Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping

Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P < 5 × 10−8). More than 70 prostate cancer susceptibility loci, explaining ~30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies.

Referral patterns and proximity to palliative care inpatient services by level of socio-economic disadvantage : a national study using spatial analysis

Background: A range of health outcomes at a population level are related to differences in levels of social disadvantage. Understanding the impact of any such differences in palliative care is important. The aim of this study was to assess, by level of socio-economic disadvantage, referral patterns to specialist palliative care and proximity to inpatient services. Methods: All inpatient and community palliative care services nationally were geocoded (using postcode) to one nationally standardised measure of socio-economic deprivation – Socio-Economic Index for Areas (SEIFA; 2006 census data). Referral to palliative care services and characteristics of referrals were described through data collected routinely at clinical encounters. Inpatient location was measured from each person’s home postcode, and stratified by socio-economic disadvantage. Results: This study covered July – December 2009 with data from 10,064 patients. People from the highest SEIFA group (least disadvantaged) were significantly less likely to be referred to a specialist palliative care service, likely to be referred closer to death and to have more episodes of inpatient care for longer time. Physical proximity of a person’s home to inpatient care showed a gradient with increasing distance by decreasing levels of socio-economic advantage. Conclusion: These data suggest that a simple relationship of low socioeconomic status and poor access to a referral-based specialty such as palliative care does not exist. Different patterns of referral and hence different patterns of care emerge.

Integrated TEM, XRD and electron-microprobe investigation of mixed-layer chlorite smectite from the Point-Sal ophiolite, California

Five basalt samples from the Point Sal ophiolite, California, were examined using HRTEM and AEM in order to compare observations with interpretations of XRD patterns and microprobe analyses. XRD data from ethylene-glycol-saturated samples indicate the following percentages of chlorite in mixed-layer chlorite-smectite identified for each specimen: (i) L2036 almost-equal-to 50%, (ii) L2035 almost-equal-to 70 and 20%, (iii) 1A-13 almost-equal-to 70%, (iv) 1B-42 almost-equal-to 70%, and (v) 1B-55 = 100%. Detailed electron microprobe analyses show that 'chlorite' analyses with high Si, K, Na and Ca contents are the result of interlayering with smectite-like layers. The Fe/(Fe + Mg) ratios of mixed-layer phyllosilicates from Point Sal samples are influenced by the bulk rock composition, not by the percentage of chlorite nor the structure of the phyllosilicate. Measurements of lattice-fringe images indicate that both smectite and chlorite layers are present in the Point Sal samples in abundances similar to those predicted with XRD techniques and that regular alternation of chlorite and smectite occurs at the unit-cell scale. Both 10- and 14-angstrom layers were recorded with HRTEM and interpreted to be smectite and chlorite, respectively. Regular alternation of chlorite and smectite (24-angstrom periodicity) occurs in upper lava samples L2036 and 1A-13, and lower lava sample 1B-42 for as many as seven alternations per crystallite with local layer mistakes. Sample L2035 shows disordered alternation of chlorite and smectite, with juxtaposition of smectite-like layers, suggesting that randomly interlayered chlorite (< 0.5)-smectite exists. Images of lower lava sample 1B-55 show predominantly 14-angstrom layers. Units of 24 angstrom tend to cluster in what may otherwise appear to be disordered mixtures, suggesting the existence of a corrensite end-member having thermodynamic significance.

Oxide reduction in NiO-containing solid solution systems during transmission electron microscopy

The effects of electron irradiation on NiO-containing solid solution systems are described. Partially hydrated NiO solid solutions, e. g. , NiO-MgO, undergo surface reduction to Ni metal after examination by TEM. This surface layer results in the formation of Moire interference patterns.

