Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

IL28B polymorphism is significantly correlated with ifn anti-viral effectiveness already on first day of pegylated interferon-alpha and ribavirin therapy of chronic HCV infection

Background and Aims: Recently, single nucleotide polymorphisms (SNPs) in IL28B were shown to correlate with response to pegylated interferon-a (IFN) and ribavirin therapy of chronic HCV infection. However, the cause for the SNPs effect on therapy response and its application for direct anti-viral (DAV) treatment are not clear. Here, we analyze early HCV kinetics as function of IL28B SNPs to determine its specific effect on viral dynamics. Methods: IL28B SNPs rs8099917, rs12979860 and rs12980275 were genotyped in 252 chronically HCV infected Caucasian naïve patients (67% HCV genotype 1, 28% genotype 2-3) receiving peginterferonalfa- 2a (180 mg/qw) plus ribavirin (1000-1200 mg/qd) in the DITTO study. HCV-RNA was measured (LD = 50 IU/ml) frequently during first 28 days. Results: RVR was achieved in 33% of genotype 1 patients with genotype CC at rs12979860 versus 12-16% for genotypes TT and CT (P < 0.03). Significant (P < 0.001) difference in viral decline was observed already at day 1 (see Figure). First phase decline was significantly (P < 0.001) larger in patients with genotype CC (2.0 log) than for TT and CT genotypes (0.6 and 0.8), indicating IFN anti-viral effectiveness in blocking virion production of 99% versus 75-84%. There was no significant association between second phase slope and rs12979860 genotype in patients with a first phase decline larger than 1 log. HCV kinetics as function of IL28b SNP. The same trend (not shown) was observed for HCV genotype 2-3 patients with different SNP genotype distribution that may indicate differential selection pressure as function of HCV genotype. Similar results were observed for SNPs rs8099917 and rs12980275, with a strong linkage disequilibrium among the 3 loci allowing to define the composite haplotype best associated with IFN effectiveness. Conclusions: IFN effectiveness in blocking virion production/ release is strongly affected by IL28B SNPs, but not other viral dynamic properties such as infected cell loss rate. Thus, IFN based therapy, as standard-of-care or in combination with DAV, should consider IL28B SNPs for prediction and personalized treatment, while response to pure DAV treatment may be less affected by IL28B SNPs. Additional analyses are undergoing to pinpoint the SNP effect on IFN anti-viral effectiveness.

Blood pressure change and outcome in acute ischemic stroke: the impact of baseline values, previous hypertensive disease and previous antihypertensive treatment.

BACKGROUND: Management of blood pressure (BP) in acute ischemic stroke is controversial. The present study aims to explore the association between baseline BP levels and BP change and outcome in the overall stroke population and in specific subgroups with regard to the presence of arterial hypertensive disease and prior antihypertensive treatment. METHODS: All patients registered in the Acute STroke Registry and Analysis of Lausanne (ASTRAL) between 2003 and 2009 were analyzed. Unfavorable outcome was defined as modified Rankin score more than 2. A local polynomial surface algorithm was used to assess the effect of BP values on outcome in the overall population and in predefined subgroups. RESULTS: Up to a certain point, as initial BP was increasing, optimal outcome was seen with a progressively more substantial BP decrease over the next 24-48 h. Patients without hypertensive disease and an initially low BP seemed to benefit from an increase of BP. In patients with hypertensive disease, initial BP and its subsequent changes seemed to have less influence on clinical outcome. Patients who were previously treated with antihypertensives did not tolerate initially low BPs well. CONCLUSION: Optimal outcome in acute ischemic stroke may be determined not only by initial BP levels but also by the direction and magnitude of associated BP change over the first 24-48 h.

The Evolution of the Climate Change Regime: Beyond a North-South Divide?

This research primarily analyses relevant climate bargaining dynamics that have been informed by a North-South impasse. This working paper argues that the first stage of negotiations for a climate convention indeed witnessed a North-South divide which became institutionalized in the Framework Convention on Climate Change. However, in subsequent negotiation rounds the key loci of bargaining struggles was centered between developed countries, in which relevant North-South cooperation dynamics were also present. Finally, this paper assesses the unfinished post-Kyoto bargaining process in which two trends are already being observed: both the emergence of a new geopolitics between the United States and major developing countries, and a fragmentation process within the South, in which the Copenhagen Accord itself has begun to institutionalize such fragmentation.

Stability and change in party preferences.

This article analyses stability and volatility of party preferences using data from the Swiss Household-Panel (SHP), which, for the first time, allow studying transitions and stability of voters over several years in Switzerland. Analyses cover the years 1999- 2007 and systematically distinguish changes between party blocks and changes within party blocks. The first part looks at different patterns of change, which show relatively high volatility. The second part tests several theories on causes of such changes applying a multinomial random-effects model. Results show that party preferences stabilise with their duration and with age and that the electoral cycle, political sophistication, socio-structural predispositions, the household-context as well as party size and the number of parties each explain part of electoral volatility. Different results for withinand between party-block changes underlie the importance of that differentiation.

