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Additional file 16: Fig S11. Flow chart for the bioinformatic strategy used to identify candidate proximal and distal regulatory sequences upstream of schizont stage-expressed genes.

Additional file 7: Fig S5. Correlations between expression level and histones and their modifications across transcriptional units. Log2 (ChIP/input) plotted from 2500 bp upstream (−2500) to 2500 bp downstream (2500) of the transcriptional start (TSS) and stop (TES) sites for 7612 ring stage transcripts and 7711 trophozoite stage transcripts assembled by Cufflinks ranked in descending order by transcript abundance (fpkm). The Spearman r correlation value (r) for the upstream and downstream enrichment of each histone or histone modification is indicated below the plots.

Additional file 8: Fig S6. Average enrichment profiles of histones and their modifications across genes binned by expression level. The average profile of H2A.Z, H3K18ac, H3K27ac, H3K4me1 and H3 over the coding sequences ± 2500 bp for genes grouped into terciles by expression level (top green, middle orange, bottom purple) and for silent genes (pink). The enrichment profile of each chromatin mark was presented as the log2 ratio over the input control. In rings, trophozoites and schizonts gene expression categories were, respectively, the top (n = 1636, 1603, 1613), middle (n = 1495, 1539, 1519) and bottom (n = 1580, 1356, 1386) terciles, and silent genes (nn= 476, 530, 602). 5′End: the start codon of a gene; 3′End: the stop codon of a gene.

Additional file 9: Fig S7. A) Average enrichment profiles of chromatin features and RNA levels from this study across the summits ± 1.8 kb of intergenic, peaks of H3K4me1 ChIP from this study relative to H3K4me3 from [38] B) Average enrichment profiles of chromatin features and RNA levels from this study across the intergenic peaks of H3K4me1 identified by Ubhe et al [48]. Average profile plots ± SE covering 1.5 kb up and downstream of published, “strong” H3K4me1 intergenic peaks longer than 1 bp (n = 259) [48] oriented according to the closest downstream gene. Top panel is the log2 ratio of ChIP over input average enrichment profiles of H3K4me1, H3K27ac, H3K18ac, H3 and Pf H2A.Z, middle panel is GC content and ATACseq normalised to gDNA and the bottom panel is RNA separated by strand. C) The number of intergenic peaks and their intersections from the H3K4me1/input from this study, the H3K4me1 from this study over the H3K4me3 from [38], and the H3K4me1 enriched intergenic regions from [48]. D) Spearman correlations for the single schizont H3K4me1 ChIP sample and matched input (Ubhe) analysed in [48] and for our two schizont replicates (S1 and S2) of H3K4me1 ChIP and matched input.

Neural interface devices that replace human biological parts are now becoming available to consumers. A negligence action has yet to be commenced against a person with a neural interface device in circumstances where harm to another’s property or person has occurred. This paper considers how the current law of negligence, the combination of common law and legislation, will be applied and concludes that the law may need to be adapted or modified. In particular, breach of the duty of care may recognise a standard of care different from that of an individual without a neural interface device while factual causation will experience difficulties. The courts will need to decide negligence proceedings where mind and machine are merged through the integration of a neural interface device and a human being, circumstances the courts have not considered before.

Neural interface devices and the melding of mind and machine, challenge the law in determining where civil liability for injury, damage or loss should lie. The ability of the human mind to instruct and control these devices means that in a negligence action against a person with a neural interface device, determining the standard of care owed by him or her will be of paramount importance. This article considers some of the factors that may influence the court’s determination of the appropriate standard of care to be applied in this situation, leading to the conclusion that a new standard of care might evolve.

