Software Metrics and Dashboard

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process. Our aim is to develop and evaluate a metrics dashboard to support Computational Science and Engineering (CSE) software development projects. This task requires us to perform the following activities: Assess how metrics are used and which general classes/types of metrics will be useful in CSE projects. Develop a metrics dashboard that will work for teams using sites like Github, Bitbucket etc. Assess the effectiveness of the dashboard in terms of project success and developer attitude towards metrics and process. Our current focus is on identifying requirements for the metrics dashboard which include the types of metrics that will help understand and improve the software quality. We have also started the development on the metrics dashboard based on the currently identified metrics types. We plan to provide a reliable metrics dashboard which could be used by the CSE development teams to improve their software quality, this will be done by instrumenting the metrics dashboard to gather usage statistics. In this way the dashboard evolves continuously

Towards Sustainable Digital Humanities Software

Our work in software quality for digital humanities was borne of an effort to address sustainable practices in scientific software development, where the speaker (Thiruvathukal) co-authored a position paper on the case for software engineering in scientific software development as part of an all-encompassing strategy to create more sustainable scientific software (an example of a well-known scientific software package is LINPACK). In this position paper, we addressed how “progress in scientific research is dependent on the quality and accessibility of software at all levels . This progress depends on embracing the best traditional--and emergent--practices in software engineering, especially agile practices that intersect with the more formal tradition of software engineering. Although this paper was about scientific software development, it could just as easily have been about any interdisciplinary software development community. Our interest in applying what we’ve learned to DH, however, comes from work Thiruvathukal and Hayward have done and/or supervised in DH, especially WoolfOnline and a Richmond Times Dispatch viewer, where more software engineering could have been helpful

Oral human papillomavirus infection in England and associated risk factors: a case control study.

Objectives - This study was conducted to determine the prevalence of and associated risk factors for infection with oral high-risk human papillomavirus (HR-HPV) in adult participants within England, and to explore any association with oral mucosal buccal epithelial cell and whole blood folate concentration. Design - This was an observational study to determine oral HR-HPV prevalence in the study population. A case-control study was performed to explore the association between infection and folate status. Setting - This study was conducted in Sheffield, United Kingdom between April 2013 and August 2014. Participants - Seven hundred participants, aged 18-60 yr, were recruited from university students (n=179), university and hospital staff (n=163), dental hospital patients (n=13), Sexual Health Sheffield patients (n=122) and the general public (n=223). Interventions - Participants completed a lifestyle and sexual behaviour questionnaire, provided an oral rinse and gargle sample for the detection of oral HR-HPV and an oral mucosal buccal epithelial cell sample for the measurement of oral mucosal buccal epithelial cell folate. A blood sample was collected for measurement of whole blood folate concentration. Outcome measures - The prevalence of oral HR-HPV infection in the study population was the primary outcome measure. Secondary outcome measures included associations between risk factors, folate status and infection. Results - The prevalence of oral HR-HPV infection in this cohort was 2.2% (15/680) with 0.7% (5/680) positive for HPV16 or HPV18. Twenty samples were excluded due to insufficient material for HPV detection. Participants with oral HR-HPV infection were more likely to be a former smoker, and have a greater number of sexual and oral sexual partners. Folate status was not linked to likelihood of HPV infection. Conclusions - The prevalence of oral infection with HR-HPV in adult men and women in Sheffield in the north of England was low. Smoking and sexual behaviour were associated with HR-HPV positivity

Individual differences in search and monitoring for color targets in dynamic visual displays

Many jobs now involve the monitoring visual representations of data that change over time. Monitoring dynamically changing displays for the onset of targets can be done in two ways: detecting targets directly post their onset or predicting their onset from the prior state of distractors. In the present study, participants? eye movements were measured as they monitored arrays of 108 colored squares whose colors changed systematically over time. Across three experiments, the data show that participants detected the onset of targets both directly and predictively. Experiments 1 and 2 showed that predictive detection was only possible when supported by sequential color changes that followed a scale ordered in color space. Experiment 3 included measures of individual differences in working memory capacity (WMC) and anxious affect and a manipulation of target prevalence in the search task. It found that predictive monitoring for targets, and decisions about target onsets, were influenced by interactions between individual differences in verbal and spatial WMC and intolerance of uncertainty, a characteristic that reflects worry about uncertain future events. The results have implications for the selection of individuals tasked with monitoring dynamic visual displays for target onsets

