Genome-wide interaction analysis reveals replicated epistatic effects on brain structure

The discovery of several genes that affect the risk for Alzheimer's disease ignited a worldwide search for single-nucleotide polymorphisms (SNPs), common genetic variants that affect the brain. Genome-wide search of all possible SNP-SNP interactions is challenging and rarely attempted because of the complexity of conducting approximately 1011 pairwise statistical tests. However, recent advances in machine learning, for example, iterative sure independence screening, make it possible to analyze data sets with vastly more predictors than observations. Using an implementation of the sure independence screening algorithm (called EPISIS), we performed a genome-wide interaction analysis testing all possible SNP-SNP interactions affecting regional brain volumes measured on magnetic resonance imaging and mapped using tensor-based morphometry. We identified a significant SNP-SNP interaction between rs1345203 and rs1213205 that explains 1.9% of the variance in temporal lobe volume. We mapped the whole brain, voxelwise effects of the interaction in the Alzheimer's Disease Neuroimaging Initiative data set and separately in an independent replication data set of healthy twins (Queensland Twin Imaging). Each additional loading in the interaction effect was associated with approximately 5% greater brain regional brain volume (a protective effect) in both Alzheimer's Disease Neuroimaging Initiative and Queensland Twin Imaging samples.

Genome-wide association identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects

Deficits in lentiform nucleus volume and morphometry are implicated in a number of genetically influenced disorders, including Parkinson's disease, schizophrenia, and ADHD. Here we performed genome-wide searches to discover common genetic variants associated with differences in lentiform nucleus volume in human populations. We assessed structural MRI scans of the brain in two large genotyped samples: the Alzheimer's Disease Neuroimaging Initiative (ADNI; N = 706) and the Queensland Twin Imaging Study (QTIM; N = 639). Statistics of association from each cohort were combined meta-analytically using a fixed-effects model to boost power and to reduce the prevalence of false positive findings. We identified a number of associations in and around the flavin-containing monooxygenase (FMO) gene cluster. The most highly associated SNP, rs1795240, was located in the FMO3 gene; after meta-analysis, it showed genome-wide significant evidence of association with lentiform nucleus volume (PMA = 4. 79 × 10-8). This commonly-carried genetic variant accounted for 2. 68 % and 0. 84 % of the trait variability in the ADNI and QTIM samples, respectively, even though the QTIM sample was on average 50 years younger. Pathway enrichment analysis revealed significant contributions of this gene to the cytochrome P450 pathway, which is involved in metabolizing numerous therapeutic drugs for pain, seizures, mania, depression, anxiety, and psychosis. The genetic variants we identified provide replicated, genome-wide significant evidence for the FMO gene cluster's involvement in lentiform nucleus volume differences in human populations.

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.

Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity

Aberrant connectivity is implicated in many neurological and psychiatric disorders, including Alzheimer's disease and schizophrenia. However, other than a few disease-associated candidate genes, we know little about the degree to which genetics play a role in the brain networks; we know even less about specific genes that influence brain connections. Twin and family-based studies can generate estimates of overall genetic influences on a trait, but genome-wide association scans (GWASs) can screen the genome for specific variants influencing the brain or risk for disease. To identify the heritability of various brain connections, we scanned healthy young adult twins with high-field, highangular resolution diffusion MRI. We adapted GWASs to screen the brain's connectivity pattern, allowing us to discover genetic variants that affect the human brain's wiring. The association of connectivity with the SPON1 variant at rs2618516 on chromosome 11 (11p15.2) reached connectome-wide, genome-wide significance after stringent statistical corrections were enforced, and it was replicated in an independent subsample. rs2618516 was shown to affect brain structure in an elderly population with varying degrees of dementia. Older people who carried the connectivity variant had significantly milder clinical dementia scores and lower risk of Alzheimer's disease. As a posthoc analysis, we conducted GWASs on several organizational and topological network measures derived from the matrices to discover variants in and around genes associated with autism (MACROD2), development (NEDD4), and mental retardation (UBE2A) significantly associated with connectivity. Connectome-wide, genome-wide screening offers substantial promise to discover genes affecting brain connectivity and risk for brain diseases.

