Enabling Proteomics: The Need for an Extendable ‘Workbench’ for User-Configurable Solutions

Proteomics has the capability to generate overwhelming quantities of data in relatively short timescales, and it is not uncommon to see experimenters investing substantially more time in data analysis than in data gathering. Although several sophisticated tools for data reduction and analysis are available, they lack the flexibility to cope with increasingly innovative experimental strategies and new database resources that encode both qualitative and quantitative data. I will outline a specification of a flexible proteomics tool that could address many current bottlenecks and deficiencies

Weak lensing predictions for coupled dark energy cosmologies at non-linear scales

We present non-linear weak lensing predictions for coupled dark energy models using the CoDECS simulations. We calculate the shear correlation function and error covariance expected for these models, for forthcoming ground-based (such as DES) and space-based (Euclid) weak lensing surveys. We obtain predictions for the discriminatory power of a ground-based survey similar to DES and a space-based survey such as Euclid in distinguishing between $\Lambda$CDM and coupled dark energy models; we show that using the non-linear lensing signal we could discriminate between $\Lambda$CDM and exponential constant coupling models with $\beta_0\geq0.1$ at $4\sigma$ confidence level with a DES-like survey, and $\beta_0\geq0.05$ at $5\sigma$ confidence level with Euclid. We also demonstrate that estimating the coupled dark energy models' non-linear power spectrum, using the $\Lambda$CDM Halofit fitting formula, results in biases in the shear correlation function that exceed the survey errors.Comment: 9 pages, 5 figures, v2: accepted for publication in MNRA

Medical Investigation and Documentation of Torture: A Handbook for Health Professionals

This Handbook is primarily aimed at raising awareness of relevant medical ethical, legal and professional standards of the many health professionals who would wish to do the most conscientious job, with a view to helping victims of torture and contributing to efforts to eliminate the practice. The key task is to establish the most scientifically valid documentation concerning possible torture of individuals, consistent with the often difficult conditions under which the work sometimes has to be undertaken. It is inspired by The Istanbul Protocol, approved by United Nations bodies, which lays down the best professional standards for physicians working in the field. Yet it recognises that not all health professionals called on to do the work will have extensive experience in this field and it presents the material in a way that aims to be accessible to all these professionals. Guidance is given in the general skills of interviewing, as well as the medical examination and documentation. In addition to the relevant ethical and legal principles, the Handbook also points to sources of advice for those who wish to further their knowledge or gain support and advice on particular situations

Trends in drop out, drug free discharge and rates of re-presentation: a retrospective cohort study of drug treatment clients in the North West of England

Background: Governments aim to increase treatment participation by problematic drug users. In the UK this has been achieved by fiscal investment, an expanded workforce, reduced waiting times and coercive measures (usually criminal justice (CJ) led). No assessment of these measures on treatment outcomes has been made. Using established monitoring systems we assessed trends in 'dropped out' and 'discharged drug free' (DDF), since the launch of the national drug strategy, and rates of treatment re-presentation for these cohorts. Methods: A longitudinal dataset of drug users (1997 to 2004/05, n = 26,415) was used to identify people who dropped out of, and were DDF from, services for years 1998 to 2001/02, and representations of these people in years to 2004/05. Trends in drop out and DDF, baseline comparisons of those DDF and those who dropped out and outcome comparisons for those referred from the CJ system versus other routes of referral were examined using chi square. Logistic regression analyses identified variables predicting drop out versus DDF and subsequent representation versus no re-presentation. Results: The proportion of individuals dropping out has increased from 7.2% in 1998 to 9.6% in 2001/02 (P < 0.001). The proportion DDF has fallen from 5.8% to 3.5% (P < 0.001). Drop out was more likely in later years, by those of younger age and by CJ referrals. The proportion re-presenting to treatment in the following year increased from 27.8% in 1998 to 44.5% in 2001/02 (P < 0.001) for those DDF, and from 22.9% to 48.6% (P < 0.001) for those who dropped out. Older age and prior treatment experience predicted re-presentation. Outcome (drop out or DDF) did not predict re-presentation. Conclusion: Increasing numbers in treatment is associated with an increased proportion dropping out and an ever-smaller proportion DDF. Rates of drop out are significantly higher for those coerced into treatment via the CJ system. Rates of re-presentation are similar for those dropping out and those DDF. Encouragingly, those who need to re-engage with treatment, particularly those who drop out, are doing so more quickly. The impact of coercion on treatment outcomes and the appropriateness of aftercare provision require further consideration

