Difficulties in distinguishing coherent from fragmental kimberlite: A case study of the Muskox pipe (Northern Slave Province, Nunavut, Canada)

Kimberlite drill core from the Muskox pipe (Northern Slave Province, Nunavut, Canada) highlights the difficulties in distinguishing coherent from fragmental kimberlite and assessing the volcanological implications of the apparent gradational contact between the two facies. Using field log data, petrography, and several methods to quantify crystal and xenolith sizes and abundances, the pipe is divided into two main facies, dark-coloured massive kimberlite (DMK) and light-coloured fragmental kimberlite (LFK). DMK is massive and homogeneous, containing country-rock lithic clasts (~ 10%) and olivine macrocrysts (~ 15%) set in a dark, typically well crystallised, interstitial medium containing abundant microphenocrysts of olivine (~ 15%), opaques and locally monticellite, all of which are enclosed by mostly serpentine. In general, LFK is also massive and structureless, containing ~ 20% country-rock lithic clasts and ~ 12% olivine macrocrysts. These framework components are supported in a matrix of serpentinized olivine microphenocrysts (10%), microlites of clinopyroxene, and phlogopite, all of which are enclosed by serpentine. The contact between DMK and LFK facies is rarely sharp, and more commonly is gradational (from 5 cm to ~ 10 m). The contact divides the pipe roughly in half and is sub-vertical with an irregular shape, locally placing DMK facies both above and below the fragmental rocks. Most features of DMK are consistent with a fragmental origin, particularly the crystal- and xenolith-rich nature (~ 55-65%), but there are some similarities with rocks described as coherent kimberlite in the literature. We discuss possible origins of gradational contacts and consider the significance for understanding the origin of the DMK facies, with an emphasis on the complications of alteration overprinting of primary textures.

Confirmatory factory analysis of the Neck Disability Index in a general problematic neck population indicates a one-factor model

BACKGROUND CONTEXT: The Neck Disability Index frequently is used to measure outcomes of the neck. The statistical rigor of the Neck Disability Index has been assessed with conflicting outcomes. To date, Confirmatory Factor Analysis of the Neck Disability Index has not been reported for a suitably large population study. Because the Neck Disability Index is not a condition-specific measure of neck function, initial Confirmatory Factor Analysis should consider problematic neck patients as a homogenous group. PURPOSE: We sought to analyze the factor structure of the Neck Disability Index through Confirmatory Factor Analysis in a symptomatic, homogeneous, neck population, with respect to pooled populations and gender subgroups. STUDY DESIGN: This was a secondary analysis of pooled data. PATIENT SAMPLE: A total of 1,278 symptomatic neck patients (67.5% female, median age 41 years), 803 nonspecific and 475 with whiplash-associated disorder. OUTCOME MEASURES: The Neck Disability Index was used to measure outcomes. METHODS: We analyzed pooled baseline data from six independent studies of patients with neck problems who completed Neck Disability Index questionnaires at baseline. The Confirmatory Factor Analysis was considered in three scenarios: the full sample and separate sexes. Models were compared empirically for best fit. RESULTS: Two-factor models have good psychometric properties across both the pooled and sex subgroups. However, according to these analyses, the one-factor solution is preferable from both a statistical perspective and parsimony. The two-factor model was close to significant for the male subgroup (p<.07) where questions separated into constructs of mental function (pain, reading headaches and concentration) and physical function (personal care, lifting, work, driving, sleep, and recreation). CONCLUSIONS: The Neck Disability Index demonstrated a one-factor structure when analyzed by Confirmatory Factor Analysis in a pooled, homogenous sample of neck problem patients. However, a two-factor model did approach significance for male subjects where questions separated into constructs of mental and physical function. Further investigations in different conditions, subgroup and sex-specific populations are warranted.

Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Genetic correlation (rg) analysis determines how much of the correlation between two measures is due to common genetic influences. In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on white matter integrity, measured by fractional anisotropy (FA), at all points of the brain, yielding an NxN genetic correlation matrix rg(x,y) between FA values at all pairs of voxels in the brain. With hierarchical clustering, we identified brain regions with relatively homogeneous genetic determinants, to boost the power to identify causal single nucleotide polymorphisms (SNP). We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix. We identified a network of genes, with a scale-free topology, that influences white matter integrity over multiple brain regions.

A perfusion fMRI investigation of thematic and categorical context effects in the spoken production of object names

The context in which objects are presented influences the speed at which they are named. We employed the blocked cyclic naming paradigm and perfusion functional magnetic resonance imaging (fMRI) to investigate the mechanisms responsible for interference effects reported for thematicallyand categorically related compared to unrelated contexts. Naming objects in categorically homogeneous contexts induced a significant interference effect that accumulated from the second cycle onwards. This interference effect was associated with significant perfusion signal decreases in left middle and posterior lateral temporal cortex and the hippocampus. By contrast, thematically homogeneous contexts facilitated naming latencies significantly in the first cycle and did not differ from heterogeneous contexts thereafter, nor were they associated with any perfusion signal changes compared to heterogeneous contexts. These results are interpreted as being consistent with an account in which the interference effect both originates and has its locus at the lexical level, with an incremental learning mechanism adapting the activation levels of target lexical representations following access. We discuss the implications of these findings for accounts that assume thematic relations can be active lexical competitors or assume mandatory involvement of top-down control mechanisms in interference effects during naming.

The microwell-mesh: A novel device and protocol for the high throughput manufacturing of cartilage microtissues

Microwell platforms are frequently described for the efficient and uniform manufacture of 3-dimensional (3D) multicellular microtissues. Multiple partial or complete medium exchanges can displace microtissues from discrete microwells, and this can result in either the loss of microtissues from culture, or microtissue amalgamation when displaced microtissues fall into common microwells. Herein we describe the first microwell platform that incorporates a mesh to retain microtissues within discrete microwells; the microwell-mesh. We show that bonding a nylon mesh with an appropriate pore size over the microwell openings allows single cells to pass through the mesh into the microwells during the seeding process, but subsequently retains assembled microtissues within discrete microwells. To demonstrate the utility of this platform, we used the microwell-mesh to manufacture hundreds of cartilage microtissues, each formed from 5 × 10(3) bone marrow-derived mesenchymal stem/stromal cells (MSC). The microwell-mesh enabled reliable microtissue retention over 21-day cultures that included multiple full medium exchanges. Cartilage-like matrix formation was more rapid and homogeneous in microtissues than in conventional large diameter control cartilage pellets formed from 2 × 10(5) MSC each. The microwell-mesh platform offers an elegant mechanism to retain microtissues in microwells, and we believe that this improvement will make this platform useful in 3D culture protocols that require multiple medium exchanges, such as those that mimic specific developmental processes or complex sequential drug exposures.

Pyroxene thermometry of rhyolite lavas of the Bruneau–Jarbidge eruptive center, Central Snake River Plain