A genome-wide association study identifies five loci influencing facial morphology in Europeans

Inter-individual variation in facial shape is one of the most noticeable phenotypes in humans, and it is clearly under genetic regulation; however, almost nothing is known about the genetic basis of normal human facial morphology. We therefore conducted a genome-wide association study for facial shape phenotypes in multiple discovery and replication cohorts, considering almost ten thousand individuals of European descent from several countries. Phenotyping of facial shape features was based on landmark data obtained from three-dimensional head magnetic resonance images (MRIs) and two-dimensional portrait images. We identified five independent genetic loci associated with different facial phenotypes, suggesting the involvement of five candidate genes-PRDM16, PAX3, TP63, C5orf50, and COL17A1-in the determination of the human face. Three of them have been implicated previously in vertebrate craniofacial development and disease, and the remaining two genes potentially represent novel players in the molecular networks governing facial development. Our finding at PAX3 influencing the position of the nasion replicates a recent GWAS of facial features. In addition to the reported GWA findings, we established links between common DNA variants previously associated with NSCL/P at 2p21, 8q24, 13q31, and 17q22 and normal facial-shape variations based on a candidate gene approach. Overall our study implies that DNA variants in genes essential for craniofacial development contribute with relatively small effect size to the spectrum of normal variation in human facial morphology. This observation has important consequences for future studies aiming to identify more genes involved in the human facial morphology, as well as for potential applications of DNA prediction of facial shape such as in future forensic applications.

Trick or treaty?: The Australian debate over the Anti-Counterfeiting Trade Agreement

The secretive 2011 Anti-Counterfeiting Trade Agreement – known in short by the catchy acronym ACTA – is a controversial trade pact designed to provide for stronger enforcement of intellectual property rights. The preamble to the treaty reads like pulp fiction – it raises moral panics about piracy, counterfeiting, organised crime, and border security. The agreement contains provisions on civil remedies and criminal offences; copyright law and trademark law; the regulation of the digital environment; and border measures. Memorably, Susan Sell called the international treaty a TRIPS Double-Plus Agreement, because its obligations far exceed those of the World Trade Organization's TRIPS Agreement 1994, and TRIPS-Plus Agreements, such as the Australia-United States Free Trade Agreement 2004. ACTA lacks the language of other international intellectual property agreements, which emphasise the need to balance the protection of intellectual property owners with the wider public interest in access to medicines, human development, and transfer of knowledge and technology. In Australia, there was much controversy both about the form and the substance of ACTA. While the Department of Foreign Affairs and Trade was a partisan supporter of the agreement, a wide range of stakeholders were openly critical. After holding hearings and taking note of the position of the European Parliament and the controversy in the United States, the Joint Standing Committee on Treaties in the Australian Parliament recommended the deferral