Cinnamon Shows Antidiabetic Properties that Are Species-Specific : Effects on Enzyme Activity Inhibition and Starch Digestion

The study was funded by the Rural and Environment Science and Analytical Services Division of the Scottish government (RESAS). The authors are grateful to Phyllis Nicol for assisting with AGE measurements.Peer reviewedPublisher PD

Correlating tephras and cryptotephras using glass compositional analyses and numerical and statistical methods:Review and evaluation

We define tephras and cryptotephras and their components (mainly ash-sized particles of glass ± crystals in distal deposits) and summarize the basis of tephrochronology as a chronostratigraphic correlational and dating tool for palaeoenvironmental, geological, and archaeological research. We then document and appraise recent advances in analytical methods used to determine the major, minor, and trace elements of individual glass shards from tephra or cryptotephra deposits to aid their correlation and application. Protocols developed recently for the electron probe microanalysis of major elements in individual glass shards help to improve data quality and standardize reporting procedures. A narrow electron beam (diameter ~3-5 μm) can now be used to analyze smaller glass shards than previously attainable. Reliable analyses of ‘microshards’ (defined here as glass shards <32 µm in diameter) using narrow beams are useful for fine-grained samples from distal or ultra-distal geographic locations, and for vesicular or microlite-rich glass shards or small melt inclusions. Caveats apply, however, in the microprobe analysis of very small microshards (<=~5 µm in diameter), where particle geometry becomes important, and of microlite-rich glass shards where the potential problem of secondary fluorescence across phase boundaries needs to be recognised. Trace element analyses of individual glass shards using laser ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS), with crater diameters of 20 μm and 10 μm, are now effectively routine, giving detection limits well below 1 ppm. Smaller ablation craters (<10 μm) can be subject to significant element fractionation during analysis, but the systematic relationship of such fractionation with glass composition suggests that analyses for some elements at these resolutions may be quantifiable. In undertaking analyses, either by microprobe or LA-ICP-MS, reference material data acquired using the same procedure, and preferably from the same analytical session, should be presented alongside new analytical data. In part 2 of the review, we describe, critically assess, and recommend ways in which tephras or cryptotephras can be correlated (in conjunction with other information) using numerical or statistical analyses of compositional data. Statistical methods provide a less subjective means of dealing with analytical data pertaining to tephra components (usually glass or crystals/phenocrysts) than heuristic alternatives. They enable a better understanding of relationships among the data from multiple viewpoints to be developed and help quantify the degree of uncertainty in establishing correlations. In common with other scientific hypothesis testing, it is easier to infer using such analysis that two or more tephras are different rather than the same. Adding stratigraphic, chronological, spatial, or palaeoenvironmental data (i.e. multiple criteria) is usually necessary and allows for more robust correlations to be made. A two-stage approach is useful, the first focussed on differences in the mean composition of samples, or their range, which can be visualised graphically via scatterplot matrices or bivariate plots coupled with the use of statistical tools such as distance measures, similarity coefficients, hierarchical cluster analysis (informed by distance measures or similarity or cophenetic coefficients), and principal components analysis (PCA). Some statistical methods (cluster analysis, discriminant analysis) are referred to as ‘machine learning’ in the computing literature. The second stage examines sample variance and the degree of compositional similarity so that sample equivalence or otherwise can be established on a statistical basis. This stage may involve discriminant function analysis (DFA), support vector machines (SVMs), canonical variates analysis (CVA), and ANOVA or MANOVA (or its two-sample special case, the Hotelling two-sample T² test). Randomization tests can be used where distributional assumptions such as multivariate normality underlying parametric tests are doubtful. Compositional data may be transformed and scaled before being subjected to multivariate statistical procedures including calculation of distance matrices, hierarchical cluster analysis, and PCA. Such transformations may make the assumption of multivariate normality more appropriate. A sequential procedure using Mahalanobis distance and the Hotelling two-sample T² test is illustrated using glass major element data from trachytic to phonolitic Kenyan tephras. All these methods require a broad range of high-quality compositional data which can be used to compare ‘unknowns’ with reference (training) sets that are sufficiently complete to account for all possible correlatives, including tephras with heterogeneous glasses that contain multiple compositional groups. Currently, incomplete databases are tending to limit correlation efficacy. The development of an open, online global database to facilitate progress towards integrated, high-quality tephrostratigraphic frameworks for different regions is encouraged

