Costs and benefits of ivory-billed woodpecker re-discovery

Several years ago, the purported re-discovery of the ivory-billed woodpecker (Campephilus principalis) in eastern Arkansas generated lively discussion in renowned scientific journals. The debate concerned both the central question of whether the bird videotaped in April 2004 really was an ivorybilled woodpecker (eg Fitzpatrick et al. 2005; Sibley et al. 2006) and the controversy around the resulting species recovery plan and its costs (McKelvey et al. 2008; Dalton 2010): was $14 million pointlessly spent?

Issues to consider when developing mandatory reporting legislation and policy to improve discovery of child abuse

In the United Kingdom, recent investigations into child sexual abuse occurring within schools, the Catholic Church and the British Broadcasting Corporation, have intensified debate on ways to improve the discovery of child sexual abuse, and child maltreatment generally. One approach adopted in other jurisdictions to better identify cases of severe child maltreatment is the introduction of some form of legislative mandatory reporting to require designated persons to report known and suspected cases. The debate in England has raised the prospect of whether adopting a strategy of some kind of mandatory reporting law is advisable. The purpose of this article is to add to this debate by identifying fundamental principles, issues and complexities underpinning policy and even legislative developments in the interests of children and society. The article will first highlight the data on the hidden nature of child maltreatment and the background to the debate. Secondly, it will identify some significant gaps in knowledge that need to be filled. Thirdly, the article will summarise the barriers to reporting abuse and neglect. Fourthly, we will identify a range of options for, and clarify the dilemmas in developing, legislative mandatory reporting, addressing two key issues: who should be mandated to report, and what types of child maltreatment should they be required to report? Finally, we draw attention to some inherently different goals and competing interests, both between and within the various institutions involved in the safeguarding of children and the criminal prosecution of some offenders. Based on this analysis we offer some concluding observations that we hope contribute to informed and careful debate about mandatory reporting.

Secular and religious moral grounds resonating across state schools in Indonesia

This paper describes moral education in Indonesia, more particularly, how teachers have implemented the Character Education policy issued by the Ministry of Education and Culture (MOEC) in 2010. This policy required teachers to instil certain values in every lesson, including EFL lessons, to contribute towards building a shared national moral character. Drawing on Durkheim's distinction between secular and religious morality, this paper considers how state schools accommodated and promoted this ‘rational moral education' or secular morality (Durkheim, 1925) in government schools, and how it interacted with religious moral education. This paper uses Bernstein's concepts of pedagogic discourse, instructional and regulative discourses to analyse how teachers have recontextualised this policy in the micro pedagogic settings of their EFL classes. Three types of data were collected for this study: interviews, class observations and teachers' lesson plans. In this way, four EFL teachers working in state schools were interviewed on two occasions and three of their classes were observed. The first interview identified teachers' beliefs and perceptions regarding the Character Education policy. Their classroom and lesson plans were observed to augment this information. Then the final interview asked about the teacher's thinking behind their actions in the observed classes. Since character education was issued within the broader frame of school based curriculum that offered schools and teachers more choices to develop the local curriculum and its intent, the analysis will focus on what moral premises were evident in their school and classes, and how such morality was transmitted through the EFL lessons. The conclusion suggests that teachers' implementation of moral education in their classes was dominated by their school communities and the teachers' own preferred value of religiosity. Such value played out in the classes through both the regulative discourse and the instructional discourse.

BPMN Miner: Automated Discovery of BPMN Process Models with Hierarchical Structure

Existing techniques for automated discovery of process models from event logs gen- erally produce flat process models. Thus, they fail to exploit the notion of subprocess as well as error handling and repetition constructs provided by contemporary process modeling notations, such as the Business Process Model and Notation (BPMN). This paper presents a technique for automated discovery of hierarchical BPMN models con- taining interrupting and non-interrupting boundary events and activity markers. The technique employs functional and inclusion dependency discovery techniques in order to elicit a process-subprocess hierarchy from the event log. Given this hierarchy and the projected logs associated to each node in the hierarchy, parent process and subprocess models are then discovered using existing techniques for flat process model discovery. Finally, the resulting models and logs are heuristically analyzed in order to identify boundary events and markers. By employing approximate dependency discovery tech- niques, it is possible to filter out noise in the event log arising for example from data entry errors or missing events. A validation with one synthetic and two real-life logs shows that process models derived by the proposed technique are more accurate and less complex than those derived with flat process discovery techniques. Meanwhile, a validation on a family of synthetically generated logs shows that the technique is resilient to varying levels of noise.

Basic Religious Charities

Just over 44,000 registered charities filed their first Annual Information Statement (AIS) return with the Australian Charities and Not-for-profits Commission (ACNC) before the end of October 2014. Of these, 10,918 charities self-identified as Basic Religious Charities (BRCs). These are usually, but not always, unincorporated religious congregations which receive no or little government funding. Having a central agency for reporting, in the form of the ACNC, having access to information supplied in the AIS by registered organisations has allowed access to new measures of charities and their activities. In September 2014 the ACNC, in conjunction with Curtin University Not-for-profit Initiative, released a high-level report on the first AIS, and the data were also made available digitally through the Australian Government Data Repository. This factsheet builds on that report by focusing on BRCs.

