Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

A Study of Restaurateurs\u27 Attitudes and Practices in Relation to Obesity

The dramatic increase in the rate of obesity in the United States is raising new public health concerns. Each year, obesity-related problems cause at least 300,000 deaths and cost around 100 billion dollars. Take a walk down the street, go to a shopping center or sport event, or pick up a newspaper or magazine and the severity of the obesity problem in the United States is becoming a critical problem to solve. About 65% of the U.S. adult population is overweight (35%) or obese (30%), which has doubled in only two decades. Obesity-related diseases such as type 2 diabetes, heart disease and stroke, arthritis, respiratory problems, cancer, and sleep apnea have become a major concern in our health care crisis. Poor diet and physical inactivity leading to excess body weight was identified as the second leading cause of death in the United States. While Americans are consuming more food outside the home, it may seem easy to assume a relationship between the increases in the success of the restaurant industry and national obesity rates. The growth in food away from home has created concern about its possible effect on dietary quality. Because so much food is eaten outside the home, restaurants do have a significant impact on the food consumption of the United States and play a considerable role in the shaping of American diets

Nucleotide specificity of the enzymatic and motile activities of dynein, kinesin, and heavy meromyosin.

The substrate specificities of dynein, kinesin, and myosin substrate turnover activity and cytoskeletal filament-driven translocation were examined using 15 ATP analogues. The dyneins were more selective in their substrate utilization than bovine brain kinesin or muscle heavy meromyosin, and even different types of dyneins, such as 14S and 22S dynein from Tetrahymena cilia and the beta-heavy chain-containing particle from the outer-arm dynein of sea urchin flagella, could be distinguished by their substrate specificities. Although bovine brain kinesin and muscle heavy meromyosin both exhibited broad substrate specificities, kinesin-induced microtubule translocation varied over a 50-fold range in speed among the various substrates, whereas heavy meromyosin-induced actin translocation varied only by fourfold. With both kinesin and heavy meromyosin, the relative velocities of filament translocation did not correlate well with the relative filament-activated substrate turnover rates. Furthermore, some ATP analogues that did not support the filament translocation exhibited filament-activated substrate turnover rates. Filament-activated substrate turnover and power production, therefore, appear to become uncoupled with certain substrates. In conclusion, the substrate specificities and coupling to motility are distinct for different types of molecular motor proteins. Such nucleotide "fingerprints" of enzymatic activities of motor proteins may prove useful as a tool for identifying what type of motor is involved in powering a motility-related event that can be reconstituted in vitro

Investigating the Effects of Finite Resolution on Observed Transverse Jet Profiles

Both the emission properties and evolution of Active Galactic Nuclei (AGN) radio jets are dependent on the magnetic fields that thread them. Faraday Rotation gradients are a very important way of investigating these magnetic fields, and can provide information on the orientation and structure of the magnetic field in the immediate vicinity of the jet; for example, a toroidal or helical field component should give rise to a systematic gradient in the observed Faraday rotation across the jet, as well as characteristic intensity and polarization profiles. However, real observed radio images have finite resolution, usually expressed via convolution with a Gaussian beam whose size corresponds to the central lobe of the point source response function. This will tend to blur transverse structure in the jet profile, raising the question of how well resolved a jet must be in the transverse direction in order to reliably detect transverse structure associated with a helical jet magnetic field. We present results of simulated intensity, polarization and Faraday rotation images designed to directly and empirically investigate the effect of finite resolution on observed transverse jet structures

Dark Matter at the Center and in the Halo of the Galaxy

All presently known stellar-dynamical constraints on the size and mass of the supermassive compact dark object at the Galactic center are consistent with a ball of self-gravitating, nearly non-interacting, degenerate fermions with mass between 76 and 491 keV, for degeneracy factor g=2. Sterile neutrinos of 76 keV mass, which are mixed with at least one of the active neutrinos with a mixing angele ~10^{-7}, are produced in about the right amount in the early Universe by incoherent resonant and non-resonant scattering of active neutrinos having asymmetry of ~0.01. The former process yields sterile neutrinos with a quasi-degenerate spectrum while the latter leads to a thermal spectrum. As the production mechanism of the sterile neutrino is consistent with the constraints from large scale structure formation, core collapse supernovae, and diffuse X-ray background, it could be the dark matter particle of the Universe.Comment: 6 pages, to appear in the Beyond 2003 conference proceeding

The cross-frequency mediation mechanism of intracortical information transactions

