Parallelization of whole genome alignment

With the advent of High performance computing, it is now possible to achieve orders of magnitude performance and computation e ciency gains over conventional computer architectures. This thesis explores the potential of using high performance computing to accelerate whole genome alignment. A parallel technique is applied to an algorithm for whole genome alignment, this technique is explained and some experiments were carried out to test it. This technique is based in a fair usage of the available resource to execute genome alignment and how this can be used in HPC clusters. This work is a rst approximation to whole genome alignment and it shows the advantages of parallelism and some of the drawbacks that our technique has. This work describes the resource limitations of current WGA applications when dealing with large quantities of sequences. It proposes a parallel heuristic to distribute the load and to assure that alignment quality is mantained.

Emissió ràdio a baixa freqüència en fenòmens eruptius i en fonts esteses de raigs gamma d'alta i molt alta energia

La tasca investigadora presentada en aquesta memòria s'ha centrat en les fonts galàctiques de raigs gamma de molt alta energia LS I +61 303, HESS J1708-410 i HESS J1858+020. La primera és una binària de raigs gamma molt estudiada, formada per una estrella massiva i un objecte compacte. S'ha proposat un escenari on l'objecte compacte seria un púlsar jove, i la interacció del seu vent amb el vent de l'estrella generaria els raigs gamma. De totes formes, no s'ha detectat polsos procedents d'aquest putatiu púlsar. L'investigador va realitzar observacions en fase a 1280 MHz amb el radiotelescopi GMRT, sense trobar-hi polsos, cosa que implica un estricte límit superior de 0,38 mJy a la densitat mitjana de flux polsat en un putatiu púlsar amb un període major que 2 mil•lisegons en el sistema binari LS I +61 303. Per altra banda, HESS J1708-410 i HESS J1858+020 són dues fonts esteses de raigs gamma de molt alta energia de les quals no es coneix cap contrapart a d'altres longituds d'ona. L'investigador les va observar amb el GMRT, quatre vegades HESS J1708-410 (dues a 610 MHz i dues a 1400 MHz) i dues vegades HESS J1858+020 (una a cada freqüència). En les imatges realitzades amb aquestes dades no hi ha emissió estesa coincident amb les regions d'emissió de raigs gamma. HESS J1858+020 se solapa parcialment amb una font estesa que podria ser un SNR. De confirmar-se la falta de contrapartida ràdio de HESS J1708-410, estaríem parlant d'un accelerador hadrònic extraordinàriament eficient, d'una classe desconeguda fins ara.

El comportamiento penalmente relevante en el delito de defraudación tributaria: una propuesta político-criminal

El sistema tributario es fundamental en el Estado social y democrático de Derecho, pues el ejercicio y efectivo disfrute de muchos derechos fundamentales depende del correcto funcionamiento de la actividad tributaria. Además de esto, la situación económica actual demanda una adecuada política en contra del fraude tributario, lo que necesariamente implica analizar si el modelo penal vigente es el más adecuado para enfrentar el fraude fiscal. Teniendo en cuenta que muchas de las características de la criminalidad tributaria no son exclusivas de un país, pues ésta trasciende habitualmente las fronteras de los países por medio del recurso a empresas multinacionales o la localización de empresas en “paraísos fiscales”, el análisis del fraude tributario no debe limitarse al examen jurídico del modelo legislativo español, debiendo trascender a un estudio de política criminal que vincula consideraciones criminológicas y jurídicas. En consecuencia, en esta investigación se propone un análisis que no se reduce a los debates exclusivamente jurídicos. Se busca, además, efectuar un examen que tenga por fundamento una perspectiva criminológica y de Law in action a fin de evaluar críticamente la respuesta a la criminalidad tributaria por parte del modelo de regulación penal vigente en España. Esta orientación permitirá una más amplia comprensión del fenómeno de la criminalidad tributaria, así como de las categorías jurídicas adecuadas político criminalmente para su prevención. Este estudio interdisciplinario nos conducirá, al final de la investigación, tanto a proponer la interpretación del modelo de legislación penal vigente, como una reforma al mismo que pretenda solucionar algunos de los problemas de prevención que a lo largo de la investigación se señalan.

