Academic Computing Newsletter: April 1991

Academic Computing Newsletter (Vol. 6 Number 3, April 1991) is published on an irregular schedule by Academic Computing Services, State University of New York, College at Brockport. This issue reviews the development of computing services on the Brockport campus over the previous 6 years, and talks about the current state of computing, as well.https://digitalcommons.brockport.edu/lits_news/1041/thumbnail.jp

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

<p>Abstract</p> <p>Background</p> <p>Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input.</p> <p>Results</p> <p>TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified.</p> <p>Conclusions</p> <p>TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at <url>http://apollo11.isto.unibo.it/software/</url>, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes.</p

Software para aprender y para hacer estadística y probabilidad – Mirando atrás y adelante desde una perspectiva personal

III Congreso Internacional Virtual de Educación Estadística (CIVEEST), 21-24 febrero de 2019. [www.ugr.es/local/fqm126/civeest.html]The paper discusses requirements for software that supports both the learning and the doing of statistics. It looks back into the 1990s and looks forward to new challenges for such tools stemming from an updated conception of statistical literacy and challenges from big data, the exploding use of data in society and the emergence of data science. A focus is on Fathom, TinkerPlots and Codap, which are looked at from the perspective of requirements for tools for statistics education. Experiences and success conditions for using these tools in various educational contexts are reported, namely in primary and secondary education and pre-service and in-service teacher education. New challenges from data science require new tools for education with new features. The paper finishes with some ideas and experience from a recent project on data science education at the upper secondary levelEl artículo discute los requisitos que el software debe cumplir para que pueda apoyar tanto el aprendizaje como la práctica de la estadística. Mira hacia la década de 1990 y hacia el futuro, para identificar los nuevos desafíos que para estas herramientas surgen de una concepción actualizada de la alfabetización estadística y los desafíos que plantean el uso de big data, la explosión del uso masivo de datos en la sociedad y la emergencia de la ciencia de los datos. Se centra en Fathom, TinkerPlots y Codap, que se analizan desde la perspectiva de los requisitos que deben cumplir las herramientas para la educación estadística. Se informa de experiencias realizadas con éxito y condiciones de uso de estas herramientas en varios contextos educativos, tanto en educación primaria como secundaria y la formación inicial y en servicio de los profesores. Los nuevos desafíos que plantea la ciencia de los datos requieren nuevas herramientas para la educación con nuevas características. El artículo termina con algunas ideas y experiencias de un proyecto reciente sobre educación en ciencia de los datos en el nivel de bachillerato

Zika virus preferentially replicates in the female reproductive tract after vaginal inoculation of rhesus macaques.

Zika virus (ZIKV) is a mosquito-transmitted virus that can cause severe defects in an infected fetus. ZIKV is also transmitted by sexual contact, although the relative importance of sexual transmission is unclear. To better understand the role of sexual transmission in ZIKV pathogenesis, a nonhuman primate (NHP) model of vaginal transmission was developed. ZIKV was readily transmitted to mature cycling female rhesus macaque (RM) by vaginal inoculation with 104-106 plaque-forming units (PFU). However, there was variability in susceptibility between the individual RM with 1-&gt;8 vaginal inoculations required to establish infection. After treatment with Depoprovera, a widely used contraceptive progestin, two RM that initially resisted 8 vaginal ZIKV inoculations became infected after one ZIKV inoculation. Thus, Depoprovera seemed to enhance susceptibility to vaginal ZIKV transmission. Unexpectedly, the kinetics of virus replication and dissemination after intravaginal ZIKV inoculation were markedly different from RM infected with ZIKV by subcutaneous (SQ) virus inoculation. Several groups have reported that after SQ ZIKV inoculation vRNA is rapidly detected in blood plasma with vRNA less common in urine and saliva and only rarely detected in female reproductive tract (FRT) secretions. In contrast, in vaginally inoculated RM, plasma vRNA is delayed for several days and ZIKV replication in, and vRNA shedding from, the FRT was found in all 6 animals. Further, after intravaginal transmission ZIKV RNA shedding from FRT secretions was detected before or simultaneously with plasma vRNA, and persisted for at least as long. Thus, ZIKV replication in the FRT was independent of, and often preceded virus replication in the tissues contributing to plasma vRNA. These results support the conclusion that ZIKV preferentially replicates in the FRT after vaginal transmission, but not after SQ transmission, and raise the possibility that there is enhanced fetal infection and pathology after vaginal ZIKV transmission compared to a mosquito transmitted ZIKV

