Briefings for Minister Reilly and Fitzgerald as released for FOI

FOI decision for each document as per schedule Ireland has made very significant strides in relation to the health of its people in recent decades. People now live longer and with a greater quality of life than ever before. We have seen improvements in standards of living, education, health behaviours, access to and quality of health services, health technologies and a range of other important trends. This has led to gains in important measures of public health that have improved Irelandâ?Ts health not only in absolute terms but also relative to other countries in the EU and theOECD.   Click here to download PDF 2.12MB

A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations.

To develop a comprehensive overview of copy number aberrations (CNAs) in stage-II/III colorectal cancer (CRC), we characterized 302 tumors from the PETACC-3 clinical trial. Microsatellite-stable (MSS) samples (n = 269) had 66 minimal common CNA regions, with frequent gains on 20 q (72.5%), 7 (41.8%), 8 q (33.1%) and 13 q (51.0%) and losses on 18 (58.6%), 4 q (26%) and 21 q (21.6%). MSS tumors have significantly more CNAs than microsatellite-instable (MSI) tumors: within the MSI tumors a novel deletion of the tumor suppressor WWOX at 16 q23.1 was identified (p<0.01). Focal aberrations identified by the GISTIC method confirmed amplifications of oncogenes including EGFR, ERBB2, CCND1, MET, and MYC, and deletions of tumor suppressors including TP53, APC, and SMAD4, and gene expression was highly concordant with copy number aberration for these genes. Novel amplicons included putative oncogenes such as WNK1 and HNF4A, which also showed high concordance between copy number and expression. Survival analysis associated a specific patient segment featured by chromosome 20 q gains to an improved overall survival, which might be due to higher expression of genes such as EEF1B2 and PTK6. The CNA clustering also grouped tumors characterized by a poor prognosis BRAF-mutant-like signature derived from mRNA data from this cohort. We further revealed non-random correlation between CNAs among unlinked loci, including positive correlation between 20 q gain and 8 q gain, and 20 q gain and chromosome 18 loss, consistent with co-selection of these CNAs. These results reinforce the non-random nature of somatic CNAs in stage-II/III CRC and highlight loci and genes that may play an important role in driving the development and outcome of this disease.

Vibration training elicits a mixed aerobic and resistance-type exercise in sedentary subjects.

Objective. Vibration training (VT) is a new exercise method, with good acceptance among sedentary subjects, due to its passive principle: the machine moves the subject, not the opposite. We hypothesize that untrained subjects can benefit from a greater cardiovascular and metabolic stimulation than trained athletes, resembling classical aerobic-type activity, in addition of eliciting strength gains shown in diverse studies. Methods. 3 group of male subjects, inactive (SED), endurance trained athletes (END) and strength trained athletes (STR) underwent fitness (VO2max) and lower-body strength tests (isokinetic). Subjects were submitted to a session of oscillating VT, composed of 3 exercises (isometric half-squat, dynamic squat, dynamic squat with added load), each of 3 minutes duration, and repeated at 3 frequencies. VO2, heart rate and Borg scale were monitored. Results. 27 healthy subjects (10 SED, 9 END and 8 STR), mean age 24.5 (SED), 25.0 (STR) and 29.8 (END) were included. VO2max was significantly different as expected (47.9 vs. 52.9 vs. 63.9 ml/kg/min, resp. for SED, STR and END). Isokinetic dominant leg extensors strength was higher in STR (3.32 Nm/kg vs. 2.60 and 2.74 in SED and END). During VT, peak oxygen consumption (% of VO2max) attained was 59.3 in SED, 50.8 in STR and 48.0 in END (P<0.001 between SED and other subjects). Peak heart rate (% of heart rate max) was 82.7 in SED, 80.4 in STR and 72.4 in END. In SED, dynamic exercises without extra load elicited 51.0% of VO2max and 72.1% of heart rate max, and perceived effort reached 15.1/20. Conclusions. VT is an unconventional type of exercise, which has been shown to enhance strength, bone density, balance and flexibility. Users are attracted by the relative passivity. In SED, we show that VT elicits sufficient cardiovascular response to benefit overall fitness in addition to the known strength effects. VT's higher acceptance as an exercise in sedentary people, compared to jogging or cycling for example, can lead to better adherence to physical activity. Although long-term effects of VT on health are not avalaible, we believe this type of combination of aerobic and resistance-type exercise can be beneficial on multiple health parameters, especially cardiovascular health.

