Novel Modifications of Parallel Jacobi Algorithms

We describe two main classes of one-sided trigonometric and hyperbolic Jacobi-type algorithms for computing eigenvalues and eigenvectors of Hermitian matrices. These types of algorithms exhibit significant advantages over many other eigenvalue algorithms. If the matrices permit, both types of algorithms compute the eigenvalues and eigenvectors with high relative accuracy. We present novel parallelization techniques for both trigonometric and hyperbolic classes of algorithms, as well as some new ideas on how pivoting in each cycle of the algorithm can improve the speed of the parallel one-sided algorithms. These parallelization approaches are applicable to both distributed-memory and shared-memory machines. The numerical testing performed indicates that the hyperbolic algorithms may be superior to the trigonometric ones, although, in theory, the latter seem more natural.Comment: Accepted for publication in Numerical Algorithm

Jacobi Polynomials as su(2, 2) Unitary Irreducible Representation

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Threat of an influenza pandemic: family physicians in the front line

<p>Abstract</p> <p>Background</p> <p>The chance of an influenza pandemic is real and clinicians should keep themselves informed about the rationale and science behind preventive and therapeutic principles relating to an (impending) influenza pandemic.</p> <p>Discussion</p> <p>Vaccination is considered the best prevention in case of a pandemic threat and first choice to contain the impact of a pandemic. Pending the availability of an effective pandemic vaccine, antivirals are likely the only effective agents for prevention and treatment. When an influenza pandemic is impending, all interventions aim to prevent people becoming infected and to suppress replication and transmission of the virus as much as possible. Antivirals will be prescribed to patients with laboratory confirmed pre-pandemic influenza as well as to their contacts (post-exposure prophylaxis) which may delay development of or even prevent a pandemic. During a manifest influenza pandemic, however, there is large-scale spreading of the influenza virus. Therefore, preventive use of antivirals is less efficient to prevent transmission. Delaying the pandemic is then important in order to prevent exhausting public health resources and disruption of society. Thus, during a manifest pandemic everyone with influenza symptoms should receive antivirals as quickly as possible, regardless of virological confirmation. To ensure optimal effectiveness of antivirals and to minimize development of drug resistant viral strains, the use of antivirals for annual influenza should be restrictive. The crucial position of family physicians during an (impending) influenza pandemic necessitates the development of primary health care guidelines on this topic for all countries.</p> <p>Summary</p> <p>Family physicians will play a key role in assessing and treating victims of a new influenza virus, and in reassuring the worried well. We outline various possible interventions in the event of an impending and a manifest influenza pandemic, such as non-medial measures, prescription of antivirals, and vaccination, and emphasize the need for pandemic influenza preparedness.</p

Human Health Risk Assessment (HHRA) for environmental development and transfer of antibiotic resistanc

This is the final version of the article. Available from NIEHS via the DOI in this record.Open access journalBACKGROUND: Only recently has the environment been clearly implicated in the risk of antibiotic resistance to clinical outcome, but to date there have been few documented approaches to formally assess these risks. OBJECTIVE: We examined possible approaches and sought to identify research needs to enable human health risk assessments (HHRA) that focus on the role of the environment in the failure of antibiotic treatment caused by antibiotic-resistant pathogens. METHODS: The authors participated in a workshop held 4-8 March 2012 in Québec, Canada, to define the scope and objectives of an environmental assessment of antibiotic-resistance risks to human health. We focused on key elements of environmental-resistance-development "hot spots," exposure assessment (unrelated to food), and dose response to characterize risks that may improve antibiotic-resistance management options. DISCUSSION: Various novel aspects to traditional risk assessments were identified to enable an assessment of environmental antibiotic resistance. These include a) accounting for an added selective pressure on the environmental resistome that, over time, allows for development of antibiotic-resistant bacteria (ARB); b) identifying and describing rates of horizontal gene transfer (HGT) in the relevant environmental "hot spot" compartments; and c) modifying traditional dose-response approaches to address doses of ARB for various health outcomes and pathways. CONCLUSIONS: We propose that environmental aspects of antibiotic-resistance development be included in the processes of any HHRA addressing ARB. Because of limited available data, a multicriteria decision analysis approach would be a useful way to undertake an HHRA of environmental antibiotic resistance that informs risk managers.This manuscript was conceived at a workshop (Antimicrobial Resistance in the Environment: Assessing and Managing Effects of Anthropogenic Activities) held 4–8 March 2012 in Montebello, Québec, Canada. The workshop was sponsored by the Canadian Society of Microbiologists, with financial support from AstraZeneca Ltd.; Pfizer Animal Health; F. Hoffman-La Roche Ltd.; GlaxoSmithKline; Unilever; Huvepharma; the American Cleaning Institute; the Canadian Animal Health Institute; the German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety; Health Canada; and the Public Health Agency of Canada

