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

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

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

Pancreatic complications following orthotopic liver transplantation

During fiscal year 1986, 40 out of 196 patients (21%) developed hyperamylasemia following orthotopic liver transplantation. The placement of a retropancreatic aortohepatic arterial interposition graft was associated with hyperamylasemia (p < 0.025). Eight patients (20%) developed clinically significant acute pancreatitis and its sequelae; abscesses and pseudocysts each in 2. Pancreatitis was attributable to the retropancreatic arterial graft in 4, viral infection in 2 and obstruction of the pancreatic duct in 1 patient. All 4 patients with arterial graft-related pancreatitis exhibited poor graft function immediately postoperatively, of whom 2 required retransplantation - both of which failed to function. Five patients died (63%); 2 from primary graft non-function, 2 due to sepsis and 1 from systemic cytomegalovirus infection. We conclude that acute pancreatitis after liver transplantation is a life-threatening complication which is often associated with graft non-function

Deciphering interplay between Salmonella invasion effectors

Bacterial pathogens have evolved a specialized type III secretion system (T3SS) to translocate virulence effector proteins directly into eukaryotic target cells. Salmonellae deploy effectors that trigger localized actin reorganization to force their own entry into non-phagocytic host cells. Six effectors (SipC, SipA, SopE/2, SopB, SptP) can individually manipulate actin dynamics at the plasma membrane, which acts as a ‘signaling hub’ during Salmonella invasion. The extent of crosstalk between these spatially coincident effectors remains unknown. Here we describe trans and cis binary entry effector interplay (BENEFIT) screens that systematically examine functional associations between effectors following their delivery into the host cell. The results reveal extensive ordered synergistic and antagonistic relationships and their relative potency, and illuminate an unexpectedly sophisticated signaling network evolved through longstanding pathogen–host interaction

Phase Contrast Imaging with Coded Apertures Using Laboratory-Based X-ray Sources

X‐ray phase contrast imaging is a powerful technique that allows detection of changes in the phase of x‐ray wavefronts as they pass through a sample. As a result, details not visible in conventional x‐ray absorption imaging can be detected. Until recently the majority of applications of phase contrast imaging were at synchrotron facilities due to the availability of their high flux and coherence; however, a number of techniques have appeared recently that allow phase contrast imaging to be performed using laboratory sources. Here we describe a phase contrast imaging technique, developed at University College London, that uses two coded apertures. The x‐ray beam is shaped by the pre‐sample aperture, and small deviations in the x‐ray propagation direction are detected with the help of the detector aperture. In contrast with other methods, it has a much more relaxed requirement for the source size (it works with source sizes up to 100 μm). A working prototype coded‐aperture system has been built. An x‐ray detector with directly deposited columnar CsI has been used to minimize signal spill‐over into neighboring pixels. Phase contrast images obtained with the system have demonstrated its effectiveness for imaging low‐absorption materials