How does monetary policy change? evidence on inflation targeting countries

We examine the evolution of monetary policy rules in a group of inflation targeting countries (Australia, Canada, New Zealand, Sweden and the United Kingdom) applying moment- based estimator at time-varying parameter model with endogenous regressors. Using this novel flexible framework, our main findings are threefold. First, monetary policy rules change gradually pointing to the importance of applying time-varying estimation framework. Second, the interest rate smoothing parameter is much lower that what previous time-invariant estimates of policy rules typically report. External factors matter for all countries, albeit the importance of exchange rate diminishes after the adoption of inflation targeting. Third, the response of interest rates on inflation is particularly strong during the periods, when central bankers want to break the record of high inflation such as in the U.K. or in Australia at the beginning of 1980s. Contrary to common wisdom, the response becomes less aggressive after the adoption of inflation targeting suggesting the positive effect of this regime on anchoring inflation expectations. This result is supported by our finding that inflation persistence as well as policy neutral rate typically decreased after the adoption of inflation targeting.

Contact melting of a three-dimensional phase change material on a flat substrate

In this paper a model is developed to describe the three dimensional contact melting process of a cuboid on a heated surface. The mathematical description involves two heat equations (one in the solid and one in the melt), the Navier-Stokes equations for the flow in the melt, a Stefan condition at the phase change interface and a force balance between the weight of the solid and the countering pressure in the melt. In the solid an optimised heat balance integral method is used to approximate the temperature. In the liquid the small aspect ratio allows the Navier-Stokes and heat equations to be simplified considerably so that the liquid pressure may be determined using an igenfunction expansion and finally the problem is reduced to solving three first order ordinary differential equations. Results are presented showing the evolution of the melting process. Further reductions to the system are made to provide simple guidelines concerning the process. Comparison of the solutions with experimental data on the melting of n-octadecane shows excellent agreement.

Effects of genetic alterations in arbuscular mycorrhizal fungi on plant growth and on their response to a change of host

Abstract :The majority of land plants form the symbiosis with arbuscular mycorrhizal fungi (AMF). The AM symbiosis has existed for hundreds of millions of years but little or no specificity seems to have co- evolved between the partners and only about 200 morphospecies of AMF are known. The fungi supply the plants most notably with phosphate in exchange for carbohydrates. The fungi improve plant growth, protect them against pathogens and herbivores and the symbiosis plays a key role in ecosystem productivity and plant diversity. The fungi are coenocytic, grow clonally and no sexual stage in their life cycle is known. For these reasons, they are presumed ancient asexuals. Evidence suggests that AMF contain populations of genetically different nucleotypes coexisting in a common cytoplasm. Consequently, the nucleotype content of new clonal offspring could potentially be altered by segregation of nuclei at spore formation and by genetic exchange between different AMF. Given the importance of AMF, it is surprising that remarkably little is known about the genetics and genomics of the fungi.The main goal of this thesis was to investigate the combined effects of plant species differences and of genetic exchange and segregation in AMF on the symbiosis. This work showed that single spore progeny can receive a different assortment of nucleotypes compared to their parent and compared to other single spore progeny. This is the first direct evidence that segregation occurs in AMF. We then showed that both genetic exchange and segregation can lead to new progeny that differentially alter plant growth compared to their parents. We also found that genetic exchange and segregation can lead to different development of the fungus during the establishment of the symbiosis. Finally, we found that a shift of host species can differentially alter the phenotypes and genotypes of AMF progeny obtained by genetic exchange and segregation compared to their parents.Overall, this study confirms the multigenomic state of the AMF Glomus intraradices because our findings are possible only if the fungus contains genetically different nuclei. We demonstrated the importance of the processes of genetic exchange and segregation to produce, in a very short time span, new progeny with novel symbiotic effects. Moreover, our results suggest that different host species could affect the fate of different nucleotypes following genetic exchange and segregation in AMF, and can potentially contribute to the maintenance of genetic diversity within AMF individuals. This work brings new insights into understanding how plants and fungi have coevolved and how the genetic diversity in AMF can be maintained. We recommend that the intra-ir1dividual AMF diversity and these processes should be considered in future research on this symbiosis.Résumé :La majorité des plantes terrestres forment des symbioses avec les champignons endomycorhiziens arbusculaires (CEA). Cette symbiose existe depuis plusieurs centaines de millions d'années mais peu ou pas de spécificité semble avoir co-évoluée entre les partenaires et seulement 200 morpho-espèces de CEA sont connues. Le champignon fournit surtout aux plantes du phosphate en échange de carbohydrates. Le champignon augmente la croissance des plantes, les protège contre des pathogènes et herbivores et la symbiose joue un rôle clé dans la productivité des écosystèmes et de la diversité des plantes. Les CEA sont coenocytiques, se reproduisent clonalement et aucune étape sexuée n'est connue dans leur cycle de vie. Pour ces raisons, ils sont présumés comme anciens asexués. Des preuves suggèrent que les CEA ont des populations de nucleotypes différents coexistant dans un cytoplasme commun. Par conséquent, le contenu en nucleotype des nouveaux descendants clonaux pourrait être altéré par la ségrégation des noyaux lors de la fonnation des spores et par l'échange génétique entre différents CEA. Etant donné l'importance des CEA, il est surprenant que si peu soit connu sur la génétique et la génomique du champignon.Le principal but de cette thèse a été d'étudier les effets combinés de différentes espèces de plantes et des mécanismes d'échange génétique et de ségrégation chez les CEA sur la symbiose. Ce travail a montré que chaque nouvelle spore produite pouvait recevoir un assortiment différent de noyaux comparé au parent ou comparé à d'autres nouvelles spores. Ceci est la première preuve directe que la ségrégation peut se produire chez les CEA. Nous avons ensuite montré qu'à la fois l'échange génétique et la ségrégation pouvaient mener à de nouveaux descendants qui altèrent différemment la croissance des plantes, comparé à leurs parents. Nous avons également trouvé que l'échange génétique et la ségrégation pouvaient entraîner des développements différents du champignon pendant l'établissement de la symbiose. Pour finir, nous avons trouvé qu'un changement d'espèce de l'hôte pouvait altérer différemment les phénotypes et génotypes des descendants issus d'échange génétique et de ségrégation, comparé à leurs parents.Globalement, cette étude confirme l'état multigénomique du CEA Glumus intraradices car nous résultats sont possibles seulement si le champignon possède des noyaux génétiquement différents. Nous avons démontrés l'importance des mécanismes d'échange génétique et de ségrégation pour produire en très peu de temps de nouveaux descendants ayant des effets symbiotiques nouveaux. De plus, nos résultats suggèrent que différentes espèces de plantes peuvent agir sur le devenir des nucleotypes après l'échange génétique et la ségrégation chez les CEA, et pourraient contribuer à la maintenance de la diversité génétique au sein d'un même CEA. Ce travail apporte des éléments nouveaux pour comprendre comment les plantes et les champignons ont coévolué et comment la diversité génétique chez les CEA peut être maintenue. Nous recommandons de considérer la diversité génétique intra-individuelle des CEA et ces mécanismes lors de futures recherches sur cette symbiose.