The Bruneau–Jarbidge eruptive center of the central Snake River Plain in southern Idaho, USA produced multiple rhyolite lava flows with volumes of <10 km³ to 200 km³ each from ~11.2 to 8.1 Ma, most of which follow its climactic phase of large-volume explosive volcanism, represented by the Cougar Point Tuff, from 12.7 to 10.5 Ma. These lavas represent the waning stages of silicic volcanism at a major eruptive center of the Yellowstone hotspot track. Here we provide pyroxene compositions and thermometry results from several lavas that demonstrate that the demise of the silicic volcanic system was characterized by sustained, high pre-eruptive magma temperatures (mostly ≥950 °C) prior to the onset of exclusively basaltic volcanism at the eruptive center. Pyroxenes display a variety of textures in single samples, including solitary euhedral crystals as well as glomerocrysts, crystal clots and annealed microgranular inclusions of pyroxene ±magnetite± plagioclase. Pigeonite and augite crystals are unzoned, and there are no detectable differences in major and minor element compositions according to textural variety — mineral compositions in the microgranular inclusions and crystal clots are identical to those of phenocrysts in the host lavas. In contrast to members of the preceding Cougar Point Tuff that host polymodal glass and mineral populations, pyroxene compositions in each of the lavas are characterized by single rather than multiple discrete compositional modes. Collectively, the lavas reproduce and extend the range of Fe–Mg pyroxene compositional modes observed in the Cougar Point Tuff to more Mg-rich varieties. The compositionally homogeneous populations of pyroxene in each of the lavas, as well as the lack of core-to-rim zonation in individual crystals suggest that individual eruptions each were fed by compositionally homogeneous magma reservoirs, and similarities with the Cougar Point Tuff suggest consanguinity of such reservoirs to those that supplied the polymodal Cougar Point Tuff. Pyroxene thermometry results obtained using QUILF equilibria yield pre-eruptive magma temperatures of 905 to 980 °C, and individual modes consistently record higher Ca content and higher temperatures than pyroxenes with equivalent Fe–Mg ratios in the preceding Cougar Point Tuff. As is the case with the Cougar Point Tuff, evidence for up-temperature zonation within single crystals that would be consistent with recycling of sub- or near-solidus material from antecedent magma reservoirs by rapid reheating is extremely rare. Also, the absence of intra-crystal zonation, particularly at crystal rims, is not easily reconciled with cannibalization of caldera fill that subsided into pre-eruptive reservoirs. The textural, compositional and thermometric results rather are consistent with minor re-equilibration to higher temperatures of the unerupted crystalline residue from the explosive phase of volcanism, or perhaps with newly generated magmas from source materials very similar to those for the Cougar Point Tuff. Collectively, the data suggest that most of the pyroxene compositional diversity that is represented by the tuffs and lavas was produced early in the history of the eruptive center and that compositions across this range were preserved or duplicated through much of its lifetime. Mineral compositions and thermometry of the multiple lavas suggest that unerupted magmas residual to the explosive phase of volcanism may have been stored at sustained, high temperatures subsequent to the explosive phase of volcanism. If so, such persistent high temperatures and large eruptive magma volumes likewise require an abundant and persistent supply of basalt magmas to the lower and/or mid-crust, consistent with the tectonic setting of a continental hotspot.

Immunochip analysis identifies multiple susceptibility loci for systemic sclerosis

In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry. Following this strategy, we identified and validated three SSc risk loci, including DNASE1L3 at 3p14, the SCHIP1-IL12A locus at 3q25, and ATG5 at 6q21, as well as a suggested association of the TREH-DDX6 locus at 11q23. The associations of several previously reported SSc risk loci were validated and further refined, and the observed peak of association in PXK was related to DNASE1L3. Our study has increased the number of known genetic associations with SSc, provided further insight into the pleiotropic effects of shared autoimmune risk factors, and highlighted the power of dense mapping for detecting previously overlooked susceptibility loci.

An immunodiagnostic assay for quantitation of specific ige to the major pollen allergen component, pas n 1, of the subtropical bahia grass