Five Years Of Denosumab Treatment In Women With Postmenopausal Osteoporosis: Preliminary Results From The Freedom Extension Study

Aims: The pivotal FREEDOM study evaluated the effi cacy and safety of 3 years' denosumab treatment in women with postmenopausal osteoporosis (PMO).1 Since osteoporosis is a chronic condition requiring long-term therapy, FREEDOM was extended to further elucidate the safety and effi cacy of long-term denosumab administration. We present data from the fi rst 2 years of this extension, representing up to 5 years' continuous exposure to denosumab.Methods: Patients who completed FREEDOM were eligible for the extension. Women continued to receive (long-term group), or started after 3 years' placebo (cross-over group), denosumab 60 mg sc every 6 months and daily calcium and vitamin D. These data refl ect 5 years' (long-term) or 2 years' (cross-over) continuous denosumab treatment. Effi cacy measures include changes in BMD from extension study baseline and bone turnover markers (BTM). P-values are descriptive.Results: Of the 83.0% of subjects who completed FREEDOM, 70.2% (N = 4550) agreed to participate in the extension (long-term: 2343; cross-over: 2207). In the long-term group, there were further signifi cant gains (P < 0.0001) in BMD in years 4 and 5: 1.9% and 1.7% at the lumbar spine to a total of 13.7% from FREEDOM baseline and 0.7% and 0.6% at the total hip to a total of 7.0%. During their fi rst 2 years' denosumab treatment, women in the cross-over group had signifi cant improvements in lumbar spine (7.9%) and total hip BMD (4.1%) (P < 0.0001). Serum C-telopeptide (CTX) was rapidly reduced following denosumab dosing in both groups, with the characteristic attenuation of CTX reduction observed at the end of the dosing interval. A low incidence of new vertebral and nonvertebral fractures was reported for both groups. The denosumab safety profi le did not change over time.Conclusions: Denosumab treatment for up to 5 years in women with PMO remains well tolerated, maintains reduction of BTMs and continues to significantly increase BMD.Reference1. Cummings. NEJM 2009;361:756.

The fine-scale architecture of structural variants in 17 mouse genomes.

BACKGROUND: Accurate catalogs of structural variants (SVs) in mammalian genomes are necessary to elucidate the potential mechanisms that drive SV formation and to assess their functional impact. Next generation sequencing methods for SV detection are an advance on array-based methods, but are almost exclusively limited to four basic types: deletions, insertions, inversions and copy number gains. RESULTS: By visual inspection of 100 Mbp of genome to which next generation sequence data from 17 inbred mouse strains had been aligned, we identify and interpret 21 paired-end mapping patterns, which we validate by PCR. These paired-end mapping patterns reveal a greater diversity and complexity in SVs than previously recognized. In addition, Sanger-based sequence analysis of 4,176 breakpoints at 261 SV sites reveal additional complexity at approximately a quarter of structural variants analyzed. We find micro-deletions and micro-insertions at SV breakpoints, ranging from 1 to 107 bp, and SNPs that extend breakpoint micro-homology and may catalyze SV formation. CONCLUSIONS: An integrative approach using experimental analyses to train computational SV calling is essential for the accurate resolution of the architecture of SVs. We find considerable complexity in SV formation; about a quarter of SVs in the mouse are composed of a complex mixture of deletion, insertion, inversion and copy number gain. Computational methods can be adapted to identify most paired-end mapping patterns.

Evolution of a cellular immune response in Drosophila: a phenotypic and genomic comparative analysis.

