MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

The robustness of carbon fibre members bonded to aluminium connectors in aerial delivery systems

In this paper a framework for robust design solution of an adhesively bonded joint between a composite material and an aluminum connector is developed. To this end, an approach has been developed to automate the process of robust design by linking Ansys workbench and an in-house MATLAB code. The model employed in this study investigated the possibility of joining composite materials to aluminum components which is a problematic process in terms of preparation, implementation, etc. Before designing such a join, it is necessary to fully understand the behaviour of the proposed aluminum connector with the carbon fibre member. To achieve this, the investigation of the adhesive layer’s behaviour and the uncertainties involved in such structures was identified. The behaviour of the adhesive between the carbon fibre composite and the aluminum connector was modelled based on the assumption that this layer acts as a “spring system” within a “cohesive” zone. Initially, the properties of Permabond ET5428 BLACK adhesive were used for validating the finite element model using the obtained test data. A robust design method is then employed to identify the right adhesive for the joint which not only maximizes the debonding force and sliding distance but is also robust with respect to the variation in its mechanical properties. A wide range of adhesive properties have been employed and a robust design technique based on uncertainty analysis is proposed

The Convergence of Explanatory Coherence and the Story Model: A Case Study in Juror Decision

This paper presents an integration of two approaches to complex decision-making from very different traditions: from the psychology of jury decision, the Story Model, and from the philosophy of science, the Theory of Explanatory Coherence and its con^utational instantiation, ECHO . The subjects in Pennington & Hastie (1993) generated causal "stories" to represent the events related to a particular trial. These stories were modeled with ECHO , and ECH O reached the same verdicts as did the human subjects. The ECH O simulations were also linked to the trial testimony, which, despite the inconsistent nature of the testimony, actually increased the coherence of stories for two jurors with very different verdicts. Implication

Cyanobacterial endobionts within a major marine, planktonic, calcifier (Globigerina bulloides, Foraminifera) revealed by 16S rRNA metabarcoding

We investigated the possibility of bacterial symbiosis in Globigerina bulloides, a palaeoceanographically important, planktonic foraminifer. This marine protist is commonly used in micropalaeontological investigations of climatically sensitive subpolar and temperate water masses as well as wind-driven upwelling regions of the world's oceans. G. bulloides is unusual because it lacks the protist algal symbionts that are often found in other spinose species. In addition, it has a large offset in its stable carbon and oxygen isotopic compositions compared to other planktonic foraminifer species, and also that predicted from seawater equilibrium. This is suggestive of novel differences in ecology and life history of G. bulloides, making it a good candidate for investigating the potential for bacterial symbiosis as a contributory factor influencing shell calcification. Such information is essential to evaluate fully the potential response of G. bulloides to ocean acidification and climate change. To investigate possible ecological interactions between G. bulloides and marine bacteria, 18S rRNA gene sequencing, fluorescence microscopy, 16SrRNA gene metabarcoding and transmission electron microscopy (TEM) were performed on individual specimens ofG. bulloides(type IId) collected from two locations in the California Current. Intracellular DNA extracted from fiveG. bulloidesspecimens was subjected to 16S rRNA gene metabarcoding and, remarkably, 37–87 % of all 16S rRNA gene sequences recovered were assigned to operational taxonomic units (OTUs) from the picocyanobacterium Synechococcus. This finding was supported by TEM observations of intact Synechococcus cells in both the cytoplasm and vacuoles of G. bulloides. Their concentrations were up to 4 orders of magnitude greater inside the foraminifera than those reported for the California Current water column and approximately 5 % of the intracellular Synechococcus cells observed were undergoing cell division. This suggests that Synechococcus is an endobiont of G. bulloides type IId, which is the first report of a bacterial endobiont in the planktonic foraminifera. We consider the potential roles of Synechococcus and G. bulloides within the relationship and the need to determine how widespread the association is within the widely distributed G. bulloides morphospecies. The possible influence of Synechococcus respiration on G. bulloides shell geochemistry is also explored

CAN System and Car Hacking

The CAN (Controller Area Network) bus is a communication network that is found in every car manufactured since 1986. It allows the internal components of the car, known as Electronic Control Units (ECUs), to communicate with each other. The CAN bus consists of two wires only, high and low, and modern vehicles can contain more than 100 ECUs. Our goal is to find vulnerabilities in a parking assist ECU we obtained from Bosch and exploit them to make the ECU exhibit unintended behavior. In order to do this, first we needed to understand CAN system protocols. Then, we needed to figure out how to send and receive CAN messages from the ECU. This required the use of both hardware and software to identify how the ECU interacts with the CAN system. Currently, we are communicating with the ECU to try to find unintended behavior. In 2016, Charlie Miller and Chris Valasek managed to remotely hack into a 2014 Jeep Cherokee. They performed this through telnetting into the car’s entertainment system. Using this connection, they flashed an update to the car’s operating system, giving them access to the CAN bus. This allowed them to directly send messages and control the car, leading to a recall of over 1.4 million vehicles by Chrysler. Today, cars have a larger attack surface with more electronics that can be exploited. If an attacker were to gain control over a parking assist unit, they could potentially steer the car, operate the brakes, and change the speed, presenting a serious threat to safety. That is why we have undertaken this project, to uncover any vulnerabilities and address the risks they pose