of ratification of ACTA. This was striking as representatives of all the main parties agreed on the recommendation. The committee was concerned about the lack of transparency, due process, public participation, and substantive analysis of the treaty. There were also reservations about the ambiguity of the treaty text, and its potential implications for the digital economy, innovation and competition, plain packaging of tobacco products, and access to essential medicines. The treaty has provoked much soul-searching as to whether the Trick or Treaty reforms on the international treaty-making process in Australia have been compromised or undermined. Although ACTA stalled in the Australian Parliament, the debate over it is yet to conclude. There have been concerns in Australia and elsewhere that ACTA will be revived as a ‘zombie agreement’. Indeed, in March 2013, the Canadian government introduced a bill to ensure compliance with ACTA. Will it be also resurrected in Australia? Has it already been revived? There are three possibilities. First, the Australian government passed enhanced remedies with respect to piracy, counterfeiting and border measures in a separate piece of legislation – the Intellectual Property Laws Amendment (Raising the Bar) Act 2012 (Cth). Second, the Department of Foreign Affairs and Trade remains supportive of ACTA. It is possible, after further analysis, that the next Australian Parliament – to be elected in September 2013 – will ratify the treaty. Third, Australia is involved in the Trans-Pacific Partnership negotiations. The government has argued that ACTA should be a template for the Intellectual Property Chapter in the Trans-Pacific Partnership. The United States Trade Representative would prefer a regime even stronger than ACTA. This chapter provides a portrait of the Australian debate over ACTA. It is the account of an interested participant in the policy proceedings. This chapter will first consider the deliberations and recommendations of the Joint Standing Committee on Treaties on ACTA. Second, there was a concern that ACTA had failed to provide appropriate safeguards with respect to civil liberties, human rights, consumer protection and privacy laws. Third, there was a concern about the lack of balance in the treaty’s copyright measures; the definition of piracy is overbroad; the suite of civil remedies, criminal offences and border measures is excessive; and there is a lack of suitable protection for copyright exceptions, limitations and remedies. Fourth, there was a worry that the provisions on trademark law, intermediary liability and counterfeiting could have an adverse impact upon consumer interests, competition policy and innovation in the digital economy. Fifth, there was significant debate about the impact of ACTA on pharmaceutical drugs, access to essential medicines and health-care. Sixth, there was concern over the lobbying by tobacco industries for ACTA – particularly given Australia’s leadership on tobacco control and the plain packaging of tobacco products. Seventh, there were concerns about the operation of border measures in ACTA. Eighth, the Joint Standing Committee on Treaties was concerned about the jurisdiction of the ACTA Committee, and the treaty’s protean nature. Finally, the chapter raises fundamental issues about the relationship between the executive and the Australian Parliament with respect to treaty-making. There is a need to reconsider the efficacy of the Trick or Treaty reforms passed by the Australian Parliament in the 1990s.

