Review of deaths related to taking ecstasy, England and Wales, 1997-2000

Original article can be found at: http://www.bmj.com/archive/--Copyright BMJ Publishing Group Ltd DOI : 10.1136/bmj.326.7380.80Peer reviewe

From treebank resources to LFG F-structures

We present two methods for automatically annotating treebank resources with functional structures. Both methods define systematic patterns of correspondence between partial PS configurations and functional structures. These are applied to PS rules extracted from treebanks, or directly to constraint set encodings of treebank PS trees

The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.

The human genome is structurally organized in three-dimensional space to facilitate functional partitioning of transcription. We learned that the latent episome of the human Epstein-Barr virus (EBV) preferentially associates with gene-poor chromosomes and avoids gene-rich chromosomes. Kaposi's sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not. Contacts on the EBV side localize to OriP, the latent origin of replication. This genetic element and the EBNA1 protein that binds there are sufficient to reconstitute chromosome association preferences of the entire episome. Contacts on the human side localize to gene-poor and AT-rich regions of chromatin distant from transcription start sites. Upon reactivation from latency, however, the episome moves away from repressive heterochromatin and toward active euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during reactivation. Involvement of myriad interchromosomal associations also suggests a role for this type of long-range association in gene regulation.IMPORTANCE The human genome is structurally organized in three-dimensional space, and this structure functionally affects transcriptional activity. We set out to investigate whether a double-stranded DNA virus, Epstein-Barr virus (EBV), uses mechanisms similar to those of the human genome to regulate transcription. We found that the EBV genome associates with repressive compartments of the nucleus during latency and with active compartments during reactivation. This study advances our knowledge of the EBV life cycle, adding three-dimensional relocalization as a novel component to the molecular events that occur during reactivation. Furthermore, the data add to our understanding of nuclear compartments, showing that disperse interchromosomal interactions may be important for regulating transcription

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

The prediction of the operating conditions on the permeate flux and on protein aggregation during membrane processing of monoclonal antibodies

The lack of available material during early stage bioprocess development poses numerous processing challenges such as limiting the number of full-scale experiments. Extended fundamental process understanding could be gained with the use of an ultra scale-down (USD) device using as little as 1.7 mL per experimental run. The USD system is used to predict diafiltration and ultrafiltration/diafiltration (UF/DF) performance of a pilot-scale tangential flow filtration (TFF) system, fitted with a flat-sheet cassette, operating at 500-fold larger scale. Both systems were designed by maintaining a volumetric loading of 8.1 L of feed per m2. Permeate flux was predicted for monoclonal antibody solutions with the USD system across a range of transmembrane pressure drops, feed concentrations and flow conditions during diafiltration, and desired retentate concentrations during UF/DF operations. The resulting USD data were in good agreement with the pilot-scale TFF when scaled based on similar shear rates over the membrane surface. Little change in soluble aggregates was observed in both systems but there were significantly higher increases in product turbidity in the USD system. A correlation was established to relate turbidity increase based on the volume fraction of high shear stress zone for USD systems and various pilot-scale TFF systems. The correlation was extended to encompass the processing time and concentration for a wide range of membrane processing challenges in both scales

Biochemical and clinical response after umbilical cord blood transplant in a boy with early childhood-onset beta-mannosidosis.

BACKGROUND: Deficiency in the enzyme β-mannosidase was described over three decades ago. Although rare in occurrence, the presentation of childhood-onset β-mannosidase deficiency consists of hypotonia in the newborn period followed by global development delay, behavior problems, and intellectual disability. No effective pharmacologic treatments have been available. METHODS: We report 2-year outcomes following the first umbilical cord blood transplant in a 4-year-old boy with early childhood-onset disease. RESULTS: We show restoration of leukocyte β-mannosidase activity which remained normal at 2 years posttransplant, and a simultaneous increase in plasma β-mannosidase activity and dramatic decrease in urine-free oligosaccharides were also observed. MRI of the brain remained stable. Neurocognitive evaluation revealed test point gains, although the magnitude of improvement was less than expected for age, causing lower IQ scores that represent a wider developmental gap between the patient and unaffected peers. CONCLUSION: Our findings suggest that hematopoietic cell transplant can correct the biochemical defect in β-mannosidosis, although preservation of the neurocognitive trajectory may be a challenge