Does the impact of osteoarthritis vary by age, gender and social deprivation? A community study using the International Classification of Functioning, Disability and Health

The aim of the study was to explore if the impact of osteoarthritis varies with respect to age, gender and social deprivation. Impact was defined as impairment, activity limitations and participation restriction (International Classification of Functioning, Disability and Health (ICF)). Investigating the functioning of the ICF model for subgroups is important both practically and theoretically.  The sample comprised a community sample of 763 people diagnosed with osteoarthritis. Uncontaminated measures of the ICF constructs were developed using discriminant content validity from a pool of 134 items, including the WOMAC and SF-36. Multigroup Structural Equation Modelling was used to explore if the same pathways exist for subgroups of gender, age and social deprivation. Results: Different significant paths were found for gender and social deprivation: impairment did not predict participation restriction for women and those most deprived, whereas these paths were significant for men and those less deprived. No difference in the paths was found for age. The impact of osteoarthritis appears to vary with respect to gender and social deprivation but not age. This suggests both that osteoarthritis per se does not adequately explain the health outcomes observed and that different clinical approaches may be appropriate for people of different gender and levels of deprivation. Implications of Rehabilitation • The ICF model appears to vary with respect to gender and social deprivation for people with osteoarthritis. • The ICF model did not appear to vary with respect to age for people with osteoarthritis. • Different treatments and interventions for osteoarthritis may need to be targeted for specific gender and social deprivation groups

Linking the sectoral employment structure and household poverty in the United Kingdom

Structural changes in the labour markets of developed economies, and changes in their institutional characteristics, have led to growing unease about the nature of low-paid employment. Related concerns have been expressed about the persistence of low-pay, the fragmentation of work and the growth of under-employment. While all these factors have potential implications for individuals’ earnings, less is known about the connection between labour market change, patterns of sectoral growth and decline and household poverty outcomes. This article shows distinct patterns of poverty outcomes by sector of employment, after controlling for other factors. However, household characteristics, in particular the presence of a second earner, do strongly mitigate the poverty risk. Overall, the findings demonstrate that policymakers need to develop a coherent policy towards poverty that recognises the nature of jobs growth and the distribution of ‘good jobs’ across households

Modelling of Short-Term Interactions Between Concrete Support and the Excavated Damage Zone Around Galleries Drilled in Callovo–Oxfordian Claystone

peer reviewedProduction of energy from nuclear power plants generates high-level radioactive nuclear waste, harmful during dozens of thousand years. Deep geological disposal of nuclear waste represents the most reliable solutions for its safe isolation. Confinement of radioactive wastes relies on the multi-barrier concept in which isolation is provided by a series of engineered (canister, backfill) and natural (host rock) barriers. Few underground research laboratories have been built all over the world to test and validate storage solutions. The underground drilling process of disposal drifts may generate cracks, fractures/strain localisation in shear bands within the rock surrounding the gallery especially in argillaceous rocks. These degradations affect the hydro-mechanical properties of the material, such as permeability, e.g. creating a preferential flow path for radionuclide migration. Hydraulic conductivity increase within this zone must remain limited to preserve the natural barrier. In addition galleries are currently reinforced by different types of concrete supports such as shotcrete and/or prefab elements. Their purpose is twofold: avoiding partial collapse of the tunnel during drilling operations and limiting convergence of the surrounding rock. Properties of both concrete and rock mass are time dependent, due to shotcrete hydration and hydromechanical couplings within the host rock. By the use of a hydro-mechanical coupled Finite Element Code with a Second Gradient regularization, this paper aims at investigating and predicting support and rock interactions (convergence, stress field). The effect of shotcrete hydration evolution, spraying time and use of compressible wedges is studied in order to determine their relative influence

An active registry for bioinformatics web services

Summary: The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks

Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans

Background: Examples of heterozygote advantage in humans are scarce and limited to protein-coding sequences. Here, we attempt a genome-wide functional inference of advantageous heterozygosity at cis-regulatory regions. Results: The single-nucleotide polymorphisms bearing the signatures of balancing selection are enriched in active cis-regulatory regions of immune cells and epithelial cells, the latter of which provide barrier function and innate immunity. Examples associated with ancient trans-specific balancing selection are also discovered. Allelic imbalance in chromatin accessibility and divergence in transcription factor motif sequences indicate that these balanced polymorphisms cause distinct regulatory variation. However, a majority of these variants show no association with the expression level of the target gene. Instead, single-cell experimental data for gene expression and chromatin accessibility demonstrate that heterozygous sequences can lower cell-to-cell variability in proportion to selection strengths. This negative correlation is more pronounced for highly expressed genes and consistently observed when using different data and methods. Based on mathematical modeling, we hypothesize that extrinsic noise from fluctuations in transcription factor activity may be amplified in homozygotes, whereas it is buffered in heterozygotes. While high expression levels are coupled with intrinsic noise reduction, regulatory heterozygosity can contribute to the suppression of extrinsic noise. Conclusions: This mechanism may confer a selective advantage by increasing cell population homogeneity and thereby enhancing the collective action of the cells, especially of those involved in the defense systems in humansope