Barcoding of the cytochrome oxidase I (COI) indicates a recent introduction of Ciona savignyi into New Zealand and provides a rapid method for Ciona species discrimination

Mitochondrial cytochrome oxidase I (COI) gene sequencing (DNA barcoding) of Ciona specimens from New Zealand (NZ) led to the first record of the solitary ascidian Ciona savignyi in the Southern Hemisphere. We sought to quantify C. savignyi COI genetic diversity around the NZ archipelago and to compare this with diversity within C. savignyi's native range in the north-west Pacific. Ciona savignyi specimens were collected from two NZ sites and from three sites around Japan. COI sequences (595 bp) were amplified and measures of genetic diversity were calculated. Based on differences between their COI sequences we developed a PCR-based assay to distinguish C. savignyi from the morphologically similar C. intestinalis. A total of 12 C. savignyi COI haplotypes were recovered from the 76 samples. Of the four haplotypes observed in NZ, two were unique. From the 10 haplotypes observed in the Japan samples, eight were unique. The C. savignyi populations in Japan were found to contain higher haplotype diversity when compared with those in NZ. The NZ samples contained only a small subset of the haplotype variation of the Japan samples, however, NZ samples did harbor two haplotypes not observed in the Japan samples. A PCR-based assay developed from the COI sequences was able to reliably discriminate the two Ciona species. The low COI genetic diversity within the two NZ C. savignyi populations sampled is consistent with a founder effect associated loss of genetic diversity. The robust PCR-based assay for distinguishing C. savignyi and C. intestinalis may find application in ecological and taxonomic studies and can be applied to both archival materials and live animals

Skip-Thought Vectors

We describe an approach for unsupervised learning of a generic, distributed sentence encoder. Using the continuity of text from books, we train an encoder-decoder model that tries to reconstruct the surrounding sentences of an encoded passage. Sentences that share semantic and syntactic properties are thus mapped to similar vector representations. We next introduce a simple vocabulary expansion method to encode words that were not seen as part of training, allowing us to expand our vocabulary to a million words. After training our model, we extract and evaluate our vectors with linear models on 8 tasks: semantic relatedness, paraphrase detection, image-sentence ranking, question-type classification and 4 benchmark sentiment and subjectivity datasets. The end result is an off-the-shelf encoder that can produce highly generic sentence representations that are robust and perform well in practice. We will make our encoder publicly available.Comment: 11 page

Introducing random walk measures to space syntax

We introduce Random Walk Closeness (RWC) to the space syntax computational paradigm. Random walks are stochastic processes in which an unbiased walker traverses a network purely based on his current location. Random walks have been used by space syntax in an agent based scenario, where results are simulation based. Here, the results are mathematical based, i.e. RWC is derived from access times, which are the average number of steps it takes to walk between locations. Results suggest an improvement in correlating pedestrian movement over Integration, RA and network Closeness

Adherence to antiretroviral therapy in adolescents living with HIV: systematic review and meta-analysis

OBJECTIVE: Adolescent and young adult (AYA) populations (12–24 years) represent over 40% of new HIV infections globally. Adolescence is sometimes characterized by high-risk sexual behaviour and a lack of engagement with healthcare services that can affect adherence to antiretroviral therapy (ART). Despite adherence to ART being critical in controlling viral replication, maintaining health and reducing onward viral transmission, there are limited data on ART adherence amongst AYA globally. We undertook a systematic review and meta-analysis of published studies reporting adherence to ART for AYA living with HIV. DESIGN AND METHODS: Searches included Embase, Medline and PsychINFO databases up to 14 August 2013. Eligible studies defined adequate adherence as at least 85% on self-report or undetectable blood plasma virus levels. A random effects meta-analysis was performed and heterogeneity examined using meta-regression. RESULTS: We identified 50 eligible articles reporting data from 53 countries and 10 725 patients. Using a pooled analysis of all eligible studies, 62.3% [95% confidence interval (CI) 57.1–67.6; I(2) : 97.2%] of the AYA population were adherent to therapy. The lowest average ART adherence was in North America [53% (95% CI 46–59; I(2) : 91%)], Europe [62% (95% CI 51–73; I(2) : 97%)] and South America [63% (95% CI 47–77; I(2) : 85%] and, with higher levels in Africa [84% (95% CI 79–89; I(2) : 93%)] and Asia [84% (95% CI 77–91; I(2) : 0%]. CONCLUSION: Review of published literature from Africa and Asia indicate more than 70% of HIV-positive AYA populations receiving ART are adherent to therapy and lower rates of adherence were shown in Europe and North America at 50–60%. The global discrepancy is probably multifactorial reflecting differences between focused and generalised epidemics, access to healthcare and funding