Discovery of genes that affect human brain connectivity: A genome-wide analysis of the connectome

Human brain connectivity is disrupted in a wide range of disorders from Alzheimer's disease to autism but little is known about which specific genes affect it. Here we conducted a genome-wide association for connectivity matrices that capture information on the density of fiber connections between 70 brain regions. We scanned a large twin cohort (N=366) with 4-Tesla high angular resolution diffusion imaging (105-gradient HARDI). Using whole brain HARDI tractography, we extracted a relatively sparse 70×70 matrix representing fiber density between all pairs of cortical regions automatically labeled in co-registered anatomical scans. Additive genetic factors accounted for 1-58% of the variance in connectivity between 90 (of 122) tested nodes. We discovered genome-wide significant associations between variants and connectivity. GWAS permutations at various levels of heritability, and split-sample replication, validated our genetic findings. The resulting genes may offer new leads for mechanisms influencing aberrant connectivity and neurodegeneration. © 2012 IEEE.

Discovery and replication of gene influences on brain structure using LASSO regression

We implemented least absolute shrinkage and selection operator (LASSO) regression to evaluate gene effects in genome-wide association studies (GWAS) of brain images, using an MRI-derived temporal lobe volume measure from 729 subjects scanned as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sparse groups of SNPs in individual genes were selected by LASSO, which identifies efficient sets of variants influencing the data. These SNPs were considered jointly when assessing their association with neuroimaging measures. We discovered 22 genes that passed genome-wide significance for influencing temporal lobe volume. This was a substantially greater number of significant genes compared to those found with standard, univariate GWAS. These top genes are all expressed in the brain and include genes previously related to brain function or neuropsychiatric disorders such as MACROD2, SORCS2, GRIN2B, MAGI2, NPAS3, CLSTN2, GABRG3, NRXN3, PRKAG2, GAS7, RBFOX1, ADARB2, CHD4, and CDH13. The top genes we identified with this method also displayed significant and widespread post hoc effects on voxelwise, tensor-based morphometry (TBM) maps of the temporal lobes. The most significantly associated gene was an autism susceptibility gene known as MACROD2.We were able to successfully replicate the effect of the MACROD2 gene in an independent cohort of 564 young, Australian healthy adult twins and siblings scanned with MRI (mean age: 23.8±2.2 SD years). Our approach powerfully complements univariate techniques in detecting influences of genes on the living brain.

Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N1198) using genome-wide search

The caudate is a subcortical brain structure implicated in many common neurological and psychiatric disorders. To identify specific genes associated with variations in caudate volume, structural magnetic resonance imaging and genome-wide genotypes were acquired from two large cohorts, the Alzheimer's Disease NeuroImaging Initiative (ADNI; N=734) and the Brisbane Adolescent/Young Adult Longitudinal Twin Study (BLTS; N=464). In a preliminary analysis of heritability, around 90% of the variation in caudate volume was due to genetic factors. We then conducted genome-wide association to find common variants that contribute to this relatively high heritability. Replicated genetic association was found for the right caudate volume at single-nucleotide polymorphism rs163030 in the ADNI discovery sample (P=2.36 × 10 -6) and in the BLTS replication sample (P=0.012). This genetic variation accounted for 2.79 and 1.61% of the trait variance, respectively. The peak of association was found in and around two genes, WDR41 and PDE8B, involved in dopamine signaling and development. In addition, a previously identified mutation in PDE8B causes a rare autosomal-dominant type of striatal degeneration. Searching across both samples offers a rigorous way to screen for genes consistently influencing brain structure at different stages of life. Variants identified here may be relevant to common disorders affecting the caudate.

Five years of GWAS discovery

The past five years have seen many scientific and biological discoveries made through the experimental design of genome-wide association studies (GWASs). These studies were aimed at detecting variants at genomic loci that are associated with complex traits in the population and, in particular, at detecting associations between common single-nucleotide polymorphisms (SNPs) and common diseases such as heart disease, diabetes, auto-immune diseases, and psychiatric disorders. We start by giving a number of quotes from scientists and journalists about perceived problems with GWASs. We will then briefly give the history of GWASs and focus on the discoveries made through this experimental design, what those discoveries tell us and do not tell us about the genetics and biology of complex traits, and what immediate utility has come out of these studies. Rather than giving an exhaustive review of all reported findings for all diseases and other complex traits, we focus on the results for auto-immune diseases and metabolic diseases. We return to the perceived failure or disappointment about GWASs in the concluding section. © 2012 The American Society of Human Genetics.

Genetics of rheumatoid arthritis contributes to biology and drug discovery

A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)1. Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ~10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2, 3, 4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation5, cis-acting expression quantitative trait loci6 and pathway analyses7, 8, 9—as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes—to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.