Understanding the genomic basis of evolutionary adaptation requires insight into the molecular basis underlying phenotypic variation. However, even changes in molecular pathways associated with extreme variation, gains and losses of specific phenotypes, remain largely uncharacterized. Here, we investigate the large interspecific differences in the ability to survive infection by parasitoids across 11 Drosophila species and identify genomic changes associated with gains and losses of parasitoid resistance. We show that a cellular immune defense, encapsulation, and the production of a specialized blood cell, lamellocytes, are restricted to a sublineage of Drosophila, but that encapsulation is absent in one species of this sublineage, Drosophila sechellia. Our comparative analyses of hemopoiesis pathway genes and of genes differentially expressed during the encapsulation response revealed that hemopoiesis-associated genes are highly conserved and present in all species independently of their resistance. In contrast, 11 genes that are differentially expressed during the response to parasitoids are novel genes, specific to the Drosophila sublineage capable of lamellocyte-mediated encapsulation. These novel genes, which are predominantly expressed in hemocytes, arose via duplications, whereby five of them also showed signatures of positive selection, as expected if they were recruited for new functions. Three of these novel genes further showed large-scale and presumably loss-of-function sequence changes in D. sechellia, consistent with the loss of resistance in this species. In combination, these convergent lines of evidence suggest that co-option of duplicated genes in existing pathways and subsequent neofunctionalization are likely to have contributed to the evolution of the lamellocyte-mediated encapsulation in Drosophila.

In-depth assessment delivers the verdict on the Government�۪s promise of a more equal society

An independent and detailed expert analysis of a decade of reforms (published 25 February) takes up the challenge made by Peter Mandelson in 1997 to “judge us after ten years of success in office. For one of the fruits of that success will be that Britain has become a more equal society.����”Commissioned by the Joseph Rowntree Foundation, the study, by a team led by LSE’s Centre for Analysis of Social Exclusion, shows sharp contrasts between different policy areas. Notable success stories include reductions in child and pensioner poverty, improved education outcomes for the poorest children and schools, and narrowing economic and other divides between deprived and other areas.But health inequalities continued to widen, gaps in incomes between the very top and very bottom grew, and poverty increased for working-age people without children.����In several policy areas there was a marked contrast between the first half of the New Labour period and the second half, when progress has slowed or even stalled.John Hills, one of the leaders of study, said, “Whether Britain has moved towards becoming a ‘more equal society’ depends on what you look at, and when. Where clear initiatives were taken, results followed. But as the growth of living standards slowed, even well before the recession, and public finances tightened, momentum seems to have been lost in several key areas.”Kitty Stewart added, “The government can take heart from achievements such as the reduction in child poverty up to 2004.����Recent data show that by then, child well-being in the UK had begun to move up the European league table from its dismal showing at the start of the decade that formed the basis of UNICEF’s damning 2007 report. But even with improved figures, Britain was still left with one of the highest rates of child poverty out of the 15 original EU members, and the latest figures show it had increased again by 2006/7.”����The study concludes that the decade from 1997 was favourable to an egalitarian agenda in several ways: the economy grew continuously; the government had large majorities and aspired to create more equality; and public attitudes surveys suggested pent-up demand for more public expenditure. But that environment now looks very uncertain, not just in the near future, but also in the longer term.����Fiscal pressures from an ageing society could further constrain resources available for redistribution, and public attitudes towards the benefit system have hardened while support for redistribution has declined.Hills added, “The 1980s and 1990s showed that hoping that rapid growth in living standards at the top would ‘trickle down’ to those at the bottom did not work.����The period since 1997 has shown that gains are possible through determined interventions, but they require intensive and continuous effort to be sustained.”JRF Chief Executive Julia Unwin added, “We know the potential impact the deepening recession will have on those already living in poverty. This book provides an important, timely and comprehensive assessment of where we are and what remains to be done.”

Fully engaged: tackling health inequalities through public health interventions

The evolving role of Primary Care Trusts (PCTs) is currently centre stage, with fundamental debate emerging from Commissioning a patient-led NHS and Our health, our care, our say a new direction for community services. This paper argues that PCTs have a crucial role to play in the public health agenda, specifically tackling health inequalities. This responsibility will become even stronger as the present wave of reforms gains momentum. There is also a lively debate on whether these reforms will make inroads into the persistent problem of health inequality or will exacerbate them even further unless robust, additional intervention levers and mechanisms are introduced. This paper suggests that PCTs will be central to ensuring the balance of reforms is tilted towards a more rather than a less equitable NHS. One of the key responsibilities for PCTs outlined by the Department of Health1 will be to act as the anchor at local level to the increasingly diverse and potentially3fragmented NHS. By using their crucial commissioning role to provide overall coherence to the health system, acting as leading local champions of the NHS and continuing the drive for improvement in access and quality, PCTs will have to act as enforcer and guardian of the equity of the NHS at local level. There is widespread evidence of the tenacity of health inequalities in Great Britain. This report looks at the measures that a fully engaged۝3 PCT has taken to grapple with the issues and draws some conclusions as to their possible wider application.refer to the resource

Binary classification of dyslipidemia from the waist-to-hip ratio and body mass index: a comparison of linear, logistic, and CART models.