Multisensory mechanisms in temporo-parietal cortex support self-location and first-person perspective.

Self-consciousness has mostly been approached by philosophical enquiry and not by empirical neuroscientific study, leading to an overabundance of diverging theories and an absence of data-driven theories. Using robotic technology, we achieved specific bodily conflicts and induced predictable changes in a fundamental aspect of self-consciousness by altering where healthy subjects experienced themselves to be (self-location). Functional magnetic resonance imaging revealed that temporo-parietal junction (TPJ) activity reflected experimental changes in self-location that also depended on the first-person perspective due to visuo-tactile and visuo-vestibular conflicts. Moreover, in a large lesion analysis study of neurological patients with a well-defined state of abnormal self-location, brain damage was also localized at TPJ, providing causal evidence that TPJ encodes self-location. Our findings reveal that multisensory integration at the TPJ reflects one of the most fundamental subjective feelings of humans: the feeling of being an entity localized at a position in space and perceiving the world from this position and perspective.

Etiology of first-ever ischaemic stroke in European young adults: the 15 cities young stroke study.

BACKGROUND AND PURPOSE: Risk factors for IS in young adults differ between genders and evolve with age, but data on the age- and gender-specific differences by stroke etiology are scare. These features were compared based on individual patient data from 15 European stroke centers. METHODS: Stroke etiology was reported in detail for 3331 patients aged 15-49 years with first-ever IS according to Trial of Org in Acute Stroke Treatment (TOAST) criteria: large-artery atherosclerosis (LAA), cardioembolism (CE), small-vessel occlusion (SVO), other determined etiology, or undetermined etiology. CE was categorized into low- and high-risk sources. Other determined group was divided into dissection and other non-dissection causes. Comparisons were done using logistic regression, adjusting for age, gender, and center heterogeneity. RESULTS: Etiology remained undetermined in 39.6%. Other determined etiology was found in 21.6%, CE in 17.3%, SVO in 12.2%, and LAA in 9.3%. Other determined etiology was more common in females and younger patients, with cervical artery dissection being the single most common etiology (12.8%). CE was more common in younger patients. Within CE, the most frequent high-risk sources were atrial fibrillation/flutter (15.1%) and cardiomyopathy (11.5%). LAA, high-risk sources of CE, and SVO were more common in males. LAA and SVO showed an increasing frequency with age. No significant etiologic distribution differences were found amongst southern, central, or northern Europe. CONCLUSIONS: The etiology of IS in young adults has clear gender-specific patterns that change with age. A notable portion of these patients remains without an evident stroke mechanism according to TOAST criteria.