Abortion in public reason

What abortion laws a liberal political community ought to have? Much has been said about the moral problem of abortion, but there has not been yet (to my knowledge) a fully articulate account of the bearing of the competing answers to this ethical problem on liberal public reason. The first part of my project consists in a critical review of the different attempts to solve the various philosophical puzzles, both metaphysical and moral, posed by the abortion problem. Why is it wrong to kill beings like you and me? By answering this question we shall gain a better insight into those properties we have that give us such strong reasons against killing beings like us. Here we face a tremendous philosophical diffuculty, for it is not possible to determine what the robustest account of the wrongness of killing is without dealing with deeper metaethical and metaphysical problems. Indeed, consequentialist and nonconsequentialist moral theories differ in what it is that makes an action morally wrong -is it just the outcome of the action as compared with the outcomes of its alternatives? Or is it something else? Also, what are we essentially? Is the foetus merely our precursor? Then killing a foetus is relevantly similar to contraception. Or is the foetus one of us? If so, when we kill it, are we depriving it of a future as valuable as ours? Perhaps the relation of identity (the fact that it is its future as opposed to someone else's) doesn't matter. That may be because the foetus is an aggregate of biological and psychological facts and perhaps aggregates are not substances. Or maybe it is a substance but only psychological realtions matter, not personal identity. The second part of my project has to do with the different status these metaphisical and ethical positions ought to have in liberal public reason. Though this is the part in which most research is still needed, my own intuition is that, given the depth of the philosphical views in competition, restrictive abortion laws ought to be considered unrespectful to citizens' autonomy.

El perdó de l’ofés: la via adequada per alleugerir les càrregues de la justícia? Estudi de la institució i de les alternatives per rendibilitzar els recursos de l’Administració de justícia

En aquesta recerca aportem les conclusions de la nostra investigació sobre la figura del perdó de l’ofès i la seva possible virtualitat com a mitjà per alleugerir l’Administració de Justícia. En primer lloc, analitzem la institució del perdó de l’ofès, en concret, la seva regulació en el nostre Codi penal, els seus antecedents històrics i aportem certes dades de Dret comparat que poden ajudar a l’estudi crític de la institució (1). En la segona part, estudiem els arguments a favor i en contra del perdó de l’ofès dins el sistema penal i ens pronunciem sobre la seva legitimitat com a mecanisme per rendibilitzar l’Administració de Justícia (2). En la tercera part, sobre la base de les conclusions anteriors, aportem una reflexió sobre les alternatives al perdó de l’ofès (3). Per últim, en la darrera part, formulem la nostra proposta final sobre els mecanismes per rendibilitzar els recursos de l’Administració de Justícia (4). Segons el nostre estudi, el perdó de l’ofès no és un bon mecanisme per alleugerir la feina de l’Administració de Justícia. En canvi, la reparació i la conciliació si poden operar com a substitutius de la pena en els supòsits de delictes de menor gravetat; en els processos penals per aquests delictes caldria introduir un intent obligatori de conciliació, com el del § 380 StPO alemany i, a més, convindria preveure en el Codi penal la facultat del jutge d’eliminar la responsabilitat penal en determinats supòsits de reparació de l’autor a la víctima del delicte.

Scores de mesure fonctionnelle articulaire pour le praticien [Joint functional outcome score for the clinician].

The sports clinician faces multiple treatment options when dealing with overload injuries, and it is important to evaluate their outcomes. Multiple scores exist, some clincian rated (CRO), others patient rated (PRO), the latter being currently favoured. This review presents some of these scores and we selected the ones we feel are the most appropriate for a sports clinician. We considered these common problems: tennis elbow, rotator cuff issues, groin pain, patellofemoral pain syndrome, achilles tendinopathy and ankle instability. In addition, an activity level score is useful to weigh the result in the context of return to performance. These scores help to create a common language between therapists and to evaluate treatments objectively.

BCR and TLR signalling pathways are recurrently targeted by genetic changes in splenic marginal zone lymphomas.

The genetics and pathogenesis of splenic marginal zone lymphoma are poorly understood. The lymphoma lacks chromosome translocation, and ~30% of cases are featured by 7q deletion, but the gene targeted by the deletion is unknown. A recent study showed inactivation of A20, a 'global' NF-kB negative regulator, in 1 of 12 splenic marginal zone lymphoma. To investigate further whether deregulation of the NF-kB pathway plays a role in the pathogenesis of splenic marginal zone lymphoma, we screened several NF-kB regulators for genetic changes by PCR and sequencing. Somatic mutations were found in A20 (6/46=13%), MYD88 (6/46=13%), CARD11 (3/34=8.8%), but not in CD79A, CD79B and ABIN1. Interestingly, these genetic changes are largely mutually exclusive from each other and MYD88 mutation was also mutually exclusive from 7q deletion. These results strongly suggest that deregulation of the TLR (toll like receptor) and BCR (B-cell receptor) signalling pathway may play an important role in the pathogenesis of splenic marginal zone lymphoma.

