The MC@NLO 4.0 Event Generator

This is the user's manual of MC@NLO 4.0. This package is a practical implementation, based upon the Fortran HERWIG and Herwig++ event generators, of the MC@NLO formalism, which allows one to incorporate NLO QCD matrix elements consistently into a parton shower framework. Processes available in this version include the hadroproduction of single vector and Higgs bosons, vector boson pairs, heavy quark pairs, single top, single top in association with a W, single top in association with a charged Higgs in type I or II 2HDM models, lepton pairs, and Higgs bosons in association with a W or Z. Spin correlations are included for all processes except ZZ production. This document is self-contained, but we emphasise the main differences with respect to previous versions.Comment: 36 pages, no figure

Linking pollution, meteorology and climate change

This thesis examines the relationship between synoptic meteorology and particulate matter (PM10). PM10 is a pollutant of high interest to UK health policy (DEFRA, 2016) and this study evaluates the importance of Rossby wave breaking (RWB) on UK PM10 concentration ([PM10]). RWB can result in atmospheric blocking, which is one extreme of mid-latitude synoptic meteorological variability that favours the accumulation of PM10. This study finds significant increases (p<0.01) in UK Midlands [PM10] resulting from winter-time northeast Atlantic/ European RWB. Furthermore, this study shows that northeast Atlantic/ European RWB increases the probability of exceeding a hazardous [PM10] threshold. We have identified the Omega block as the most hazardous RWB subset, with a probability of exceeding a hazardous [PM10] threshold (0.383) over three times that for days without RWB (0.129). We have implemented a tracer framework within a Hadley centre Met-Office climate model (HADGEM3-GA4) to identify flow regimes influencing the UK throughout northeast Atlantic/European RWB events. A present-day HADGEM3-GA4 simulation, nudged to ERA-Interim reanalysis data, is used to verify the tracer framework and to identify the flow regimes influencing Omega block events. This study finds that the advection of European tracer and the accumulation of locally sourced tracer contribute to hazardous [PM10] throughout Omega block events. This study’s principal aim is to determine climatic shifts in both the frequency of synoptic meteorological conditions conducive to UK PM10 accumulation and in the corresponding flow regimes. Using a further two HADGEM3-GA4 simulations, we find a north-eastward climate shift in northeast Atlantic/ European RWB, with an overall reduction in events. Additionally, we find that uture RWB events result in significantly (p<0.01) increased European and reduced stagnant air masses within the UK. This result indicates a reduced frequency of UK [PM10] exceedances, however a tendency for increased transport of toxic particles from Europe

Crowdsourcing concurrent relations

While discourse relations can be signaled explicitly with conjunctions (Ex. 1) or adverbials (Ex. 2), (1) “We’ve started trying just about anything to keep sales moving in the stores, ” says Kim Renk, a Swank vice president. But there are limits. [wsj0280]1 (2) They both called it a “welcome home ” gathering. Nevertheless, an ANC rally by any other name is still an ANC rally. [wsj0559] we also find sentences (Ex. 3–5) with both forms of DRD: (3) If that became public knowledge, the last bit of influence she had over her bank would be gone. So instead she hardened her soul and pretended to be a banker who was working her own will. [COCA] (4) It’s past ten. I could go to bed but instead I crawl out the window onto my little roof with the joint behind my ear. [COCA] (5) Appealing to a young audience, he scraps an old reference to Ozzie and Harriet and instead quotes the Grateful Dead. [wsj 1615] In such cases, the conjunction and adverbial can each signal a distinct discourse relation. A previous crowd-sourced study of four adverbials that can co-occur with conjunctions (Jiang, 2013) asked respon

Investigations on path indexing for graph databases

Graph databases have become an increasingly popular choice for the management of the massive network data sets arising in many contemporary applications. We investigate the effectiveness of path indexing for accelerating query processing in graph database systems, using as an exemplar the widely used open-source Neo4j graph database. We present a novel path index design which supports efficient ordered access to paths in a graph dataset. Our index is fully persistent and designed for external memory storage and retrieval. We also describe a compression scheme that exploits the limited differences between consecutive keys in the index, as well as a workload-driven approach to indexing. We demonstrate empirically the speed-ups achieved by our implementation, showing that the path index yields query run-times from 2x up to 8000x faster than Neo4j. Empirical evaluation also shows that our scheme leads to smaller indexes than using general-purpose LZ4 compression. The complete stand-alone implementation of our index, as well as supporting tooling such as a bulk-loader, are provided as open source for further research and development

