Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods

A number of studies have suggested using comparisons between DNA sequences of closely related bacterial isolates to estimate the relative rate of recombination to mutation for that bacterial species. We consider such an approach which uses single-locus variants: pairs of isolates whose DNA differ at a single gene locus. One way of deriving point estimates for the relative rate of recombination to mutation from such data is to use composite likelihood methods. We extend recent work in this area so as to be able to construct confidence intervals for our estimates, without needing to resort to computationally-intensive bootstrap procedures, and to develop a test for whether the relative rate varies across loci. Both our test and method for constructing confidence intervals are obtained by modeling the dependence structure in the data, and then applying asymptotic theory regarding the distribution of estimators obtained using a composite likelihood. We applied these methods to multi-locus sequence typing (MLST) data from eight bacteria, finding strong evidence for considerable rate variation in three of these: Bacillus cereus, Enterococcus faecium and Klebsiella pneumoniae.Comment: Published at http://dx.doi.org/10.1214/14-AOAS795 in the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Semi-automatic selection of summary statistics for ABC model choice

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data

Glazing of tool dies for semi-solid steel forming

This paper describes an analysis conducted into the effect of CO2 laser processing parameters on the surface modification and heat treatment of steels. The CO2 laser and in house developed apparatus for movement of the samples allowed for high speed surface heat treatment. The operation of these components in conjunction allowed a wide variation in the heat treatments and sample properties to be obtained. In particular, the mechanism to pass the steel samples at high speeds (700 — 1200 mm/s), kept the focus spot exposure times below 1 x 10-3 s. Laser power from 825 to 1050W and continuous beam mode were used. Both laser hardened and laser glazed samples were analysed using optical microscopy, Vickers and micro hardness testing, and XRD. The samples showed functionally graded surface morphologies and corresponding hardness and stiffness responses. For more rapidly process samples three layers of distinct hardness were noted. In all cases crystal and property modification to approximately 500ttm was found. Results show how the laser treatment is directly related to the hardness profile through the surface and resultant microstructures. The results from all the samples show increased hardness due to (a) the formation of martensite and ferrite in the laser hardened samples and (b) a complete microstructural transformation to an amorphous state in the glazed samples. It is noted that the higher stiffness and hardness of the glazed samples can expect to result in a more wear resistant coating for the semi-steel forming process. The amorphous layer may also be expected to act as a thermal barrier to the higher temperatures encountered in semi-solid steel forming

Distribution and Abundance of Phytoplankton, Zooplankton, Ichthyoplankton, and Micronekton in the Deepwater Gulf of Mexico

Expeditions in the 1960s and 1970s are the basis for the general paradigm that standing stocks and productivity of phytoplankton are both low ( \u3c0.1 mg chl·m-3; \u3c150 mg C.m-2·d-1) seaward of the shelf-slope break in the Gulf of Mexico. The present review supports this description of the mean (stable) state but also shows hot spots in primary production (\u3e2 g C·m-2·d-1) occur when/where nutrient availability is locally enhanced seaward of the shelf-slope break. Recent collections with Bongo and MOCNESS nets, midwater trawls, and bioacoustic surveys of the Loop Current and associated cyclonic and anticyclonic eddies in the Gulf of Mexico show that these deepwater hot spots have higher stocks of zooplankton and micronekton as well. The local aggregations ranged in size from coarse- to meso- spatial scales (10s to 100s of kilometers) though locations of such oases were spatially variable along the continental margin

Coleridge’s Imperfect Circles

This thesis takes as its starting point Coleridge’s assertion that “[t]he common end of all . . . Poems is . . . to make those events which in real or imagined History move in a strait [sic] Line, assume to our Understandings a circular motion” (CL 4: 545). Coleridge’s so-called “Conversation” poems seem to conform most conspicuously to this aesthetic theory, structured as they are to return to their starting points at their conclusions. The assumption, however, that this comforting circular structure is commensurate with the sense of these poems can be questioned, for the conclusions of the “Conversation” poems are rarely, if ever, reassuring. The formal circularity of these poems is frequently achieved more by persuasive rhetoric than by any cohesion of elements. The circular structure encourages the reader’s expectations of unity and synthesis, but ultimately these expectations are disappointed, and instead the reader is surprised by an ending more troubling than the rhetoric of return and reassurance would suggest. Taking three “Conversation” poems as case studies (“The Eolian Harp,” “This Lime-Tree Bower My Prison,” and “Frost at Midnight”), this thesis attempts to explicate those tensions which exist in the “Conversation” poems between form and effect, between structure and sense

De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus)

BACKGROUND: The tuatara (Sphenodon punctatus) is a species of extraordinary zoological interest, being the only surviving member of an entire order of reptiles which diverged early in amniote evolution. In addition to their unique phylogenetic placement, many aspects of tuatara biology, including temperature-dependent sex determination, cold adaptation and extreme longevity have the potential to inform studies of genome evolution and development. Despite increasing interest in the tuatara genome, genomic resources for the species are still very limited. We aimed to address this by assembling a transcriptome for tuatara from an early-stage embryo, which will provide a resource for genome annotation, molecular marker development and studies of development and adaptation in tuatara. RESULTS: We obtained 30 million paired-end 50 bp reads from an Illumina Genome Analyzer and assembled them with Velvet and Oases using a range of kmers. After removing redundancy and filtering out low quality transcripts, our transcriptome dataset contained 32911 transcripts, with an N50 of 675 and a mean length of 451 bp. Almost 50% (15965) of these transcripts could be annotated by comparison with the NCBI non-redundant (NR) protein database or the chicken, green anole and zebrafish UniGene sets. A scan of candidate genes and repetitive elements revealed genes involved in immune function, sex differentiation and temperature-sensitivity, as well as over 200 microsatellite markers. CONCLUSIONS: This dataset represents a major increase in genomic resources for the tuatara, increasing the number of annotated gene sequences from just 60 to almost 16,000. This will facilitate future research in sex determination, genome evolution, local adaptation and population genetics of tuatara, as well as inform studies on amniote evolution

The Relationship Between Social Vulnerability and COVID-19 Incidence Among Louisiana Census Tracts

Objective: To examine the association between the Centers for Disease Control and Prevention (CDC)\u27s Social Vulnerability Index (SVI) and COVID-19 incidence among Louisiana census tracts. Methods: An ecological study comparing the CDC SVI and census tract-level COVID-19 case counts was conducted. Choropleth maps were used to identify census tracts with high levels of both social vulnerability and COVID-19 incidence. Negative binomial regression with random intercepts was used to compare the relationship between overall CDC SVI percentile and its four sub-themes and COVID-19 incidence, adjusting for population density. Results: In a crude stratified analysis, all four CDC SVI sub-themes were significantly associated with COVID-19 incidence. Census tracts with higher levels of social vulnerability were associated with higher COVID-19 incidence after adjusting for population density (adjusted RR: 1.52, 95% CI: 1.41-1.65). Conclusions: The results of this study indicate that increased social vulnerability is linked with COVID-19 incidence. Additional resources should be allocated to areas of increased social disadvantage to reduce the incidence of COVID-19 in vulnerable populations