Talking of many things : using topical networks to study discussions in social media

This paper outlines a method for studying online activity using both qualitative and quantitative methods: topical network analysis. A topical network refers to "the collection of sites commenting on a particular event or issue, and the links between them" (Highfield, Kirchhoff, & Nicolai, 2011, p. 341). The approach is a complement for the analysis of large datasets enabling the examination and comparison of different discussions as a means of improving our understanding of the uses of social media and other forms of online communication. Developed for an analysis of political blogging, the method also has wider applications for other social media websites such as Twitter.

Quantitative approaches to comparing communication patterns on Twitter

To date, the available literature mainly discusses Twitter activity patterns in the context of individual case studies, while comparative research on a large number of communicative events and their dynamics and patterns is missing. By conducting a comparative study of more than 40 different cases (covering topics such as elections, natural disasters, corporate crises, and televised events) we identify a number of distinct types of discussion that can be observed on Twitter. Drawing on a range of communicative metrics, we show that thematic and contextual factors influence the usage of different communicative tools available to Twitter users, such as original tweets, @replies, retweets, and URLs. Based on this first analysis of the overall metrics of Twitter discussions, we also demonstrate stable patterns in the use of Twitter in the context of major topics and events.

Urban agriculture : a growing field of research workshop at INTERACT 2013

Growing food presents diverse challenges and opportunities within the urban environment. As cities develop, population density rises, land prices rise, and the opportunity to use land for traditional farming and gardening diminishes. Counter to this trend there are a growing number of both community gardens, city farms, guerrilla gardening, rooftop and vertical gardens, pot plants, windowsill herbs, and other balcony or backyard gardens cropping up in different cities, all with a purpose to produce food. This workshop brings to-gether practitioners and researchers in the field of urban agriculture and Hu-man-Computer Interaction to explore and opportunities for technology design to support the different forms of growing practice and foster local food production in cities. This 1-day workshop will serve as an active forum for researchers and practi-tioners across various fields including, but not limited to, agriculture and gar-dening, education, urban planning, human-computer interaction, and communi-ty engagement. This workshop has three distinct points of focus: i) Individual and small-scale gardening and food production, and how to connect like minded people who are involved in these practices to share their knowledge ii) Com-munities involved in urban agriculture, either through community gardens, city farms, or grassroots movements, often dependant on volunteer participation, providing the challenge of managing limited resources iii) Environmental and sociocultural sustainability through urban agriculture. The participants will have an opportunity to present their own work. This will be followed by a visit to a nearby city farm, which will provide a local context for a group design exercise. Finally the workshop will conclude with panel dis-cussions to review opportunities for further research and collaborations beyond the conference. For more information, please visit the workshop website, at http://www.urbaninformatics.net/resources/interact2013cfp/

Isolation of two phenylethanoid glycosides from Eremophila gilesii

The leaves of Eremophila gilesii have been used traditionally to treat colds, headaches, sores, and chest pains. Our previous screening of Australian native plants showed that the methanol extract of the aerial parts of E. gilesii demonstrated notable inhibition of ADP-induced human platelet aggregation and serotonin release. Subsequent fractionation on the methanol extract led to the isolation of two phenylethanoid glycosides, verbascoside (1) and poliumoside (2). This is the first study reporting the presence of phenylethanoid glycosides in E. gilesii.

Shared caregiving responsibilities of adult siblings with elderly parents

This paper uses a nonstructural, ordered discrete choice model to measure the effects of various parent and child characteristics upon the independent caregiving decisions of the adult children of elderly parents sampled in the 1982 and 1984 National Long Term Care Survey (NLTCS). While significant effects are noted, emphasis is placed on test statistics constructed to measure the independence of caregiving decisions. The test statistic results are conclusive: The caregiving decisions of adult children are dependent across time and family members. Structural models taking dependencies among family members into account note effects similar to those in the nonstructural model.