In a seminal paper by von Stein and Sarnthein (2000), it was hypothesized that "bottom-up" information processing of "content" elicits local, high frequency (beta-gamma) oscillations, whereas "top-down" processing is "contextual", characterized by large scale integration spanning distant cortical regions, and implemented by slower frequency (theta-alpha) oscillations. This corresponds to a mechanism of cortical information transactions, where synchronization of beta-gamma oscillations between distant cortical regions is mediated by widespread theta-alpha oscillations. It is the aim of this paper to express this hypothesis quantitatively, in terms of a model that will allow testing this type of information transaction mechanism. The basic methodology used here corresponds to statistical mediation analysis, originally developed by (Baron and Kenny 1986). We generalize the classical mediator model to the case of multivariate complex-valued data, consisting of the discrete Fourier transform coefficients of signals of electric neuronal activity, at different frequencies, and at different cortical locations. The "mediation effect" is quantified here in a novel way, as the product of "dual frequency RV-coupling coefficients", that were introduced in (Pascual-Marqui et al 2016, http://arxiv.org/abs/1603.05343). Relevant statistical procedures are presented for testing the cross-frequency mediation mechanism in general, and in particular for testing the von Stein & Sarnthein hypothesis.Comment: https://doi.org/10.1101/119362 licensed as CC-BY-NC-ND 4.0 International license: http://creativecommons.org/licenses/by-nc-nd/4.0

Isolated effective coherence (iCoh): causal information flow excluding indirect paths

A problem of great interest in real world systems, where multiple time series measurements are available, is the estimation of the intra-system causal relations. For instance, electric cortical signals are used for studying functional connectivity between brain areas, their directionality, the direct or indirect nature of the connections, and the spectral characteristics (e.g. which oscillations are preferentially transmitted). The earliest spectral measure of causality was Akaike's (1968) seminal work on the noise contribution ratio, reflecting direct and indirect connections. Later, a major breakthrough was the partial directed coherence of Baccala and Sameshima (2001) for direct connections. The simple aim of this study consists of two parts: (1) To expose a major problem with the partial directed coherence, where it is shown that it is affected by irrelevant connections to such an extent that it can misrepresent the frequency response, thus defeating the main purpose for which the measure was developed, and (2) To provide a solution to this problem, namely the "isolated effective coherence", which consists of estimating the partial coherence under a multivariate auto-regressive model, followed by setting all irrelevant associations to zero, other than the particular directional association of interest. Simple, realistic, toy examples illustrate the severity of the problem with the partial directed coherence, and the solution achieved by the isolated effective coherence. For the sake of reproducible research, the software code implementing the methods discussed here (using lazarus free-pascal "www.lazarus.freepascal.org"), including the test data as text files, are freely available at: https://sites.google.com/site/pascualmarqui/home/icoh-isolated-effective-coherenceComment: 2014-02-21 pre-print, technical report, KEY Institute for Brain-Mind Research, University of Zurich, et a

Identification of children who may benefit from self-hypnosis at a pediatric pulmonary center

BACKGROUND: Emotional difficulties can trigger respiratory symptoms. Thus, children presenting with respiratory complaints may benefit from a psychological intervention. The purpose of this study was to define the proportion of patients referred to a Pediatric Pulmonary Center who may benefit from instruction in self-hypnosis, as a psychological intervention. METHODS: A retrospective chart review was conducted for all newly referred patients to the SUNY Upstate Medical University Pediatric Pulmonary Center during an 18 month period beginning January 1, 2000. Patients were offered hypnosis if they presented with symptoms or signs suggestive of psychological difficulties. Hypnosis was taught in one or two 15–45 minute sessions by a pediatric pulmonologist. RESULTS: Of 725 new referrals, 424 were 0–5 years old, 193 were 6–11 years old, and 108 were 12–18 years old. Diagnoses of anxiety, habit cough, or vocal cord dysfunction accounted for 1% of the 0–5 year olds, 20% of the 6–11 year olds, and 31% of the 12–18 year olds. Hypnotherapy was offered to 1% of 0–5 year olds, 36% of 6–11 year olds, and 55% of 12–18 year olds. Of 81 patients who received instruction in self-hypnosis for anxiety, cough, chest pain, dyspnea, or inspiratory difficulties, 75% returned for follow-up, and among the returning patients 95% reported improvement or resolution of their symptoms. CONCLUSION: A large number of patients referred to a Pediatric Pulmonary Center appeared to benefit from instruction in self-hypnosis, which can be taught easily as a psychological intervention

Coral bleaching from a single cell perspective

© 2018 The Author(s). Ocean warming is resulting in increased occurrence of mass coral bleaching; a response in which the intracellular algal endosymbionts (Symbiodinium sp.) are expelled from the coral host due to physiological stress. This detrimental process is often attributed to overproduction of reactive oxygen species (ROS) that leak out of the endosymbionts and causes damage to the host cell, though direct evidence validating this link is limited. Here, for the first time, we used confocal microscopy and fluorescent dyes to investigate if endosymbiont ROS production significantly and predictably affects physiological parameters in its host cell. Heat treatment resulted in a 60% reduction in coral symbiont density, a ~70% increase in median endosymbiont ROS and a small reduction in photosystem efficiency (F V/F M, 11%), indicating absence of severe light stress. Notably, no other physiological parameters were affected in either endosymbionts or host cells, including reduced glutathione and ROS-induced lipid peroxidation. Taken together, the increase in endosymbiont ROS could not be linked to physiological damage in either partner, suggesting that oxidative stress is unlikely to have been the driver for symbiont expulsion in this study