Background Pollens of the Panicoideae subfamily of grasses including Bahia (Paspalum notatum) are important allergen sources in subtropical regions of the world. An assay for specific IgE to the major molecular allergenic component, Pas n 1, of Bahia grass pollen (BaGP) would have immunodiagnostic utility for patients with pollen allergy in these regions. Methods Biotinylated Pas n 1 purified from BaGP was coated onto streptavidin ImmunoCAPs. Subjects were assessed by clinical history of allergic rhinitis and skin prick test (SPT) to aeroallergens. Serum total, BaGP-specific and Pas n 1-specific IgE were measured. Results: Pas n 1 IgE concentrations were highly correlated with BaGP SPT (r = 0.795, p < 0.0001) and BaGP IgE (r = 0.915, p < 0.0001). At 0.23 kU/l Pas n 1 IgE, the diagnostic sensitivity (92.4%) and specificity (93.1%) for the detection of BaGP allergy was high (area under receiver operator curve 0.960, p < 0.0001). The median concentrations of Pas n 1 IgE in non-Atopic subjects (0.01 kU/l, n = 67) and those with other allergies (0.02 kU/l, n = 59) showed no inter-group difference, whilst grass pollen-Allergic patients with allergic rhinitis showed elevated Pas n 1 IgE (6.71 kU/l, n = 182, p < 0.0001). The inter-Assay coefficient of variation for the BaGP-Allergic serum pool was 6.92%. Conclusions Pas n 1 IgE appears to account for most of the BaGP-specific IgE. This molecular component immunoassay for Pas n 1 IgE has potential utility to improve the sensitivity and accuracy of diagnosis of BaGP allergy for patients in subtropical regions.

Towards the pathogenesis of autoimmune liver disease

There have been recent improvements in the clinical understanding and definition of the major types of autoimmune liver disease. However, still lacking is knowledge of their prevalence and pathogenesis. Three areas of study are in progress in our laboratory. First, in type 1 autoimmune hepatitis, the search continues to identify a liver/disease-specific autoantigenic reactant. Using hepatocyte membrane preparations, immunoblotting has underlined the problem of distinguishing, among multiple reactants, those that may be causally rather than consequentially related to hepatocellular damage. Second, in primary biliary cirrhosis (PBC), the need for population screening to ascertain prevalence and detect preclinical cases can be met by a rapid automated procedure for detection, by specific enzyme inhibition in microtitre wells, of antibody (anti-M2) to the pyruvate dehydrogenase complex E2 subunit (PDC-E2). Third, the structure of the conformational epitope within the inner lipoyl domain of PDC-E2 is being investigated by screening random phage-displayed peptide libraries using PBC sera. This has yielded phage clones in which the sequence of the peptide insert portrays the structure of this epitope, as judged by clustering of PBC-derived sequences to particular branches of a guide-tree that shows relatedness of peptides, and by reactivity of selected phage clones with anti-PDC-E2. Thus phage display identifies a peptide 'mimotope' of the antibody epitope in the inner lipoyl domain of PDC-E2.

Reconfiguring Guangzhou identity – a study of place and locality on Sina Weibo

This thesis investigates the role of Chinese microblogging platform Sina Weibo in how the people of Guangzhou understand and negotiate their sense of locality. The geo-identity approach used in this thesis opens up a new approach to explore the complex power relationships that structure our society in and through digital media. It finds that although the Chinese government is trying to orchestrate a homogeneous sense of national belonging, Weibo is constantly reinforcing people's awareness of and identification with the local. The findings show that as new communication technologies and practices reconfigure people's daily experience and social lives, they redefine our sense of self and belonging.

Mapping bound plasmon propagation on a nanoscale stripe waveguide using quantum dots: Influence of spacer layer thickness

In this paper we image the highly confined long range plasmons of a nanoscale metal stripe waveguide using quantum emitters. Plasmons were excited using a highly focused 633 nm laser beam and a specially designed grating structure to provide stronger incoupling to the desired mode. A homogeneous thin layer of quantum dots was used to image the near field intensity of the propagating plasmons on the waveguide. We observed that the photoluminescence is quenched when the QD to metal surface distance is less than 10 nm. The optimised spacer layer thickness for the stripe waveguides was found to be around 20 nm. Authors believe that the findings of this paper prove beneficial for the development of plasmonic devices utilising stripe waveguides.