Identification and characterization of a novel non-structural protein of bluetongue virus

Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77–79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell

Multiple Imputation Ensembles (MIE) for dealing with missing data

Missing data is a significant issue in many real-world datasets, yet there are no robust methods for dealing with it appropriately. In this paper, we propose a robust approach to dealing with missing data in classification problems: Multiple Imputation Ensembles (MIE). Our method integrates two approaches: multiple imputation and ensemble methods and compares two types of ensembles: bagging and stacking. We also propose a robust experimental set-up using 20 benchmark datasets from the UCI machine learning repository. For each dataset, we introduce increasing amounts of data Missing Completely at Random. Firstly, we use a number of single/multiple imputation methods to recover the missing values and then ensemble a number of different classifiers built on the imputed data. We assess the quality of the imputation by using dissimilarity measures. We also evaluate the MIE performance by comparing classification accuracy on the complete and imputed data. Furthermore, we use the accuracy of simple imputation as a benchmark for comparison. We find that our proposed approach combining multiple imputation with ensemble techniques outperform others, particularly as missing data increases

Corvid Re-Caching without ‘Theory of Mind’: A Model

Scrub jays are thought to use many tactics to protect their caches. For instance, they predominantly bury food far away from conspecifics, and if they must cache while being watched, they often re-cache their worms later, once they are in private. Two explanations have been offered for such observations, and they are intensely debated. First, the birds may reason about their competitors' mental states, with a ‘theory of mind’; alternatively, they may apply behavioral rules learned in daily life. Although this second hypothesis is cognitively simpler, it does seem to require a different, ad-hoc behavioral rule for every caching and re-caching pattern exhibited by the birds. Our new theory avoids this drawback by explaining a large variety of patterns as side-effects of stress and the resulting memory errors. Inspired by experimental data, we assume that re-caching is not motivated by a deliberate effort to safeguard specific caches from theft, but by a general desire to cache more. This desire is brought on by stress, which is determined by the presence and dominance of onlookers, and by unsuccessful recovery attempts. We study this theory in two experiments similar to those done with real birds with a kind of ‘virtual bird’, whose behavior depends on a set of basic assumptions about corvid cognition, and a well-established model of human memory. Our results show that the ‘virtual bird’ acts as the real birds did; its re-caching reflects whether it has been watched, how dominant its onlooker was, and how close to that onlooker it has cached. This happens even though it cannot attribute mental states, and it has only a single behavioral rule assumed to be previously learned. Thus, our simulations indicate that corvid re-caching can be explained without sophisticated social cognition. Given our specific predictions, our theory can easily be tested empirically

Quality of life in South East Asian patients who consult for dyspepsia: Validation of the short form Nepean Dyspepsia Index

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

UVB phototherapy in an outpatient setting or at home: a pragmatic randomised single-blind trial designed to settle the discussion. The PLUTO study