Biological threats: A Health Response for Ireland

In the light of recent worldwide events it is clear that there is a need in this and every country for preparedness for dealing with people who have been exposed to or infected with agents associated with bioterrorism. It seems unlikely that a country such as Ireland would be the target of a primary bioterrorist attack. It is more likely that those who have been covertly exposed to bioterrorist agents abroad could enter this country before they develop signs of illness and could have their illness diagnosed in this country. Due to the high infectivity of many of the diseases associated with these bioterrorist agents it is necessary to have protocols in place to deal with all contingencies. Download document here

Towards a tobacco free society : Report of the Tobacco Free policy Review Group

This report is the latest of four reports dealing with various aspects of smoking. There is some inevitable overlap in these reports and the actual recommendations may be somewhat different but there is a common objective of seeking the most effective measures possible to dramatically reduce the level of smoking in our society and above all to prevent our children from starting to smoke Download the Report here

Speech by Mr. Micheál Martin TD – Meeting The Challenges Of Cultural Diversity In The Irish Healthcare Sector

It gives me great pleasure to accept the invitation to address this conference on “Meeting the Challenges of Cultural Diversity in the Irish Healthcare Sector” which is being organised by the Irish Health Services Management Institute in partnership with the National Consultative Committee on Racism and Interculturalism. The conference provides an important opportunity to develop our knowledge and understanding of the issues surrounding cultural diversity in the health sector from the twin perspectives of patients and staff. Cultural diversity has over recent years become an increasingly visible aspect of Irish society bringing with it both opportunities and challenges. It holds out great possibilities for the enrichment of all who live in Ireland but it also challenges us to adapt creatively to the changes required to realise this potential and to ensure that the experience is a positive one for all concerned but particularly for those in the minority ethnic groups. In the last number of years in particular, the focus has tended to be on people coming to this country either as refugees, asylum seekers or economic migrants. Government figures estimate that as many as 340,000 immigrants are expected in the next six years. However ethnic and cultural diversity are not new phenomena in Ireland. Travellers have a long history as an indigenous minority group in Ireland with a strong culture and identity of their own. The changing experience and dynamics of their relationship with the wider society and its institutions over time can, I think, provide some valuable lessons for us as we seek to address the more numerous and complex issues of cultural diversity which have arisen for us in the last decade. Turning more specifically to the health sector which is the focus of this conference, culture and identity have particular relevance to health service policy and provision in that The first requirement is that we in the health service acknowledge cultural diversity and the differences in behaviours and in the less obvious areas of values and beliefs that this often implies. Only by acknowledging these differences in a respectful way and informing ourselves of them can we address them. Our equality legislation – The Employment Equality Act, 1998 and the Equal Status Act, 2000 – prohibits discrimination on nine grounds including race and membership of the Traveller community. The Equal Status Act prohibits discrimination on an individual basis in relation to the nine grounds while for groups it provides for the promotion of equality of opportunity. The Act applies to the provision of services including health services. I will speak first about cultural diversity in relation to the patient. In this respect it is worth mentioning that the recognition of cultural diversity and appropriate responses to it were issues which were strongly emphasised in the public consultation process which we held earlier this year in the context of developing National Anti-Poverty targets for the health sector and also our new national health strategy. Awareness and sensitivity training for staff is a key requirement for adapting to a culturally diverse patient population. The focus of this training should be the development of the knowledge and skills to provide services sensitive to cultural diversity. Such training can often be most effectively delivered in partnership with members of the minority groups themselves. I am aware that the Traveller community, for example, is involved in in-service training for health care workers. I am also aware that the National Consultative Committee on Racism and Interculturalism has been involved in training with the Eastern Regional Health Authority. We need to have more such initiatives. A step beyond the sensitivity training for existing staff is the training of members of the minority communities themselves as workers in our health services. Again the Traveller community has set an example in this area with its Primary Health Care Project for Travellers. The Primary Health Care for Travellers Project was established in 1994 as a joint partnership initiative with the Eastern Health Board and Pavee Point, with ongoing technical assistance being provided from the Department of Community Health and General Practice, Trinity College, Dublin. This project was the first of its kind in the country and has facilitated The project included a training course which concentrated on skills development, capacity building and the empowerment of Travellers. This confidence and skill allowed the Community Health Workers to go out and conduct a baseline survey to identify and articulate Travellers’ health needs. This was the first time that Travellers were involved in this process; in the past their needs were assumed. The results of the survey were fed back to the community and they prioritised their needs and suggested changes to the health services which would facilitate their access and utilisation. Ongoing monitoring and data collection demonstrates a big improvement in levels of satisfaction and uptake and ulitisation of health services by Travellers in the pilot area. This Primary Health Care for Travellers initiative is being replicated in three other areas around the country and funding has been approved for a further 9 new projects. This pilot project was the recipient of a