Annotation of SBML Models Through Rule-Based Semantic Integration

*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.
*Results:* We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.
*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RB

Time Zones As Cues For Coordination: Latitude, Longitude, And Letterman

Market productivity is often greater, and leisure and other household activities more enjoyable, when people perform them simultaneously. Beyond pointing out the positive externalities of synchronicity, economists have not attempted to identify exogenous determinants of timing. We develop a theory illustrating conditions under which synchronicity will vary and identify three factors — the amount of daylight, the timing of television programming, and differences in time zones — that can alter timing. Using the American Time Use Survey for 2003 and 2004, we first show that an exogenous shock to time in one area due to non-adherence to daylight-saving time leads its residents to alter their work schedules to continue coordinating their activities with those of people elsewhere. With time use data from Australia, we also demonstrate the same response to a similar shock there. We then show that both television timing and the benefits of coordinating across time zones in the U.S. generally affect the timing of market work and sleep, the two most time-consuming activities people undertake. While these impacts do not differ greatly by people's demographic characteristics,workers in industries where we would expect more coordination outside of their local areas are more responsive to the effects of time zones.banking, market discipline

Time Zones as Cues for Coordination: Latitude, Longitude, and Letterman

Market productivity is often greater, and leisure and other household activities more enjoyable, when people perform them simultaneously. Beyond pointing out the positive externalities of synchronicity, economists have not attempted to identify exogenous determinants of timing. We develop a theory illustrating conditions under which synchronicity will vary and identify three factors %u2014 the amount of daylight, the timing of television programming, and differences in time zones %u2014 that can alter timing. Using the American Time Use Survey for 2003 and 2004, we first show that an exogenous shock to time in one area due to non-adherence to daylight-saving time leads its residents to alter their work schedules to continue coordinating their activities with those of people elsewhere. With time use data from Australia, we also demonstrate the same response to a similar shock there. We then show that both television timing and the benefits of coordinating across time zones in the U.S. generally affect the timing of market work and sleep, the two most time-consuming activities people undertake. While these impacts do not differ greatly by people's demographic characteristics, workers in industries where we would expect more coordination outside of their local areas are more responsive to the effects of time zones.

Categorisation of continuous risk factors in epidemiological publications: a survey of current practice

BACKGROUND: Reports of observational epidemiological studies often categorise (group) continuous risk factor (exposure) variables. However, there has been little systematic assessment of how categorisation is practiced or reported in the literature and no extended guidelines for the practice have been identified. Thus, we assessed the nature of such practice in the epidemiological literature. Two months (December 2007 and January 2008) of five epidemiological and five general medical journals were reviewed. All articles that examined the relationship between continuous risk factors and health outcomes were surveyed using a standard proforma, with the focus on the primary risk factor. Using the survey results we provide illustrative examples and, combined with ideas from the broader literature and from experience, we offer guidelines for good practice. RESULTS: Of the 254 articles reviewed, 58 were included in our survey. Categorisation occurred in 50 (86%) of them. Of those, 42% also analysed the variable continuously and 24% considered alternative groupings. Most (78%) used 3 to 5 groups. No articles relied solely on dichotomisation, although it did feature prominently in 3 articles. The choice of group boundaries varied: 34% used quantiles, 18% equally spaced categories, 12% external criteria, 34% other approaches and 2% did not describe the approach used. Categorical risk estimates were most commonly (66%) presented as pairwise comparisons to a reference group, usually the highest or lowest (79%). Reporting of categorical analysis was mostly in tables; only 20% in figures. CONCLUSIONS: Categorical analyses of continuous risk factors are common. Accordingly, we provide recommendations for good practice. Key issues include pre-defining appropriate choice of groupings and analysis strategies, clear presentation of grouped findings in tables and figures, and drawing valid conclusions from categorical analyses, avoiding injudicious use of multiple alternative analyses

Challenges to pre-migration interventions to prevent human trafficking: Results from a before-and-after learning assessment of training for prospective female migrants in Odisha, India

