Probabilistic assignment of formulas to mass peaks in metabolomics experiments

<b>Motivation</b>: High-accuracy mass spectrometry is a popular technology for high-throughput measurements of cellular metabolites (metabolomics). One of the major challenges is the correct identification of the observed mass peaks, including the assignment of their empirical formula, based on the measured mass.<p></p> <b>Results</b>: We propose a novel probabilistic method for the assignment of empirical formulas to mass peaks in high-throughput metabolomics mass spectrometry measurements. The method incorporates information about possible biochemical transformations between the empirical formulas to assign higher probability to formulas that could be created from other metabolites in the sample. In a series of experiments, we show that the method performs well and provides greater insight than assignments based on mass alone. In addition, we extend the model to incorporate isotope information to achieve even more reliable formula identification.<p></p&gt

Conditional Sampling for Max-Stable Processes with a Mixed Moving Maxima Representation

This paper deals with the question of conditional sampling and prediction for the class of stationary max-stable processes which allow for a mixed moving maxima representation. We develop an exact procedure for conditional sampling using the Poisson point process structure of such processes. For explicit calculations we restrict ourselves to the one-dimensional case and use a finite number of shape functions satisfying some regularity conditions. For more general shape functions approximation techniques are presented. Our algorithm is applied to the Smith process and the Brown-Resnick process. Finally, we compare our computational results to other approaches. Here, the algorithm for Gaussian processes with transformed marginals turns out to be surprisingly competitive.Comment: 35 pages; version accepted for publication in Extremes. The final publication is available at http://link.springer.co

Effectiveness of pharmacist home visits for individuals at risk of medication-related problems: A systematic review and meta-analysis of randomised controlled trials

This is the final version. Available on open access from BMC via the DOI in this recordAvailability of data and materials: Not applicable, as this research article reviewed the published literature. The data published may be found in the original manuscripts cited in the references list.Background: Medication mismanagement is a major cause of both hospital admission and nursing home placement of frail older adults. Medication reviews by community pharmacists aim to maximise therapeutic benefit but also minimise harm. Pharmacist-led medication reviews have been the focus of several systematic reviews, but none have focussed on the home setting. Review methods: To determine the effectiveness of pharmacist home visits for individuals at risk of medication-related problems we undertook a systematic review and meta-analysis of randomised controlled trials (RCTs). Thirteen databases were searched from inception to December 2018. Forward and backward citation of included studies was also performed. Articles were screened for inclusion independently by two reviewers. Randomised controlled studies of home visits by pharmacists for individuals at risk of medication-related problems were eligible for inclusion. Data extraction and quality appraisal were performed by one reviewer and checked by a second. Random-effects meta-analyses were performed where sufficient data allowed and narrative synthesis summarised all remaining data. Results: Twelve RCTs (reported in 15 articles), involving 3410 participants, were included in the review. The frequency, content and purpose of the home visit varied considerably. The data from eight trials were suitable for meta-analysis of the effects on hospital admissions and mortality, and from three trials for the effects on quality of life. Overall there was no evidence of reduction in hospital admissions (risk ratio (RR) of 1.01 (95%CI 0.86 to 1.20, I2 = 69.0%, p = 0.89; 8 studies, 2314 participants)), or mortality (RR of 1.01 (95%CI 0.81 to 1.26, I2 = 0%, p = 0.94; 8 studies, 2314 participants)). There was no consistent evidence of an effect on quality of life, medication adherence or knowledge. Conclusion: A systematic review of twelve RCTs assessing the impact of pharmacist home visits for individuals at risk of medication related problems found no evidence of effect on hospital admission or mortality rates, and limited evidence of effect on quality of life. Future studies should focus on using more robust methods to assess relevant outcomes.National Institute for Health Research (NIHR

Appropriation from a common pool resource: effects of the characteristics of the common pool resource, the appropriators and the existence of communication