WHO 50th anniversary commemorative award in 1998. The project is developing as a model of good practice which could inspire further initiatives of this type for other minority groups. Access to information has been identified in numerous consultative processes as a key factor in enabling people to take a proactive approach to managing their own health and that of their families and in facilitating their access to health services. Honouring our commitment to equity in these areas requires that information is provided in culturally appropriate formats. The National Health Promotion Strategy 2000-2005, for example, recognises that there exists within our society many groups with different requirements which need to be identified and accommodated when planning and implementing health promotion interventions. These groups include Travellers, refugees and asylum seekers, people with intellectual, physical or sensory disability and the gay and lesbian community. The Strategy acknowledges the challenge involved in being sensitive to the potential differences in patterns of poor health among these different groups. The Strategic aim is to promote the physical, mental and social well-being of individuals from these groups. The objective of the Strategy on these issues are: While our long term aim may be to mainstream responses so that our health services is truly multicultural, we must recognise the need at this point in time for very specific focused responses particularly for groups with poor health status such as Travellers and also for refugees and asylum seekers. In the case of refugees and asylum seekers examples of targeted services are screening for communicable diseases – offered on a voluntary basis – and psychological support services for those who have suffered trauma before coming here. The two approaches of targeting and mainstreaming are not mutually exclusive. A combination of both is required at this point in time but the balance between them must be kept under constant review in the light of changing needs. A major requirement if we are to meet the challenge of cultural diversity is an appropriate data and research base. I think it is important that we build up our information and research data base in partnership with the minority groups themselves. We must establish what the health needs of diverse groups are; we must monitor uptake of services and how well we are responding to needs and we must monitor outcomes and health status. We must also examine the impact of the policies in other sectors on the health of minority groups. The National Health Information Strategy, currently being developed, and the recently published National Strategy for Health Research – Making Knowledge Work for Health provide important frameworks within which we can improve our data and research base. A culturally diverse health sector workforce – challenges and opportunities The Irish health service can benefit greatly from successful international recruitment. There has been a strong non-national representation amongst the medical profession for more than 30 years. More recently there have been significant increases in other categories of health service workers from overseas. The Department recognises the enormous value that overseas recruitment brings over a wide range of services and supports the development of effective and appropriate recruitment strategies in partnership with health service employers. These changes have made cultural diversity an important issue for all health service organisations. Diversity in the workplace is primarily about creating a culture that seeks, respects, values and harnesses difference. This includes all the differences that when added together make each person unique. So instead of the focus being on particular groups, diversity is about all of us. Change is not about helping “them” to join “us” but about critically looking at “us” and rooting out all aspects of our culture that inappropriately exclude people and prevent us from being inclusive in the way we relate to employees, potential employees and clients of the health service. International recruitment benefits consumers, Irish employees and the overseas personnel alike. Regardless of whether they are employed by the health service, members of minority groups will be clients of our service and consequently we need to be flexible in order to accommodate different cultural needs. For staff, we recognise that coming from other cultures can be a difficult transition. Consequently health service employers have made strong efforts to assist them during this period. Many organisations provide induction courses, religious facilities (such as prayer rooms) and help in finding suitable accommodation. The Health Service Employers Agency (HSEA) is developing an equal opportunities/diversity strategy and action plans as well as training programmes to support their implementation, to ensure that all health service employment policies and practices promote the equality/diversity agenda to continue the development of a culturally diverse health service. The management of this new environment is extremely important for the health service as it offers an opportunity to go beyond set legal requirements and to strive for an acceptance and nurturing of cultural differences. Workforce cultural diversity affords us the opportunity to learn from the working practices and perspectives of others by allowing personnel to present their ideas and experience through teamwork, partnership structures and other appropriate fora, leading to further improvement in the services we provide. It is important to ensure that both personnel units and line managers communicate directly with their staff and demonstrate by their actions that they intend to create an inclusive work place which doesn´t demand that minority staff fit. Contented, valued employees who feel that there is a place for them in the organisation will deliver a high quality health service. Your conference here today has two laudable aims – to heighten awareness and assist health care staff to work effectively with their colleagues from different cultural backgrounds and to gain a greater understanding of the diverse needs of patients from minority ethnic backgrounds. There is a synergy in these aims and in the tasks to which they give rise in the management of our health service. The creative adaptations required for one have the potential to feed into the other. I would like to commend both organisations which are hosting this conference for their initiative in making this event happen, particularly at this time – Racism in the Workplace Week. I look forward very much to hearing the outcome of your deliberations. Thank you.

