiler (ITP) has been developed for deployment on perennial sea ice in polar oceans to measure changes in upper ocean temperature and salinity in all seasons. The ITP system consists of three components: a surface instrument that sits atop an ice floe, a weighted, plastic-jacketed wire-rope tether of arbitrary length (up to 800 m) suspended from the surface instrument, and an instrumented underwater unit that profiles up and down the wire tether. The profiling underwater unit is similar in shape and dimension to an ARGO float except that the float's variable-buoyancy system is replaced with a traction drive unit. Deployment of ITPs may be conducted either from ice caps or icebreakers, utilizing a self contained tripod/winch system that requires no power. Careful selection of an appropriate multiyear ice floe is needed to prolong the lifetime of the system (up to 3 years depending on the profiling schedule). Shortly after deployment, each ITP begins profiling the water column at its programmed sampling interval. After each acquired temperature and salinity profile, the underwater unit (PROCON) transfers the data and engineering files using an inductive modem to the surface controller (SURFCON). SURFCON also accumulates battery voltages, buoy temperature, and locations from GPS at specified intervals in status files, and queues that information for transmission at the start of each new day. At frequent intervals, an Iridium satellite transceiver in the surface package calls and transmits queued status and CTD data files onto a WHOI logger computer, which are subsequently processed and displayed in near-real time at http://www.whoi.edu/itp. In 2004 and 2005, three ITP prototypes were deployed in the Arctic Ocean. Each system was programmed with accelerated sampling schedules of multiple one-way traverses per day between 10 and 750-760 m depth in order to quickly evaluate endurance and component fatigue. Two of the ITPs are continuing to function after more than 10 months and 1200 profiles. Larger motor currents are observed at times of fast ice floe motion when larger wire angles develop and drag forces on the profiler are increased. The CTD profile data so far obtained document interesting spatial variations in the major water masses of the Beaufort Gyre, show the double-diffusive thermohaline staircase that lies above the warm, salty Atlantic layer, and many mesoscale eddys. Deployed together with CRREL Ice Mass Balance (IMB) buoys, these ITP systems also operate as part of an Ice Based Observatory (IBO). Data returned from an array of IBOs within an Arctic Observing Network will provide valuable real time observations, support studies of ocean processes, and facilitate numerical model initialization and validation.Funding was provided by the National Science Foundation under Contract Nos. OCE-0324233 and ARC-0519899

Higher intensity walking improves global cognition during inpatient rehabilitation: A secondary analysis of a randomized control trial

Cognitive deficits are common poststroke. Cognitive rehabilitation is typically used to improve cognitive deficits. It is unknown whether higher doses of exercise to promote motor recovery influence cognitive outcomes. Our recent trial, Determining Optimal Post-Stroke Exercise (DOSE), shows more than double the steps and aerobic minutes can be achieved during inpatient rehabilitation versus usual care, and translates to improved long-term walking outcomes. Thus, the secondary analysis aim was to determine the effect of the DOSE protocol on cognitive outcomes over 1-year poststroke. The DOSE protocol progressively increased step number and aerobic minutes during inpatient stroke rehabilitation over 20 sessions. The Montreal Cognitive Assessment (MoCA), Digit Symbol Substitution Test (DSST), and Trail Making Test B were completed at baseline, post-intervention, and 6- and 12-months poststroke, administered using standardized guidelines. Using the DOSE data, we used mixed-effect spline regression to model participants\u27 trajectories of cognitive recovery, controlling for relevant covariates. Participants (Usual Car

Assessment of regression-based methods to adjust for publication bias through a comprehensive simulation study

<p>Abstract</p> <p>Background</p> <p>In meta-analysis, the presence of funnel plot asymmetry is attributed to publication or other small-study effects, which causes larger effects to be observed in the smaller studies. This issue potentially mean inappropriate conclusions are drawn from a meta-analysis. If meta-analysis is to be used to inform decision-making, a reliable way to adjust pooled estimates for potential funnel plot asymmetry is required.</p> <p>Methods</p> <p>A comprehensive simulation study is presented to assess the performance of different adjustment methods including the novel application of several regression-based methods (which are commonly applied to detect publication bias rather than adjust for it) and the popular Trim & Fill algorithm. Meta-analyses with binary outcomes, analysed on the log odds ratio scale, were simulated by considering scenarios with and without i) publication bias and; ii) heterogeneity. Publication bias was induced through two underlying mechanisms assuming the probability of publication depends on i) the study effect size; or ii) the p-value.</p> <p>Results</p> <p>The performance of all methods tended to worsen as unexplained heterogeneity increased and the number of studies in the meta-analysis decreased. Applying the methods conditional on an initial test for the presence of funnel plot asymmetry generally provided poorer performance than the unconditional use of the adjustment method. Several of the regression based methods consistently outperformed the Trim & Fill estimators.</p> <p>Conclusion</p> <p>Regression-based adjustments for publication bias and other small study effects are easy to conduct and outperformed more established methods over a wide range of simulation scenarios.</p