High Resolution mid-Infrared Imaging of SN 1987A

Using the Thermal-Region Camera and Spectrograph (T-ReCS) attached to the Gemini South 8m telescope, we have detected and resolved 10 micron emission at the position of the inner equatorial ring (ER) of supernova SN 1987A at day 6067. ``Hot spots'' similar to those found in the optical and near-IR are clearly present. The morphology of the 10 micron emission is globally similar to the morphology at other wavelengths from X-rays to radio. The observed mid-IR flux in the region of SN1987A is probably dominated by emission from dust in the ER. We have also detected the ER at 20 micron at a 4 sigma level. Assuming that thermal dust radiation is the origin of the mid-IR emission, we derive a dust temperature of 180^{+20}_{-10} K, and a dust mass of 1.- 8. 10^{-5} Mo for the ER. Our observations also show a weak detection of the central ejecta at 10 micron. We show that previous bolometric flux estimates (through day 2100) were not significantly contaminated by this newly discovered emission from the ER. If we assume that the energy input comes from radioactive decays only, our measurements together with the current theoretical models set a temperature of 90 leq T leq 100 K and a mass range of 10^{-4} - 2. 10^{-3} Mo for the dust in the ejecta. With such dust temperatures the estimated thermal emission is 9(+/-3) 10^{35} erg s^{-1} from the inner ring, and 1.5 (+/-0.5) 10^{36} erg s^{-1} from the ejecta. Finally, using SN 1987A as a template, we discuss the possible role of supernovae as major sources of dust in the Universe.Comment: aastex502, 14 pages, 4 figures; Accepted for publication in ApJ Content changed: new observations, Referee's comments and suggestion

SUMOylation of DISC1: a potential role in neural progenitor proliferation in the developing cortex

DISC1 is a multifunctional, intracellular scaffold protein. At the cellular level, DISC1 plays a pivotal role in neural progenitor proliferation, migration, and synaptic maturation. Perturbation of the biological pathways involving DISC1 is known to lead to behavioral changes in rodents, which supports a clinical report of a Scottish pedigree in which the majority of family members with disruption of the DISC1 gene manifest depression, schizophrenia, and related mental conditions. The discrepancy between modest evidence in genetics and strong biological support for the role of DISC1 in mental conditions suggests a working hypothesis that regulation of DISC1 at the protein level, such as posttranslational modification, may play a role in the pathology of mental conditions. In this study, we report on the SUMOylation of DISC1. This posttranslational modification occurs on lysine residues where the small ubiquitin-related modifier (SUMO) and its homologs are conjugated to a large number of cellular proteins, which in turn regulates their subcellular distribution and protein stability. By using in silico, biochemical, and cell-biological approaches, we now demonstrate that human DISC1 is SUMOylated at one specific lysine 643 (K643). We also show that this residue is crucial for proper neural progenitor proliferation in the developing cortex

Expression profiling identifies genes involved in emphysema severity

Chronic obstructive pulmonary disease (COPD) is a major public health problem. The aim of this study was to identify genes involved in emphysema severity in COPD patients

Spin-Charge Separation, Anomalous Scaling and the Coherence of Hopping in exactly solved Two Chain Models

The coherence of transport between two one-dimensional interacting Fermi liquids, coupled by single particle hopping and interchain interaction, is examined in the context of two exactly soluble models. It is found that the coherence of the inter-chain hopping depends on the interplay between inter-chain hopping and inter-chain interaction terms, and not simply on the ground state spectral properties of an isolated chain. Specifically, the splitting of levels in associated with interchain hopping in a $g_4$ soluble model is found to be enhanced by the introduction of interchain interaction. It is also shown that, for an exactly solvable model with both $g_2$ and $g_4$ interactions, coherent interchain hopping coexists with anomalous scaling and non-Fermi liquid behavior in the chain direction.Comment: Two postscript figure