Freshwater snails and Schistosomiasis mansoni in the state of Rio de Janeiro, Brazil: III - Baixadas Mesoregion

In this paper, the third of a series dealing with the survey of freshwater gastropods of the state of Rio de Janeiro, the results of collections carried out in the Mesoregion Baixadas from 2000 to 2002 are presented. Twenty-two species, belonging to seven families, were found. As to the snail intermediate hosts of Schistosoma mansoni, the most frequent species was Biomphalaria tenagophila besides some new findings of Biomphalaria straminea. No specimens were found harboring larval forms of S. mansoni although different kinds of cercariae had been observed.

Report of the Consultation on the Health Act, 2004 (Part 9) - Complaints

Part 9 of the Health Act 2004 makes provision for the introduction of a statutory complaints system within the HSE. The purpose of this Department of Health and Children Consultation is to establish a shared understanding of the requirements and priorities attaching to this particular part of the Act as well as providing an opportunity for those experienced in complaints handling to contribute to and inform the Regulations which will specify how the HSE will establish a statutory framework for dealing with complaints received under Part 9 of the Health Act, 2004. Read the report (PDF, 387kb)  

Projecte web "Viatges a Patrimonis de la Humanitat" (Ass. Amics Unesco Barcelona)

Treball Final Carrera sobre la gestió d'un projecte web, de gestió de continguts multimèdia, de creació i coordinació d'un equip de voluntaris per a la divulgació en línia i el foment dels viatges culturals als llocs Patrimoni de la Humanitat realitzats per una entitat intercultural catalana, Amics de la UNESCO de Barcelona.

Divorce in the barn owl: securing a compatible or better mate entails the cost of re-pairing with a less ornamented female mate.

Two nonmutually exclusive hypotheses can explain why divorce is an adaptive strategy to improve reproductive success. Under the 'better option hypothesis', only one of the two partners initiates divorce to secure a higher-quality partner and increases reproductive success after divorce. Under the 'incompatibility hypothesis', partners are incompatible and hence they may both increase reproductive success after divorce. In a long-term study of the barn owl (Tyto alba), we address the question of whether one or the two partners derive fitness benefits by divorcing. Our results support the hypothesis that divorce is adaptive: after a poor reproductive season, at least one of the two divorcees increase breeding success up to the level of faithful pairs. By breeding more often together, faithful pairs improve coordination and thereby gain in their efficiency to produce successful fledglings. Males would divorce to obtain a compatible mate rather than a mate of higher quality: a heritable melanin-based signal of female quality did not predict divorce (indicating that female absolute quality may not be the cause of divorce), but the new mate of divorced males was less melanic than their previous mate. This suggests that, at least for males, a cost of divorce may be to secure a lower-quality but compatible mate. The better option hypothesis could not be formally rejected, as only one of the two divorcing partners commonly succeeded in obtaining a higher reproductive success after divorce. In conclusion, incompatible partners divorce to restore reproductive success, and by breeding more often together, faithful partners improve coordination.

National Drugs Strategy 2009 - 2016 - End of Year Progress Report for 2013

Drugs misuse continues to be one of the most significant challenges facing our country.   It is highly destructive and has devastating effects on individuals, relationships, families, communities and society in general. Implementation of the National Drugs Strategy 2009-2016, which sets out Government policy in dealing with the drugs problem, is being pursued across a range of Government Departments and Agencies.  Solid progress is being made across the 63 Actions of the Strategy, which are based around the five pillars of supply reduction, prevention, treatment, rehabilitation and research. The Oversight Forum on Drugs, which is Chaired by Minister Mr Alex White, meets on a quarterly basis and reviews the implementation of the Strategy. The 2013 Annual Progress Report on the implementation of the actions of the National Drugs Strategy is available here.