A Submission to the Joint Standing Committee on Treaties on the Anti-Counterfeiting Trade Agreement 2011 (# ACTA)

“If Hollywood could order intellectual property laws for Christmas, what would they look like? This is pretty close.” David Fewer “While European and American IP maximalists have pushed for TRIPS-Plus provisions in FTAs and bilateral agreements, they are now pushing for TRIPS-Plus-Plus protections in these various forums.” Susan Sell “ACTA is a threat to the future of a free and open Internet.” Alexander Furnas “Implementing the agreement could open a Pandora's box of potential human rights violations.” Amnesty International. “I will not take part in this masquerade.” Kader Arif, Rapporteur for the Anti-Counterfeiting Trade Agreement 2011 in the European Parliament Executive Summary As an independent scholar and expert in intellectual property, I am of the view that the Australian Parliament should reject the adoption of the Anti-Counterfeiting Trade Agreement 2011. I would take issue with the Department of Foreign Affairs and Trade’s rather partisan account of the negotiations, the consultations, and the outcomes associated with the Anti-Counterfeiting Trade Agreement 2011. In my view, the negotiations were secretive and biased; the local consultations were sometimes farcical because of the lack of information about the draft texts of the agreement; and the final text of the Anti-Counterfeiting Trade Agreement 2011 is not in the best interests of Australia, particularly given that it is a net importer of copyright works and trade mark goods and services. I would also express grave reservations about the quality of the rather pitiful National Interest Analysis – and the lack of any regulatory impact statement – associated with the Anti-Counterfeiting Trade Agreement 2011. The assertion that the Anti-Counterfeiting Trade Agreement 2011 does not require legislative measures is questionable – especially given the United States Trade Representative has called the agreement ‘the highest-standard plurilateral agreement ever achieved concerning the enforcement of intellectual property rights.’ It is worthwhile reiterating that there has been much criticism of the secretive and partisan nature of the negotiations surrounding the Anti-Counterfeiting Trade Agreement 2011. Sean Flynn summarizes these concerns: "The negotiation process for ACTA has been a case study in establishing the conditions for effective industry capture of a lawmaking process. Instead of using the relatively transparent and inclusive multilateral processes, ACTA was launched through a closed and secretive “‘club approach’ in which like-minded jurisdictions define enforcement ‘membership’ rules and then invite other countries to join, presumably via other trade agreements.” The most influential developing countries, including Brazil, India, China and Russia, were excluded. Likewise, a series of manoeuvres ensured that public knowledge about the specifics of the agreement and opportunities for input into the process were severely limited. Negotiations were held with mere hours notice to the public as to when and where they would be convened, often in countries half away around the world from where public interest groups are housed. Once there, all negotiation processes were closed to the public. Draft texts were not released before or after most negotiating rounds, and meetings with stakeholders took place only behind closed doors and off the record. A public release of draft text, in April 2010, was followed by no public or on-the-record meetings with negotiators." Moreover, it is disturbing that the Anti-Counterfeiting Trade Agreement 2011 has been driven by ideology and faith, rather than by any evidence-based policy making Professor Duncan Matthews has raised significant questions about the quality of empirical evidence used to support the proposal of Anti-Counterfeiting Trade Agreement 2011: ‘There are concerns that statements about levels of counterfeiting and piracy are based either on customs seizures, with the actual quantities of infringing goods in free circulation in any particular market largely unknown, or on estimated losses derived from industry surveys.’ It is particularly disturbing that, in spite of past criticism, the Department of Foreign Affairs and Trade has supported the Anti-Counterfeiting Trade Agreement 2011, without engaging the Productivity Commission or the Treasury to do a proper economic analysis of the proposed treaty. Kader Arif, Rapporteur for the Anti-Counterfeiting Trade Agreement 2011 in the European Parliament, quit his position, and said of the process: "I want to denounce in the strongest possible manner the entire process that led to the signature of this agreement: no inclusion of civil society organisations, a lack of transparency from the start of the negotiations, repeated postponing of the signature of the text without an explanation being ever given, exclusion of the EU Parliament's demands that were expressed on several occasions in our assembly. As rapporteur of this text, I have faced never-before-seen manoeuvres from the right wing of this Parliament to impose a rushed calendar before public opinion could