explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots.

explorase: Multivariate Exploratory Analysis and Visualization for Systems Biology

The datasets being produced by high-throughput biological experiments, such as microarrays, have forced biologists to turn to sophisticated statistical analysis and visualization tools in order to understand their data. We address the particular need for an open-source exploratory data analysis tool that applies numerical methods in coordination with interactive graphics to the analysis of experimental data. The software package, known as explorase, provides a graphical user interface (GUI) on top of the R platform for statistical computing and the GGobi software for multivariate interactive graphics. The GUI is designed for use by biologists, many of whom are unfamiliar with the R language. It displays metadata about experimental design and biological entities in tables that are sortable and filterable. There are menu shortcuts to the analysis methods implemented in R, including graphical interfaces to linear modeling tools. The GUI is linked to data plots in GGobi through a brush tool that simultaneously colors rows in the entity information table and points in the GGobi plots

An Excess of Jupiter Analogs in Super-Earth Systems

We use radial velocity observations to search for long-period gas giant companions in systems hosting inner super-Earth (1-4 R_Earth, 1-10 M_Earth) planets to constrain formation and migration scenarios for this population. We consistently re-fit published RV datasets for 65 stars and find 9 systems with statistically significant trends indicating the presence of an outer companion. We combine these RV data with AO images to constrain the masses and semi-major axes of these companions. We quantify our sensitivity to the presence of long-period companions by fitting the sample with a power law distribution and find an occurrence rate of 39+/-7% for companions 0.5-20 M_Jup and 1-20 AU. Half of our systems were discovered by the transit method and half were discovered by the RV method. While differences in RV baselines and number of data points between the two samples lead to different sensitivities to distant companions, we find that occurrence rates of gas giant companions in each sample are consistent at the 0.5$\sigma$ level. We compare the frequency of Jupiter analogs in these systems to the equivalent rate from field star surveys and find that Jupiter analogs are more common around stars hosting super-Earths. We conclude that the presence of outer gas giants does not suppress the formation of inner super-Earths, and that these two populations of planets instead appear to be correlated. We also find that the stellar metallicities of systems with gas giant companions are higher than those without companions, in agreement with the well-established metallicity correlation from RV surveys of field stars.Comment: published in A

Effectiveness of melarsoprol and eflornithine as first-line regimens for gambiense sleeping sickness in nine Médecins Sans Frontières programmes

This paper describes the effectiveness of first-line regimens for stage 2 human African trypanosomiasis (HAT) due to Trypanosoma brucei gambiense infection in nine Médecins Sans Frontières HAT treatment programmes in Angola, Republic of Congo, Sudan and Uganda. Regimens included eflornithine and standard- and short-course melarsoprol. Outcomes for 10461 naïve stage 2 patients fitting a standardised case definition and allocated to one of the above regimens were analysed by intention-to-treat analysis. Effectiveness was quantified by the case fatality rate (CFR) during treatment, the proportion probably and definitely cured and the Kaplan-Meier probability of relapse-free survival at 12 months and 24 months post admission. The CFR was similar for the standard- and short-course melarsoprol regimens (4.9% and 4.2%, respectively). The CFR for eflornithine was 1.2%. Kaplan-Meier survival probabilities varied from 71.4-91.8% at 1 year and 56.5-87.9% at 2 years for standard-course melarsoprol, to 73.0-91.1% at 1 year for short-course melarsoprol, and 79.9-97.4% at 1 year and 68.6-93.7% at 2 years for eflornithine. With the exception of one programme, survival at 12 months was >90% for eflornithine, whilst for melarsoprol it was <90% except in two sites. Eflornithine is recommended where feasible, especially in areas with low melarsoprol effectivenes

A systematic review of interventions to increase the use of standardized outcome measures by rehabilitation professionals

Objective: To determine the types and effectiveness of interventions to increase the knowledge about, attitudes towards, and use of standardized outcome measures in rehabilitation professionals.&nbsp; Data Sources: An electronic search using Medline, EMBASE, PsycINFO, CINAHL, Ergonomics Abstracts, Sports Discus. The search is current to February 2016.&nbsp; Study Selection: All study designs testing interventions were included as were all provider and patient types. Two reviewers independently conducted a title and abstract review, followed by a full-text review.&nbsp; Data extraction: Two reviewers independently extracted a priori variables and used consensus for disagreements. Quality assessment was conducted using the Assessment of Quantitative Studies published by the Effective Public Health Practice Group.&nbsp; Data Synthesis: We identified 11 studies involving at least 1200 providers. Nine of the studies showed improvements in outcome measure use rates but only three of these studies used an experimental or quasi-experimental design. Eight of the studies used an educational approach in the intervention and three used audit and feedback. Poor intervention description and quality of studies limited recommendations.&nbsp; Conclusions: Increased attention to testing interventions focused on known barriers, matched to behavior change techniques, and with stronger designs is warranted

Knowledge Translation Activities in Occupational Therapy Organizations: The Canadian Landscape

Despite acknowledging the importance of knowledge translation (KT), the occupational therapy profession has demonstrated only emerging KT activity. Organizations are seen as playing an important role in supporting KT. To date, there have been no known attempts to explore KT activities conducted by occupational therapy organizations in Canada. The purpose of this study was to identify and describe KT activities occurring in Canadian occupational therapy organizations. An environmental scan was used to identify KT activities. The websites of occupational therapy national and provincial associations and/or regulatory bodies and the educational programs were searched. A Knowledge Mobilization Matrix (KMM) website was applied to each organizational website. The total KMM scores were highest for universities and lowest for regulatory organizations. The type and nature of the KT activities varied according to the type of organization. Canadian occupational therapy leadership organizations play an important role in supporting KT