Bayesian correlated clustering to integrate multiple datasets

Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct – but often complementary – information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured via parameters that describe the agreement among the datasets. Results: Using a set of 6 artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real S. cerevisiae datasets. In the 2-dataset case, we show that MDI’s performance is comparable to the present state of the art. We then move beyond the capabilities of current approaches and integrate gene expression, ChIP-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques – as well as to non-integrative approaches – demonstrate that MDI is very competitive, while also providing information that would be difficult or impossible to extract using other methods

School industry partnerships: An innovative strategy for vocational education

One of the challenges confronting contemporary education internationally is to ensure that students are provided with opportunities to make informed choices about future careers and to acquire the capacity to transition into these careers. Schools need to manage their curricula, teacher capacity, timetables, and diversity of student populations by offering pathways that are seen as engaging and meaningful to life beyond schooling. Traditionally, education in the senior years has privileged those students who intend to progress to advanced studies at university or in other professional careers. In more recent times, in response the need for more sophisticated technical knowledge in the trades and a growing skills shortages in these fields, schools have paid more attention to vocational education. It has been argued that the vocational aspect of the school curriculum is less well understood and poorly implemented in comparison with the traditional academic curricula. One attempt to address this issue is through the establishment of school-industry partnerships. This paper explores the process of knowledge transfer between industry and schools in these partnerships. The paper theorises how knowledge that is valued and foundational in workplace employment can inform school curricula and pedagogical practices. The paper draws on theories of organisational knowledge, workplace learning and experiential learning to explore strategies that enhance school-to-employment transition outcomes

Cooperative education through a large scale industry-school partnership

In most of the advanced economies, students are losing interest in careers especially in en¬gineering and related industries. Hence, western economies are confronting a critical skilled labour shortage in areas of technology, science and engineering. Decisions about career pathways are made as early as the primary years of schooling and hence cooperation be¬tween industry and schools to attract students to the professions is crucial. The aim of this paper is to document how the organisational and institutional elements of one industry-school partnerships initiative — The Gateway Schools Program — contribute to productive knowledge sharing and networking. In particular this paper focuses on an initiative of an Australian State government in response to a perceived crisis around the skills shortage in an economy transitioning from a localised to a global knowledge production economy. The Gateway Schools initiative signals the first sustained attempt in Australia to incorporate schools into production networks through strategic partnerships linking them to partner organisations at the industry level. We provide case examples of how four schools opera¬tionalise the partnerships with the minerals and energy industries and how these partner¬ships as knowledge assets impact the delivery of curriculum and capacity building among teachers. Our ultimate goal is to define those characteristics of successful partnerships that do contribute to enhanced interest and engagement by students in those careers that are currently experiencing critical shortages

DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia

We performed a systematic analysis of blood DNA methylation profiles from 4483 participants from seven independent cohorts identifying differentially methylated positions (DMPs) associated with psychosis, schizophrenia, and treatment-resistant schizophrenia. Psychosis cases were characterized by significant differences in measures of blood cell proportions and elevated smoking exposure derived from the DNA methylation data, with the largest differences seen in treatment-resistant schizophrenia patients. We implemented a stringent pipeline to meta-analyze epigenome-wide association study (EWAS) results across datasets, identifying 95 DMPs associated with psychosis and 1048 DMPs associated with schizophrenia, with evidence of colocalization to regions nominated by genetic association studies of disease. Many schizophrenia-associated DNA methylation differences were only present in patients with treatment-resistant schizophrenia, potentially reflecting exposure to the atypical antipsychotic clozapine. Our results highlight how DNA methylation data can be leveraged to identify physiological (e.g., differential cell counts) and environmental (e.g., smoking) factors associated with psychosis and molecular biomarkers of treatment-resistant schizophrenia.Peer reviewe