PubChem: a public information system for analyzing bioactivities of small molecules

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within PubChem. These web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure–activity analysis, and target selectivity examination. This article reviews these bioactivity analysis tools and discusses their uses. Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually

An overview of the PubChem BioAssay resource

The PubChem BioAssay database (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs) hosted by the US National Institutes of Health (NIH). It archives experimental descriptions of assays and biological test results and makes the information freely accessible to the public. A PubChem BioAssay data entry includes an assay description, a summary and detailed test results. Each assay record is linked to the molecular target, whenever possible, and is cross-referenced to other National Center for Biotechnology Information (NCBI) database records. ‘Related BioAssays’ are identified by examining the assay target relationship and activity profile of commonly tested compounds. A key goal of PubChem BioAssay is to make the biological activity information easily accessible through the NCBI information retrieval system-Entrez, and various web-based PubChem services. An integrated suite of data analysis tools are available to optimize the utility of the chemical structure and biological activity information within PubChem, enabling researchers to aggregate, compare and analyze biological test results contributed by multiple organizations. In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein

The relationship between gambling advertising and gambling attitudes, intentions and behaviours:a critical and meta-analytic review

Gambling advertising has become ubiquitous in westernised countries in the last two decades, yet there is little understanding of the relationship between exposure to gambling advertising and gambling attitudes, intentions and behaviour. We conduct a critical and meta-analytic review of the past two decades of empirical research. The research suggests a positive association between exposure to gambling advertising and gambling-related attitudes, intentions and behaviour. The association is greatest for gambling behaviour. There is some evidence for a dose-response relationship. The quality and breadth of research on gambling advertising are weaker than those in comparable areas (e.g., alcohol, tobacco), with an absence of longitudinal and experimental studies. Gaps in, and methodological problems with, the field are discussed, and research directions recommended

Cognitive Bias Modification for behavior change in alcohol and smoking addiction: a Bayesian meta-analysis of individual participant data.

Cognitive Bias Modification (CBM) refers to a family of interventions targeting substance-related cognitive biases, which have been found to play a role in the maintenance of addictive behaviors. In this study, we conducted a Bayesian meta-analysis of individual patient data from studies investigating the effects of CBM as a behavior change intervention for the treatment of alcohol and tobacco use disorders, in individuals aware of the behavior change goal of the studies. Main outcomes included reduction in the targeted cognitive biases after the intervention and in substance use or relapse rate at the short-to-long term follow-up. Additional moderators, both at the study-level (type of addiction and CBM training) and at the participant-level (amount of completed training trials, severity of substance use), were progressively included in a series of hierarchical mixedeffects models. We included 14 studies involving 2435 participants. CBM appeared to have a small effect on cognitive bias (0.23, 95% credible interval = 0.06–0.41) and relapse rate (−0.27, 95% credible interval = −0.68 – 0.22), but not on reduction of substance use. Increased training practice showed a paradoxical moderation effect on relapse, with a relatively lower chance of relapse in the control condition with increased practice, compared to the training condition. All effects were associated with extremely wide 95% credible intervals, which indicate the absence of enough evidence in favor or against a reliable effect of CBM on cognitive bias and relapse rate in alcohol and tobacco use disorders. Besides the need for a larger body of evidence, research on the topic would benefit from a stronger adherence to the current methodological standards in randomized controlled trial design and the systematic investigation of shared protocols of CBM

Standardizing Clinical Trials Workflow Representation in UML for International Site Comparison

BACKGROUND: With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. METHODS: Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. RESULTS: Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. CONCLUSIONS: This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials workflows

QUERI and implementation research: Emerging from adolescence into adulthood: QUERI Series