When, in 1977, the Australian electorate provided a double majority to effect a change of section 72 of the Commonwealth Constitution requiring judges of the High Court of Australia to retire at the age of 70 years old, I doubt we understood the continuing capacity of these esteemed members of the judiciary. For the opportunity to sit and talk with Ian Callinan AC who, in compliance with that amendment, retired from the High Court in September 2007, I needed to wait until he returned from The Hague where he was sitting as a Judge ad hoc on the International Court of Justice. Although a native of Casino, New South Wales, Mr Callinan is regarded as a Queenslander. Indeed, he grew up in Brisbane, finished high school at Brisbane Grammar and graduated in law at The University of Queensland. Appointed in 1978 as a Queen’s Counsel, Mr Callinan enjoyed this period of his legal career and we discussed an aspect of the Christopher Skase case, which reinforced my belief that Mr Callinan is an incredibly skilful advocate. On 14 September 1998, ABC Four Corners broadcasted the views of some prominent Australians on the appointment of Mr Callinan to the High Court. In assessing the type of person Mr Callinan is, Tony Morris QC said: “Ian Callinan isn't a coward”, while former Commonwealth Attorney-General, Michael Lavarch, said: “He was regarded as an absolutely outstanding criminal lawyer within the Queensland legal profession, I mean really a top-notch advocate”. I was not interested in raising any of the controversial issues that Mr Callinan has encountered as an advocate in high profile matters. I wanted to know how he felt about his time on the High Court, what his thoughts are on the operation of the High Court, the IP cases he decided, the real life issues that he feels impact on counsel who are appearing before the High Court and the people he regarded as role models. During our conversation, Mr Callinan laughed often and when he did his eyes lit up, revealing his passion for life. He is an incredibly genuine Australian who loved his time as a barrister, enjoyed his role on the High Court, enjoys his current job as mediator, loves writing novels, has a great desire for continual improvement in the quality of legal education and legal advocacy and sees a need for change in IP law. When I asked: “So, what might the future hold for you?”, he laughed and said: “Well, at my age I don’t have a long horizon time”. I said: “Just enjoy the journey?”, to which Mr Callinan responded: “Exactly”.

In an age where digital innovation knows no boundaries, research in the area of brain-computer interface and other neural interface devices go where none have gone before. The possibilities are endless and as dreams become reality, the implications of these amazing developments should be considered. Some of these new devices have been created to correct or minimise the effects of disease or injury so the paper discusses some of the current research and development in the area, including neuroprosthetics. To assist researchers and academics in identifying some of the legal and ethical issues that might arise as a result of research and development of neural interface devices, using both non-invasive techniques and invasive procedures, the paper discusses a number of recent observations of authors in the field. The issue of enhancing human attributes by incorporating these new devices is also considered. Such enhancement may be regarded as freeing the mind from the constraints of the body, but there are legal and moral issues that researchers and academics would be well advised to contemplate as these new devices are developed and used. While different fact situation surround each of these new devices, and those that are yet to come, consideration of the legal and ethical landscape may assist researchers and academics in dealing effectively with matters that arise in these times of transition. Lawyers could seek to facilitate the resolution of the legal disputes that arise in this area of research and development within the existing judicial and legislative frameworks. Whether these frameworks will suffice, or will need to change in order to enable effective resolution, is a broader question to be explored.

The statutory derivative action was introduced in Australia in 2000. This right of action has been debated in the literature and introduced in a number of other jurisdictions as well. However, it is by no means clear that all issues have been resolved despite its operation in Australia for over 10 years. This article considers the application of Pt 2F.1A of the Corporations Act to companies in liquidation under Ch 5. It demonstrates that the application involves consideration of not only proper statutory interpretation but also policy matters around the role and the supervision by the court of a liquidator once a company has entered liquidation.

This article discusses some recent judicial decisions to assist legal practitioners to overcome some of the problems encountered when serving Bankruptcy Notices and Creditor’s Petitions. Some of the issues covered in the discussion are: What the valid last-known address of the debtor can be, whether a Bankruptcy Notice can be validly served by email on a debtor who is located outside Australia, whether service of a Bankruptcy Notice is valid when the debtor is outside Australia when service on the debtor occurs in Australia, whether the creditor’s failure to obtain leave for service of a Bankruptcy Notice can be excused, what can be done regarding personal service of a Creditor’s Petition when a debtor is outside Australia and whether the Court can set aside a sequestration order. The article goes on to place the issues in the context of broader bankruptcy policies noting that effective service of bankruptcy documents is challenging in a world where mobility of debtors is global and new modes of communication ever changing.