Fatal consequences: An analysis of the failed employee voice system at the Bundaberg Hospital

In this paper we discuss the failure of the employee voice system at the Bundaberg Base Hospital (BBH) in Australia. Surgeon Jayant Patel was arrested over the deaths of patients on whom he operated when he was the director of surgery at the hospital. Our interest is in the reasons the established employee voice mechanisms failed when employees attempted to bring serious issues to the attention of managers. Our data is based on an analysis of the sworn testimonies of participants who participated in two inquiries concerning these events. An analysis of the events with a particular focus on the failings of the voice system is presented. We ask the following: how and why did the voice systems in the case of the BBH fail?

Genetic and environmental influences on neuroimaging phenotypes: A meta-analytical perspective on twin imaging studies

Because brain structure and function are affected in neurological and psychiatric disorders, it is important to disentangle the sources of variation in these phenotypes. Over the past 15 years, twin studies have found evidence for both genetic and environmental influences on neuroimaging phenotypes, but considerable variation across studies makes it difficult to draw clear conclusions about the relative magnitude of these influences. Here we performed the first meta-analysis of structural MRI data from 48 studies on >1,250 twin pairs, and diffusion tensor imaging data from 10 studies on 444 twin pairs. The proportion of total variance accounted for by genes (A), shared environment (C), and unshared environment (E), was calculated by averaging A, C, and E estimates across studies from independent twin cohorts and weighting by sample size. The results indicated that additive genetic estimates were significantly different from zero for all metaanalyzed phenotypes, with the exception of fractional anisotropy (FA) of the callosal splenium, and cortical thickness (CT) of the uncus, left parahippocampal gyrus, and insula. For many phenotypes there was also a significant influence of C. We now have good estimates of heritability for many regional and lobar CT measures, in addition to the global volumes. Confidence intervals are wide and number of individuals small for many of the other phenotypes. In conclusion, while our meta-analysis shows that imaging measures are strongly influenced by genes, and that novel phenotypes such as CT measures, FA measures, and brain activation measures look especially promising, replication across independent samples and demographic groups is necessary.

Alzheimer's disease risk gene, GAB2, is associated with regional brain volume differences in 755 young healthy twins

The development of late-onset Alzheimer's disease (LOAD) is under strong genetic control and there is great interest in the genetic variants that confer increased risk. The Alzheimer's disease risk gene, growth factor receptor bound protein 2-associated protein (GAB2), has been shown to provide a 1.27- 1.51 increased odds of developing LOAD for rs7101429 major allele carriers, in case-control analysis. GAB2 is expressed across the brain throughout life, and its role in LOAD pathology is well understood. Recent studies have begun to examine the effect of genetic variation in the GAB2 gene on differences in the brain. However, the effect of GAB2 on the young adult brain has yet to be considered. Here we found a significant association between the GAB2 gene and morphological brain differences in 755 young adult twins (469 females) (M = 23.1, SD = 3.1 years), using a gene-based test with principal components regression (PCReg). Detectable differences in brain morphology are therefore associated with variation in the GAB2 gene, even in young adults, long before the typical age of onset of Alzheimer's disease.

Does the technique employed for skin temperature assessment alter outcomes? A systematic review

Skin temperature is an important physiological measure that can reflect the presence of illness and injury as well as provide insight into the localised interactions between the body and the environment. The aim of this systematic review was to analyse the agreement between conductive and infrared means of assessing skin temperature which are commonly employed in in clinical, occupational, sports medicine, public health and research settings. Full-text eligibility was determined independently by two reviewers. Studies meeting the following criteria were included in the review: 1) the literature was written in English, 2) participants were human (in vivo), 3) skin surface temperature was assessed at the same site, 4) with at least two commercially available devices employed—one conductive and one infrared—and 5) had skin temperature data reported in the study. A computerised search of four electronic databases, using a combination of 21 keywords, and citation tracking was performed in January 2015. A total of 8,602 were returned. Methodology quality was assessed by 2 authors independently, using the Cochrane risk of bias tool. A total of 16 articles (n = 245) met the inclusion criteria. Devices are classified to be in agreement if they met the clinically meaningful recommendations of mean differences within ±0.5 °C and limits of agreement of ±1.0 °C. Twelve of the included studies found mean differences greater than ±0.5 °C between conductive and infrared devices. In the presence of external stimulus (e.g. exercise and/or heat) five studies foundexacerbated measurement differences between conductive and infrared devices. This is the first review that has attempted to investigate presence of any systemic bias between infrared and conductive measures by collectively evaluating the current evidence base. There was also a consistently high risk of bias across the studies, in terms of sample size, random sequence generation, allocation concealment, blinding and incomplete outcome data. This systematic review questions the suitability of using infrared cameras in stable, resting, laboratory conditions. Furthermore, both infrared cameras and thermometers in the presence of sweat and environmental heat demonstrate poor agreement when compared to conductive devices. These findings have implications for clinical, occupational, public health, sports science and research fields.

