Targeted Assembly of Short Sequence Reads

As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled strin-gently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming ge-nomic mutations, polymorphism, fusion and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly

Prediction of landing gear loads using machine learning techniques

This article investigates the feasibility of using machine learning algorithms to predict the loads experienced by a landing gear during landing. For this purpose, the results on drop test data and flight test data will be examined. This article will focus on the use of Gaussian process regression for the prediction of loads on the components of a landing gear. For the learning task, comprehensive measurement data from drop tests are available. These include measurements of strains at key locations, such as on the side-stay and torque link, as well as acceleration measurements of the drop carriage and the gear itself, measurements of shock absorber travel, tyre closure, shock absorber pressure and wheel speed. Ground-to-tyre loads are also available through measurements made with a drop test ground reaction platform. The aim is to train the Gaussian process to predict load at a particular location from other available measurements, such as accelerations, or measurements of the shock absorber. If models can be successfully trained, then future load patterns may be predicted using only these measurements. The ultimate aim is to produce an accurate model that can predict the load at a number of locations across the landing gear using measurements that are readily available or may be measured more easily than directly measuring strain on the gear itself (for example, these may be measurements already available on the aircraft, or from a small number of sensors attached to the gear). The drop test data models provide a positive feasibility test which is the basis for moving on to the critical task of prediction on flight test data. For this, a wide range of available flight test measurements are considered for potential model inputs (excluding strain measurements themselves), before attempting to refine the model or use a smaller number of measurements for the prediction

Double differentiation in a cross-national comparison of populist political movements and online media uses in the United States and the Netherlands

In a context of highly visible and politically influential populist movements, this study considers the online self-representation of the Tea Party Patriots (TPP) in the United States and the Party for Freedom (PVV) in the Netherlands. A multi-methodological approach was adopted to compare the discursive manifestation of key populism concepts: leadership characteristics, adversary definition and mobilizing information. Analyses reconstruct and account for similarities and differences in discursive framing strategies of 'double differentiation' through which both movements attempt inclusion in and exclusion from the political establishment, and, in doing so, mobilize communities of support. Altogether, this study advances the understanding of what constitutes 'unmediated' content that is presented through user-generated media production, and how self-determined media spaces have facilitated shifts in populist media legitimation and political representation in two politically unique countries

X Chromosome Inactivation and Differentiation Occur Readily in ES Cells Doubly-Deficient for MacroH2A1 and MacroH2A2

Macrohistones (mH2As) are unusual histone variants found exclusively in vertebrate chromatin. In mice, the H2afy gene encodes two splice variants, mH2A1.1 and mH2A1.2 and a second gene, H2afy2, encodes an additional mH2A2 protein. Both mH2A isoforms have been found enriched on the inactive X chromosome (Xi) in differentiated mammalian female cells, and are incorporated into the chromatin of developmentally-regulated genes. To investigate the functional significance of mH2A isoforms for X chromosome inactivation (XCI), we produced male and female embryonic stem cell (ESC) lines with stably-integrated shRNA constructs that simultaneously target both mH2A1 and mH2A2. Surprisingly, we find that female ESCs deficient for both mH2A1 and mH2A2 readily execute and maintain XCI upon differentiation. Furthermore, male and female mH2A-deficient ESCs proliferate normally under pluripotency culture conditions, and respond to several standard differentiation procedures efficiently. Our results show that XCI can readily proceed with substantially reduced total mH2A content

Introduction to Khovanov Homologies. I. Unreduced Jones superpolynomial

An elementary introduction to Khovanov construction of superpolynomials. Despite its technical complexity, this method remains the only source of a definition of superpolynomials from the first principles and therefore is important for development and testing of alternative approaches. In this first part of the review series we concentrate on the most transparent and unambiguous part of the story: the unreduced Jones superpolynomials in the fundamental representation and consider the 2-strand braids as the main example. Already for the 5_1 knot the unreduced superpolynomial contains more items than the ordinary Jones.Comment: 33 page

New uses of the Migraine Screen Questionnaire (MS-Q): validation in the Primary Care setting and ability to detect hidden migraine. MS-Q in Primary Care