be alerted, thus depriving the Parliament of its right to expression and of the tools at its disposal to convey citizens' legitimate demands.” Everyone knows the ACTA agreement is problematic, whether it is its impact on civil liberties, the way it makes Internet access providers liable, its consequences on generic drugs manufacturing, or how little protection it gives to our geographical indications. This agreement might have major consequences on citizens' lives, and still, everything is being done to prevent the European Parliament from having its say in this matter. That is why today, as I release this report for which I was in charge, I want to send a strong signal and alert the public opinion about this unacceptable situation. I will not take part in this masquerade." There have been parallel concerns about the process and substance of the Anti-Counterfeiting Trade Agreement 2011 in the context of Australia. I have a number of concerns about the substance of the Anti-Counterfeiting Trade Agreement 2011. First, I am concerned that the Anti-Counterfeiting Trade Agreement 2011 fails to provide appropriate safeguards in respect of human rights, consumer protection, competition, and privacy laws. It is recommended that the new Joint Parliamentary Committee on Human Rights investigate this treaty. Second, I argue that there is a lack of balance to the copyright measures in the Anti-Counterfeiting Trade Agreement 2011 – the definition of piracy is overbroad; the suite of civil remedies, criminal offences, and border measures is excessive; and there is a lack of suitable protection for copyright exceptions, limitations, and remedies. Third, I discuss trade mark law, intermediary liability, and counterfeiting. I express my concerns, in this context, that the Anti-Counterfeiting Trade Agreement 2011 could have an adverse impact upon consumer interests, competition policy, and innovation in the digital economy. I also note, with concern, the lobbying by tobacco industries for the Anti-Counterfeiting Trade Agreement 2011 – and the lack of any recognition in the treaty for the capacity of countries to take measures of tobacco control under the World Health Organization Framework Convention on Tobacco Control. Fourth, I note that the Anti-Counterfeiting Trade Agreement 2011 provides no positive obligations to promote access to essential medicines. It is particularly lamentable that Australia and the United States of America have failed to implement the Doha Declaration on the TRIPS Agreement and Public Health 2001 and the WTO General Council Decision 2003. Fifth, I express concerns about the border measures in the Anti-Counterfeiting Trade Agreement 2011. Such measures lack balance – and unduly favour the interests of intellectual property owners over consumers, importers, and exporters. Moreover, such measures will be costly, as they involve shifting the burden of intellectual property enforcement to customs and border authorities. Interdicting, seizing, and destroying goods may also raise significant trade issues. Finally, I express concern that the Anti-Counterfeiting Trade Agreement 2011 undermines the role of existing international organisations, such as the United Nations, the World Intellectual Property Organization and the World Trade Organization, and subverts international initiatives such as the WIPO Development Agenda 2007. I also question the raison d'être, independence, transparency, and accountability of the proposed new ‘ACTA Committee’. In this context, I am concerned by the shift in the position of the Labor Party in its approach to international treaty-making in relation to intellectual property. The Australian Parliament adopted the Australia-United States Free Trade Agreement 2004, which included a large Chapter on intellectual property. The treaty was a ‘TRIPs-Plus’ agreement, because the obligations were much more extensive and prescriptive than those required under the multilateral framework established by the TRIPS Agreement 1994. During the debate over the Australia-United States Free Trade Agreement 2004, the Labor Party expressed the view that it would seek to mitigate the effects of the TRIPS-Plus Agreement, when at such time it gained power. Far from seeking to ameliorate the effects of the Australia-United States Free Trade Agreement 2004, the Labor Government would seek to lock Australia into a TRIPS-Double Plus Agreement – the Anti-Counterfeiting Trade Agreement 2011. There has not been a clear political explanation for this change in approach to international intellectual property. For both reasons of process and substance, I conclude that the Australian Parliament and the Australian Government should reject the Anti-Counterfeiting Trade Agreement 2011. The Australian Government would do better to endorse the Washington Declaration on Intellectual Property and the Public Interest 2011, and implement its outstanding obligations in respect of access to knowledge, access to essential medicines, and the WIPO Development Agenda 2007. The case study of the Anti-Counterfeiting Trade Agreement 2011 highlights the need for further reforms to the process by which Australia engages in international treaty-making.