Role of enhanced vector transmission of a new West Nile virus strain in an outbreak of equine disease in Australia in 2011

Background In 2011, a variant of West Nile virus Kunjin strain (WNVKUN) caused an unprecedented epidemic of neurological disease in horses in southeast Australia, resulting in almost 1,000 cases and a 9% fatality rate. We investigated whether increased fitness of the virus in the primary vector, Culex annulirostris, and another potential vector, Culex australicus, contributed to the widespread nature of the outbreak. Methods Mosquitoes were exposed to infectious blood meals containing either the virus strain responsible for the outbreak, designated WNVKUN2011, or WNVKUN2009, a strain of low virulence that is typical of historical strains of this virus. WNVKUN infection in mosquito samples was detected using a fixed cell culture enzyme immunoassay and a WNVKUN- specific monoclonal antibody. Probit analysis was used to determine mosquito susceptibility to infection. Infection, dissemination and transmission rates for selected days post-exposure were compared using Fisher’s exact test. Virus titers in bodies and saliva expectorates were compared using t-tests. Results There were few significant differences between the two virus strains in the susceptibility of Cx. annulirostris to infection, the kinetics of virus replication and the ability of this mosquito species to transmit either strain. Both strains were transmitted by Cx. annulirostris for the first time on day 5 post-exposure. The highest transmission rates (proportion of mosquitoes with virus detected in saliva) observed were 68% for WNVKUN2011 on day 12 and 72% for WNVKUN2009 on day 14. On days 12 and 14 post-exposure, significantly more WNVKUN2011 than WNVKUN2009 was expectorated by infected mosquitoes. Infection, dissemination and transmission rates of the two strains were not significantly different in Culex australicus. However, transmission rates and the amount of virus expectorated were significantly lower in Cx. australicus than Cx. annulirostris. Conclusions The higher amount of WNVKUN2011 expectorated by infected mosquitoes may be an indication that this virus strain is transmitted more efficiently by Cx. annulirostris compared to other WNVKUN strains. Combined with other factors, such as a convergence of abundant mosquito and wading bird populations, and mammalian and avian feeding behaviour by Cx. annulirostris, this may have contributed to the scale of the 2011 equine epidemic.

Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

Founder p.Arg 446* mutation in the PDHX gene explains over half of cases with congenital lactic acidosis in Roma children

Investigation of 31 of Roma patients with congenital lactic acidosis (CLA) from Bulgaria identified homozygosity for the R446* mutation in the PDHX gene as the most common cause of the disorder in this ethnic group. It accounted for around 60% of patients in the study and over 25% of all CLA cases referred to the National Genetic Laboratory in Bulgaria. The detection of a homozygous patient from Hungary and carriers among population controls from Romania and Slovakia suggests a wide spread of the mutation in the European Roma population. The clinical phenotype of the twenty R446* homozygotes was relatively homogeneous, with lactic acidosis crisis in the first days or months of life as the most common initial presentation (15/20 patients) and delayed psychomotor development and/or seizures in infancy as the leading manifestations in a smaller group (5/20 patients). The subsequent clinical picture was dominated by impaired physical growth and a very consistent pattern of static cerebral palsy-like encephalopathy with spasticity and severe to profound mental retardation seen in over 80% of cases. Most patients had a positive family history. We propose testing for the R446* mutation in PDHX as a rapid first screening in Roma infants with metabolic acidosis. It will facilitate and accelerate diagnosis in a large proportion of cases, allow early rehabilitation to alleviate the chronic clinical course, and prevent further affected births in high-risk families.

Raman spectroscopy techniques for detection of energetic materials at high and low concentration

This thesis presents the development of a rapid, sensitive and reproducible spectroscopic method for the detection of TNT in forensic and environmental applications. Simple nano sensors prepared by cost effective methods were utilized as sensitive platforms for the detection of TNT by surface enhanced Raman spectroscopy. The optimization of the substrate and the careful selection of a suitable recognition molecule contributed to the significant improvements of sensitive and selective targeting over current detection methods. The work presented in this thesis paves the way for effective detection and monitoring of explosives residues in law enforcement and environmental health applications.