Speech by Mr Micheál Martin TD at Launch of Pre-Registration Nursing Degree Programme

Good afternoon ladies and gentlemen. I am very pleased that you were all able to accept my invitation to join me here today on this landmark occasion for nursing education. It is fitting that all of the key stakeholders from the health and education sectors should be so well represented at the launch of an historic new development. Rapid and unpredictable change throughout society has been the hallmark of the twenty-first century, and healthcare is no exception. Regardless of what change occurs, no one doubts that nursing is intrinsic to the health of this nation. However, significant changes in nurse education are now needed if the profession is to deliver on its social mandate to promote people´s health by providing excellent and sensitive care. As science, technology and the demands of the public for sophisticated and responsive health care become increasingly complex, it is essential that the foundation of nursing education is redesigned. Pre-registration nursing education has already undergone radical change over the past eight years, during which time it has moved from an apprenticeship model of education and training to a diploma based programme firmly rooted in higher education. The Secretary General of my Department, Michael Kelly, played a leading role in bringing about this transformation, which has greatly enhanced the way students are prepared for entry to the nursing profession. The benefits of the revised model of education are clearly evident from the quality of the nurses graduating from the diploma programme. The Commission on Nursing examined the whole area of nursing education, and set out a very convincing case for educating nursing students to degree level. It argued that nurses of the future would be required to possess increased flexibility and the ability to work autonomously. A degree programme would provide nurses with a theoretical underpinning that would enable them to develop their clinical skills to a greater extent and to respond to future challenges in health care, for the benefit of patients and clients of the health services. The Commission has provided a solid framework for the professional development of nurses and midwives, including a process that is already underway for the creation of clinical nurse specialist and advanced nurse practitioner posts. This process will facilitate the transfer of skills across divisions of nursing. In this scenario, it is clearly desirable that the future benchmark qualification for registration as a nurse should be a degree in nursing studies. A Nursing Education Forum was established in early 1999 to prepare a strategic framework for the implementation of a nursing degree programme. When launching the Forum´s report last January, I indicated that the Government had agreed in principle to the introduction of the proposed degree programme next year. At the time two substantial outstanding issues had yet to be resolved, namely the basis on which nurse teachers would transfer from the health sector to the education sector and the amount of capital and revenue funding required to operate the degree programme. My Department has brokered agreements between the Nursing Alliance and the Higher Education Institutions for the assimilation of nurse teachers as lecturers into their affiliated institutions. The terms of these agreements have been accepted by all four nursing unions following a ballot of their nurse teacher members. I would like to pay particular tribute to all nurse teachers who have contributed to shaping the position, relevance and visibility of nursing through leadership, which embodies scholarship and excellence in the profession of nursing itself. In response to a recommendation of the Nursing Education Forum, I established an Inter-Departmental Steering Committee, chaired by Bernard Carey of my Department, to consider all the funding and policy issues. This Steering Committee includes representatives of the Department of Finance and the Department of Education and Science as well as the Higher Education Authority. The Steering Committee has been engaged in intensive negotiations with representatives of the Conference of Heads of Irish Universities and the Institutes of Technology in relation to their capital and revenue funding requirements. These negotiations were successfully concluded within the past few weeks. The satisfactory resolution of the industrial relations and funding issues cleared the way for me to go to the Government with concrete proposals for the implementation of degree level education for nursing students. I am delighted to announce here today that the Government has approved all of my proposals, and that a four-year undergraduate pre-registration nursing degree programme will be implemented on a nation-wide basis at the start of the next academic year, 2002/2003. The Government has approved the provision of capital funding totalling £176 million pounds for a major building and equipment programme to facilitate the full integration of nursing students into the higher education sector. This programme is due to be completed by September 2004, and will ensure that nursing students are accommodated in purpose built schools of nursing studies with state of the art clinical skills and human science laboratories at thirteen higher education sites throughout the country. The Government has also agreed to make available the substantial additional revenue funding required to support the nursing degree programme. By 2006, the full year cost of operating the programme will rise to some £43 million pounds. The scale of this investment in pre-registration nursing education is enormous by any yardstick. It demonstrates the firm commitment of myself and my Government colleagues to the full implementation of the recommendations of the Commission on Nursing, of which the introduction of pre-registration degree level education is arguably the most important. This historic decision, and it is truly historic, will finally put the education of nurses on a par with the education of other health care professionals. The nursing profession has long been striving for parity, and my own involvement in the achievement of it is a matter of deep personal satisfaction to me. I am also pleased to announce that the Government has approved my plans for increasing the number of nursing training places to coincide with the implementation of the degree programme next year. Ninety-three additional places in mental handicap and psychiatric nursing will be created at Athlone, Letterkenny, Tralee and Waterford Institutes of Technology. This will yield 392 extra places over the four years of the degree programme. A total of 1,640 places annually on the new degree programme will thus be available. This is an all-time record, and maintaining the annual student intake at this level for the foreseeable future is a key element of my overall strategy for ensuring that we produce sufficient “home-grown” nurses for our health services. I am aware that the Nursing Alliance were anxious that some funding would be provided for the further academic career development of nurse teachers who transfer to one of the six Universities that will be involved in the delivery of the degree programme. I am happy to confirm that up to £300,000 in total per year will be available for this purpose over the first four years of the degree programme. In line with a recommendation of the Commission on Nursing, my Department will have responsibility for the administration of the nursing degree budget until the programme has been bedded down in the higher education sector. A primary concern will be to ensure that the substantial capital and revenue funding involved is ring-fenced for nursing studies. It is intended that responsibility for the budget will be transferred to the Department of Education and Science after the first cohort of nursing degree students have graduated in 2006. In the context of today´s launch, it is relevant to refer to a special initiative that I introduced last year to assist registered nurses wishing to undertake part-time nursing degree courses. Under this initiative, nurses are entitled to have their course fees paid by their employers in return for a commitment to continue working in the public health service for a period following completion of the course. This initiative has proved extremely popular with large numbers of nurses availing of it. I want to confirm here today that the free fees initiative will continue in operation until 2005, at a total cost of at least £15 million pounds. I am giving this commitment in order to assure this year´s intake of nursing students to the final diploma programmes that fee support for a part-time nursing degree course will be available to them when they graduate in three years time. The focus of today´s celebration is rightly on the landmark Government decision to implement the nursing degree programme next year. As Minister for Health and Children, and as a former Minister for Education, I also have a particular interest in the educational opportunities available to other health service workers to upgrade their skills. I am pleased to announce that the Government has approved my proposals for the introduction of a sponsorship scheme for suitable, experienced health care assistants who wish to become nurses. This new scheme will commence next year and will be administered by the health boards. Successful applicants will be allowed to retain their existing salaries throughout the four years of the degree programme in return for a commitment to work as nurses for their health service employer for a period of five years following registration. Up to forty sponsorships will be available annually. The new scheme will enable suitable applicants to undertake nursing education and training without suffering financial hardship. The greatest advantage of the scheme will be the retention by the public health service of staff who are supported under it, since they will have had practical experience of working in the service and their own personal commitment to upgrading their skills will be informed by that experience. I am confident that the sponsorship scheme will be warmly welcomed by health service unions representing care assistants as providing an exciting new career development path for their members. Education and health are now the two pillars upon which the profession of nursing rests. We must continue to build bridges, even tunnels where needed to strengthen this partnership. We must all understand partnerships donâ?Tt just happen they are designed and must be worked at. The changes outlined here today are powerful incentives for those in healthcare agencies, academic institutions and regulatory bodies to design revolutionary programmes capable of shaping a critical mass of excellent practitioners. You have an opportunity, greater perhaps than has been granted to any other generation in history to make certain those changes are for the good. Ultimately changes that will make the country a healthier and more equitable place to live. The challenge relates to building a seamless preparatory programme which equally respects both education and practise as an indivisible duo whilst ensuring that high tech does not replace the human touch. This is a special day in the history of the development of the Irish nursing profession, and I would like to thank everybody for their contribution. I want to express my particular appreciation of two people who by this stage are well known to all of you – Bernard Carey of my Department and Siobhán O´Halloran of the National Implementation Committee. Bernard and Siobhán have devoted considerable time and energy to the project on my behalf over the past fourteen months or so. That we are here today celebrating the launch of degree level education is due in no small part to their successful execution of the mandate that I gave them. We live in a rapidly changing world, one in which nursing can no longer rely on systems of the past to guide it through the new millennium. In terms of contemporary healthcare, nursing is no longer just a reciprocal kindness but rather a highly complex set of professional behaviours, which require serious educational investment. Pre-registration nurse education will always need development and redesign to ensure our health care system meets the demands of modern society. Nothing is finite. Today more than ever the health system is dependent on the resourcefulness of nursing. I have no doubt that the new educational landscape painted will ensure that nurses of the future will be increasingly innovative, independent and in demand. The unmistakable message from my Department is that nursing really matters. Thank you.

