Kronos: a workflow assembler for genome analytics and informatics.

BackgroundThe field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.ResultsWe present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows.ConclusionsThe Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos

Immediate and delayed hypersensitivity reactions to a single dose of oxaliplatin

Hypersensitivity reaction (HSR), occurring during or immediately after oxaliplatin infusions are well documented and occur more commonly after multiple courses of therapy.A 69-year-old white woman with Stage Ill colon cancer commenced adjuvant chemotherapy with oxaliplatin and capecitabine. Ten minutes after the completion of the oxaliplatin infusion she experienced a severe hypersensitivity reaction. Symptoms resolved after treatment With corticosteroids, antihistamines, and bronchodilators. Nineteen hours later, a similar reaction Occurred.A review of the literature found 2 similar cases of delayed reactions to oxaliplatin occurring 20 and 10 hours after infusion, respectively. The first case occurred after the initial dose and again with cycle 2. The second case happened after the sixth infusion.This is the first reported case, to our knowledge, of immediate and delayed hypersensitivity reactions occurring after the initial dose of oxaliplatin

Research on mechanisms of alloy strengthening. Part 1 - Strengthening through fine particle dispersion. Part 2 - Control of structure and properties by means of rapid quenching of liquid metals /splat cooling/ Semiannual report

Alloy strengthening mechanisms - strengthening by fine particle dispersion, and structure and properties control by rapid quenching or splat cooling of liquid metal

The assessment of usability of electronic shopping: A heuristic evaluation

Today there are thousands of electronic shops accessible via the Web. Some provide user-friendly features whilst others seem not to consider usability factors at all. Yet, it is critical that the electronic shopping interface is user-friendly so as to help users to obtain their desired results. This study applied heuristic evaluation to examine the usability of current electronic shopping. In particular, it focused on four UK-based supermarkets offering electronic services: including ASDA, Iceland, Sainsbury, and Tesco. The evaluation consists of two stages: a free-flow inspection and a task-based inspection. The results indicate that the most significant and common usability problems have been found to lie within the areas of ‘User Control and Freedom’ and ‘Help and Documentation’. The findings of this study are applied to develop a set of usability guidelines to support the future design of effective interfaces for electronic shopping

Inverse problem of photoelastic fringe mapping using neural networks

This paper presents an enhanced technique for inverse analysis of photoelastic fringes using neural networks to determine the applied load. The technique may be useful in whole-field analysis of photoelastic images obtained due to external loading, which may find application in a variety of specialized areas including robotics and biomedical engineering. The presented technique is easy to implement, does not require much computation and can cope well within slight experimental variations. The technique requires image acquisition, filtering and data extraction, which is then fed to the neural network to provide load as output. This technique can be efficiently implemented for determining the applied load in applications where repeated loading is one of the main considerations. The results presented in this paper demonstrate the novelty of this technique to solve the inverse problem from direct image data. It has been shown that the presented technique offers better result for the inverse photoelastic problems than previously published works

Long-Term Stability of an Area-Reversible Atom-Interferometer Sagnac Gyroscope

We report on a study of the long-term stability and absolute accuracy of an atom interferometer gyroscope. This study included the implementation of an electro-optical technique to reverse the vector area of the interferometer for reduced systematics and a careful study of systematic phase shifts. Our data strongly suggests that drifts less than 96 $\mu$deg/hr are possible after empirically removing shifts due to measured changes in temperature, laser intensity, and several other experimental parameters.Comment: 4 pages, 4 figures, submitted to PR

Neighbourhood, Route and Workplace-Related Environmental Characteristics Predict Adults' Mode of Travel to Work

Commuting provides opportunities for regular physical activity which can reduce the risk of chronic disease. Commuters' mode of travel may be shaped by their environment, but understanding of which specific environmental characteristics are most important and might form targets for intervention is limited. This study investigated associations between mode choice and a range of objectively assessed environmental characteristics.Participants in the Commuting and Health in Cambridge study reported where they lived and worked, their usual mode of travel to work and a variety of socio-demographic characteristics. Using geographic information system (GIS) software, 30 exposure variables were produced capturing characteristics of areas around participants' homes and workplaces and their shortest modelled routes to work. Associations between usual mode of travel to work and personal and environmental characteristics were investigated using multinomial logistic regression.Of the 1124 respondents, 50% reported cycling or walking as their usual mode of travel to work. In adjusted analyses, home-work distance was strongly associated with mode choice, particularly for walking. Lower odds of walking or cycling rather than driving were associated with a less frequent bus service (highest versus lowest tertile: walking OR 0.61 [95% CI 0.20–1.85]; cycling OR 0.43 [95% CI 0.23–0.83]), low street connectivity (OR 0.22, [0.07–0.67]; OR 0.48 [0.26–0.90]) and free car parking at work (OR 0.24 [0.10–0.59]; OR 0.55 [0.32–0.95]). Participants were less likely to cycle if they had access to fewer destinations (leisure facilities, shops and schools) close to work (OR 0.36 [0.21–0.62]) and a railway station further from home (OR 0.53 [0.30–0.93]). Covariates strongly predicted travel mode (pseudo r-squared 0.74).Potentially modifiable environmental characteristics, including workplace car parking, street connectivity and access to public transport, are associated with travel mode choice, and could be addressed as part of transport policy and infrastructural interventions to promote active commuting

Control of human endometrial stromal cell motility by PDGF-BB, HB-EGF and trophoblast-secreted factors

Human implantation involves extensive tissue remodeling at the fetal-maternal interface. It is becoming increasingly evident that not only trophoblast, but also decidualizing endometrial stromal cells are inherently motile and invasive, and likely contribute to the highly dynamic processes at the implantation site. The present study was undertaken to further characterize the mechanisms involved in the regulation of endometrial stromal cell motility and to identify trophoblast-derived factors that modulate migration. Among local growth factors known to be present at the time of implantation, heparin-binding epidermal growth factor-like growth factor (HB-EGF) triggered chemotaxis (directed locomotion), whereas platelet-derived growth factor (PDGF)-BB elicited both chemotaxis and chemokinesis (non-directed locomotion) of endometrial stromal cells. Supernatants of the trophoblast cell line AC-1M88 and of first trimester villous explant cultures stimulated chemotaxis but not chemokinesis. Proteome profiling for cytokines and angiogenesis factors revealed neither PDGF-BB nor HB-EGF in conditioned media from trophoblast cells or villous explants, while placental growth factor, vascular endothelial growth factor and PDGF-AA were identified as prominent secretory products. Among these, only PDGF-AA triggered endometrial stromal cell chemotaxis. Neutralization of PDGF-AA in trophoblast conditioned media, however, did not diminish chemoattractant activity, suggesting the presence of additional trophoblast-derived chemotactic factors. Pathway inhibitor studies revealed ERK1/2, PI3 kinase/Akt and p38 signaling as relevant for chemotactic motility, whereas chemokinesis depended primarily on PI3 kinase/Akt activation. Both chemotaxis and chemokinesis were stimulated upon inhibition of Rho-associated, coiled-coil containing protein kinase. The chemotactic response to trophoblast secretions was not blunted by inhibition of isolated signaling cascades, indicating activation of overlapping pathways in trophoblast-endometrial communication. In conclusion, trophoblast signals attract endometrial stromal cells, while PDGF-BB and HB-EGF, although not identified as trophoblast-derived, are local growth factors that may serve to fine-tune directed and non-directed migration at the implantation site