Interoperability of Remote Laboratories Systems

There has been growing interest in, and development of, remotely accessible laboratories as a mechanism for improving access and flexibility, and enabling sharing of facilities. Differences in focus, philosophy, approach or domain have led to quite different technical solutions in supporting remote laboratories. Whilst this diversity represents a significant strength in terms of the ability to explore different issues and support diverse applications, it does however potentially hamper the sharing of labs between different institutions. Investigation into interoperability between two remote lab platforms has realized a need for a common application protocol to achieve the goals remote labs aims to provide. We describe our approach to providing a bridge between two current remote laboratory architectures Labshares Sahara and MITs iLabs and report on the issues that arise with regard to the protocol translations

Bayesian Gaussian Copula Factor Models for Mixed Data.

Gaussian factor models have proven widely useful for parsimoniously characterizing dependence in multivariate data. There is a rich literature on their extension to mixed categorical and continuous variables, using latent Gaussian variables or through generalized latent trait models acommodating measurements in the exponential family. However, when generalizing to non-Gaussian measured variables the latent variables typically influence both the dependence structure and the form of the marginal distributions, complicating interpretation and introducing artifacts. To address this problem we propose a novel class of Bayesian Gaussian copula factor models which decouple the latent factors from the marginal distributions. A semiparametric specification for the marginals based on the extended rank likelihood yields straightforward implementation and substantial computational gains. We provide new theoretical and empirical justifications for using this likelihood in Bayesian inference. We propose new default priors for the factor loadings and develop efficient parameter-expanded Gibbs sampling for posterior computation. The methods are evaluated through simulations and applied to a dataset in political science. The models in this paper are implemented in the R package bfa

An integrated biostratigraphy and seismic stratigraphy for the late Neogene continental margin succession in northern Taranaki Basin, New Zealand

Our aim has been to develop an integrated biostratigraphy and seismic stratigraphy for the Pliocene and Pleistocene formations (Ariki, Mangaa, Giant Foresets) in northern Taranaki Basin to better understand the evolution of the modern continental margin offshore central-western North Island, New Zealand. Detailed mapping of seismic reflectors in part of the basin, when compared with correlations of late Neogene stage boundaries between 11 well sections, has highlighted crossover between the datasets. To help resolve this issue, the biostratigraphy of the Pliocene-Pleistocene parts of each of four well sections (Arawa-1, Ariki-1, Kora-1, and Wainui-1) has been re-examined using a dense suite of samples. In addition, the biostratigraphy of seven other well sections (Awatea-1, Kahawai-1, Mangaa-1, Taimana-1, Tangaroa-1, Te Kumi-1, and Turi-1) has been re-evaluated. The crossover is partly attributed to a combination of sampling resolution inherent in exploration well sections, the mixed nature of cuttings samples, and the general scarcity of age-diagnostic planktic foraminifera in the late Neogene formations. The achievement of seismic closure suggests that error in the mapping of the seismic reflectors is not a significant source of the uncertainty (crossover). We have developed a workable time-stratigraphic framework by qualitatively weighting the biostratigraphic data in each of the well sections, thereby identifying the parts of particular well sections with the highest resolution microfossil data and the optimal stratigraphic position of stage boundaries with respect to the mapped seismic horizons/seismic units. Hence, it is possible to assign the known numerical ages for these stage boundaries to reflection horizons/seismic units mapped within the basin. We have applied this information to produce a series of isopach maps for successive stage boundaries that help show the sedimentary evolution of the continental margin succession west of central North Island

Evidence for the role of EPHX2 gene variants in anorexia nervosa.

Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P<0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P<0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition

The Impact of HAART on the Respiratory Complications of HIV Infection: Longitudinal Trends in the MACS and WIHS Cohorts