Complete nucleotide sequence analysis of a Brazilian dengue virus type 2 strain

In the last decade, dengue fever (DF) in Brazil has been recognized as an important public health problem, and an increasing number of dengue haemorrhagic fever (DHF) cases have been reported since the introduction of dengue virus type 2 (DEN-2) into the country in 1990. In order to analyze the complete genome sequence of a DEN-2 Brazilian strain (BR64022/98), we designed primers to amplify contiguous segments of approximately 500 base pairs across the entire sequence of the viral genome. Twenty fragments amplified by reverse transcriptase-PCR were cloned, and the complete nucleotide and the deduced amino acid sequences were determined. This constitutes the first complete genetic characterization of a DEN-2 strain from Brazil. All amino acid changes differentiating strains related to the Asian/American-Asian genotype were observed in BR64022/98, indicating the Asiatic origin of the strain.

2nd Report of the Independent Monitoring Group on A Vision For Change

This is the Second Annual Report of the Independent Monitoring Group for A Vision for Change the Report of the Expert Group on Mental Health Policy. The Monitoring Group was established in March 2006 to monitor and assess progress on the implementation of A Vision for Change. In this Second Report, the Monitoring Group has found that by and large the recommendations in its first report were not addressed in 2007, although some have been prioritised for implementation in 2008. Download document here

Implementation of the Action Plan for Health Research 2009-13 - First year report 2009-2010

In November 2009 the Government published an Action Plan for Health Research. The Plan was prepared by the Health Research Group following a commitment set out in Building Ireland’s Smart Economy (December 2008). The Action Plan, which was approved by the Cabinet Committee on Science, Technology and Innovation, provides the lead on national priorities and resource allocation in health research. The Action Plan was prepared to prioritise a programme of actions essential to creating a health research system which supports outstanding individuals, working in world class facilities and conducting leading edge research focused on the needs of patients and the public. The HRG is committed to measuring the success of the Action Plan by the extent to which it meets these deliverables by 2013. One year on, this report reviews the progress being made to implement the Plan.  