BACKGROUND: We sought to improve upon previously published statistical modeling strategies for binary classification of dyslipidemia for general population screening purposes based on the waist-to-hip circumference ratio and body mass index anthropometric measurements. METHODS: Study subjects were participants in WHO-MONICA population-based surveys conducted in two Swiss regions. Outcome variables were based on the total serum cholesterol to high density lipoprotein cholesterol ratio. The other potential predictor variables were gender, age, current cigarette smoking, and hypertension. The models investigated were: (i) linear regression; (ii) logistic classification; (iii) regression trees; (iv) classification trees (iii and iv are collectively known as "CART"). Binary classification performance of the region-specific models was externally validated by classifying the subjects from the other region. RESULTS: Waist-to-hip circumference ratio and body mass index remained modest predictors of dyslipidemia. Correct classification rates for all models were 60-80%, with marked gender differences. Gender-specific models provided only small gains in classification. The external validations provided assurance about the stability of the models. CONCLUSIONS: There were no striking differences between either the algebraic (i, ii) vs. non-algebraic (iii, iv), or the regression (i, iii) vs. classification (ii, iv) modeling approaches. Anticipated advantages of the CART vs. simple additive linear and logistic models were less than expected in this particular application with a relatively small set of predictor variables. CART models may be more useful when considering main effects and interactions between larger sets of predictor variables.

Normalització d'un volum d'arxius en format MP3

Aquest projecte es pot dividir en tres parts: una primera part d'extracció dels components freqüencials de les trames d'arxius MP3, una segona part d'anàlisi i càlcul d'un factor de normalització a partir de les dades dels components freqüencials de diversos arxius MP3, i una última part amb la modificació correcta dels guanys de les trames dels arxius MP3 a partir del factor de normalització generat en la part anterior. En aquest treball de final de carrera s'implementen la primera i la tercera de les parts descrites anteriorment.

A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni

To provide a novel resource for analysis of the genome of Biomphalaria glabrata, members of the international Biomphalaria glabrata Genome Initiative (biology.unm.edu/biomphalaria-genome.html), working with the Arizona Genomics Institute (AGI) and supported by the National Human Genome Research Institute (NHGRI), produced a high quality bacterial artificial chromosome (BAC) library. The BB02 strain B. glabrata, a field isolate (Belo Horizonte, Minas Gerais, Brasil) that is susceptible to several strains of Schistosoma mansoni, was selfed for two generations to reduce haplotype diversity in the offspring. High molecular weight DNA was isolated from ovotestes of 40 snails, partially digested with HindIII, and ligated into pAGIBAC1 vector. The resulting B. glabrata BAC library (BG_BBa) consists of 61824 clones (136.3 kb average insert size) and provides 9.05 × coverage of the 931 Mb genome. Probing with single/low copy number genes from B. glabrata and fingerprinting of selected BAC clones indicated that the BAC library sufficiently represents the gene complement. BAC end sequence data (514 reads, 299860 nt) indicated that the genome of B. glabrata contains ~ 63% AT, and disclosed several novel genes, transposable elements, and groups of high frequency sequence elements. This BG_BBa BAC library, available from AGI at cost to the research community, gains in relevance because BB02 strain B. glabrata is targeted whole genome sequencing by NHGRI.