© 2017 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. There is a growing literature that studies the management of Common Pool Resources (CPRs) within the context of controlled laboratory experiments. A major thesis of this work is that non-binding communication (cheap talk) among appropriators of the commons may be sufficient to permit them to manage the commons efficiently without requiring an outside regulator. In this chapter we compare three CPR environments in controlled laboratory sessions with and without non-binding communication. We identify the nature of the differences across the environments and propose several new environments that may support a conjecture that cognitive differences induced by the framing of the sessions leads to the differences we find. Our results suggest that the success of nonbinding communication in reducing over-appropriation from a CPR may be dependent upon the characteristics of the CPR's yield function, the nature of the communication and the number of appropriators

Forty years of SNOMED: a literature review

BACKGROUND: Over a period of 40 years, SNOMED has developed from a pathology-specific nomenclature (SNOP) into a logic-based health care terminology. In spite of its long existence and continuous evolvement, it is yet unknown to what extent SNOMED is used in clinical practice, and what benefits were achieved. The aim of this paper is to investigate this by providing an overview of published studies in which a version of SNOMED was studied or applied. METHODS: This paper analyzes the use of SNOMED over time, as reflected in scientific publications, by means of Medline literature search in PubMed. The search included papers from 1966 until June 2006. For each selected paper the following characteristics were classified: version, medical domain, coding moment (during or after the care process), usage, and type of evaluation (e.g., does SNOMED work, does SNOMED help). RESULTS: 250 papers were included in this research. The number of annual publications has increased, as has the number of domains in which SNOMED is being used. Theoretical studies mainly concern comparison of SNOMED to other terminological systems and SNOMED as an illustration of a terminological systems' theory. Few studies are available on the usage of SNOMED in clinical practice, largely involving coding information and retrieval/aggregation based on SNOMED codes. CONCLUSION: The clinical application of SNOMED is broadening beyond pathology. The majority of studies concern proving the value of SNOMED in theory. Fewer studies are available on the usage of SNOMED in clinical practice. Literature gives no indication of the use of SNOMED for direct care purposes such as decision suppor

Improving the normalization of complex interventions: measure development based on normalization process theory (NoMAD): study protocol

<b>Background</b> Understanding implementation processes is key to ensuring that complex interventions in healthcare are taken up in practice and thus maximize intended benefits for service provision and (ultimately) care to patients. Normalization Process Theory (NPT) provides a framework for understanding how a new intervention becomes part of normal practice. This study aims to develop and validate simple generic tools derived from NPT, to be used to improve the implementation of complex healthcare interventions.<p></p> <b>Objectives</b> The objectives of this study are to: develop a set of NPT-based measures and formatively evaluate their use for identifying implementation problems and monitoring progress; conduct preliminary evaluation of these measures across a range of interventions and contexts, and identify factors that affect this process; explore the utility of these measures for predicting outcomes; and develop an online users’ manual for the measures.<p></p> <b>Methods</b> A combination of qualitative (workshops, item development, user feedback, cognitive interviews) and quantitative (survey) methods will be used to develop NPT measures, and test the utility of the measures in six healthcare intervention settings.<p></p> <b>Discussion</b> The measures developed in the study will be available for use by those involved in planning, implementing, and evaluating complex interventions in healthcare and have the potential to enhance the chances of their implementation, leading to sustained changes in working practices

A Sense-Making Approach to Understanding Adolescents' Selection of Health Information Sources

The authors propose that information sources are best understood as constructed by individuals in an attempt to find answers to questions of immediate relevance. Contact profiles, or patterns of source use for particular information, determine what constitutes a source for an individual. The study explores how adolescents acquire and use health information. Data analyses based on a probability sample of 200 adolescents identified nine contact profiles and supported four study hypotheses. Contact profiles differ according to health topics and are related to message sending and seeking regarding human sexuality and birth control. Adolescents with peer-media, home-oriented or multi-source contact profiles about human sexuality and birth control were more likely than others to be the peer advisors on this topic, and those with peer-media and multi-source profiles the ones more likely to be the information seekers about it. Contact profiles are also related to adolescents' health decision making capacity. Adolescents with peer-media and multi-source profiles for human sexuality and birth control information and those with home- oriented profiles for alcohol and smoking information engaged in more health decision making steps than those with other profiles. Finally, contact profiles are also related to awareness and contact with new information sources. Adolescents with peer-oriented and multi-source profiles were more likely than others to be aware of and have contacted a new peer education program in the school.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68266/2/10.1177_109019818401100403.pd