Forging Links between Human Mental Retardation–Associated CNVs and Mouse Gene Knockout Models

Rare copy number variants (CNVs) are frequently associated with common neurological disorders such as mental retardation (MR; learning disability), autism, and schizophrenia. CNV screening in clinical practice is limited because pathological CNVs cannot be distinguished routinely from benign CNVs, and because genes underlying patients' phenotypes remain largely unknown. Here, we present a novel, statistically robust approach that forges links between 148 MR–associated CNVs and phenotypes from ∼5,000 mouse gene knockout experiments. These CNVs were found to be significantly enriched in two classes of genes, those whose mouse orthologues, when disrupted, result in either abnormal axon or dopaminergic neuron morphologies. Additional enrichments highlighted correspondences between relevant mouse phenotypes and secondary presentations such as brain abnormality, cleft palate, and seizures. The strength of these phenotype enrichments (>100% increases) greatly exceeded molecular annotations (<30% increases) and allowed the identification of 78 genes that may contribute to MR and associated phenotypes. This study is the first to demonstrate how the power of mouse knockout data can be systematically exploited to better understand genetically heterogeneous neurological disorders

Bias of Selection on Human Copy-Number Variants

Although large-scale copy-number variation is an important contributor to conspecific genomic diversity, whether these variants frequently contribute to human phenotype differences remains unknown. If they have few functional consequences, then copy-number variants (CNVs) might be expected both to be distributed uniformly throughout the human genome and to encode genes that are characteristic of the genome as a whole. We find that human CNVs are significantly overrepresented close to telomeres and centromeres and in simple tandem repeat sequences. Additionally, human CNVs were observed to be unusually enriched in those protein-coding genes that have experienced significantly elevated synonymous and nonsynonymous nucleotide substitution rates, estimated between single human and mouse orthologues. CNV genes encode disproportionately large numbers of secreted, olfactory, and immunity proteins, although they contain fewer than expected genes associated with Mendelian disease. Despite mouse CNVs also exhibiting a significant elevation in synonymous substitution rates, in most other respects they do not differ significantly from the genomic background. Nevertheless, they encode proteins that are depleted in olfactory function, and they exhibit significantly decreased amino acid sequence divergence. Natural selection appears to have acted discriminately among human CNV genes. The significant overabundance, within human CNVs, of genes associated with olfaction, immunity, protein secretion, and elevated coding sequence divergence, indicates that a subset may have been retained in the human population due to the adaptive benefit of increased gene dosage. By contrast, the functional characteristics of mouse CNVs either suggest that advantageous gene copies have been depleted during recent selective breeding of laboratory mouse strains or suggest that they were preferentially fixed as a consequence of the larger effective population size of wild mice. It thus appears that CNV differences among mouse strains do not provide an appropriate model for large-scale sequence variations in the human population

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

In the above-mentioned article, one result reported in the third paragraph of the Results subsection “ceRNAts of individual lnceRNAs tend to be functionally related” was in error. This paragraph should now read: “On average, mESC-expressed lnceRNAs have 20.2 predicted MREs per kb of transcript that are specific to 12 different mESC-expressed miRNAs. This MRE density is similar to the density within 3′ UTRs of ceRNAts (20.4 MREs predicted per kb; P = 0.34, two-tailed Mann-Whitney U test) (Supplemental Fig. S9; Supplemental Table S8). A single lnceRNA might, therefore, be as likely as an mRNA to regulate post-transcriptionally the transcript abundance of many mRNAs via crosstalk with many miRNAs.” Corrected versions of Supplemental Figure S9 and Supplemental Table S8 are also now provided online. This correction does not affect any of the conclusions of the paper. The authors apologize for any confusion caused by this error

Bristol and Bath by Design; To understand the economic and cultural value of design in the Bristol and Bath region

The aim of the project was to collect data on designcompanies in the Bristol and Bath region, and to gain abetter understanding of the economic and cultural valueof the design-led sector. To do this, our primary researchwas to develop a range of qualitative and quantitativemethods that could gather and then analyse the data