A Submission to the Joint Standing Committee on Treaties on the Korea-Australia Free Trade Agreement (KAFTA)

Australia and South Korea have signed a new free trade agreement - the Korea-Australia Free Trade Agreement (KAFTA). Is it a fair trade fairytale? Or is it a dirty deal done dirt cheap? Or somewhere in between? It is hard to tell, given the initial secrecy of the negotiations, and the complexity of the texts of the agreement There has been much debate in Parliament over the transparency of the trade agreement; the scope of market access provided under the deal; the impact of the investment chapter, with its investor-state dispute settlement clause; the intellectual property chapter; the environment chapter; its impact upon public health; and the labor rights chapter. KAFTA provides an indication of the approach of the new Conservative Government in Australia to other trade deals – such as the Trans-Pacific Partnership.

A Submission to the Senate Legal and Constitutional Affairs Committee on the Copyright Amendment (Online Infringement) Bill 2015 (Cth)

The film company, Roadshow, the pay television company Foxtel, and Rupert Murdoch’s News Corp and News Limited — as well as copyright industries — have been clamouring for new copyright powers and remedies. In the summer break, the Coalition Government has responded to such entreaties from its industry supporters and donors, with a new package of copyright laws and policies. There has been significant debate over the proposals between the odd couple of Attorney-General George Brandis and the Minister for Communications, Malcolm Turnbull. There has been deep, philosophical differences between the two Ministers over the copyright agenda. The Attorney-General George Brandis has supported a model of copyright maximalism, with strong rights and remedies for the copyright empires in film, television, and publishing. He has shown little empathy for the information technology companies of the digital economy. The Attorney-General has been impatient to press ahead with a copyright regime. The Minister for Communications, Malcolm Turnbull, has been somewhat more circumspect,recognising that there is a need to ensure that copyright laws do not adversely impact upon competition in the digital economy. The final proposal is a somewhat awkward compromise between the discipline-and-punish regime preferred by Brandis, and the responsive regulation model favoured by Turnbull. In his new book, Information Doesn’t Want to Be Free: Laws for the Internet Age, Cory Doctorow has some sage advice for copyright owners: Things that don’t make money: * Complaining about piracy. * Calling your customers thieves. * Treating your customers like thieves. In this context, the push by copyright owners and the Coalition Government to have a copyright crackdown may well be counter-productive to their interests. This submission considers a number of key elements of the Coalition Government’s Copyright Crackdown. Part 1 examines the proposals in respect of the Copyright Amendment (Online Infringement) Bill 2015 (Cth). Part 2 focuses upon the proposed Copyright Code. Part 3 considers the question of safe harbours for intermediaries. Part 4 examines the question of copyright exceptions – particularly looking at the proposal of the Australian Law Reform Commission for the introduction of a defence of fair use. Part 5 highlights the recommendations of the IT Pricing Inquiry and the Harper Competition Policy Review in respect of copyright law, consumer rights, and competition law.

Submission to Senate Economics References Committee, An Inquiry in to Affordable Housing

Developer paid fees or infrastructure charges are a commonly used mechanism for local governments to pay for new infrastructure. However, property developers claim that these costs are merely passed on to home buyers, with adverse effects to housing affordability. Despite numerous government reports and many years of industry advocacy, there remains no empirical evidence in Australia to confirm or quantify this passing on effect to home buyers and the consequent effect on housing affordability. Hence there remains no data from which governments can base policy decision on, and the debate continues. This research examines the question of the impact of infrastructure charges on housing affordability in Australia. It employs hedonic regression methods to estimate the impact of infrastructure charges on house prices and vacant lot prices in Brisbane, Australia during 2005-2011, using a data set of 29,752 house sales, comprising 4,699 new house sales and 25,053 existing house sales and 13,739 lot sales. The regression results for the effect of infrastructure charges on house prices in Brisbane indicated that for every $1.00 of infrastructure charge levied on developers, all house prices increase by $3.69 or a 369% overpassing of these government levies onto home buyers. Thus, this one government levy could be responsible for $877 per month on home owner mortgage repayments in Brisbane, Queensland. This research is consistent with international findings, that support the proposition that developer paid infrastructure charges are passed on to home buyers and are a significant contributor to increasing house prices and reduced housing affordability. Understanding who really pays for urban infrastructure is critical to both the housing affordability and infrastructure funding debates in Australia and this research provides the first empirical data for policy makers to assess their policy objectives and outcomes against.

After 10 years of clinical trials with liraglutide, do we know whether it is beneficial in diabetes?

Type 2 diabetes remains an escalating world-wide problem, despite a range of treatments. The revelation that insulin secretion is under the control of a gut hormone, glucagon-like peptide 1 (GLP-1), led to a new paradigm in the management of type 2 diabetes. Liraglutide is a long acting GLP-1 receptor agonist used in the treatment of type 2 diabetes. The review considers the clinical trials with liraglutide. There are many comparator trials between liraglutide and other medicines for the treatment of type 2 diabetes, and these trials have shown that liraglutide lowers HbA1c and body weight, and is well tolerated. A large cardiovascular safety trial with liraglutide is presently being undertaken. After 10 years of clinical trials with liraglutide, we do not know whether liraglutide has cardiovascular safety in subjects with type 2 diabetes and high cardiovascular risk. Although this is not a requirement for registration by the Food and Drug Administration (FDA), in my opinion, they should reconsider this. We also do not presently know whether liraglutide has any beneficial effects on clinical cardiovascular outcomes.