RGtk2: A Graphical User Interface Toolkit for R

Graphical user interfaces (GUIs) are growing in popularity as a complement or alternative to the traditional command line interfaces to R. RGtk2 is an R package for creating GUIs in R. The package provides programmatic access to GTK+ 2.0, an open-source GUI toolkit written in C. To construct a GUI, the R programmer calls RGtk2 functions that map to functions in the underlying GTK+ library. This paper introduces the basic concepts underlying GTK+ and explains how to use RGtk2 to construct GUIs from R. The tutorial is based on simple and pratical programming examples. We also provide more complex examples illustrating the advanced features of the package. The design of the RGtk2 API and the low-level interface from R to GTK+ are discussed at length. We compare RGtk2 to alternative GUI toolkits for R.

RGtk2: A Graphical User Interface Toolkit for R

Graphical user interfaces (GUIs) are growing in popularity as a complement or alternative to the traditional command line interfaces to R. RGtk2 is an R package for creating GUIs in R. The package provides programmatic access to GTK+ 2.0, an open-source GUI toolkit written in C. To construct a GUI, the R programmer calls RGtk2 functions that map to functions in the underlying GTK+ library. This paper introduces the basic concepts underlying GTK+ and explains how to use RGtk2 to construct GUIs from R. The tutorial is based on simple and pratical programming examples. We also provide more complex examples illustrating the advanced features of the package. The design of the RGtk2 API and the low-level interface from R to GTK+ are discussed at length. We compare RGtk2 to alternative GUI toolkits for R

Determining the Relationship Between Mean Paraspinal Muscle Area Ratios and Percent Inter-Vertebral Foraminal Area Change in Flexion Versus Extension Positions of Military Working Dogs Using Computed Tomography

Core (paraspinal) muscle strengthening exercises are increasingly applied as methods for management of lower back pain in military working dogs. However, more evidence-based studies are needed to justify these methods. A previous publication correlated increased flexion/extension changes in lumbosacral intervertebral foraminal area (positional foraminal stenosis) with lower back pain in dogs. Aims of this thesis project were to test hypotheses that 1) lumbosacral paraspinal muscle areas will be associated with positional changes in inter-vertebral foraminal areas, 2) muscle areas will significantly differ by positioning, and 3) lumbosacral angles and range of motion values will significantly differ by measurement technique. A retrospective cross-sectional study was conducted using archived computed tomography (CT) scans of the lumbosacral region in 39 military working Labrador Retrievers. Scans had been acquired for another research project, using standardized flexion and extension positioning. For the current study, CT scans were retrieved and a single observer performed triplicate measurements of transverse sectional areas for the vertebral body and each paraspinal muscle at three vertebral locations, for both right and left sides, and for both flexion and extension positions. Vertebral body areas were used for calculation of muscle area ratios. The same observer also measured intervertebral foraminal areas for both sides and both positions at each vertebral location, using 2 previously published techniques. A second observer recorded lumbosacral angles in both positions using 2 previously published techniques. In consultation with a statistician, mean values for each variable were calculated and compared. Very weak associations were found for mean muscle area ratios and absolute intervertebral foraminal area percent change. Significant differences were identified between flexion/extension positions for all mean muscle area ratios. Significant differences between technique 1 and technique 2 were found in both flexion and extension for mean lumbosacral angles. Mean values for lumbosacral range of motion did not significantly differ by measurement technique. These findings indicated that core muscle strengthening exercises may not be the most effective way of managing dogs with positional foraminal stenosis. Findings also indicated that patient positioning and lumbosacral angle measurement techniques should be standardized for future studies when determining the effectiveness of exercise prescriptions