Objective: To review the incidence of respiratory conditions and their effect on mortality in HIV-infected and uninfected individuals prior to and during the era of highly active antiretroviral therapy (HAART). Design: Two large observational cohorts of HIV-infected and HIV-uninfected men (Multicenter AIDS Cohort Study [MACS]) and women (Women's Interagency HIV Study [WIHS]), followed since 1984 and 1994, respectively. Methods: Adjusted odds or hazards ratios for incident respiratory infections or non-infectious respiratory diagnoses, respectively, in HIV-infected compared to HIV-uninfected individuals in both the pre-HAART (MACS only) and HAART eras; and adjusted Cox proportional hazard ratios for mortality in HIV-infected persons with lung disease during the HAART era. Results: Compared to HIV-uninfected participants, HIV-infected individuals had more incident respiratory infections both pre-HAART (MACS, odds ratio [adjusted-OR], 2.4; 95% confidence interval [CI], 2.2-2.7; p<0.001) and after HAART availability (MACS, adjusted-OR, 1.5; 95%CI 1.3-1.7; p<0.001; WIHS adjusted-OR, 2.2; 95%CI 1.8-2.7; p<0.001). Chronic obstructive pulmonary disease was more common in MACS HIV-infected vs. HIV-uninfected participants pre-HAART (hazard ratio [adjusted-HR] 2.9; 95%CI, 1.02-8.4; p = 0.046). After HAART availability, non-infectious lung diseases were not significantly more common in HIV-infected participants in either MACS or WIHS participants. HIV-infected participants in the HAART era with respiratory infections had an increased risk of death compared to those without infections (MACS adjusted-HR, 1.5; 95%CI, 1.3-1.7; p<0.001; WIHS adjusted-HR, 1.9; 95%CI, 1.5-2.4; p<0.001). Conclusion: HIV infection remained a significant risk for infectious respiratory diseases after the introduction of HAART, and infectious respiratory diseases were associated with an increased risk of mortality. © 2013 Gingo et al

Top-Down Feedback in an HMAX-Like Cortical Model of Object Perception Based on Hierarchical Bayesian Networks and Belief Propagation

PubMed ID: 2313976

Search for Gravitational Waves from Primordial Black Hole Binary Coalescences in the Galactic Halo

We use data from the second science run of the LIGO gravitational-wave detectors to search for the gravitational waves from primordial black hole (PBH) binary coalescence with component masses in the range 0.2--$1.0 M_\odot$. The analysis requires a signal to be found in the data from both LIGO observatories, according to a set of coincidence criteria. No inspiral signals were found. Assuming a spherical halo with core radius 5 kpc extending to 50 kpc containing non-spinning black holes with masses in the range 0.2--$1.0 M_\odot$, we place an observational upper limit on the rate of PBH coalescence of 63 per year per Milky Way halo (MWH) with 90% confidence.Comment: 7 pages, 4 figures, to be submitted to Phys. Rev.

Volcanic ash ice-nucleating activity can be enhanced or depressed by ash-gas interaction in the eruption plume

Volcanic ash can trigger ice nucleation when immersed in supercooled water. This will impact several processes (e.g., electrification, aggregation, precipitation) in the eruption plume and cloud and in the wider atmosphere upon ash dispersal. Previous studies show that ash bulk properties, reflecting the chemistry and phase state of the source magma, likely contribute to the ice-nucleating activity (INA) of ash. However, it remains unexplored how interaction with magmatic gases in the hot eruption plume, which inevitably leads to altered ash surface properties, affects the ash INA. Here we demonstrate that the INA of tephra is raised by exposure to H2O(g) mixed with SO2(g) at both 800 and 400 °C, but is substantially reduced by exposure to H2O(g) alone or mixed with HCl(g) at the same temperatures. In contrast, the INA of K-feldspar and quartz is reduced by all three eruption plume processing treatments. The decrease in INA of all silicates after heating with H2O(g) might relate to a loss of ice-active sites by surface dehydroxylation and/or oxidation. In the presence of HCl(g) or SO2(g), respectively, metal chloride or sulphate salts form on the tephra surfaces only. While NaCl and CaCl2 seem to have no effect on the tephra INA, CaSO4 is inferred to create ice-active sites, potentially through a particular combination of surface chemistry and topography. Overall, our findings suggest a complex interplay of bulk mineralogy and surface alteration in influencing ice nucleation by volcanic ash, and highlight the general sensitivity (enhancement or depression) of ash INA to interaction with magmatic gases in the eruption plume

Derivation of Suitability Metrics for Remote Access Mode Experiments

When considering the possible use of an online mode of experimentation it is important to evaluate the suitability of the remote access mode to a particular learning exercise. Within a large and diverse set of possible experiment-oriented learning exercises, it follows that not all laboratory experiments are well-suited for conversion to the remote access mode. In this paper we consider a range of factors that should be considered before the decision is taken to implement a remote laboratory. These factors fit broadly into four categories: learning factors, equipment factors, cohort factors and accreditation factors. Some of the factors may demonstrate a tendency to belong to more than one category, and some may present with a more significant weighting than others, but the categorical organization of the factors adds an ability to apply an objective assessment to remote access mode suitability