In an age where financial transactions are conducted worldwide and mobility of citizens throughout the world is common, lawyers seeking to serve Bankruptcy Notices and Creditor’s Petitions encounter many problems. To assist lawyers in overcoming some of the service problems that are arising as a result of this changing world, a number of recent cases are considered that highlight a number of issues, including American Express Australia Limited v Michaels [2010] FMCA 103, Deputy Commissioner of Taxation v Barnes (2008) 70 ATR 776; [2008] FMCA 7, Battenberg v Restom & Ors (2005) 223 ALR 692; upheld by the Full Federal Court in Battenberg v Restrom and Ors (2006) 149 FCR 128 at 133; [2006] FCAFC 20 and Envee Energy Pty Ltd (In Liquidation) v Stockford [2007] FMCA 1426. While the fact situation of every bankruptcy case will differ, recent decisions may assist lawyers in dealing effectively with bankruptcy matters in these times of transition. Lawyers can facilitate completion of the litigious process within the relevant legislative framework in order to satisfy their responsibility to clients and to the Court by considering this case law.

This Report analyses the copyright law framework needed to ensure open access to outputs of the Australian academic and research sector such as datasets, articles and theses. It is written in the context of an increasing recognition, in Australia and internationally, that access to knowledge is a key driver of social, cultural and economic development and that publicly funded research should be openly accessible. With the objective of enabling access to knowledge, this Report proposes the development of clear protocols for copyright management (designed as practical and effective tools) for implementation in the Australian academic and research sector The Report explains that with the rise of networked digital technologies our knowledge landscape and innovation system is more and more reliant on best practice copyright management strategies. Furthermore in the 21st century these strategies need to accommodate both the demands for open sharing of knowledge and traditional commercialisation models. To this end, this Report examines the way in which practices for managing copyright, interact with the new web based frameworks that have developed for knowledge creation and dissemination. It focuses on specific areas that are central to the promotion of innovation and creativity in Australia, with emphasis on various types of repositories. More specifically, this Report provides an overview of the principles of copyright law, the concept of open access to knowledge, the recently developed open content models of copyright licensing and proposes a framework for enhancing the management of copyright interests in research and academic output (including electronic theses and dissertations (ETD)). The Report describes a forward work program which, upon implementation, will provide the platform for the development of systems and practices designed to effectively promote open access to knowledge within the Australian academic and research sector. The Report calls upon Australian research and funding institutions to consider their commitment to open access and articulate this in clear polices and copyright management frameworks. It proposes a survey of researchers about their understanding of, attitudes towards and experience with publishing agreements and the provision of model agreements that can facilitate open access and commercialisation objectives. The Report details a methodology for cataloguing and better understanding publishers’ attitudes towards open access. This list aims to be interoperable with the existing SHERPA list based in the UK and accessible through a web interface known as the OAK List. Finally the Report looks at copyright management of open access to ETD and makes proposals for better managing this process. In all of these endeavours the OAK Law Project aims to undertake work that will be of relevance to and can be utilised by key stakeholders.

The OAK Law Project aims to facilitate seamless access to knowledge and improve social, economic and cultural outcomes. This guide aims to provide practical guidance for academic authors interested in making their work more openly accessible to readers and other researchers. The guide provides authors with an overview of the concept of and rationale for open access to research outputs and how they may be involved in its implementation and with what effect. In doing so it considers the central role of copyright law and publishing agreements in structuring an open access framework as well as the increasing involvement of funders and academic institutions. The guide also explains different methods available to authors for making their outputs openly accessible, such as publishing in an open access journal or depositing work into an open access repository. Importantly, the guide addresses how open access goals can affect an author’s relationship with their commercial publisher and provides guidance on how to negotiate a proper allocation of copyright interests between an author and publisher. A Copyright Toolkit is provided to further assist authors in managing their copyright.

The Legal Framework for e-Research Project lead by Professor Brian Fitzgerald and hosted by the Queensland University of Technology (QUT) is funded by the Australian Commonwealth Department of Education, Employment and Workplace Relations (DEEWR), formerly Education, Science and Training (DEST), under the Systemic Infrastructure Initiative (SII), Research Information Infrastructure Framework for Australian Higher Education, as part of the Commonwealth Government’s Backing Australia’s Ability – An Innovation Action Plan for the Future (BAA). The Project involves mapping out a sophisticated legal framework for e- Research and collaborative innovation. As we transition into the National Collaborative Research Infrastructure Strategy (NCRIS)2 era it is vitally important that social and legal aspects of the e-Research framework are developed in step with the rapid advances in technology. Only little work has been done in this area worldwide. This project is linking with key international actors to provide an internationally significant project. While the Open Access to Knowledge (OAK) Law Project3 aims to examine the role of open access to all in an Internet world, this project also focuses on open innovation within secure knowledge communities – both are vital aspects of the e-Research framework. The critical issue is working out legal models for e-Research that reflect the capacity of the technologies involved and can be implemented quickly, effectively and (in many instances) in an automated way.

The OAK Law Project aims to facilitate seamless access to knowledge and improve social, economic and cultural outcomes. This guide aims to provide practical guidance for academic authors interested in making their work more openly accessible to readers and other researchers. The guide provides authors with an overview of the concept of and rationale for open access to research outputs and how they may be involved in its implementation and with what effect. In doing so it considers the central role of copyright law and publishing agreements in structuring an open access framework as well as the increasing involvement of funders and academic institutions. The guide also explains different methods available to authors for making their outputs openly accessible, such as publishing in an open access journal or depositing work into an open access repository. Importantly, the guide addresses how open access goals can affect an author’s relationship with their commercial publisher and provides guidance on how to negotiate a proper allocation of copyright interests between an author and publisher. A Copyright Toolkit is provided to further assist authors in managing their copyright.

This Report analyses the copyright law framework needed to ensure open access to outputs of the Australian academic and research sector such as datasets, articles and theses. It is written in the context of an increasing recognition, in Australia and internationally, that access to knowledge is a key driver of social, cultural and economic development and that publicly funded research should be openly accessible. With the objective of enabling access to knowledge, this Report proposes the development of clear protocols for copyright management (designed as practical and effective tools) for implementation in the Australian academic and research sector The Report explains that with the rise of networked digital technologies our knowledge landscape and innovation system is more and more reliant on best practice copyright management strategies. Furthermore in the 21st century these strategies need to accommodate both the demands for open sharing of knowledge and traditional commercialisation models. To this end, this Report examines the way in which practices for managing copyright, interact with the new web based frameworks that have developed for knowledge creation and dissemination. It focuses on specific areas that are central to the promotion of innovation and creativity in Australia, with emphasis on various types of repositories. More specifically, this Report provides an overview of the principles of copyright law, the concept of open access to knowledge, the recently developed open content models of copyright licensing and proposes a framework for enhancing the management of copyright interests in research and academic output (including electronic theses and dissertations (ETD)). The Report describes a forward work program which, upon implementation, will provide the platform for the development of systems and practices designed to effectively promote open access to knowledge within the Australian academic and research sector. The Report calls upon Australian research and funding institutions to consider their commitment to open access and articulate this in clear polices and copyright management frameworks. It proposes a survey of researchers about their understanding of, attitudes towards and experience with publishing agreements and the provision of model agreements that can facilitate open access and commercialisation objectives. The Report details a methodology for cataloguing and better understanding publishers’ attitudes towards open access. This list aims to be interoperable with the existing SHERPA list based in the UK and accessible through a web interface known as the OAK List. Finally the Report looks at copyright management of open access to ETD and makes proposals for better managing this process. In all of these endeavours the OAK Law Project aims to undertake work that will be of relevance to and can be utilised by key stakeholders.