Background: Awareness-raising and pre-migration training are popular strategies to prevent human trafficking. Programmatic theories assume that when prospective migrants are equipped with information about risks, they will make more-informed choices, ultimately resulting in safe migration. In 2016, India was estimated to have 8 million people in modern slavery, including those who migrate internally for work. Work in Freedom (WiF) was a community-based trafficking prevention intervention. This study evaluated WiF’s pre-migration knowledge-building activities for female migrants in Odisha to prevent future labour-related exploitation. / Methods: Pre- and post- training questionnaires were administered to women (N = 347) who participated in a two-day pre-migration training session. Descriptive analysis and unadjusted analyses (paired t-tests, McNemar’s tests, Wilcoxon signed ranks tests) examined differences in women’s knowledge scores before and after training. Adjusted analyses used mixed effects models to explore whether receiving information on workers’ rights or working away from home prior to the training was associated with changes in scores. Additionally, we used data from a household survey (N = 4,671) and survey of female migrants (N = 112) from a population sample in the same district to evaluate the intervention’s rationale and implementation strategy. / Results: Female participants were on average 37.3 years-old (SD 11) and most (67.9%) had no formal education. Only 11 participants (3.2%) had previous migration experience. Most participants (90.5%) had previously received information or advice on workers’ rights or working away from home. Compared to female migrants in the population, training participants were different in age, caste and religion. Awareness about migration risks, rights and collective bargaining was very low initially and remained low post-training, e.g. of 13 possible migration risks, before the training, participants named an average of 1.2 risks, which increased only slightly to 2.1 risks after the training (T(346) = -11.64, p<0.001). Changes were modest for attitudes about safe and risky migration practices, earnings and savings. Before the training, only 34 women (10.4%) considered migrating, which reduced to 25 women (7.7%) post-training (X2 = 1.88, p = 0.169)—consistent with the low prevalence (7% of households) of female migration locally. Women’s attitudes remained relatively fixed about the shame associated with paid domestic work. Survey data indicated focusing on domestic work did not correspond to regional migration trends, where women migrate primarily for construction or agriculture work. / Conclusion: The apparent low effectiveness of the WiF short-duration migration training may be linked to the assumption that individual changes in knowledge will lead to shifts in social norms. The narrow focus on such individual-level interventions may overestimate an individual’s agency. Findings indicate the importance of intervention development research to ensure activities are conducted in the right locations, target the right populations, and have relevant content. Absent intervention development research, this intervention suffered from operating in a site that had very few migrant women and a very small proportion migrating for domestic work—the focus of the training. To promote better development investments, interventions should be informed by local evidence and subjected to rigorous theory-based evaluation to ensure interventions achieve the most robust design to foster safe labour migration for women

Issues in the reporting of epidemiological studies: a survey of recent practice.

OBJECTIVES: To review current practice in the analysis and reporting of epidemiological research and to identify limitations. DESIGN: Examination of articles published in January 2001 that investigated associations between risk factors/exposure variables and disease events/measures in individuals. SETTING: Eligible English language journals including all major epidemiological journals, all major general medical journals, and the two leading journals in cardiovascular disease and cancer. MAIN OUTCOME MEASURE: Each article was evaluated with a standard proforma. RESULTS: We found 73 articles in observational epidemiology; most were either cohort or case-control studies. Most studies looked at cancer and cardiovascular disease, even after we excluded specialty journals. Quantitative exposure variables predominated, which were mostly analysed as ordered categories but with little consistency or explanation regarding choice of categories. Sample selection, participant refusal, and data quality received insufficient attention in many articles. Statistical analyses commonly used odds ratios (38 articles) and hazard/rate ratios (23), with some inconsistent use of terminology. Confidence intervals were reported in most studies (68), though use of P values was less common (38). Few articles explained their choice of confounding variables; many performed subgroup analyses claiming an effect modifier, though interaction tests were rare. Several investigated multiple associations between exposure and outcome, increasing the likelihood of false positive claims. There was evidence of publication bias. CONCLUSIONS: This survey raises concerns regarding inadequacies in the analysis and reporting of epidemiological publications in mainstream journals