Virus Sharing, Genetic Sequencing, and Global Health Security

The WHO’s Pandemic Influenza Preparedness (PIP) Framework was a milestone global agreement designed to promote the international sharing of biological samples to develop vaccines, while that ensuring poorer countries would have access to those vaccines. Since the PIP Framework was negotiated, scientists have developed the capacity to use genetic sequencing data (GSD) to develop synthetic viruses rapidly for product development of life-saving technologies in a time-sensitive global emergency—threatening to unravel the Framework. Access to GSD may also have major implications for biosecurity, biosafety, and intellectual property (IP). By rendering the physical transfer of viruses antiquated, GSD may also undermine the effectiveness of the PIP Framework itself, with disproportionate impacts on poorer countries. We examine the changes that need to be made to the PIP Framework to address the growing likelihood that GSD might be shared instead of physical virus samples. We also propose that the international community harness this opportunity to expand the scope of the PIP Framework beyond only influenza viruses with pandemic potential. In light of non-influenza pandemic threats such as the Middle East Respiratory Syndrome (MERS) and Ebola, we call for an international agreement on the sharing of the benefits of research – such as vaccines and treatments – for other infectious diseases to ensure not only a more secure and healthy world, but also a more just world, for humanity

Phase 2 of the Multiple Provider Employment Zones Qualitative Study, DWP Research Report 399

This report presents the findings of a qualitative study of the operation and impact of the Multiple Provider Employment Zone (MPEZ) initiatives that have operated in four cities (London, Birmingham, Liverpool and Glasgow) since 20041. The study builds on earlier work by Cambridge Policy Consultants (Hirst et al. 2006), which concentrated on issues related to the early establishment of the MPEZ initiative and the initial experiences of Providers, Jobcentre Plus districts and customers. The Phase 2 research took place approximately one year on from the Phase 1 study and focused on tracking developments in the operation of MPEZ as the initiative became more established. The study involved interviews with EZ Providers (managers and Advisers), Jobcentre Plus representatives (managers and Advisers) and customers (young people (aged 18-24) claiming Jobseeker’s Allowance (JSA), who would otherwise have returned to New Deal for Young People (NDYP)2, lone parents receiving Income Support and early entrants – see section 1.6 for full details). In order to gain a wider perspective, researchers also spoke to representatives of organisations that have employed MPEZ participants and a number of stakeholder organisations with a broad interest in local labour market policies and programmes in the MPEZ areas. In total, the research involved interviews or group discussions with over 300 individuals, providing a range and depth of qualitative information that allows a detailed picture to be established of the way that MPEZs developed between mid- 2005 and mid-2006, including the experiences of employers and the labour market destinations of MPEZ participants. A central issue addressed in the research and in this report is the ‘multiple’ element of the initiative and the value that is added through the existence of more than one Provider in each MPEZ area. Questions of allocation, choice, specialisation, competition and innovation are considered from the perspectives of Providers, Jobcentre Plus, customers, employers and stakeholders and the final sections present some conclusions and issues for consideration in relation to these topics

Bone mineral density optimisation in adults with perinatally acquired HIV infection in routine care

We report on BMD and factors associated with reductions in BMD for all adults with perinatally acquired HIV who attended a London clinic between May 2014 and October 2016. We observed a high prevalence of reductions in BMD and a higher than expected prevalence of factors associated with adverse bone health, namely vitamin D deficiency

Niche inheritance: a cooperative pathway to enhance cancer cell fitness though ecosystem engineering

Cancer cells can be described as an invasive species that is able to establish itself in a new environment. The concept of niche construction can be utilized to describe the process by which cancer cells terraform their environment, thereby engineering an ecosystem that promotes the genetic fitness of the species. Ecological dispersion theory can then be utilized to describe and model the steps and barriers involved in a successful diaspora as the cancer cells leave the original host organ and migrate to new host organs to successfully establish a new metastatic community. These ecological concepts can be further utilized to define new diagnostic and therapeutic areas for lethal cancers.Comment: 8 pages, 1 Table, 4 Figure