The Quality Enhancement Research Initiative (QUERI) program and implementation research have both come of age in the 10 years since QUERI was established. Looking forward, if QUERI and the field of implementation science are to mature successfully, we will need to address a series of challenges. First, we need to more clearly demonstrate how applying principles of implementation science leads to more effective implementation and communicate those lessons to our partners and funders. Second, we will need to engage in the ongoing debate over methodological standards in quality improvement and implementation research. Third, a program like QUERI needs to become more relevant to the daily decisions of key stakeholders. Fourth, if we hope to sustain interest in implementation science, we will need to demonstrate the business case for more effective implementation. Fifth, we need to think creatively about how to nurture the next generations of implementation researchers and front-line "connectors," who are critical for accelerating implementation. Finally, we need to strengthen the connections between implementation research and the other operational and research activities that influence change in healthcare systems

Registered Replication Report: Dijksterhuis and van Knippenberg (1998)

Dijksterhuis and van Knippenberg (1998) reported that participants primed with a category associated with intelligence ("professor") subsequently performed 13% better on a trivia test than participants primed with a category associated with a lack of intelligence ("soccer hooligans"). In two unpublished replications of this study designed to verify the appropriate testing procedures, Dijksterhuis, van Knippenberg, and Holland observed a smaller difference between conditions (2%-3%) as well as a gender difference: Men showed the effect (9.3% and 7.6%), but women did not (0.3% and -0.3%). The procedure used in those replications served as the basis for this multilab Registered Replication Report. A total of 40 laboratories collected data for this project, and 23 of these laboratories met all inclusion criteria. Here we report the meta-analytic results for those 23 direct replications (total N = 4,493), which tested whether performance on a 30-item general-knowledge trivia task differed between these two priming conditions (results of supplementary analyses of the data from all 40 labs, N = 6,454, are also reported). We observed no overall difference in trivia performance between participants primed with the "professor" category and those primed with the "hooligan" category (0.14%) and no moderation by gender

Quantification in cardiac MRI: advances in image acquisition and processing

Cardiac magnetic resonance (CMR) imaging enables accurate and reproducible quantification of measurements of global and regional ventricular function, blood flow, perfusion at rest and stress as well as myocardial injury. Recent advances in MR hardware and software have resulted in significant improvements in image quality and a reduction in imaging time. Methods for automated and robust assessment of the parameters of cardiac function, blood flow and morphology are being developed. This article reviews the recent advances in image acquisition and quantitative image analysis in CMR

Biomedical informatics and translational medicine

Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams

Predictors of enhancing human physical attractiveness: Data from 93 countries

People across the world and throughout history have gone to great lengths to enhance their physical appearance. Evolutionary psychologists and ethologists have largely attempted to explain this phenomenon via mating preferences and strategies. Here, we test one of the most popular evolutionary hypotheses for beauty-enhancing behaviors, drawn from mating market and parasite stress perspectives, in a large cross-cultural sample. We also test hypotheses drawn from other influential and non-mutually exclusive theoretical frameworks, from biosocial role theory to a cultural media perspective. Survey data from 93,158 human participants across 93 countries provide evidence that behaviors such as applying makeup or using other cosmetics, hair grooming, clothing style, caring for body hygiene, and exercising or following a specific diet for the specific purpose of improving ones physical attractiveness, are universal. Indeed, 99% of participants reported spending >10 min a day performing beauty-enhancing behaviors. The results largely support evolutionary hypotheses: more time was spent enhancing beauty by women (almost 4 h a day, on average) than by men (3.6 h a day), by the youngest participants (and contrary to predictions, also the oldest), by those with a relatively more severe history of infectious diseases, and by participants currently dating compared to those in established relationships. The strongest predictor of attractiveness-enhancing behaviors was social media usage. Other predictors, in order of effect size, included adhering to traditional gender roles, residing in countries with less gender equality, considering oneself as highly attractive or, conversely, highly unattractive, TV watching time, higher socioeconomic status, right-wing political beliefs, a lower level of education, and personal individualistic attitudes. This study provides novel insight into universal beauty-enhancing behaviors by unifying evolutionary theory with several other complementary perspectives