The ball in play demands of international rugby union

Objectives: Rugby union is a high intensity intermittent sport, typically analysed via set time periods or rolling average methods. This study reports the demands of international rugby union via global positioning system (GPS) metrics expressed as mean ball in play (BiP), maximum BiP (max BiP), and whole match outputs. Design: Single cohort cross sectional study involving 22 international players, categorised as forwards and backs. Methods: A total of 88 GPS files from eight international test matches were collected during 2016. An Opta sportscode timeline was integrated into the GPS software to split the data into BiP periods. Metres per min (m.min-1), high metabolic load per min (HML), accelerations per min (Acc), high speed running per min (HSR), and collisions per min (Coll) were expressed relative to BiP periods and over the whole match (>60min). Results: Whole match metrics were significantly lower than all BiP metrics (p < 0.001). Mean and max BiP HML, (p < 0.01) and HSR (p < 0.05) were significantly higher for backs versus forwards, whereas Coll were significantly higher for forwards (p < 0.001). In plays lasting 61s or greater, max BiP m.min-1 were higher for backs. Max BiP m.min-1, HML, HSR and Coll were all time dependant (p < 0.05) showing that both movement metrics and collision demands differ as length of play continues. Conclusions: This study uses a novel method of accurately assessing the BiP demands of rugby union. It also reports typical and maximal demands of international rugby union that can be used by practitioners and scientists to target training of worst-case scenario's equivalent to international intensity. Backs covered greater distances at higher speeds and demonstrated higher HML, in general play as well as 'worst case scenarios'; conversely forwards perform a higher number of collisions

The Phylogenetic Diversity of Metagenomes

Phylogenetic diversity—patterns of phylogenetic relatedness among organisms in ecological communities—provides important insights into the mechanisms underlying community assembly. Studies that measure phylogenetic diversity in microbial communities have primarily been limited to a single marker gene approach, using the small subunit of the rRNA gene (SSU-rRNA) to quantify phylogenetic relationships among microbial taxa. In this study, we present an approach for inferring phylogenetic relationships among microorganisms based on the random metagenomic sequencing of DNA fragments. To overcome challenges caused by the fragmentary nature of metagenomic data, we leveraged fully sequenced bacterial genomes as a scaffold to enable inference of phylogenetic relationships among metagenomic sequences from multiple phylogenetic marker gene families. The resulting metagenomic phylogeny can be used to quantify the phylogenetic diversity of microbial communities based on metagenomic data sets. We applied this method to understand patterns of microbial phylogenetic diversity and community assembly along an oceanic depth gradient, and compared our findings to previous studies of this gradient using SSU-rRNA gene and metagenomic analyses. Bacterial phylogenetic diversity was highest at intermediate depths beneath the ocean surface, whereas taxonomic diversity (diversity measured by binning sequences into taxonomically similar groups) showed no relationship with depth. Phylogenetic diversity estimates based on the SSU-rRNA gene and the multi-gene metagenomic phylogeny were broadly concordant, suggesting that our approach will be applicable to other metagenomic data sets for which corresponding SSU-rRNA gene sequences are unavailable. Our approach opens up the possibility of using metagenomic data to study microbial diversity in a phylogenetic context

The Force-Velocity Relation for Growing Biopolymers

The process of force generation by the growth of biopolymers is simulated via a Langevin-dynamics approach. The interaction forces are taken to have simple forms that favor the growth of straight fibers from solution. The force-velocity relation is obtained from the simulations for two versions of the monomer-monomer force field. It is found that the growth rate drops off more rapidly with applied force than expected from the simplest theories based on thermal motion of the obstacle. The discrepancies amount to a factor of three or more when the applied force exceeds 2.5kT/a, where a is the step size for the polymer growth. These results are explained on the basis of restricted diffusion of monomers near the fiber tip. It is also found that the mobility of the obstacle has little effect on the growth rate, over a broad range.Comment: Latex source, 9 postscript figures, uses psfig.st