NICaN Regional Supportive & Palliative Care Network

NICaN Regional Supportive & Palliative Care Network Friday 30th May 2008 Lecture Theatre, Fern House Antrim 2.00 pm - 5.00 pm Welcome, Introductions Stuart MacDonnell, Chair of the Supportive and Palliative Care network welcomed everyone to the meeting. This meeting had been rescheduled to accommodate the validation workshop for the regional palliative care model, which took place on Friday,18th April. Acknowledging the full agenda, several items were pulled forward to accommodate speakers SPC_0809_03 Modernisation and Reform of Supportive and Palliative care Mr MacDonnell welcomed Dr Sonja McIlfatrick and Dr Donna Fitzimons, members of the Phase 1 Project Team for the Modernisation and Reform of palliative care. Their presentation highlighted the journey taken by the Project Team since January 2008 - May 2008. Seeking to deliver the network vision, for any person with palliative care need, cancer or non - cancer, the project team incorporated several methodologies. The literature review identified best practice. An assessment of need including epidemiological data and review of service provision. Consultation reflected the engagement with patients, carers and professional forums, primary care and non-malignant focus groups. The breadth of consultation confirmed the evidence for the identified components of the model. These were validated at the April workshop. External review of the work was provided by Dr Phil Larkin (Galway Uni) Prof David Clark (End of Life Care Observatory, Lancaster University) and Mr Bob Neillans (Chair of the Mid Trent Palliative care network, which has been involved in the Delivering choice programme within Lincolnshire). The Guiding Principles of the model reinforced Patient and family centred care, enhanced community provision and supported by specialists. The components of the model are · Identification of patient with Palliative careened · Holistic Assessment · Integration of services · Coordination of care · End of Life Care and Bereavement Care The consultation process also highlighted the need for Increased Public and Professional Awareness. This was recognised as an encompassing component. Underpinning the model is the need for robust Education and common core values e.g. dignity, choice, advocacy, empowerment, partnership working. Stuart MacDonnell, who also chaired the steering group during the project, congratulated the Project Team for delivering the comprehensive document on schedule. The Report has been submitted to the NICaN Board and the DHSSPSNI. In addition, an outline for Phase 2 of this work has been submitted. Mr MacDonnell recognised that there is real opportunity for palliative care to benefit from the DHSSPSNI commitment to concrete developments. Phase 2 will progress the current high-level components of the model into quality services developments at a local level, demonstrating integration throughout. The methods propose continued engagement with the Delivering Choice Programme enabled through a Central and also Local Teams. The report and the Appendices care available on the NICaN website www.nican@n-i.nhs.uk SPC_0809_01 Chairman's Business · Update on the Cancer Service Framework, the document has been submitted and presented to the Departmental Programme Board. Next stages will include the review of costs and development of a implementation guidance It is hoped that the completed document should be available for public consultation in Autumn 2008. with a launch of the framework document and accompanying implementation guide in Spring 2009. Some funding has already been identified to advance key areas of work including, Advanced communication skills training, peer review and an appointment of a post to develop the cancerni.net, focusing on children and e-learning tools. · Children's and Adolescent Cancer network group , Liz Henderson is to convene a group to consider how this is to be taken forward. · NICaN appointments Recognition was given to the significant contribution made by Dr Gerard Daly during his position as NICaN Lead Clinician, particularly throughout the early establishment of the NICaN. Dr Dermott Hughes (Western Trust) has been appointed as the NICaN Medical Director. The Primary Care Director post has been advertised and it is hoped that the Director of Network will be advertised later in Summer. Endorsement of End of Life care paper. The Paper was presented and endorsed at the March 2008 NICaN Board meeting. Mr David Galloway (Director of Secondary Care) emphasised the need for this important work to be recognised within the regional model to ensure that it is reflected in future models of service delivery Congratulations were again echoed to the Chair of the End of Life Group for this work, Dr Glynis Henry, and the working group Other recognition Mr MacDonnell congratulated the significant achievements across the network. These include: · Dr Francis Robinson (Consultant Palliative Medicine, Western Trust) Awarded - Consultant of the year at the NI Health Care awards. · Mrs Evelyn Whittaker Hospice Nurse Specialist, NI Hospice, Joint Second Prize in the Development award within the International Journal of Palliative Nursing Awards, for her work in development of palliative care education in nursing homes. · Mr Ray Elder is the newly appointed Team Leader of Community Palliative care, SE Trust. · Mrs Bridget Denvir, who managed the establishment of one of the first community multiprofessional palliative care teams is moving to work with establishing integrated teams within the Belfast Trust. Bridget has been an active core member of the network and here contribution has been much appreciated. Mrs Sharon Barr will attend in future. SPC_0809_02 Minutes & matters Arising from Meeting, 