Making progress in genetic kin recognition among vertebrates

A recent study in BMC Evolutionary Biology has shown that genetically similar individual ring-tailed lemurs are also more similar in their scent composition, suggesting a possible mechanism of kin recognition. Theoretical and experimental studies reveal challenges ahead in achieving a true systems-level understanding of this process and its outcomes

Innovation performance and the role of clustering at the local enterprise level: a fuzzy-set qualitative comparative analysis approach

This study, utilizes an innovative methodological approach, fuzzy-set Qualitative Comparative Analysis (fsQCA), investigating the drivers of heterogeneous geographies characterizing English Local Economic Partnerships (LEPs). The fsQCA technique offers a novel configurational alternative to regression-based approaches investigating the effects of clustering in conjunction with firm-level innovation, university third-sector activity (TSA) and entrepreneurship, on LEPs innovation performance. The findings, offer contributions to the theories of industrial clusters and innovation, regional innovation systems, knowledge spillovers and entrepreneurial university innovation within LEPs. First, supporting fsQCAs, no individual variable generates either a positive/negative innovation outcome. Second, while all positive innovation recipes include presence of the cluster variable, for negative innovation recipes, only one does not identify absence of clustering as relevant. Given that the cluster variable does not appear in any recipes without at least one of the other variables suggests activity concentration does not exist in isolation to generate innovation outcomes without other localized conditions existing, e.g. firm-level innovation. Third, there is evidence for the non-cluster-based aspects of knowledge spillover theory of entrepreneurship with respect to university activity and the entrepreneurial university concept. Instead, roles of entrepreneurship and university TSA, while important, appear to be more peripheral and geographically context specific

Characterisation of a novel reverse-biased PPD CMOS image sensor

A new pinned photodiode (PPD) CMOS image sensor (CIS) has been developed and characterised. The sensor can be fully depleted by means of reverse bias applied to the substrate, and the principle of operation is applicable to very thick sensitive volumes. Additional n-type implants under the pixel p-wells, called Deep Depletion Extension (DDE), have been added in order to eliminate the large parasitic substrate current that would otherwise be present in a normal device. The first prototype has been manufactured on a 18 μm thick, 1000 Ω .cm epitaxial silicon wafers using 180 nm PPD image sensor process at TowerJazz Semiconductor. The chip contains arrays of 10 μm and 5.4 μm pixels, with variations of the shape, size and the depth of the DDE implant. Back-side illuminated (BSI) devices were manufactured in collaboration with Teledyne e2v, and characterised together with the front-side illuminated (FSI) variants. The presented results show that the devices could be reverse-biased without parasitic leakage currents, in good agreement with simulations. The new 10 μm pixels in both BSI and FSI variants exhibit nearly identical photo response to the reference non-modified pixels, as characterised with the photon transfer curve. Different techniques were used to measure the depletion depth in FSI and BSI chips, and the results are consistent with the expected full depletion

Exploring 1st- and 2nd-year chiropractic students' willingness and attitudes toward peer physical examination

Objective This study aimed to explore chiropractic students' perceptions and attitudes about the appropriateness of peer physical examination as a teaching tool and their willingness and comfort with it. Methods A modified version of a validated questionnaire was used. First- and 2nd-year chiropractic students at Murdoch University were approached during their practical sessions. The responses were analyzed using descriptive statistics reporting frequencies and percentages. Comparison between classes, age, and sex was evaluated by cross-tabulation. Results A total of 184 questionnaires were completed with a response rate of 76.6%. Our results demonstrated that most students were comfortable with and willing to participate in peer physical examination as well as trusted it as an appropriate part of their training and a valuable learning experience. Nevertheless, a small percentage were uncomfortable with peer physical examination and regarded it as an unprofessional activity. In addition, it was revealed that younger females (≤20 years) reported feeling unnecessarily exposed and therefore significantly less comfortable with peer physical examination. They were also less comfortable when examined in the inguinal area by a student of the opposite sex. Conclusion Although peer physical examination appears to be a very popular training tool, it still has a few areas of concern that need to be investigated and addressed to improve students' attitude, perception, and comfort with this teaching technique. Further studies could investigate how other factors such as religious beliefs contribute toward students' perception and attitudes regarding peer physical examination

Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic’ strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host–microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches