Geographic variations and temporal trends of Salmonella-associated hospitalization in the U.S. elderly, 1991-2004: A time series analysis of the impact of HACCP regulation

<p>Abstract</p> <p>Background</p> <p>About 1.4 million <it>Salmonella </it>infections, a common food-borne illness, occur in the U.S. annually; the elderly (aged 65 or above) are most susceptible. In 1997, the USDA introduced the Pathogen Reduction and Hazard Analysis and Critical Control Points Systems (PR/HACCP) which demands regular <it>Salmonella </it>testing in various establishments processing meat products, such as broiler chickens. Impact evaluations of PR/HACCP on hospitalizations related to <it>Salmonella </it>are lacking.</p> <p>Methods</p> <p>Hospitalization records of the U.S. elderly in 1991-2004 were obtained from the Centers of Medicare and Medicaid Services. Harmonic regression analyses were performed to evaluate the long-term trends of <it>Salmonella</it>-related hospitalizations in pre- and post-HACCP periods. Seasonal characteristics of the outcome in the nine Census divisions of the contiguous U.S. were also derived and contrasted.</p> <p>Results</p> <p>Predicted rates decreased in most divisions after 1997, except South Atlantic, East South Central, and West South Central. These three divisions also demonstrated higher overall hospitalization rates, pronounced seasonal patterns, and consistent times to peak at about 32^ndto 34^thweek of the year.</p> <p>Conclusion</p> <p>The impact of HACCP was geographically different. South Atlantic, East South Central, and West South Central divisions should be targeted in further <it>Salmonella </it>preventive programs. Further research is needed to identify the best program type and timing of implementation.</p

One stop or full stop? The continuing challenges for researchers despite the new streamlined NHS research governance process

<p>Abstract</p> <p>Background</p> <p>Obtaining the necessary approvals and permission for clinical research requires successful negotiation of the ethical and R&D layers of the NHS. Differences in structure and governance frameworks feature between the constituent nations of the UK (England, Scotland, Wales and Northern Ireland), which adds complexity to cross-national studies. Difficulties in carrying out research in the NHS in the UK due to bureaucratic and time-consuming governance processes have led to the development of a new system of application and co-ordination from 2009. This paper illustrates how this new system fails to be consistent and streamlined and is unlikely to become so unless changes are made to the implementation and management of the governance processes.</p> <p>Methods</p> <p>We present a case study of the research governance process at the survey stage of an investigation into the use, preferences and need for information by people making choices or decisions about health care. The method involved home-based, face-to-face interviewing in a questionnaire survey in relation to decisions about lymphoma treatment, Down's syndrome screening in pregnancy, and caring for people with dementia.</p> <p>Results</p> <p>Our experience of the ethics stage was very positive, noting an efficient process of application and a speedy decision, both in relation to the initial application and to subsequent substantial amendments. By contrast, the R&D stages were very slow, most with unexplained delays, but some offering contradictory advice and exhibiting a lack of clear guidance and training for NHS staff. The R&D arrangements in Scotland were far quicker and more likely to be successful than in England. Overall, the delays were so severe that substantial parts of the research could not be delivered as planned within the funding timescale.</p> <p>Conclusions</p> <p>If high-quality research in the NHS, particularly in England, is to be delivered in a timely and cost-effective way, R&D processes for gaining research governance approval need improvement. Attention is needed in process implementation and management, particularly in relation to staff training, as well as clarity in guidance and communication within and between organisations.</p

Aspects of coverage in medical DNA sequencing

<p>Abstract</p> <p>Background</p> <p>DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but many design specifications have yet to be conclusively established. Perhaps the most fundamental of these is the redundancy required to detect sequence variations, which bears directly upon genomic coverage and the consequent resolving power for discerning somatic mutations.</p> <p>Results</p> <p>We address the medical sequencing coverage problem via an extension of the standard mathematical theory of haploid coverage. The expected diploid multi-fold coverage, as well as its generalization for aneuploidy are derived and these expressions can be readily evaluated for any project. The resulting theory is used as a scaling law to calibrate performance to that of standard BAC sequencing at 8× to 10× redundancy, i.e. for expected coverages that exceed 99% of the unique sequence. A differential strategy is formalized for tumor/normal studies wherein tumor samples are sequenced more deeply than normal ones. In particular, both tumor alleles should be detected at least twice, while both normal alleles are detected at least once. Our theory predicts these requirements can be met for tumor and normal redundancies of approximately 26× and 21×, respectively. We explain why these values do not differ by a factor of 2, as might intuitively be expected. Future technology developments should prompt even deeper sequencing of tumors, but the 21× value for normal samples is essentially a constant.</p> <p>Conclusion</p> <p>Given the assumptions of standard coverage theory, our model gives pragmatic estimates for required redundancy. The differential strategy should be an efficient means of identifying potential somatic mutations for further study.</p