13th December 2007 No amendments were made to the draft minutes from the December meeting. These will be posted on the NICaN website for future reference. Palliative Care Research Following consultation, the response to the business case for the All Ireland Institute was forwarded on 22 February 2008 to Prof David Clark. Prof Judith Hill informed the group that terms of tender are now being developed. Awareness raising across academic institutions continues to engage interest in potential partnerships. Atlantic Philantrophies have offered financial support to the venture and match funding is being sought from across jurisdictions. Previous discussions at Network meetings have endorsed the need to establish a work strand for research and development within palliative and end of life care. To identify the body of interested parties and explore the strengths and weaknesses of a collaborative model for research, a workshop, - Building collaboration for Palliative and End of life Care Research -will take place on 4 June 10am - 2pm.in the Comfort Hotel.Antrim, The workshop will be chaired by Prof David Clark, Director of the International Observatory on End of Life Care. Prof Shelia Payne, Help the Hospices Chair in Hospice Studies and co director of the Cancer Experiences Collaborative will present the Experiences and Results from Research Collaborative. Feedback from this event will be brought back to the next meeting in September. SPC_0809_04 Patient Information pathways - a pathway for advanced disease Ms Danny Sinclair, NICaN Regional Coordinator for Patient Information informed the network of how patient information pathways have been developed in line with the Cancer Services Collaborative. Emerging themes, with regard to information needs of patients with advanced disease, are being identified from the work undertaken across the tumour groups. It is important to identify all information needs to develop a generic pathway of information resources for advanced disease to be endorsed by the Supportive and Palliative care network. This could be used across the all tumour specific information pathways and across organisational boundaries. The resulting pathway could potentially be used for non- cancer condition. A group is to be established to take this work forward. The group will: · Develop a list of advanced disease information themes · .Identify when they become relevant for the patient or their carer · .Identify existing resources · .Develop resources where needed · .Participate or nominate when review is required Dr Sheila Kelly nominated Helen Hume (SETrust) Paula Kealey will also contribute to this work; a nomination from the Patient and Public Information Forum has also been identified. A date will be circulated across the network to engage further interest and establish group SPC_0809_08 Development of a Regional Syringe Driver Prescription Chart Ms Kathy Stephenson reported that the second consultation of the draft regional syringe driver prescription chart and the focus group discussions, Pilots of the chart are to be undertaken within Trust, Hospices and General Practices. SPC_0809_05 A framework for Generalist and Specialist Palliative and End of Life Care Competency Dr Kathleen Dunne, lead of the Education works strand, reported on the findings following consultation of the Education framework. The report was widely appreciated across the network and valued as a significant and timely document for the commissioning of generalist and specialist adult palliative care education. Mr MacDonnell congratulated Dr Dunne and the members of the education workstrand for developing the framework aligning its significance to the underpinning needs of the regional model Amendments will be made to the document and then forwarded to the NICaN Board for endorsement. A process of implementation will be explored and reported to the network group at the September meeting. Key target areas for generalist palliative care education were highlighted within care of the elderly and general medicine. . SPC_0809_06 Pallcareni.net-a website for people with palliative care needs Ms Danny Sinclair, reminded the group of the pending amalgamation of the CAPriCORN and NICaN website. The resulting new web address will be www. cancerni.net. Recurrent funding has been secured to ensure the development of the supportive and palliative care website.www.Pallcareni.net The new website will host good information for people with palliative care needs, regardless of diagnosis. It will be accessible via the cancerni.net portal or independently as the pallcareni portal. It will signpost people with palliative care needs to condition- specific websites. The website will also enable the communication needs of the NI Regional Supportive & Palliative Care Network. This is a very significant method of seeking to enable greater understanding of palliative care for public and professionals, as highlighted within the regional model. Currently the material from the CAPriCORN website is being migrated onto cancerni and /or pallcareni.net as appropriate. To enable the further development of this opportunity a steering group of interested individuals is to be established. Their role will be to: · Drive the development of the website so it meets the needs of public and professionals through the sourcing and development of additional content · Identify any support that is needed, e.g. technical support · Review the website as a whole as it grows (coordinating condition-specific developments) · Review the functions of the website to aid communication throughout the Supportive and Palliative care network The steering group representation should reflect the constituencies within the Supportive and Palliative Care network. Current expressions of interest have come from Heather Reid and Valerie Peacock. A date will be circulated across the network to engage further interest and establish group SPC_0809_07 Update of Guidelines workstrand Dr Pauline Wilkinson presented the current work within the guidelines workstrand. 