Short-rib polydactyly and jeune syndromes are caused by mutations in WDR60

Short-rib polydactyly syndromes (SRPS I-V) are a group of lethal congenital disorders characterized by shortening of the ribs and long bones, polydactyly, and a range of extraskeletal phenotypes. A number of other disorders in this grouping, including Jeune and Ellis-van Creveld syndromes, have an overlapping but generally milder phenotype. Collectively, these short-rib dysplasias (with or without polydactyly) share a common underlying defect in primary cilium function and form a subset of the ciliopathy disease spectrum. By using whole-exome capture and massive parallel sequencing of DNA from an affected Australian individual with SRPS type III, we detected two novel heterozygous mutations in WDR60, a relatively uncharacterized gene. These mutations segregated appropriately in the unaffected parents and another affected family member, confirming compound heterozygosity, and both were predicted to have a damaging effect on the protein. Analysis of an additional 54 skeletal ciliopathy exomes identified compound heterozygous mutations in WDR60 in a Spanish individual with Jeune syndrome of relatively mild presentation. Of note, these two families share one novel WDR60 missense mutation, although haplotype analysis suggested no shared ancestry. We further show that WDR60 localizes at the base of the primary cilium in wild-type human chondrocytes, and analysis of fibroblasts from affected individuals revealed a defect in ciliogenesis and aberrant accumulation of the GLI2 transcription factor at the centrosome or basal body in the absence of an obvious axoneme. These findings show that WDR60 mutations can cause skeletal ciliopathies and suggest a role for WDR60 in ciliogenesis.

Genome-wide association studies of quantitative traits with related individuals: Little (power) lost but much to be gained

For complex disease genetics research in human populations, remarkable progress has been made in recent times with the publication of a number of genome-wide association scans (GWAS) and subsequent statistical replications. These studies have identified new genes and pathways implicated in disease, many of which were not known before. Given these early successes, more GWAS are being conducted and planned, both for disease and quantitative phenotypes. Many researchers and clinicians have DNA samples available on collections of families, including both cases and controls. Twin registries around the world have facilitated the collection of large numbers of families, with DNA and multiple quantitative phenotypes collected on twin pairs and their relatives. In the design of a new GWAS with a fixed budget for the number of chips, the question arises whether to include or exclude related individuals. It is commonly believed to be preferable to use unrelated individuals in the first stage of a GWAS because relatives are 'over-matched' for genotypes. In this study, we quantify that for GWAS of a quantitative phenotype, relative to a sample of unrelated individuals surprisingly little power is lost when using relatives. The advantages of using relatives are manifold, including the ability to perform more quality control, the choice to perform within-family tests of association that are robust to population stratification, and the ability to perform joint linkage and association analysis. Therefore, the advantages of using relatives in GWAS for quantitative traits may well outweigh the small disadvantage in terms of statistical power.

Significant evidence of one or more susceptibility loci for endometriosis with near-Mendelian inheritance on chromosome 7p13-15

