Pangea: A Workbench for Statically Analyzing Multi-Language Software Corpora

Software corpora facilitate reproducibility of analyses, however, static analysis for an entire corpus still requires considerable effort, often duplicated unnecessarily by multiple users. Moreover, most corpora are designed for single languages increasing the effort for cross-language analysis. To address these aspects we propose Pangea, an infrastructure allowing fast development of static analyses on multi-language corpora. Pangea uses language-independent meta-models stored as object model snapshots that can be directly loaded into memory and queried without any parsing overhead. To reduce the effort of performing static analyses, Pangea provides out-of-the box support for: creating and refining analyses in a dedicated environment, deploying an analysis on an entire corpus, using a runner that supports parallel execution, and exporting results in various formats. In this tool demonstration we introduce Pangea and provide several usage scenarios that illustrate how it reduces the cost of analysis.

Screening of the Open Source Malaria Box Reveals an Early Lead Compound for the Treatment of Alveolar Echinococcosis.

The metacestode (larval) stage of the tapeworm Echinococcus multilocularis causes alveolar echinococcosis (AE), a very severe and in many cases incurable disease. To date, benzimidazoles such as albendazole and mebendazole are the only approved chemotherapeutical treatment options. Benzimidazoles inhibit metacestode proliferation, but do not act parasiticidal. Thus, benzimidazoles have to be taken a lifelong, can cause adverse side effects such as hepatotoxicity, and are ineffective in some patients. We here describe a newly developed screening cascade for the evaluation of the in vitro efficacy of new compounds that includes assessment of parasiticidal activity. The Malaria Box from Medicines for Malaria Venture (MMV), comprised of 400 commercially available chemicals that show in vitro activity against Plasmodium falciparum, was repurposed. Primary screening was carried out at 10 μM by employing the previously described PGI assay, and resulted in the identification of 24 compounds that caused physical damage in metacestodes. Seven out of these 24 drugs were also active at 1 μM. Dose-response assays revealed that only 2 compounds, namely MMV665807 and MMV665794, exhibited an EC50 value below 5 μM. Assessments using human foreskin fibroblasts and Reuber rat hepatoma cells showed that the salicylanilide MMV665807 was less toxic for these two mammalian cell lines than for metacestodes. The parasiticidal activity of MMV665807 was then confirmed using isolated germinal layer cell cultures as well as metacestode vesicles by employing viability assays, and its effect on metacestodes was morphologically evaluated by electron microscopy. However, both oral and intraperitoneal application of MMV665807 to mice experimentally infected with E. multilocularis metacestodes did not result in any reduction of the parasite load.

Prognostic value of the Geneva prediction rule in patients in whom pulmonary embolism is ruled out

The prognosis of patients in whom pulmonary embolism (PE) is suspected but ruled out is poorly understood. We evaluated whether the initial assessment of clinical probability of PE could help to predict the prognosis for these patients.

The Getting-Out-of-Bed (GoB) scale: a measure of motivation and life outlook in older adults with cancer

OBJECTIVE: To develop and evaluate the psychometric properties of a measure of motivation and life outlook (Getting-Out-of-Bed [GoB]). DESIGN: Secondary analysis of baseline and 6-month data from a longitudinal follow-up study of older breast cancer survivors. PARTICIPANTS: Women (N = 660) diagnosed with primary breast cancer stage I-IIIA disease, age >or=65 years, and permission to contact from an attending physician in four geographic regions in the United States (city-based Los Angeles, California; statewide in Minnesota, North Carolina, and Rhode Island). MEASUREMENT: Data were collected over 6-months of follow-up from consenting patients' medical records and telephone interviews with patients. Data collected included the 4-item GoB, health-related quality of life (HRQoL), breast cancer, sociodemographic, and health-related characteristics. RESULTS: Factor analysis produced, as hypothesized, one principal component with eigen values of 2.74(baseline) and 2.91(6-months) which explained 68.6%(baseline) and 72.7%(6-months) of total variance. In further psychometric analyses, GoB exhibited good construct validity (divergent: low nonstatistically significant correlations with unrelated constructs; convergent: moderate statistically significant correlations with related constructs; discriminant: distinguished high HRQoL groups with a high level of significance), excellent internal reliability (Cronbach's alpha 0.84(baseline), 0.87(6-months)), and produced stable measurements over 6-months. Women with GoB scores >or=50 at baseline were more likely at 6-months to have good HRQoL, good self-perceived health, and report regular exercise, indicating good predictive ability. CONCLUSION: GoB demonstrated overall good psychometric properties in this sample of older breast cancer survivors, suggestive of a promising tool for assessing motivation and life outlook in older adults. Nevertheless, because it was developed and initially evaluated in a select sample, using measures with similar but not exact content overlap further evaluation is needed before it can be recommended for widespread use.

Cholesteatoma surgery in children: long-term results of the inside-out technique

OBJECTIVE To present the anatomical and functional results of the inside-out technique applied in pediatric cholestetaoma surgery and to evaluate functionality with good hearing results against radicality with lower recurrence rate. METHODS Retrospective analysis and evaluation of the postoperative outcome in a consecutive series of 126 children or 130 ears operated between 1992 and 2008. With the inside-out technique, cholesteatoma is eradicated from the epitympanum toward the mastoid and, as a single stage procedure, functional reconstruction of the middle ear is achieved by tympanoossiculoplasty. RESULTS In 89.2% of all cases, the ear was dry postoperatively. 80.9% of the ears reached a postoperative air-bone gap of 30 dB or less and the median air conduction hearing threshold was 29 dB; in 60.9% of all cases, hearing was postoperatively improved. The recurrence rate was 16.2% in a mean postoperative follow-up 8.5 years. Altogether, 48 ears (36.9%) underwent revision surgery. The complication rate was 3.1% and involved only minor complications. CONCLUSION The inside-out technique allows a safe removal of cholesteatoma from the epitympanum toward the mastoid with a single-stage reconstruction of the ossicular chain. For this reason we support our individual approach, which allows creation of the smallest possible cavity for the size of the cholesteatoma. Our results confirm that the inside-out technique is effective in the treatment of pediatric cholesteatoma.

The “Out of Africa Tribe” (II): Paleolithic warriors with big canoes and protective weapons

It is generally difficult to establish a timeline for the appearance of different technologies and tools during human cultural evolution. Here I use stochastic character mapping of discrete traits using human mtDNA phylogenies rooted to the Reconstructed Sapiens Reference Sequence (RSRS) as a model to address this question. The analysis reveals that the ancestral state of Homo sapiens was hunting, using material innovations that included bows and arrows, stone axes and spears. However, around 80,000 y before present, a transition occurred, from this ancestral hunting tradition, toward the invention of protective weapons such as shields, the appearance of ritual fighting as a socially accepted behavior and the construction of war canoes for the fast transport of large numbers of warriors. This model suggests a major cultural change, during the Palaeolithic, from hunters to warriors. Moreover, in the light of the recent Out of Africa Theory, it suggests that the “Out of Africa Tribe” was a tribe of warriors that had developed protective weapons such as shields and used big war canoes to travel the sea coast and big rivers in raiding expeditions.