The Sloan Digital Sky Survey Reverberation Mapping Project: Technical Overview

The Sloan Digital Sky Survey Reverberation Mapping project (SDSS-RM) is a dedicated multi-object RM experiment that has spectroscopically monitored a sample of 849 broad-line quasars in a single 7 deg$^2$ field with the SDSS-III BOSS spectrograph. The RM quasar sample is flux-limited to i_psf=21.7 mag, and covers a redshift range of 0.1<z<4.5. Optical spectroscopy was performed during 2014 Jan-Jul dark/grey time, with an average cadence of ~4 days, totaling more than 30 epochs. Supporting photometric monitoring in the g and i bands was conducted at multiple facilities including the CFHT and the Steward Observatory Bok telescopes in 2014, with a cadence of ~2 days and covering all lunar phases. The RM field (RA, DEC=14:14:49.00, +53:05:00.0) lies within the CFHT-LS W3 field, and coincides with the Pan-STARRS 1 (PS1) Medium Deep Field MD07, with three prior years of multi-band PS1 light curves. The SDSS-RM 6-month baseline program aims to detect time lags between the quasar continuum and broad line region (BLR) variability on timescales of up to several months (in the observed frame) for ~10% of the sample, and to anchor the time baseline for continued monitoring in the future to detect lags on longer timescales and at higher redshift. SDSS-RM is the first major program to systematically explore the potential of RM for broad-line quasars at z>0.3, and will investigate the prospects of RM with all major broad lines covered in optical spectroscopy. SDSS-RM will provide guidance on future multi-object RM campaigns on larger scales, and is aiming to deliver more than tens of BLR lag detections for a homogeneous sample of quasars. We describe the motivation, design and implementation of this program, and outline the science impact expected from the resulting data for RM and general quasar science.Comment: 25 pages, submitted to ApJS; project website at http://www.sdssrm.or

The Five Eras of Chiropractic & the future of chiropractic as seen through the eyes of a participant observer

Chiropractic has endured a turbulent history, marked by tremendous advances in areas such as education and licensing while marred by interprofessional conflict and a poor public image. The prolonged interprofessional conflict was instrumental in shaping the culture of chiropractic. These obstacles have long-since been removed although there are lingering effects from them

Evaluating the Quality of Research into a Single Prognostic Biomarker: A Systematic Review and Meta-analysis of 83 Studies of C-Reactive Protein in Stable Coronary Artery Disease

Background Systematic evaluations of the quality of research on a single prognostic biomarker are rare. We sought to evaluate the quality of prognostic research evidence for the association of C-reactive protein (CRP) with fatal and nonfatal events among patients with stable coronary disease. Methods and Findings We searched MEDLINE (1966 to 2009) and EMBASE (1980 to 2009) and selected prospective studies of patients with stable coronary disease, reporting a relative risk for the association of CRP with death and nonfatal cardiovascular events. We included 83 studies, reporting 61,684 patients and 6,485 outcome events. No study reported a prespecified statistical analysis protocol; only two studies reported the time elapsed (in months or years) between initial presentation of symptomatic coronary disease and inclusion in the study. Studies reported a median of seven items (of 17) from the REMARK reporting guidelines, with no evidence of change over time. The pooled relative risk for the top versus bottom third of CRP distribution was 1.97 (95% confidence interval [CI] 1.78–2.17), with substantial heterogeneity (I2 = 79.5). Only 13 studies adjusted for conventional risk factors (age, sex, smoking, obesity, diabetes, and low-density lipoprotein [LDL] cholesterol) and these had a relative risk of 1.65 (95% CI 1.39–1.96), I2 = 33.7. Studies reported ten different ways of comparing CRP values, with weaker relative risks for those based on continuous measures. Adjusting for publication bias (for which there was strong evidence, Egger's p<0.001) using a validated method reduced the relative risk to 1.19 (95% CI 1.13–1.25). Only two studies reported a measure of discrimination (c-statistic). In 20 studies the detection rate for subsequent events could be calculated and was 31% for a 10% false positive rate, and the calculated pooled c-statistic was 0.61 (0.57–0.66). Conclusion Multiple types of reporting bias, and publication bias, make the magnitude of any independent association between CRP and prognosis among patients with stable coronary disease sufficiently uncertain that no clinical practice recommendations can be made. Publication of prespecified statistical analytic protocols and prospective registration of studies, among other measures, might help improve the quality of prognostic biomarker research

Polycystin-1 Surface Localization Is Stimulated by Polycystin-2 and Cleavage at the G Protein-coupled Receptor Proteolytic Site

The localization of polycystin (PC)1) to the plasma membrane requires coexpression with PC2 and cleavage at the PC1 G protein-coupled receptor proteolytic site. Neither the PC1 binding capacity of PC2 nor its channel function is required for this effect

2nd ESMO Consensus Conference on Lung Cancer: early-stage non-small-cell lung cancer consensus on diagnosis, treatment and follow-up

This manuscript provides recommendations for the diagnosis, treatment and follow-up of early stage non-small cell lung cancer developed during the 2nd ESMO Consensus Conference on Lung Cancer in May 201