Accelerating Multiple Sequence Alignment with the Cell BE Processor

The Cell Broadband Engine (BE) Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, most notably the extensive support for vectorization, scratch pad memories and explicit programming of direct memory accesses (DMAs) and mailbox communication. While these features strongly increase programming complexity, it is generally claimed that significant speedups can be obtained by using Cell BE processors. This paper presents our experiences with using the Cell BE architecture to accelerate Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is in obtaining high performance. By making extensive use of vectorization and by parallelizing the application across all cores, we demonstrate a speedup of 24.4 times when using 16 synergistic processor units on a QS21 Cell Blade compared to single-thread execution on the power processing unit. As the Cell BE exploits a large number of slim cores, our highly optimized implementation is just 3.8 times faster than a 3-thread version running on an Intel Core2 Duo, as the latter processor exploits a small number of fat cores.

Rising incidence of Pneumocystis jirovecii pneumonia suggests iatrogenic exposure of immune compromised patients may be becoming a significant problem.

Against a background of point-source outbreaks of Pneumocystis pneumonia (PCP) in renal transplant units in Europe, we undertook a retrospective 3 year observational review of PCP in Northern Ireland. This showed an unexpected increase in incidence, with a mortality rate of 30%. Fifty-one cases were confirmed compared to 10 in the preceding 7 years. Where undiagnosed HIV infection had previously been the main risk factor for PCP, this was now equally matched by chemotherapy for haematological and non-haematological malignancy and immune suppression for a range of autoimmune conditions. Congenital immunodeficiency and transplantation were less common pre-disposing factors, but renal grafts also showed a rising incidence. Asymptomatic carriage was uncommon. At presentation both upper and lower respiratory samples were of equal use in establishing the diagnosis and treatment resulted in rapid clearance. The data suggests the need for considering PCP in at risk patients, reviewing its mode of acquisition and whether iatrogenic colonization is a treatable pre-condition. [Epub ahead of print]

Defining a Research Agenda in Value Driven Design: Questions That Need to be Asked

Value driven design is an innovative design process that utilizes the optimization of a system level value function to determine the best possible design. This contrasts with more traditional systems engineering techniques, which rely on satisfying requirements to determine the design solution. While ‘design for value’ is intuitively acceptable, the transformation of value driven design concepts into practical tools and methods for its application is challenging. This, coupled with the growing popularity of value-centric design philosophies, has led to a proposed research agenda in value driven design. This research agenda asks fundamental questions about the design philosophy and attempts to identify areas of significant challenge. The research agenda is meant to stimulate discussion in the field, as well as prompt research that will lead to the development of tools and methodologies that will facilitate the application of value driven design and further the state of the art.

“They might as well be walking around the inside of a biscuit tin”: Barriers to Employment and Reintegration for ‘Politically Motivated’ Former Prisoners in Northern Ireland

The prisoner provisions under the Northern Ireland Peace Agreement clearly emphasised the importance of the reintegration and civic inclusion of ‘politically motivated’ former prisoners; however, numerous barriers to full reintegration remain. Even though these prisoners were released as part of a peace process, based on principles of conflict transformation and reconciliation, there were still The prisoner provisions under the Northern Ireland Peace Agreement emphasised the importance of the reintegration and civic inclusion of ‘politically motivated’ former prisoners; however, numerous barriers to full reintegration remain. Notwithstanding the fact that these prisoners were released as part of a peace process, based on principles of conflict transformation and reconciliation, there were still numerous conditions placed upon them as part of their release process and they continued to hold a ‘criminal’ record upon release. As with ‘ordinary’ ex-prisoners, these ‘politically motivated’ former prisoners have subsequently faced numerous obstacles in their attempts to reintegrate back into society, particularly in the area of employment. Recognising that they needed to deal with the consequences of imprisonment, ‘politically motivated’ former prisoners formed numerous self-help organisations to assist in the reintegration process and have mobilised to lobby for protection against the discrimination and unequal treatment experienced by ex-prisoners seeking employment. This article explores the remaining barriers to employment for ‘politically motivated’ former prisoners and the consequences of these barriers. The article moves to assess how prisoner groups have subsequently used a ‘rights based’ discourse to engage local government in their struggle to overcome existing obstacles before finally concluding that any piecemeal attempt to remove barriers to full reintegration will only impede the longer term conflict transformation process in Northern Ireland.

Right to War in the Islamic Tradition:Jihad and its Compatibility with Modern International Law (will be submitted to the publisher in April 2014)

In the last century, Islam drew the world’s attention though such phenomena as the Islamic revolution in Iran, the fierce Muslim resistance against the Soviet invasion of Afghanistan, and the assassination of Egypt’s President Sadat by a radical Islamic group. But it was when Osama Bin Laden and his organization Al Qaeda were established to have been behind the 11 September attacks in the US, the age-old images of Islam, the fanatical and belligerent religion threatening what the Western world stands for, were revitalized. The impact of 9/11 attacks was so great that even balanced portrayals of Islam were eclipsed by stereotypical images of a fundamental, anti-Western and warmongering religion that bore the hallmarks of medieval prejudices and rhetoric. The popular image tailored for the Western audience reflected Islam as monolithic, intrinsically aggressive, and determined to engage in religious wars against the interests and values of the Western civilisation.
This book intends to help reduce, at least to a reasonable degree, the impact of sweeping, and at times tendentious, generalisations about Islamic laws of warfare. The main purpose of this book is to place the legal, cultural and historical practices of Islamic wars in their broader socio-political contexts, thereby establishing that there has been no undisputed understanding of what defensive or aggressive warfare entails in Islam, whether in doctrine or in practice.

Which patients with renal colic should be referred?

Around 1-2 people per thousand present with an acute episode of pain caused by renal stones each year. Renal colic is classically sudden in onset, unilateral, and radiates from loin to groin. Renal pelvic or upper ureteric stones usually cause more flank pain and tenderness while lower ureteric stones cause pain radiating towards the ipsilateral testicle or labia. Other common symptoms include nausea and vomiting, haematuria and irritative LUTS. A febrile patient with renal colic requires immediate hospital admission. Symptoms suggestive of renal colic along with a positive dipstick for haematuria have a reported sensitivity of 84% and specificity of 99% but it is important to consider other differential diagnoses. An NSAID is preferred over an opiate drug as an initial analgesic choice as the NSAID can help reduce ureteric spasm. Diclofenac has the best evidence base for this class of analgesic. About 90% of stones will pass spontaneously and thus it is often appropriate to manage renal colic at home. Patients with signs of peritonitis, systemic infection, septic shock as well as those whose diagnosis is unclear should be referred urgently to hospital. Patients who are systemically unwell with renal stones are more likely to have an infected and obstructed urinary tract system that needs urgent imaging and possible drainage. All patients who are managed at home should have renal tract imaging within a week by fast track referral to radiology or as an urgent urology outpatient referral as per local guidelines to rule out an obstructed urinary system. Patients with recurrent stones should be advised to maintain a copious fluid intake (>2 L/day) to reduce the concentration of the urine. A reduction in salt intake (ideally