Problem solving in the primary school (K-2)

This article focuses on problem solving activities in a first grade classroom in a typical small community and school in Indiana. But, the teacher and the activities in this class were not at all typical of what goes on in most comparable classrooms; and, the issues that will be addressed are relevant and important for students from kindergarten through college. Can children really solve problems that involve concepts (or skills) that they have not yet been taught? Can children really create important mathematical concepts on their own – without a lot of guidance from teachers? What is the relationship between problem solving abilities and the mastery of skills that are widely regarded as being “prerequisites” to such tasks?Can primary school children (whose toolkits of skills are limited) engage productively in authentic simulations of “real life” problem solving situations? Can three-person teams of primary school children really work together collaboratively, and remain intensely engaged, on problem solving activities that require more than an hour to complete? Are the kinds of learning and problem solving experiences that are recommended (for example) in the USA’s Common Core State Curriculum Standards really representative of the kind that even young children encounter beyond school in the 21st century? … This article offers an existence proof showing why our answers to these questions are: Yes. Yes. Yes. Yes. Yes. Yes. And: No. … Even though the evidence we present is only intended to demonstrate what’s possible, not what’s likely to occur under any circumstances, there is no reason to expect that the things that our children accomplished could not be accomplished by average ability children in other schools and classrooms.

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010 : a systematic analysis for the Global Burden of Disease Study 2010

Background Non-fatal health outcomes from diseases and injuries are a crucial consideration in the promotion and monitoring of individual and population health. The Global Burden of Disease (GBD) studies done in 1990 and 2000 have been the only studies to quantify non-fatal health outcomes across an exhaustive set of disorders at the global and regional level. Neither effort quantified uncertainty in prevalence or years lived with disability (YLDs). Methods Of the 291 diseases and injuries in the GBD cause list, 289 cause disability. For 1160 sequelae of the 289 diseases and injuries, we undertook a systematic analysis of prevalence, incidence, remission, duration, and excess mortality. Sources included published studies, case notification, population-based cancer registries, other disease registries, antenatal clinic serosurveillance, hospital discharge data, ambulatory care data, household surveys, other surveys, and cohort studies. For most sequelae, we used a Bayesian meta-regression method, DisMod-MR, designed to address key limitations in descriptive epidemiological data, including missing data, inconsistency, and large methodological variation between data sources. For some disorders, we used natural history models, geospatial models, back-calculation models (models calculating incidence from population mortality rates and case fatality), or registration completeness models (models adjusting for incomplete registration with health-system access and other covariates). Disability weights for 220 unique health states were used to capture the severity of health loss. YLDs by cause at age, sex, country, and year levels were adjusted for comorbidity with simulation methods. We included uncertainty estimates at all stages of the analysis. Findings Global prevalence for all ages combined in 2010 across the 1160 sequelae ranged from fewer than one case per 1 million people to 350 000 cases per 1 million people. Prevalence and severity of health loss were weakly correlated (correlation coefficient −0·37). In 2010, there were 777 million YLDs from all causes, up from 583 million in 1990. The main contributors to global YLDs were mental and behavioural disorders, musculoskeletal disorders, and diabetes or endocrine diseases. The leading specific causes of YLDs were much the same in 2010 as they were in 1990: low back pain, major depressive disorder, iron-deficiency anaemia, neck pain, chronic obstructive pulmonary disease, anxiety disorders, migraine, diabetes, and falls. Age-specific prevalence of YLDs increased with age in all regions and has decreased slightly from 1990 to 2010. Regional patterns of the leading causes of YLDs were more similar compared with years of life lost due to premature mortality. Neglected tropical diseases, HIV/AIDS, tuberculosis, malaria, and anaemia were important causes of YLDs in sub-Saharan Africa. Interpretation Rates of YLDs per 100 000 people have remained largely constant over time but rise steadily with age. Population growth and ageing have increased YLD numbers and crude rates over the past two decades. Prevalences of the most common causes of YLDs, such as mental and behavioural disorders and musculoskeletal disorders, have not decreased. Health systems will need to address the needs of the rising numbers of individuals with a range of disorders that largely cause disability but not mortality. Quantification of the burden of non-fatal health outcomes will be crucial to understand how well health systems are responding to these challenges. Effective and affordable strategies to deal with this rising burden are an urgent priority for health systems in most parts of the world. Funding Bill & Melinda Gates Foundation.