1. Brief Holistic Assessment & Referral Criteria to Specialist Palliative Care The development of an Holistic assessment Tool will help to identify holistic need at generalist and specialist level. Recognition of complex need prompts appropriate referral to specialist palliative care. The regional referral form is compatible with the Minimum Data set. The final drafts of this work are to be circulated widely, inclusive of service framework groups, primary care, secondary care and the supportive and palliative care network. Consultation will take place during June and July. Piloting of the forms will also be undertaken. 2. Control of Pain in Cancer Patients The original guidelines where developed 2003 and are now ready for review. The Mapping exercise, undertaken in May 2007, highlighted that the Guidelines were poorly adopted. The group have reviewed the pending SIGN 2 guidelines for pain with regard to practice in Northern Ireland. These are highly evidence based and are due to be launched this Summer. Whilst an excellent resource their comprehensiveness limits their readability, this may result in poor compliance. The Guidelines group feel it is important to have accessible and user-friendly guidelines particularly for Generalists and Out of hours. There are examples of good work that has taken place across the province, but there is a need for regional consistency. Dr Wilkinson has contacted Dr Carolyn Harper (Deputy CMO) and GAIN with regard to enabling funding to progress this work. The Guidelines group hope to approach the NICaN Primary Care Group to work in collaboratively on this piece, based on the templates already available. The works should be available in both electronic and paper versions. 3. Care of the dying & Breaking bad news Dr Gail Johnston has now completed an Audit of the Care of the Dying Pathways within the EHSSB. Gail is also seeking to examine to what extent the Regional Guidelines for Breaking Bad News are being implemented in the EHSSB with a view to identifying the need for further training or organisational structures that would facilitate future uptake. 4. Advances in new Technology Syringe Drivers Dr Wilkinson reported on a presentation made to the guidelines group by Mr Jim Elliot, Principle Engineer, Cardiology & Ann McLean, and Macmillan Palliative Care Nurse RVH. There is increasing concern with regard to how devices meet the recommended safety standards and how to reduce error. New devices have 3 point checking, automatic detection of syringe, automatic flow rates, full range of alarms, battery status and data download to provide an event log. There are now 2 companies in UK who have devices that meet these safety criteria. The current Graseby syringe drivers, which have been on the market and used predominately within Northern Ireland over the past 27 years Most new devices are not compatible with the regionally available monoject syringe, however contractual changes will lead to the withdrawal of the monoject syringes in October 2008. The Guidelines group supports a regional approach to this matter. This was echoed in the Supportive and Palliative care network. An option appraisal, identifying costs, and training issues should be developed through the engagement with Trusts and DHSSPSNI. The issue of Patient safety should be raised with the DHSSPSNI. SPC_0809_09 Evaluation of Supportive and Palliative Care network Deferred to next meeting. . SPC_0809_10 Emerging Issues Mrs Anne Coyle, Bereavement Coordinator, Southern Trust, announced that the Regional Bereavement Strategy is soon to be released. Anne supported the close alignment between the content of the strategy and the work of the regional model and other workstrands within the Supportive and Palliative care network. Ms Eleanor Donaghy, Transplant Coordinator, briefly highlighted the issue of tissue donation. Each year Northern Ireland has a dearth of corneal donations. There is no upper age limit for donation and retrieval is not limited by a cancer diagnosis. Recipients do not require immunosuppressive and the transplant is lifelong. The National Blood Service provided coordination of this donation they may be contacted via 07659180773. It is hoped that Mrs Coyle and Ms Donaghy could provide more comprehensive presentations at a future meeting. Events · Irish Psycho- Oncology Group Seminar, Cork 6 June, Exploring the Struggle for meaning in Cancer · Integrated Care: Putting Research into Practice, 13June, Trinity College, Dublin · Macmillan online conference Friday 13 June 2008, 9am - 5pm · Delivering effective end of life care: developing partnership working 15 Oct 2008, 9.30 -4.15 pm London Network Meeting was closed at 5.00pm SPC_0607_ Dates of Future Meetings (please note the change of venue) 10th September 2008, 1.30 - 5pm venue to be decided15th January 2009, 1.30 - 5pm venue to be decided12th May 2009, 1.30 - 5pm venue to be decided Attendances Apologies Stuart MacDonnellLorna NevinSonja McIlfatrick Donna FitzsimonsKathleen DunnePauline WilkinsonKathy StephensonSheila KellyMarie Nugent,Anne CoyleFiona GilmourJudith HillLorna DicksonMargaret CarlinLoretta GribbenYvonne Duff Lesley NelsonLiz HendersonSue FosterCathy PayneGraeme PaynePatricia MageeGeraldine WeatherupPaula KealyCaroline McAfeeLinda WrayValerie PeacockAnn McCleanRay Elder Martin BradleyHelen HumeGillian RankinHeather MonteverdeJulie DoyleAlison PorterYvonne SmythLiz Atkinson,Glynis HenryMaeve HullyCaroline HughesAnn FinnBob BrownSharon BarrJulie DoyleJanis McCulla .