Designing Primary Prevention for People Living with HIV

Today, there are new reasons for a sharper focus on prevention for people living with HIV. Growing numbers of people with the disease are living more healthy, sexual lives. Recent evidence suggests that risk taking among both HIV-positive and negative people is increasing. After nearly two decades of life in the shadow of AIDS, communities are growing weary of traditional prevention messages and many people are openly grappling with difficult questions of intimacy and sex. Increasingly, people living with HIV also face multiple complex economic and substance abuse challenges that complicate prevention efforts.There is an urgent need -- and sufficient expertise -- to move forward with prevention campaigns focused on helping people living with HIV and AIDS avoid passing their infection along to others. Numerous innovative interventions for people with HIV show promise, including:a social marketing campaign for gay men and a five-session group intervention for women living with HIV in Massachusetts,a chat line for positives and a group session program for Latinas/Latinos in Los Angeles,Internet chat room interventions in Atlanta,a group session for gay Asian American-Pacific Islander Americans living with HIV in San Francisco, andPrevention Case Management programs newly funded by the Centers for Disease Control

REAPR: a universal tool for genome assembly evaluation.

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/

Controls on the processing and fate of terrestrially-derived organic carbon in aquatic ecosystems: synthesis of special issue

This special issue brought together a complementary set of studies describing the range of processes affecting the cycling and fate of terrigenous organic matter within aquatic systems. It focuses in particular on headwater streams, and on peat catchments as major global sources of freshwater dissolved organic matter and of particulate organic matter in areas of peat erosion. This work is placed within the wider context of processes occurring in forested and agricultural headwaters, larger river systems and estuaries, and in a policy context in relation to national-scale carbon fluxes, the treatment of organic matter in drinking water supplies and the inclusion of aquatic carbon in international greenhouse gas accounting

A comprehensive evaluation of assembly scaffolding tools.

Background: Genome assembly is typically a two-stage process: contig assembly followed by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the focus of reported assembly statistics; longer scaffolds greatly facilitate the use of genome sequences in downstream analyses, and it is appealing to present larger numbers as metrics of assembly performance. However, scaffolds are highly prone to errors, especially when generated using short reads, which can directly result in inflated assembly statistics. Results: Here we provide the first independent evaluation of scaffolding tools for second-generation sequencing data. We find large variations in the quality of results depending on the tool and dataset used. Even extremely simple test cases of perfect input, constructed to elucidate the behaviour of each algorithm, produced some surprising results. We further dissect the performance of the scaffolders using real and simulated sequencing data derived from the genomes of Staphylococcus aureus, Rhodobacter sphaeroides, Plasmodium falciparum and Homo sapiens. The results from simulated data are of high quality, with several of the tools producing perfect output. However, at least 10% of joins remains unidentified when using real data. Conclusions: The scaffolders vary in their usability, speed and number of correct and missed joins made between contigs. Results from real data highlight opportunities for further improvements of the tools. Overall, SGA, SOPRA and SSPACE generally outperform the other tools on our datasets. However, the quality of the results is highly dependent on the read mapper and genome complexity

Non-native plants add to the British flora without negative consequences for native diversity

Plants are commonly listed as invasive species, presuming that they cause harm at both global and regional scales; ~40% of species listed as invasive within Britain are plants. Yet invasive plants are rarely linked to the national or global extinction of native plant species. The possible explanation is that competitive exclusion takes place slowly, and that invasive plants will eventually eliminate native species (the ‘time-to-exclusion hypothesis’). Using the extensive British Countryside Survey Data, we find that changes to plant occurrence and cover between 1990 and 2007 at 479 British sites do not differ between native and non-native plant species. Over 80% of the plant species that are widespread enough to be sampled are native species, and hence total cover changes have been dominated by native species (total cover increases by native species are over nine times greater than those by non-native species). This implies that factors other than plant ‘invasions’ are the key drivers of vegetation change. We also find that the diversity of native species is increasing in locations where the diversity of non-native species is increasing, suggesting that high diversities of native and non-native plant species are compatible with one another. We reject the ‘time-to-exclusion hypothesis’ as the reason why extinctions have not been observed, and suggest that non-native plant species are not a threat to floral diversity in Britain. Further research is needed in island-like environments, but we question whether it is appropriate that over three-quarters of taxa listed globally as invasive species are plants

Essential Fish Habitat project status report

: Groundfish that associate with rugged seafloor types are difficult to assess with bottom-trawl sampling gear. Simrad ME70 multibeam echosounder (MBES) data and video imagery were collected to characterize trawlable and untrawlable areas, and to ultimately improve efforts to determine habitat-specific groundfish biomass. The data were collected during two acoustic-trawl surveys of the Gulf of Alaska (GOA) during 2011 and 2012 by NOAA Alaska Fisheries Science Center (AFSC) researchers. MBES data were collected continuously along the trackline, which included parallel transects (1-20 nmi spacing) and fine-scale survey locations in 2011. Video data were collected at camera stations using a drop camera system. Multibeamderived seafloor metrics were overlaid with the locations of previously conducted AFSC bottomtrawl (BT) survey hauls and 2011 camera stations. Generalized linear models were used to identify the best combination of multibeam metrics to discriminate between trawlable and untrawlable seafloor for the region of overlap between the camera stations or haul paths and the MBES data. The most discriminatory models were chosen based on the Akaike information criterion (AIC). The two best models were developed using data collected at camera stations with either oblique incidence backscatter strength (Sb) or mosaic Sb in combination with bathymetric position index and seafloor ruggedness and described over 54% of the variation between trawlable and untrawlable seafloor types. A map of predicted seafloor trawlability produced from the model using mosaic Sb and benthic-terrain metrics demonstrated that 58% of the area mapped (5,987 km2 ) had \u3e 50% probability of being trawlable and 42% of being untrawlable. The model predicted 69% of trawlable and untrawlable haul locations correctly. Successful hauls occurred in areas with 62% probability of being trawlable and haul locations with gear damage occurred in areas with a 38% probability of being trawlable. This model and map produced from multibeamderived seafloor metrics may be used to refine seafloor interpretation for the AFSC BT surveys and to advance efforts to develop habitat-specific biomass estimates for GOA groundfish populations

Developing a low-cost beer dispensing robotic system for the service industry

As the prices of commercially available electronic and mechanical components decrease, manufacturers such as Devantech and Revolution Education have made encoded motor controller systems and microcontrollers very accessible to engineers and designers. This has made it possible to design sophisticated robotic and mechatronic systems very rapidly and at relatively low cost. A recent project in the Autonomous Systems Lab at Middlesex University, UK was to design and build a small, automated, robotic bartender based around the 5 litre Heineken 'Draughtkeg' system, which is capable of patrolling a bar and dispensing beer when signalled to by a customer. Because the system was designed as a commercial product, design constraints focused on keeping the build cost down, and so electronic components were sourced from outside companies and interfaced with a bespoke chassis and custom mechanical parts designed and manufactured on site at the University. All the programming was conducted using the proprietary BASIC language, which is freely available from the PicAXE supplier at no cost. This paper will discuss the restrictions involved in building a robot chassis around 'off-theshelf' components, and the issues arising from making the human-machine interaction intuitive whilst only using low-cost ultrasonic sensors. Programming issues will also be discussed, such as the control of accuracy when interfacing a PicAXE microcontroller with a Devantech MD25 Motor Controller board. Public live testing of the system was conducted at the Kinetica Art Fair 2010 event in London and has since been picked up by websites such as Engadget.com and many others. Feedback on the system will be described, as well as the refinements made as a result of these test