Were intercalated komatiites and dacites at the Black Swan nickel sulphide mine, Yilgarn Craton, Western Australia, emplaced as extrusive lavas or intrusive bodies? The significance of breccia textures and contact relationships

Intercalated Archean komatiites and dacites sit above a thick footwall dacite unit in the host rock succession at the Black Swan Nickel Mine, north of Kalgoorlie in the Yilgarn Craton, Western Australia. Both lithofacies occur in units that vary in scale from laterally extensive at the scale of the mine lease to localized, thin, irregular bodies, from > 100 m thick to only centimetres thick. Some dacites are only slightly altered and deformed, and are interpreted to post-date major deformation and alteration (late porphyries). However, the majority of the dacites display evidence of deformation, especially at contacts, and metamorphism, varying from silicification and chlorite alteration at contacts to pervasive low grade regional metamorphic alteration represented by common assemblages of chlorite, sericite and albite. Texturally, the dacites vary from entirely massive and coherent to partially brecciated to totally brecciated. Strangely, some dacites are coherent at the margins and brecciated internally. Breccia textures vary from cryptically defined, to blocky, closely packed, in situ jig-saw fit textures with secondary minerals in fractures between clasts, to more apparent matrix rich textures with round clast forms, giving apparent conglomerate textures. Some clast zones have multi-coloured clasts, giving the impression of varied provenance. Strangely however, all these textural variants have gradational relationships with each other, and no bedding or depositional structures are present. This indicates that all textures have an in situ origin. The komatiites are generally altered and pervasively carbonate veined. Preservation of original textures is patchy and local, but includes coarse adcumulate, mesocumulate, orthocumulate, crescumulate-harrisite and occasionally spinifex textures. Where original contacts between komatiites and dacites are preserved intact (i.e. not sheared or overprinted by alteration), the komatiites have chilled margins, whereas the dacites do not. The margins of the dacites are commonly silicified, and inclusions of dacite occur in komatiite, even at the top contacts of komatiite units, but komatiite clasts do not occur in the dacites. The komatiites therefore were emplaced as sills into the dacites, and the intercalated relationships are interpreted as intrusive. The brecciation and alteration in the dacites are interpreted as being largely due to hydraulic fracturing and alteration induced by contact metamorphic effects and hydrothermal alteration deriving from the intrusion of komatiites into the felsic pile. The absence of autobreccia and hyaloclastite textures in the dacites suggest that they were emplaced as an earlier intrusive (sill?) complex at a high level in the crust.

K from zeolite : glasshouse trial for testing K availability to the plants

MesoLite, a zeolite material manufactured by NanoChem Holdings Pty Ltd is made by caustic reaction of kaolin at temperatures between 80-95°C. This material has a moderate surface area (9~12 m2/g) and very high cation exchange capacity (500meq/100g). To measure the availability of K in K-MesoLite to plants, wheat was grown with K-MesoLite or a soluble fertiliser (e.g. KCl) in non-leached pots in a glasshouse. The weights and elemental compositions of the plants were compared after four weeks growth. Plants grown with K-MesoLite were slightly larger than those grown with KCl. The elemental compositions of the plants were similar except for Si, which was significantly higher in the plants grown with K-MesoLite than in those fertilised with KCl. K from K-MesoLite is readily available to plants.

Using patterns co-occurrence matrix for cleaning closed sequential patterns for text mining

With the overwhelming increase in the amount of texts on the web, it is almost impossible for people to keep abreast of up-to-date information. Text mining is a process by which interesting information is derived from text through the discovery of patterns and trends. Text mining algorithms are used to guarantee the quality of extracted knowledge. However, the extracted patterns using text or data mining algorithms or methods leads to noisy patterns and inconsistency. Thus, different challenges arise, such as the question of how to understand these patterns, whether the model that has been used is suitable, and if all the patterns that have been extracted are relevant. Furthermore, the research raises the question of how to give a correct weight to the extracted knowledge. To address these issues, this paper presents a text post-processing method, which uses a pattern co-occurrence matrix to find the relation between extracted patterns in order to reduce noisy patterns. The main objective of this paper is not only reducing the number of closed sequential patterns, but also improving the performance of pattern mining as well. The experimental results on Reuters Corpus Volume 1 data collection and TREC filtering topics show that the proposed method is promising.