Spectral quantification of nonlinear behaviour of the nearshore seabed and correlations with potential forcings at Duck, N.C., U.S.A

Local bathymetric quasi-periodic patterns of oscillation are identified from monthly profile surveys taken at two shore-perpendicular transects at the USACE field research facility in Duck, North Carolina, USA, spanning 24.5 years and covering the swash and surf zones. The chosen transects are the two furthest (north and south) from the pier located at the study site. Research at Duck has traditionally focused on one or more of these transects as the effects of the pier are least at these locations. The patterns are identified using singular spectrum analysis (SSA). Possible correlations with potential forcing mechanisms are discussed by 1) doing an SSA with same parameter settings to independently identify the quasi-periodic cycles embedded within three potentially linked sequences: monthly wave heights (MWH), monthly mean water levels (MWL) and the large scale atmospheric index known as the North Atlantic Oscillation (NAO) and 2) comparing the patterns within MWH, MWL and NAO to the local bathymetric patterns. The results agree well with previous patterns identified using wavelets and confirm the highly nonstationary behaviour of beach levels at Duck; the discussion of potential correlations with hydrodynamic and atmospheric phenomena is a new contribution. The study is then extended to all measured bathymetric profiles, covering an area of 1100m (alongshore) by 440m (cross-shore), to 1) analyse linear correlations between the bathymetry and the potential forcings using multivariate empirical orthogonal functions (MEOF) and linear correlation analysis and 2) identify which collective quasi-periodic bathymetric patterns are correlated with those within MWH, MWL or NAO, based on a (nonlinear) multichannel singular spectrum analysis (MSSA). (...continued in submitted paper)Comment: 50 pages, 3 tables, 8 figure

Two Earth-sized planets orbiting Kepler-20

Since the discovery of the first extrasolar giant planets around Sun-like stars, evolving observational capabilities have brought us closer to the detection of true Earth analogues. The size of an exoplanet can be determined when it periodically passes in front of (transits) its parent star, causing a decrease in starlight proportional to its radius. The smallest exoplanet hitherto discovered has a radius 1.42 times that of the Earth's radius (R Earth), and hence has 2.9 times its volume. Here we report the discovery of two planets, one Earth-sized (1.03R Earth) and the other smaller than the Earth (0.87R Earth), orbiting the star Kepler-20, which is already known to host three other, larger, transiting planets. The gravitational pull of the new planets on the parent star is too small to measure with current instrumentation. We apply a statistical method to show that the likelihood of the planetary interpretation of the transit signals is more than three orders of magnitude larger than that of the alternative hypothesis that the signals result from an eclipsing binary star. Theoretical considerations imply that these planets are rocky, with a composition of iron and silicate. The outer planet could have developed a thick water vapour atmosphere.Comment: Letter to Nature; Received 8 November; accepted 13 December 2011; Published online 20 December 201

Are autistic traits measured equivalently in individuals with and without an Autism Spectrum Disorder?:An invariance analysis of the Autism Spectrum Quotient Short Form

It is common to administer measures of autistic traits to those without autism spectrum disorders (ASDs) with, for example, the aim of understanding autistic personality characteristics in non-autistic individuals. Little research has examined the extent to which measures of autistic traits actually measure the same traits in the same way across those with and without an ASD. We addressed this question using a multi-group confirmatory factor invariance analysis of the Autism Quotient Short Form (AQ-S: Hoekstra et al. in J Autism Dev Disord 41(5):589-596, 2011) across those with (n = 148) and without (n = 168) ASD. Metric variance (equality of factor loadings), but not scalar invariance (equality of thresholds), held suggesting that the AQ-S measures the same latent traits in both groups, but with a bias in the manner in which trait levels are estimated. We, therefore, argue that the AQ-S can be used to investigate possible causes and consequences of autistic traits in both groups separately, but caution is due when combining or comparing levels of autistic traits across the two group