BACKGROUND: Endometriosis is a common disease with a heritable component. The collaborative International Endogene Study consists of two data sets (Oxford and Australia) comprising 1176 families with multiple affected. The aim was to investigate whether the apparent concentration of cases in a proportion of families could be explained by one or more rare variants with (near-)Mendelian autosomal inheritance. METHODS AND RESULTS: Linkage analyses (aimed at finding chromosomal regions harbouring disease-predisposing genes) were conducted in families with three or more affected (Oxford: n = 52; Australia: n = 196). In the Oxford data set, a non-parametric linkage score (Kong & Cox (K&C) Log of ODds (LOD)) of 3.52 was observed on chromosome 7p (genome-wide significance P = 0.011). A parametric MOD score (equal to maximum LOD maximized over 357 possible inheritance models) of 3.89 was found at 65.72 cM (D7S510) for a dominant model with reduced penetrance. After including the Australian data set, the non-parametric K&C LOD of the combined data set was 1.46 at 57.3 cM; the parametric analysis found an MOD score of 3.30 at D7S484 (empirical significance: P = 0.035) for a recessive model with high penetrance. Critical recombinant analysis narrowed the probable region of linkage down to overlapping 6.4 Mb and 11 Mb intervals containing 48 and 96 genes, respectively. CONCLUSIONS: This is the first report to suggest that there may be one or more high-penetrance susceptibility loci for endometriosis with (near-)Mendelian inheritance.

Genomewide linkage study in 1,176 affected sister pair families identifies a significant susceptibility locus for endometriosis on chromosome 10q26

Endometriosis is a common gynecological disease that affects up to 10% of women in their reproductive years. It causes pelvic pain, severe dysmenorrhea, and subfertility. The disease is defined as the presence of tissue resembling endometrium in sites outside the uterus. Its cause remains uncertain despite >50 years of hypothesis-driven research, and thus the therapeutic options are limited. Disease predisposition is inherited as a complex genetic trait, which provides an alternative route to understanding the disease. We seek to identify susceptibility loci, using a positional-cloning approach that starts with linkage analysis to identify genomic regions likely to harbor these genes. We conducted a linkage study of 1,176 families (931 from an Australian group and 245 from a U.K. group), each with at least two members--mainly affected sister pairs--with surgically diagnosed disease. We have identified a region of significant linkage on chromosome 10q26 (maximum LOD score [MLS] of 3.09; genomewide P = .047) and another region of suggestive linkage on chromosome 20p13 (MLS = 2.09). Minor peaks (with MLS > 1.0) were found on chromosomes 2, 6, 7, 8, 12, 14, 15, and 17. This is the first report of linkage to a major locus for endometriosis. The findings will facilitate discovery of novel positional genetic variants that influence the risk of developing this debilitating disease. Greater understanding of the aberrant cellular and molecular mechanisms involved in the etiology and pathophysiology of endometriosis should lead to better diagnostic methods and targeted treatments.

Genomewide significant linkage to migrainous headache on chromosome 5q21

Familial typical migraine is a common, complex disorder that shows strong familial aggregation. Using latent-class analysis (LCA), we identified subgroups of people with migraine/severe headache in a community sample of 12,245 Australian twins (60% female), drawn from two cohorts of individuals aged 23-90 years who completed an interview based on International Headache Society criteria. We report results from genomewide linkage analyses involving 756 twin families containing a total of 790 independent sib pairs (130 affected concordant, 324 discordant, and 336 unaffected concordant for LCA-derived migraine). Quantitative-trait linkage analysis produced evidence of significant linkage on chromosome 5q21 and suggestive linkage on chromosomes 8, 10, and 13. In addition, we replicated previously reported typical-migraine susceptibility loci on chromosomes 6p12.2-p21.1 and 1q21-q23, the latter being within 3 cM of the rare autosomal dominant familial hemiplegic migraine gene (ATP1A2), a finding which potentially implicates ATP1A2 in familial typical migraine for the first time. Linkage analyses of individual migraine symptoms for our six most interesting chromosomes provide tantalizing hints of the phenotypic and genetic complexity of migraine. Specifically, the chromosome 1 locus is most associated with phonophobia; the chromosome 5 peak is predominantly associated with pulsating headache; the chromosome 6 locus is associated with activity-prohibiting headache and photophobia; the chromosome 8 locus is associated with nausea/vomiting and moderate/severe headache; the chromosome 10 peak is most associated with phonophobia and photophobia; and the chromosome 13 peak is completely due to association with photophobia. These results will prove to be invaluable in the design and analysis of future linkage and linkage disequilibrium studies of migraine.