Using the R Package crlmm for Genotyping and Copy Number Estimation

Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workflow for the estimation of allele-specific copy number and integration of the marker-level estimates with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R.

Assessment of reliability in isokinetic testing among adolescent basketball players

Background. The reproducibility of day-to-day testing of isokinetic concentric and eccentric muscular actions among adolescent basketball players aged 14 to 16 years and relationships of mean within-subject variation in two isokinetic testing sessions with chronological age, biological maturation (estimated age at peak height velocity), training experience, body size, lower-body morphology, and initial strength performance were evaluated. Material and Methods. The sample included 27 basketball players who completed replicate test sessions of 5 repetitions of reciprocal concentric and eccentric knee extensions and flexions at 60 degrees s(-1). A randomly selected subsample of 8 players completed a third testing session to confirm reliability estimates. Results. Coefficients of variation (CV) between sessions 1 and 2 ranged from 8.1% to 17.4%, and intraclass coefficients (ICCs) ranged from 0.72 to 0.89. For sessions 1 and 3, CVs ranged from 3.9% to 6.0%, and ICCs ranged from 0.95 to 0.99. The initial level of strength of eccentric knee flexion (r=-0.43) and eccentric knee extension (r=-0.42) were correlated (P<0.05) with eccentric knee extension within-variation between two sessions. Training experience (r=-0.37, P<0.05) and initial values of concentric knee flexion (r=-0.62, P<0.01) were correlated with concentric knee flexion within-subject differences. Within-subject variation of eccentric knee extension was correlated (P<0.05) with chronologic age (r=0.41), estimated age at peak height velocity (r=-0.38), body size (r=0.41 to 0.47), and leg volume (r=0.39). Conclusions. Familiarization sessions may improve the reliability of concentric and eccentric knee isokinetic strength testing at 60 s(-1) in adolescent basketball players. Age, maturity status, and training experience of young athletes should be considered when testing knee isokinetic strength at 60 degrees s(-1)

Integrating Engineering Data Systems for NASA Spaceflight Projects

NASA has a large range of custom-built and commercial data systems to support spaceflight programs. Some of the systems are re-used by many programs and projects over time. Management and systems engineering processes require integration of data across many of these systems, a difficult problem given the widely diverse nature of system interfaces and data models. This paper describes an ongoing project to use a central data model with a web services architecture to support the integration and access of linked data across engineering functions for multiple NASA programs. The work involves the implementation of a web service-based middleware system called Data Aggregator to bring together data from a variety of systems to support space exploration. Data Aggregator includes a central data model registry for storing and managing links between the data in disparate systems. Initially developed for NASA's Constellation Program needs, Data Aggregator is currently being repurposed to support the International Space Station Program and new NASA projects with processes that involve significant aggregating and linking of data. This change in user needs led to development of a more streamlined data model registry for Data Aggregator in order to simplify adding new project application data as well as standardization of the Data Aggregator query syntax to facilitate cross-application querying by client applications. This paper documents the approach from a set of stand-alone engineering systems from which data are manually retrieved and integrated, to a web of engineering data systems from which the latest data are automatically retrieved and more quickly and accurately integrated. This paper includes the lessons learned through these efforts, including the design and development of a service-oriented architecture and the evolution of the data model registry approaches as the effort continues to evolve and adapt to support multiple NASA programs and priorities

Using the R Package crlmm for Genotyping and Copy Number Estimation

Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This paper illustrates a workflow for the estimation of allele-specific copy number and integration of the marker-level estimates with complimentary Bioconductor software for inferring regions of copy number gain or loss. All analyses are performed in the statistical environment R

Perfil de Aluno e Rendimento Escolar em Pedagogia: Correlacionando Variáveis na UFBA

Este artigo traça o perfil do aluno de pedagogia da Universidade Federal da Bahia – UFBA e estabelece correlações entre o rendimento escolar e diversas variáveis independentes. As análises estatísticas foram realizadas a partir do banco de dados sobre ingressos da referida universidade nos anos 1993, 1994, 1995 e 1997. Os alunos do curso de pedagogia tendem a ser mais pobres e egressos majoritariamente da escola média pública, diferentemente do que ocorre com a UFBA como um todo. O rendimento médio escolar no curso de pedagogia é superior ao da UFBA e o estudante negro obtém rendimento escolar significativamente maior que o branco. Esses resultados e outros apresentados no trabalho sugerem uma distinção do sistema de avaliação escolar utilizado no curso de pedagogia dos demais cursos da UFBA. Contudo, faz-se necessário realizar novos estudos para se conhecer melhor esses sistemas e encontrar explicações para os resultados encontrados. Palavras-chave: Avaliação da aprendizagem; desempenho acadêmico; ensino superior, curso de pedagogia. Abstract: This article profiles the pedagogy student at the Federal University of Bahia – UFBA and establishes correlations between academic acheivement and a series of independent variables. The statistical analyses were performed using data pertaining to students entering UFBA in the years 1993, 1994, 1995 and 1997. The students in the pedagogy course tend to be poorer and primarily products of public secondary school, different from what is encountered for the UFBA student body as a whole. The level of academic achievement for the pedagogy course is higher than that for UFBA in general and black students perform academically better than do while students. These findings along with others presented in the article suggest that the system of academic evaluation utilized in the pedagogy course is distinct from that used in UFBA´s other programs. This implies the need to conduct further study to better comprehend these systems and uncover explanations for the findings reported. Key words: learning evaluation; school achievement; higher education; pedagogy

Design and development of Ga-substituted Z-type hexaferrites for microwave absorber applications: mössbauer, static and dynamic properties