<p>Abstract</p> <p>Background</p> <p>PC plays an important role in early diagnosis of health disorders, particularly migraine, due to the financial impact of this disease for the society and its impact on patients' quality of life. The aim of the study was to validate the self-administered MS-Q questionnaire for detection of hidden migraine in the field of primary care (PC), and to explore its use in this setting.</p> <p>Methods</p> <p>Cross-sectional, observational, and multicentre study in subjects above 18 years of age patients attending PC centers (regardless of the reason for consultation). A MS-Q score ≥ 4 was considered possible migraine. Level of agreement with IHS criteria clinical diagnosis (kappa coefficient), and instrument's validity properties: sensitivity, specificity, positive (PPV) and negative (NPV) predictive values were determined. The ability of the instrument to identify possible new cases of migraine was calculated, as well as the ratio of hidden disease compared to the ratio obtained by IHS criteria.</p> <p>Results</p> <p>A total of 9,670 patients were included [48.9 ± 17.2 years (mean ± SD); 61.9% women], from 410 PC centers representative of the whole national territory. The clinical prevalence of migraine according to the IHS criteria was 24.7%, and 20.4% according to MS-Q: Kappa index of agreement 0.82 (p < 0.05). MS-Q sensitivity was 0.82 (95% CI, 0.81 - 0.84), specificity 0.97 (95% CI, 0.98 - 0.99), PPV 0.95 (95% CI, 0.94 - 0.96), and NPV 0.94 (95% CI, 0.93 - 0.95). No statistically significant differences were found in the percentages of patients with <it>de novo </it>and hidden migraine identified by MS-Q and by IHS criteria: 5.7% vs. 6.1% and 26.6% vs. 24.1%, respectively.</p> <p>Conclusions</p> <p>The results of the present study confirm the usefulness of the MS-Q questionnaire for the early detection and assessment of migraine in PC settings, and its ability to detect hidden migraine.</p

A participatory physical and psychosocial intervention for balancing the demands and resources among industrial workers (PIPPI): study protocol of a cluster-randomized controlled trial

Background: Need for recovery and work ability are strongly associated with high employee turnover, well-being and sickness absence. However, scientific knowledge on effective interventions to improve work ability and decrease need for recovery is scarce. Thus, the present study aims to describe the background, design and protocol of a cluster randomized controlled trial evaluating the effectiveness of an intervention to reduce need for recovery and improve work ability among industrial workers. Methods/Design: A two-year cluster randomized controlled design will be utilized, in which controls will also receive the intervention in year two. More than 400 workers from three companies in Denmark will be aimed to be cluster randomized into intervention and control groups with at least 200 workers (at least 9 work teams) in each group. An organizational resources audit and subsequent action planning workshop will be carried out to map the existing resources and act upon initiatives not functioning as intended. Workshops will be conducted to train leaders and health and safety representatives in supporting and facilitating the intervention activities. Group and individual level participatory visual mapping sessions will be carried out allowing team members to discuss current physical and psychosocial work demands and resources, and develop action plans to minimize strain and if possible, optimize the resources. At all levels, the intervention will be integrated into the existing organization of work schedules. An extensive process and effect evaluation on need for recovery and work ability will be carried out via questionnaires, observations, interviews and organizational data assessed at several time points throughout the intervention period. Discussion: This study primarily aims to develop, implement and evaluate an intervention based on the abovementioned features which may improve the work environment, available resources and health of industrial workers, and hence their need for recovery and work ability

Design of Experiments for Screening

The aim of this paper is to review methods of designing screening experiments, ranging from designs originally developed for physical experiments to those especially tailored to experiments on numerical models. The strengths and weaknesses of the various designs for screening variables in numerical models are discussed. First, classes of factorial designs for experiments to estimate main effects and interactions through a linear statistical model are described, specifically regular and nonregular fractional factorial designs, supersaturated designs and systematic fractional replicate designs. Generic issues of aliasing, bias and cancellation of factorial effects are discussed. Second, group screening experiments are considered including factorial group screening and sequential bifurcation. Third, random sampling plans are discussed including Latin hypercube sampling and sampling plans to estimate elementary effects. Fourth, a variety of modelling methods commonly employed with screening designs are briefly described. Finally, a novel study demonstrates six screening methods on two frequently-used exemplars, and their performances are compared

Molecular diet analysis of two african free-tailed bats (molossidae) using high throughput sequencing.

Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5' tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated.This study was supported by Bat Conservation International, Etatsraad Georg Bestle og Hustrus Mindelegat and the Oticon Fonden (KB and CN), the Danish Council for Independent Research Natural Sciences ‘Skou’ award (MTPG), and a Natural Sciences and Engineering Research Council of Canada post-doctoral fellowship (ELC). These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This study was also supported by the Royal Swaziland Sugar Corporation, who provided field assistance and therefore had a role in data collection

A systems approach to policy evaluation

There is growing interest in evaluating policy implementation in ways that grapple with the complexity of the process. This article offers an example of using systems methodology to explore how the child protection policy in child contact centres has functioned in practice. Rather than just asking the traditional evaluation question “is it working?” this study sought to understand how the policy was working and how it was interpreted as it interacted with other systems, producing conflicts, local variation and emergent effects. It illustrates how the systems concepts of ‘emergence’, ‘local rationality’, ‘socio-technical systems’ and ‘feedback for learning’ can contribute new knowledge and understanding to a complex policy evaluation problem