Hyperchaotic qualities of the ball motion in a ball milling device

Ball collisions in milling devices are governed by complex dynamics ruled by impredictable impulsive forces. In this paper, nonlinear dynamics techniques are employed to analyze the time series describing the trajectory of a milling ball in an empty container obtained from a numerical model. The attractor underlying the system dynamics was reconstructed by the time delay method. In order to characterize the system dynamics the calculation of the spectrum of Lyapunov exponents was performed. Six Lyapunov exponents, divided into two terns with opposite sign, were obtained. The detection of the positive tern demonstrates the occurrence of the hyperchaotic qualities of the ball motion. A fractal Lyapunov dimension, equal to 5.62, was also obtained confirming the strange features of the attractor

Onset of chaotic dynamics in a ball mill: attractors merging and crisis induced intermittency

In mechanical treatment carried out by ball milling, powder particles are subjected to repeated high-energy mechanical loads which induce heavy plastic deformations together with fracturing and cold-welding events. Owing to the continuous defect accumulation and interface renewal, both structural and chemical transformations occur. The nature and the rate of such transformations have been shown to depend on variables, such as impact velocity and collision frequency that depend, in turn, on the whole dynamics of the system. The characterization of the ball dynamics under different impact conditions is then to be considered a necessary step in order to gain a satisfactory control of the experimental set up. In this paper we investigate the motion of a ball in a milling device. Since the ball motion is governed by impulsive forces acting during each collision, no analytical expression for the complete ball trajectory can be obtained. In addition, mechanical systems exhibiting impacts are strongly nonlinear due to sudden changes of velocities at the instant of impact. Many different types of periodic and chaotic impact motions exist indeed even for simple systems with external periodic excitation forces. We present results of the analysis on the ball trajectory, obtained from a suitable numerical model, under growing degree of impact elasticity. A route to high dimensional chaos is obtained. Crisis and attractors merging are also found

Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data

Background: The genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays.|Results: We designed PCR primers to amplify specific probes (180-500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (similar to13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts.|Conclusions: This paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website

The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics

Jejunal gene expression patterns correlate with severity of systemic infection in chicken

<p>Abstract</p> <p>Background</p> <p>Not much is known about the effect of <it>Salmonella enteritidis</it> on changes in the developmental processes occurring in the intestine of young chicken. Therefore we investigated the correlation of intestinal gene expression patterns with the severity of systemic Salmonella infections.</p> <p>Methods</p> <p>The number of Salmonella colony forming units (CFUs) in the liver of infected chicken were plotted against the average intestinal expression profiles of previously identified gene expression clusters. The functional properties of all the genes taken together present in 3 clusters exhibiting positive correlation at early time-points were compared with the functional properties of the genes displaying antagonistic correlations in 1 cluster. The top 5 ranking functional groups were analysed in further detail.</p> <p>Results</p> <p>Three clusters showed gene expression profiles which were positively correlated with the severity of systemic disease as measured by the number of Salmonella colony forming units in the liver. In these clusters, genes involved in morphological processes were predominantly present. One cluster had a profile that was negatively correlated with the severity of systemic disease, as measured by numbers of CFUs in the liver. The genes in the latter cluster were mostly involved in cell turn-over and metabolism.</p> <p>Conclusions</p> <p>In the developing jejunum of young chicken, both stimulatory and inhibitory gene expression mechanisms are correlated with the severity of systemic Salmonella infections.</p