Semantic labelling for document feature patterns using ontological subjects

Finding and labelling semantic features patterns of documents in a large, spatial corpus is a challenging problem. Text documents have characteristics that make semantic labelling difficult; the rapidly increasing volume of online documents makes a bottleneck in finding meaningful textual patterns. Aiming to deal with these issues, we propose an unsupervised documnent labelling approach based on semantic content and feature patterns. A world ontology with extensive topic coverage is exploited to supply controlled, structured subjects for labelling. An algorithm is also introduced to reduce dimensionality based on the study of ontological structure. The proposed approach was promisingly evaluated by compared with typical machine learning methods including SVMs, Rocchio, and kNN.

Spatial and temporal foraging patterns of Queensland fruit fly, Bactrocera tryoni(Froggatt) (Diptera: Tephritidae), for protein and implications for management

Fruit flies require protein for reproductive development and actively feed upon protein sources in the field. Liquid protein baits mixed with insecticide are used routinely to manage pest fruit flies, such as Bactrocera tryoni (Froggatt). However, there are still some gaps in the underpinning science required to improve the efficacy of bait spray technology. The spatial and temporal foraging behaviour of B. tryoni in response to protein was investigated in the field. A series of linked trials using either wild flies in the open field or laboratory-reared flies in field cages and a netted orchard were undertaken using nectarines and guavas. Key questions investigated were the fly's response to protein relative to: height of protein within the canopy, fruiting status of the tree, time of day, season and size of the experimental arena. Canopy height had a significant response on B. tryoni foraging, with more flies foraging on protein in the mid to upper canopy. Fruiting status also had a significant effect on foraging, with most flies responding to protein when applied to fruiting hosts. B. tryoni demonstrated a repeatable diurnal response pattern to protein, with the peak response being between 12:00–16:00 h. Season showed significant but unpredictable effects on fruit fly response to protein in the subtropical environment where the work was undertaken. Relative humidity, but not temperature or rainfall, was positively correlated with protein response. The number of B. tryoni responding to protein decreased dramatically as the spatial scale increased from field cage through to the open field. Based on these results, it is recommend that, to be most effective, protein bait sprays should be applied to the mid to upper canopies of fruiting hosts. Overall, the results show that the protein used, an industry standard, has very low attractancy to B. tryoni and that further work is urgently needed to develop more volatile protein baits.

Trends in cycling patterns and interactions with pedestrians in the city centre

All levels of government continue to advocate increasing the number of people cycling for recreation and transport. However, governments and the general public still have concerns about the implications for the safety of cyclists and other road users. While there is concern about injury for bicycle-pedestrian collisions, for 2008-09 in Australia only 40 pedestrians were hospitalised as a result of a collision with a cyclist (and 33 cyclists from collisions with pedestrians). There is little research that observes changes over time in actual cyclist behaviours and interactions with other road users. This paper presents the results of an observational study of cycling in the Brisbane Central Business District based on data collected using the same methodology in October 2010 and 2012.

Infrared and Raman spectroscopic characterization of the phosphate mineral leucophosphite - K(Fe3+)2(PO4)2(OH)·2(H2O)

The phosphate mineral leucophosphite K(Fe2)3þ(PO4)2(OH) · 2H2O has been characterized by SEM-EDS, Raman, and infrared spectro- scopic measurements. The mineral is predominantly a K and Fe phosphate with some minor substitution of Al in the Fe3þ site. Raman bands at 994 and 1058 cm-1 are assigned to the symmetric stretching modes of PO3- and HPO2- units. The Raman bands at 1104, 1135, and 1177 cm-1 are assigned to the PO3- and HPO2- antisymmetric stretching modes. Raman and infrared spectra in the 2600–3800 cm-1 region show a complex set of overlapping bands, which may be resolved into the component bands. The Raman bands observed at 3325, 3355, and 3456 cm-1 are attributed to water stretching vibrations, and in the infrared spectrum, bands at 3237, 3317, and 3453 cm-1 are assigned to water stretching bands.

Citation success over time : theory or empirics?

This study investigates the citation patterns of theoretical and empirical papers published in a top economics journal, namely American Economic Review, over a period of almost 30 years, while also exploring the determinants of citation success. The results indicate that empirical papers attract more citation success than theoretical studies. However, the pattern over time is very similar. Moreover, among empirical papers it appears that the cross-country studies are more successful than single country studies focusing on North America data or other regions.