Validation of ICDPIC software injury severity scores using a large regional trauma registry.

BACKGROUND: Administrative or quality improvement registries may or may not contain the elements needed for investigations by trauma researchers. International Classification of Diseases Program for Injury Categorisation (ICDPIC), a statistical program available through Stata, is a powerful tool that can extract injury severity scores from ICD-9-CM codes. We conducted a validation study for use of the ICDPIC in trauma research. METHODS: We conducted a retrospective cohort validation study of 40,418 patients with injury using a large regional trauma registry. ICDPIC-generated AIS scores for each body region were compared with trauma registry AIS scores (gold standard) in adult and paediatric populations. A separate analysis was conducted among patients with traumatic brain injury (TBI) comparing the ICDPIC tool with ICD-9-CM embedded severity codes. Performance in characterising overall injury severity, by the ISS, was also assessed. RESULTS: The ICDPIC tool generated substantial correlations in thoracic and abdominal trauma (weighted κ 0.87-0.92), and in head and neck trauma (weighted κ 0.76-0.83). The ICDPIC tool captured TBI severity better than ICD-9-CM code embedded severity and offered the advantage of generating a severity value for every patient (rather than having missing data). Its ability to produce an accurate severity score was consistent within each body region as well as overall. CONCLUSIONS: The ICDPIC tool performs well in classifying injury severity and is superior to ICD-9-CM embedded severity for TBI. Use of ICDPIC demonstrates substantial efficiency and may be a preferred tool in determining injury severity for large trauma datasets, provided researchers understand its limitations and take caution when examining smaller trauma datasets.

Automatic verification of linear controller software

© 2015 IEEE.We consider the problem of verification of software implementations of linear time-invariant controllers. Commonly, different implementations use different representations of the controller's state, for example due to optimizations in a third-party code generator. To accommodate this variation, we exploit input-output controller specification captured by the controller's transfer function and show how to automatically verify correctness of C code controller implementations using a Frama-C/Why3/Z3 toolchain. Scalability of the approach is evaluated using randomly generated controller specifications of realistic size.

Are component positioning and prosthesis size associated with hip resurfacing failure?

BACKGROUND: Recent studies suggest that there is a learning curve for metal-on-metal hip resurfacing. The purpose of this study was to assess whether implant positioning changed with surgeon experience and whether positioning and component sizing were associated with implant longevity. METHODS: We evaluated the first 361 consecutive hip resurfacings performed by a single surgeon, which had a mean follow-up of 59 months (range, 28 to 87 months). Pre and post-operative radiographs were assessed to determine the inclination of the acetabular component, as well as the sagittal and coronal femoral stem-neck angles. Changes in the precision of component placement were determined by assessing changes in the standard deviation of each measurement using variance ratio and linear regression analysis. Additionally, the cup and stem-shaft angles as well as component sizes were compared between the 31 hips that failed over the follow-up period and the surviving components to assess for any differences that might have been associated with an increased risk for failure. RESULTS: Surgeon experience was correlated with improved precision of the antero-posterior and lateral positioning of the femoral component. However, femoral and acetabular radiographic implant positioning angles were not different between the surviving hips and failures. The failures had smaller mean femoral component diameters as compared to the non-failure group (44 versus 47 millimeters). CONCLUSIONS: These results suggest that there may be differences in implant positioning in early versus late learning curve procedures, but that in the absence of recognized risk factors such as intra-operative notching of the femoral neck and cup inclination in excess of 50 degrees, component positioning does not appear to be associated with failure. Nevertheless, surgeons should exercise caution in operating patients with small femoral necks, especially when they are early in the learning curve.

CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.

Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/.

Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates.

MOTIVATION: Technological advances that allow routine identification of high-dimensional risk factors have led to high demand for statistical techniques that enable full utilization of these rich sources of information for genetics studies. Variable selection for censored outcome data as well as control of false discoveries (i.e. inclusion of irrelevant variables) in the presence of high-dimensional predictors present serious challenges. This article develops a computationally feasible method based on boosting and stability selection. Specifically, we modified the component-wise gradient boosting to improve the computational feasibility and introduced random permutation in stability selection for controlling false discoveries. RESULTS: We have proposed a high-dimensional variable selection method by incorporating stability selection to control false discovery. Comparisons between the proposed method and the commonly used univariate and Lasso approaches for variable selection reveal that the proposed method yields fewer false discoveries. The proposed method is applied to study the associations of 2339 common single-nucleotide polymorphisms (SNPs) with overall survival among cutaneous melanoma (CM) patients. The results have confirmed that BRCA2 pathway SNPs are likely to be associated with overall survival, as reported by previous literature. Moreover, we have identified several new Fanconi anemia (FA) pathway SNPs that are likely to modulate survival of CM patients. AVAILABILITY AND IMPLEMENTATION: The related source code and documents are freely available at https://sites.google.com/site/bestumich/issues. CONTACT: yili@umich.edu.

ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat.

