The SoLid anti-neutrino detector's readout system

The SoLid collaboration have developed an intelligent readout system to reduce their 3200 silicon photomultiplier detector's data rate by a factor of 10000 whilst maintaining high efficiency for storing data from anti-neutrino interactions. The system employs an FPGA-level waveform characterisation to trigger on neutron signals. Following a trigger, data from a space time region of interest around the neutron will be read out using the IPbus protocol. In these proceedings the design of the readout system is explained and results showing the performance of a prototype version of the system are presented

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/

Assessing the effects of land use on biodiversity in the world's drylands and Mediterranean environments

Biodiversity models make an important contribution to our understanding of global biodiversity changes. The effects of different land uses vary across ecosystem types, yet most broad-scale models have failed to account for this variation. The effects of land use may be different in systems characterized by low water availability because of the unusual conditions within these systems. Drylands are expanding, currently occupying over 40% of the terrestrial land, while Mediterranean systems are highly endangered biodiversity hotspots. However, the impact of land use on biodiversity in these biomes is yet to be assessed. Using a database of local biodiversity surveys, we assess the effects of land use on biodiversity in the world’s drylands and Mediterranean ecosystems. We compare the average species richness, total abundance, species diversity, ecological dominance, endemism rates, and compositional turnover across different land uses. In drylands, there was a strong turnover in species composition in disturbed land uses compared with undisturbed natural habitat (primary vegetation), but other measures of biodiversity did not respond significantly. However, it is important to note that the sample size for drylands was very low, a gap which should be filled promptly. Mediterranean environments showed a very high sensitivity of biodiversity to land uses. In this biome, even habitat recovering after past disturbance (secondary vegetation) had substantially reduced biodiversity and altered community composition compared with primary vegetation. In an effort to maintain original biodiversity and the ecosystem functions it supports within Mediterranean biomes, conservation measures should therefore prioritize the preservation of remaining primary vegetation

A first-level track trigger architecture for super-CMS

We present an architectural concept for a first-level hardware track trigger for CMS at SLHC. The design of such a system is challenging. A primary constraint on implementation will be power consumption within the detector, in turn driven by the transmission bandwidth to offdetector electronics. We therefore emphasise the minimisation of the data flow through local filtering of track stubs on the detector. The architecture does not comprise a stand-alone track trigger, but uses muon and calorimeter trigger objects to seed track-matching within an integrated first-level system

Gene identification for the cblD defect of vitamin B12 metabolism

Background Vitamin B12 (cobalamin) is an essential cofactor in several metabolic pathways. Intracellular conversion of cobalamin to its two coenzymes, adenosylcobalamin in mitochondria and methylcobalamin in the cytoplasm, is necessary for the homeostasis of methylmalonic acid and homocysteine. Nine defects of intracellular cobalamin metabolism have been defined by means of somatic complementation analysis. One of these defects, the cblD defect, can cause isolated methylmalonic aciduria, isolated homocystinuria, or both. Affected persons present with multisystem clinical abnormalities, including developmental, hematologic, neurologic, and metabolic findings. The gene responsible for the cblD defect has not been identified. Methods We studied seven patients with the cblD defect, and skin fibroblasts from each were investigated in cell culture. Microcell-mediated chromosome transfer and refined genetic mapping were used to localize the responsible gene. This gene was transfected into cblD fibroblasts to test for the rescue of adenosylcobalamin and methylcobalamin synthesis. Results The cblD gene was localized to human chromosome 2q23.2, and a candidate gene, designated MMADHC (methylmalonic aciduria, cblD type, and homocystinuria), was identified in this region. Transfection of wild-type MMADHC rescued the cellular phenotype, and the functional importance of mutant alleles was shown by means of transfection with mutant constructs. The predicted MMADHC protein has sequence homology with a bacterial ATP-binding cassette transporter and contains a putative cobalamin binding motif and a putative mitochondrial targeting sequence. Conclusions Mutations in a gene we designated MMADHC are responsible for the cblD defect in vitamin B12 metabolism. Various mutations are associated with each of the three biochemical phenotypes of the disorder

Timing and Synchronization of the DUNE Neutrino Detector

The DUNE neutrino experiment far detector has a fiducial mass of 40 kt. The O(1M) readout channels are distributed over the four 10 kt modules and need to be synchronized with respect to each other to a precision of O(10 ns). The entire system needs to be synchronized with respect to GPS time to O(100 ns). The system needs to be reliable, simple and affordable. Clock and synchronization information encoded on the same fibre using a protocol based on duty cycle shift keying (DCSK) with 8b10b encoding to ensure DC-balance. The use of DCSK allows the clock to be recovered directly by PLL based clock generators without needing to use a separate clock and data recovery (CDR) device. Small scale tests show a timing jitter at the endpoint of approximately 10 ps with respect to the timing master.Comment: conferenc

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

Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation.

Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear nucleolus results in the clustering of rDNA. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second-generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in var gene expression. We have generated maps of chromosomal spatial affinities within the P. falciparum nucleus at 25 Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in var gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality

Adolescents' experiences of street harassment: creating a typology and assessing the emotional impact

Purpose: Research examining young people's experiences of harassment has tended to focus on the school and digital environment. Despite street harassment being identified as a common experience for adult women, very few studies have explored adolescents' experiences of street harassment. Methodology: A person centred analytical approach, based on experienced reporting, was used to create a typology of street harassment. Reports of street harassment were received from 118 (68 female, 43 male, 7 no gender reported) 11- to 15-year-olds over a 6 to 8 week period. Findings: Cluster analysis revealed four distinct groups: "predominately verbal", "non-verbal/non-direct", "other incident", and "all forms". Young women and those in the "all forms" group reported experiencing greater negative emotions following the episode of street harassment. Young men were equally as likely as young women to report experiencing street harassment. Value: The findings uniquely highlight that adolescents experience distinct types of street harassment and some of which are associated with negative emotions