BACKGROUND: Home ultraviolet B (UVB) treatment is a much-debated treatment, especially with regard to effectiveness, safety and side effects. However, it is increasingly being prescribed, especially in the Netherlands. Despite ongoing discussions, no randomised research has been performed, and only two studies actually compare two groups of patients. Thus, firm evidence to support or discourage the use of home UVB phototherapy has not yet been obtained. This is the goal of the present study, the PLUTO study (Dutch acronym for "national trial on home UVB phototherapy for psoriasis"). METHODS: We designed a pragmatic randomised single-blind multi-centre trial. This trial is designed to evaluate the impact of home UVB treatment versus UVB phototherapy in a hospital outpatient clinic as to effectiveness, quality of life and cost-effectiveness. In total 196 patients with psoriasis who were clinically eligible for UVB phototherapy were included. Normally 85% of the patients treated with UVB show a relevant clinical response. With a power of 80% and a 0.05 significance level it will be possible to detect a reduction in effectiveness of 15%. Effectiveness will be determined by calculating differences in the Psoriasis Area and Severity Index (PASI) and the Self Administered PASI (SAPASI) scores. Quality of life is measured using several validated generic questionnaires and a disease-specific questionnaire. Other outcome measures include costs, side effects, dosimetry, concomitant use of medication and patient satisfaction. Patients are followed throughout the therapy and for 12 months thereafter. The study is no longer recruiting patients, and is expected to report in 2006. DISCUSSION: In the field of home UVB phototherapy this trial is the first randomised parallel group study. As such, this trial addresses the weaknesses encountered in previous studies. The pragmatic design ensures that the results can be well generalised to the target population. Because, in addition to effectiveness, aspects such as quality of life and cost-effectiveness are also taken into consideration, this study will produce valuable evidence to either support or discourage prescription of home UVB phototherapy. TRIAL REGISTRATION: Current controlled trials/Nederlands Trial register: ISRCTN83025173. Clinicaltrials.gov: NCT0015093

The EQ-5D (Euroqol) is a valid generic instrument for measuring quality of life in patients with dyspepsia

<p>Abstract</p> <p>Background</p> <p>There is little information of the validity of generic instruments in measuring health-related quality of life (HRQOL) in patients with dyspepsia. We aimed to assess the reliability and validity of the EQ-5D, a brief and simple instrument, in measuring HRQOL in adult patients with dyspepsia.</p> <p>Methods</p> <p>Consecutive adults with dyspepsia attending the Gastroenterology clinic in a tertiary referral center were interviewed with the EQ-5D (both English and Malay versions), the short-form Nepean Dyspepsia Index (SF-NDI), the SF-36 and Leeds Dyspepsia Questionnaire (LDQ). Known-groups and convergent construct validity were investigated by testing hypotheses at attribute and overall levels. A repeat telephone interview was conducted 2 weeks later to assess test-retest reliability.</p> <p>Results</p> <p>A total of 113 patients (mean (SD) age: 53.7 (14) years; 49.5% male; 24.8% Malays, 37.2% Chinese; 70.8% functional dyspepsia) were recruited. Response rate was 100% with nil missing data. Known-groups validation revealed 20/26 hypotheses fulfillment. Patients with more severe dyspepsia reported more problems with their usual activity (p = 0.07) and pain (p = 0.06) and demonstrated lower median VAS scores (60 vs 70, p = 0.002) and EQ-5D utility scores (0.72 vs 0.78, p = 0.002). Those reporting problems in various EQ-5D dimensions had significantly lower scores in relevant SF-36 and SF-NDI dimensions. The overall EQ-5D utility score also demonstrated good correlation with the SF-36 summary physical and mental scores and the SF-NDI total score. Intraclass correlation coefficient for test-retest reliability was 0.66 (95% CI = 0.55 – 0.76).</p> <p>Conclusion</p> <p>The EQ-5D is an acceptable, valid and reliable generic instrument for measuring HRQOL in adult patients with dyspepsia.</p