Gallium substituted Z-type Sr3GaxCo2-xFe24O41 (x = 0.0–2.0 in steps of 0.4) hexaferrites were synthesised by the sol-gel auto-combustion process, and sintered at 1150 °C. The structural, morphology, magnetic, Mössbauer, dielectric and microwave absorption properties were examined. XRD results of x = 0.0, 0.4, 0.8, and 1.2 samples show the formation of a single Z-type hexagonal phase. The samples x = 1.6 and 2.0 show the formation of Z and M phases. Hysteresis loops analysis suggest that samples x < 1.6 possess a soft magnetic nature, while the samples x = 1.6 and 2.0 show a hard ferrite characteristics. All samples possess multi-domain microstructures. The composition x = 0.4 [maximum MS = 97.94 Am2kg−1] was fitted with seven sextets (Fe3+) and a paramagnetic doublet-A (Fe3+), while beyond x ≥ 0.8 two more doublets (Fe2+) were observed along with seven sextets in Mössbauer spectra. The maximum values of Fe2+ ions (1.26%) and relative area of paramagnetic doublets (1.91%) were observed for x = 1.6 composition, which is also responsible for the lowest value of MS (69.99 Am2kg−1) for this composition. The average hyperfine magnetic field was found to decrease, whereas average quadrupole splitting was found to increase, with Ga-substitution. The substitution of Ga ions enhanced permeability, dielectric constant, magnetic loss and dielectric loss, in a non-linear fashion. The reflection loss was maximum at lower frequencies for samples x = 0.0 and 0.8, and decreases with frequency. Sample x = 0.8 has maximum reflection loss of −12.44 dB at 8 GHz, a measured thickness of 3 mm, and a bandwidth of −10 dB at 1.18 GHz. The observed absorption has been discussed with the help of the input impedance matching mechanism and quarter wavelength mechanism. The observed coercivity in different samples also influenced microwave absorption which demonstrated potenial in microwave absorber applications.publishe

Multi-user investigation organizer

A system that allows a team of geographically dispersed users to collaboratively analyze a mishap event. The system includes a reconfigurable ontology, including instances that are related to and characterize the mishap, a semantic network that receives, indexes and stores, for retrieval, viewing and editing, the instances and links between the instances, a network browser interface for retrieving and viewing screens that present the instances and links to other instances and that allow editing thereof, and a rule-based inference engine, including a collection of rules associated with establishment of links between the instances. A possible conclusion arising from analysis of the mishap event may be characterized as one or more of: not a credible conclusion; an unlikely conclusion; a credible conclusion; conclusion needs analysis; conclusion needs supporting data; conclusion proposed to be closed; and an un-reviewed conclusion

Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

Modelling the location and consequences of aircraft accidents

Following the completion of two projects funded by the UK EPSRC and two for the Airports Cooperative Research Program, ACRP (2008, 2011), this paper aims to summarise the work on the location and consequence models . The projects overall focused on the development of an improved airport risk assessment methodology aimed at assessing risks related to aircraft accidents at and in the vicinity of airports and managing Runway Safety Areas (RSAs) as a risk mitigation measure. The improved methodology is more quantitative, risk-sensitive, flexible and transparent than traditional risk assessment approaches. As such, it contributes to the implementation of Safety Management Systems at airports, as stipulated by the International Civil Aviation Organisation. The innovative elements of this research are two-fold. First, an accident database covering undershoots, overruns, and veer-off crashes close to runways at airports has been compiled and data on incidents has been added. Second, accident frequency models have been developed, for example, identifying the contribution of influencing factors such as variations in meteorological conditions. To allow airport risk to then be calculated entails comparing these cases with those contained in a ‘normal operations database’ where no accidents have been recorded but where the influencing factors are also known. Subsequent models have examined the location of the accidents and their consequences. It is this work that is the focus of this paper. Future work will focus on improving these aspects of the modelling and the consequences of crashes more than 2000 ft. but less than 10 miles from a runway end as well as impacts on third parties

A sigmoidal fit for pressure-volume curves of idiopathic pulmonary fibrosis patients on mechanical ventilation: clinical implications

OBJECTIVE: Respiratory pressure-volume curves fitted to exponential equations have been used to assess disease severity and prognosis in spontaneously breathing patients with idiopathic pulmonary fibrosis. Sigmoidal equations have been used to fit pressure-volume curves for mechanically ventilated patients but not for idiopathic pulmonary fibrosis patients. We compared a sigmoidal model and an exponential model to fit pressure-volume curves from mechanically ventilated patients with idiopathic pulmonary fibrosis. METHODS: Six idiopathic pulmonary fibrosis patients and five controls underwent inflation pressure-volume curves using the constant-flow technique during general anesthesia prior to open lung biopsy or thymectomy. We identified the lower and upper inflection points and fit the curves with an exponential equation, V = A-B.e-k.P, and a sigmoid equation, V = a+b/(1+e-(P-c)/d). RESULTS: The mean lower inflection point for idiopathic pulmonary fibrosis patients was significantly higher (10.5 ± 5.7 cm H2O) than that of controls (3.6 ± 2.4 cm H2O). The sigmoidal equation fit the pressure-volume curves of the fibrotic and control patients well, but the exponential equation fit the data well only when points below 50% of the inspiratory capacity were excluded. CONCLUSION: The elevated lower inflection point and the sigmoidal shape of the pressure-volume curves suggest that respiratory system compliance is decreased close to end-expiratory lung volume in idiopathic pulmonary fibrosis patients under general anesthesia and mechanical ventilation. The sigmoidal fit was superior to the exponential fit for inflation pressure-volume curves of anesthetized patients with idiopathic pulmonary fibrosis and could be useful for guiding mechanical ventilation during general anesthesia in this condition