Percepción de las consecuencias del consumo de tabaco en fumadores adictos al juego

En una muestra de 34 adictos al juego en tratamiento, se examinan las características deconsumo de tabaco de los sujetos fumadores y la influencia de las consecuencias percibidas dela conducta de fumar en función de las etapas de cambio (Prochaska, DiClemente y Norcross,1992). Los resultados muestran que, aunque los porcentajes de fumadores doblan a los existentesen la población general, las personas fumadoras adictas al juego están representadas en lasdiferentes etapas de cambio con porcentajes parecidos a los de dicha población. Por otra parte,no se ha encontrado relación entre el nivel de dependencia medido con el Test de Fagerström yla etapa de cambio. En cuanto a la influencia de las consecuencias percibidas del consumo detabaco, en general los sujetos tienden a conceder mayor importancia a los perjuicios que a losbeneficios de fumar. En los análisis en función de las etapas de cambio, se encuentran diferenciassignificativas entre el grupo de los que piensan dejar de fumar en los próximos seis meses,(contempladores y preparados) y el grupo de los que no fuman (exfumadores y no fumadores) enel beneficio “fumar ayuda a relajarse” que es más valorado por los primeros. También seencuentran dichas diferencias entre los precontempladores y los que no fuman en dos perjuicios:“fumar produce a veces dolor de cabeza” y “fumar a veces provoca taquicardia” que son másvalorados por los segundos. Estos resultados sugieren la conveniencia de realizar las intervencionesmás adecuadas para cada etapa de cambio, a fin de que las personas adictas al juegopuedan también tener éxito en el abandono de la adicción al tabaco

Efecto de las pérdidas y ganancias recientes en el riesgo asumido por los automovilistas

Se analiza el efecto de las pérdidas y ganancias recientes sobre la conducta arriesgada y el riesgo percibido en la ejecución del simulador de conducción TIC/PC. Los modelos teóricos analizados coinciden en predecir aumento de la conducta arriesgada tras la pérdida y no modificación tras la ganancia. Los resultados obtenidos no confirman estas predicciones en cuanto al efecto de las pérdidas recientes. Tras las ganancias los sujetos no se diferencian de los controles. En cuanto al riesgo percibido, sólo la Teoría de Riesgo-Cero predice modificaciones tras la pérdida. Si bien nuestros sujetos experimentales perciben menos riesgo tras la pérdida, ello no se traduce en un aumento de la conducta arriesgada. Parece ser que percepción y conducta se rigen por mecanismos diferentes

Impact of severe epilepsy on development: Recovery potential after successful early epilepsy surgery.

Purpose: Epilepsy surgery in young children with focal lesions offers a unique opportunity to study the impact of severe seizures on cognitive development during a period of maximal brain plasticity, if immediate control can be obtained. We studied 11 children with early refractory epilepsy (median onset, 7.5 months) due to focal lesion who were rendered seizure-free after surgery performed before the age of 6 years. Methods: The children were followed prospectively for a median of 5 years with serial neuropsychological assessments correlated with electroencephalography (EEG) and surgery-related variables. Results: Short-term follow-up revealed rapid cognitive gains corresponding to cessation of intense and propagated epileptic activity [two with early catastrophic epilepsy; two with regression and continuous spike-waves during sleep (CSWS) or frontal seizures]; unchanged or slowed velocity of progress in six children (five with complex partial seizures and frontal or temporal cortical malformations). Longer-term follow-up showed stabilization of cognitive levels in the impaired range in most children and slow progress up to borderline level in two with initial gains. Discussion: Cessation of epileptic activity after early surgery can be followed by substantial cognitive gains, but not in all children. In the short term, lack of catch-up may be explained by loss of retained function in the removed epileptogenic area; in the longer term, by decreased intellectual potential of genetic origin, irreversible epileptic damage to neural networks supporting cognitive functions, or reorganization plasticity after early focal lesions. Cognitive recovery has to be considered as a "bonus," which can be predicted in some specific circumstances.

A teaching/learning support tool for introductory programming courses

In This work we present a Web-based tool developed with the aim of reinforcing teaching and learning of introductory programming courses. This tool provides support for teaching and learning. From the teacher's perspective the system introduces important gains with respect to the classical teaching methodology. It reinforces lecture and laboratory sessions, makes it possible to give personalized attention to the student, assesses the degree of participation of the students and most importantly, performs a continuous assessment of the student's progress. From the student's perspective it provides a learning framework, consisting in a help environment and a correction environment, which facilitates their personal work. With this tool students are more motivated to do programming