The role of GTPase-activating protein (GAP) that deactivates ADP-ribosylation factor 1 (ARF1) during the formation of coat protein I (COPI) vesicles has been unclear. GAP is originally thought to antagonize vesicle formation by triggering uncoating, but later studies suggest that GAP promotes cargo sorting, a process that occurs during vesicle formation. Recent models have attempted to reconcile these seemingly contradictory roles by suggesting that cargo proteins suppress GAP activity during vesicle formation, but whether GAP truly antagonizes coat recruitment in this process has not been assessed directly. We have reconstituted the formation of COPI vesicles by incubating Golgi membrane with purified soluble components, and find that ARFGAP1 in the presence of GTP promotes vesicle formation and cargo sorting. Moreover, the presence of GTPgammaS not only blocks vesicle uncoating but also vesicle formation by preventing the proper recruitment of GAP to nascent vesicles. Elucidating how GAP functions in vesicle formation, we find that the level of GAP on the reconstituted vesicles is at least as abundant as COPI and that GAP binds directly to the dilysine motif of cargo proteins. Collectively, these findings suggest that ARFGAP1 promotes vesicle formation by functioning as a component of the COPI coat.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.

Genetic deficiency of the fourth component of complement :clinical, immunological and genetical studies in a further family. IXth International Complement Workshop

info:eu-repo/semantics/published

Transformaciones en el plano utilizando software de geometría dinámica

Se presenta una experiencia sobre el estudio de las isometrías en el plano en la educación secundaria, utilizando software de geometría dinámica. Se construye y estudia las propiedades de los distintos movimientos (traslaciones, giros y simetrías). La actividad se desarrolla en la clase de informática con apoyo de programas como geogebra y applets de cabriweb. Se tratan elementos invariantes, composición de movimientos y motivos que teselan el plano.

Problemas geométricos de variación y el uso de software dinámico

En este artículo se presentan dos problemas geométricos que involucran la noción de variación, analizados desde la perspectiva de la resolución de problemas y la incorporación del software dinámico como un medio que puede potenciar el aprendizaje de los estudiantes. Los objetivos al presentar un análisis desde diferentes procedimientos de solución a estos problemas son: exhibir distintos acercamientos a situaciones, los cuales puede ir desarrollando el estudiante y el grupo al abordarlas, proporcionar al profesor elementos que le permitan proponer trayectorias hipotéticas del aprendizaje vinculadas con los conceptos y habilidades matemáticas que se requieren para abordar el problema y para comprenderlo, así como proveer de elementos al docente para identificar los momentos en los cuales puede intervenir en el proceso de solución para encauzar o enfatizar conceptos o habilidades matemáticas.

Contenidos transversales y aprendizaje de la matemática: haciendo uso de la tecnología (software libre)

El trabajo trata de mostrar los logros en el aprendizaje de la matemática –área de Geometría– a través del contenido transversal Educación para la gestión de riesgos y la conciencia ambiental, usando recursos tecnológicos como Google Maps y Google Earth. El tema desarrollado para tal fin fue el problema sismológico en el Perú. Finalmente, se señalan temas de geometría involucrados, así como temas anexos a través del uso de contenidos de Estadística, Geografía y Ciencias Naturales. La experiencia se hizo con un grupo de 50 alumnas del Tercer año de Educación Secundaria de una escuela pública del Perú.

Uso de software en la enseñanza de la matemática

Las clases de matemáticas no debieran tener como objetivo fundamental el aprendizaje de contenidos (definiciones, teoremas, axiomas…) que posteriormente serán aplicados a la resolución de un gran listado de ejercicios y problemas propuestos por el profesor y que justificará el aprendizaje de dichos contenidos, sino que, por el contrario, debieran partir con un problema concreto y familiar para el alumno. Una vez planteado éste y discutido por todos, estudiantes y profesor, traerá como consecuencia la obligación de resolverlo y por tanto la necesidad del aprendizaje de las técnicas que son necesarias para ello y recurrir al uso de tecnología disponible. Es muy importante destacar que durante todo el proceso el alumno hace conjeturas que irá verificando en cada paso. Se dará cuenta que algunas de las conjeturas que hizo son correctas y que otras no lo son, es decir, cometerá errores y aciertos, en función de los cuales irá cimentando su aprendizaje. Pero, por sobre todo, debe aprender que “va al colegio a equivocarse”, pero que no debe quedarse en el error, que en la discusión con sus compañeros y el profesorado encontrará la(s) solucione(s), que es probable que más de una sirva, pero que también unas son mejores que otras, que en algunos casos hay una solución óptima, en definitiva irá “aprendiendo a aprender”. Se ilustra lo anterior planteando resolver un clásico problema de construcción de cajas utilizando como herramienta de aprendizaje el software DERIVE 5.

El software matemático y los lenguajes de programación

Se lleva a cabo un análisis de los lenguajes de programación desde el punto de vista de sus relaciones con el software matemático. Para ello se comienza con una definición bastante flexible de software matemático, para continuar con un análisis metodológico de los lenguajes de programación, estudiando los paradigmas imperativo, funcional, la programación lógica y la orientación a objetos. Por último se realiza un estudio histórico de los lenguajes de programación, así como de los lenguajes de programación más adecuados para la implementación de algoritmos matemáticos.

Software educativo en línea para la enseñanza y el aprendizaje de temas de Cálculo Numérico

En un proyecto de investigación finalizado, se diseñó un software de escritorio para la enseñanza y el aprendizaje del tema Resolución Numérica de Ecuaciones no Lineales, usando el paquete MatLab.

Implementación del análisis en componentes principales con el software estadístico R

El Análisis en Componentes Principales (ACP) constituye la técnica base para el Análisis Multivariado de Datos. Su objetivo principal es reducir la cantidad de variables, manteniendo la máxima cantidad de información, presente en una tabla de datos de variables cuantitativas. En el presente artículo se expone un panorama general sobre la estructura que fundamenta un ACP y se implementa un caso concreto en el software estadístico R. Para ello es necesario un conocimiento básico de este software.