Utility of temporal artery biopsy samples for genome-wide analysis of giant cell arteritis

Giant Cell Arteritis (GCA) is the most common vasculitis affecting the elderly. Archived formalin-fixed paraffin-embedded (FFPE) temporal artery biopsy (TAB) specimens potentially represent a valuable resource for large-scale genetic analysis of this disease. FFPE TAB samples were obtained from 12 patients with GCA. Extracted TAB DNA was assessed by real time PCR before restoration using the Illumina HD FFPE Restore Kit. Paired FFPE-blood samples were genotyped on the Illumina OmniExpress FFPE microarray. The FFPE samples that passed stringent quality control measures had a mean genotyping success of >97%. When compared with their matching peripheral blood DNA, the mean discordant heterozygote and homozygote single nucleotide polymorphisms calls were 0.0028 and 0.0003, respectively, which is within the accepted tolerance of reproducibility. This work demonstrates that it is possible to successfully obtain high-quality microarray-based genotypes FFPE TAB samples and that this data is similar to that obtained from peripheral blood.

Making an IMPACT: Campus-wide collaboration for course and learning space transformation

At Purdue University, the Libraries participate in a provost-initiated, campus-wide course redesign program called Instruction Matters: Purdue Academic Course Transformation (IMPACT). This initiative aims to bring active-learning to foundational courses traditionally taught through lectures. Purdue librarians recognized the IMPACT initiative as one way to enter the conversations blooming on our campus about the nature of learning, curriculum design, and how space design impacts potential learning. This article presents three perspectives: 1) the information literacy coordinator, 2) a libraries’ administrator with a gift for space planning, and; 3) an in-the-trenches liaison to course redesign projects. Each discusses the IMPACT initiative from his or her unique perspective and view of its impact on librarian roles. Collectively, the article explains why we think it is essential that this kind of campus effort is supported by libraries.

Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb

To gain insight into the mechanisms by which the Myb transcription factor controls normal hematopoiesis and particularly, how it contributes to leukemogenesis, we mapped the genome-wide occupancy of Myb by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) in ERMYB myeloid progenitor cells. By integrating the genome occupancy data with whole genome expression profiling data, we identified a Myb-regulated transcriptional program. Gene signatures for leukemia stem cells, normal hematopoietic stem/progenitor cells and myeloid development were overrepresented in 2368 Myb regulated genes. Of these, Myb bound directly near or within 793 genes. Myb directly activates some genes known critical in maintaining hematopoietic stem cells, such as Gfi1 and Cited2. Importantly, we also show that, despite being usually considered as a transactivator, Myb also functions to repress approximately half of its direct targets, including several key regulators of myeloid differentiation, such as Sfpi1 (also known as Pu.1), Runx1, Junb and Cebpb. Furthermore, our results demonstrate that interaction with p300, an established coactivator for Myb, is unexpectedly required for Myb-mediated transcriptional repression. We propose that the repression of the above mentioned key pro-differentiation factors may contribute essentially to Myb's ability to suppress differentiation and promote self-renewal, thus maintaining progenitor cells in an undifferentiated state and promoting leukemic transformation. © 2011 The Author(s).

An innovative online intervention: The Steering Clear First Offender Drink Driving Program

Drink driving remains a substantial public health issue warranting investigation. First offender drink drivers are seen to be less risky than repeat offenders, though the majority of first offenders report drink driving prior to detection, and many continue to drink drive following conviction. Few first offenders are offered treatment programs, and as such there is a need to address drink driving behaviour at this stage. A comprehensive approach including first offender treatment is needed to address the problem. Online interventions have demonstrated effectiveness in reducing risky behaviours such as harmful substance use. Such interventions allow for personalised tailored content to be delivered to individuals targeting specific mechanisms of behavioural change. This method also allows for targeting screening to ensure relevance of content on an individual level. However, there have been no research based online programs to date aimed at reducing repeat drink driving by first offenders. The Steering Clear First Offender Drink Driving Program is a self-guided, research based online program aimed at reducing recidivism by first time drink driving offenders. It includes a specialised web app to track drinks and build plans to prevent future drink driving. This allows for elongation of learning and encouragement of sustained behavioural change using self-monitoring after initial program completion. An outline of the program is discussed and the qualitative experience of the program on a sample of first offenders recruited at the time of court appearance is described.