Evaluation of next-generation sequencing software in mapping and assembly

Next-generation high-throughput DNA sequencing technologies have advanced progressively in sequence-based genomic research and novel biological applications with the promise of sequencing DNA at unprecedented speed. These new non-Sanger-based technologies feature several advantages when compared with traditional sequencing methods in terms of higher sequencing speed, lower per run cost and higher accuracy. However, reads from next-generation sequencing (NGS) platforms, such as 454/Roche, ABI/SOLiD and Illumina/Solexa, are usually short, thereby restricting the applications of NGS platforms in genome assembly and annotation. We presented an overview of the challenges that these novel technologies meet and particularly illustrated various bioinformatics attempts on mapping and assembly for problem solving. We then compared the performance of several programs in these two fields, and further provided advices on selecting suitable tools for specific biological applications.published_or_final_versio

Chronic arthritis in children and adolescents in two Indian health service user populations

BACKGROUND: High prevalence rates for rheumatoid arthritis, spondyloarthopathies, and systemic lupus erythematosus have been described in American Indian and Alaskan Native adults. The impact of these diseases on American Indian children has not been investigated. METHODS: We used International Classification of Diseases-9 (ICD-9) codes to search two Indian Health Service (IHS) patient registration databases over the years 1998–2000, searching for individuals 19 years of age or younger with specific ICD-9-specified diagnoses. Crude estimates for disease prevalence were made based on the number of individuals identified with these diagnoses within the database. RESULTS: Rheumatoid arthritis (RA) / juvenile rheumatoid arthritis (JRA) was the most frequent diagnosis given. The prevalence rate for JRA in the Oklahoma City Area was estimated as 53 per 100,000 individuals at risk, while in the Billings Area, the estimated prevalence was nearly twice that, at 115 per 100,000. These rates are considerably higher than those reported in the most recent European studies. CONCLUSION: Chronic arthritis in childhood represents an important, though unrecognized, chronic health challenge within the American Indian population living in the United States

Cancer initiation and progression: an unsimplifiable complexity

BACKGROUND: Cancer remains one of the most complex diseases affecting humans and, despite the impressive advances that have been made in molecular and cell biology, how cancer cells progress through carcinogenesis and acquire their metastatic ability is still widely debated. CONCLUSION: There is no doubt that human carcinogenesis is a dynamic process that depends on a large number of variables and is regulated at multiple spatial and temporal scales. Viewing cancer as a system that is dynamically complex in time and space will, however, probably reveal more about its underlying behavioural characteristics. It is encouraging that mathematicians, biologists and clinicians continue to contribute together towards a common quantitative understanding of cancer complexity. This way of thinking may further help to clarify concepts, interpret new and old experimental data, indicate alternative experiments and categorize the acquired knowledge on the basis of the similarities and/or shared behaviours of very different tumours

Mammographic density adds accuracy to both the Tyrer-Cuzick and Gail breast cancer risk models in a prospective UK screening cohort

This work was supported by the National Institute for Health Research (NIHR) and Genesis Breast Cancer Prevention Appeal (references GA10-033 and GA13-006). This article presents independent research funded by the NIHR under its Programme Grants for Applied Research (grant RP-PG-0707-10031). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. The authors also acknowledge the support of Medical Research Council Health eResearch Centre grant MR/K006665/1

National Security vs Criminal law. Perspectives, Doubts and Concerns on the Criminalisation of Organised Crime in England and Wales

This paper will interpret and critically analyse the new offence for organised crime in England and Wales (Section 45 of the Serious Crime Act 2015) from a criminological perspective in light of evidence found in research in the country. It will argue that changes in the law relate to changes in political narratives rather than to variations in the criminal panorama of organised crime. It will discuss these changes within three perspectives, which address various levels of concern: a narrative perspective, which reflects on the overlapping of meanings in the use of the words ‘organised crime’; an evolution perspective, which reflects on the origins of the new participation offences with reference to both national and international pressures; a management perspective, which reflects on some of the immediate effects of the new offences of organised crime on the criminal justice system. This paper will conclude that political narratives have indeed influenced criminal policy, while there is no significant change in the phenomenon of organised crime to justify such narratives

The role of gender in a smoking cessation intervention: a cluster randomized clinical trial

<p>Abstract</p> <p>Background</p> <p>The prevalence of smoking in Spain is high in both men and women. The aim of our study was to evaluate the role of gender in the effectiveness of a specific smoking cessation intervention conducted in Spain.</p> <p>Methods</p> <p>This study was a secondary analysis of a cluster randomized clinical trial in which the randomization unit was the Basic Care Unit (family physician and nurse who care for the same group of patients). The intervention consisted of a six-month period of implementing the recommendations of a Clinical Practice Guideline. A total of 2,937 current smokers at 82 Primary Care Centers in 13 different regions of Spain were included (2003-2005). The success rate was measured by a six-month continued abstinence rate at the one-year follow-up. A logistic mixed-effects regression model, taking Basic Care Units as random-effect parameter, was performed in order to analyze gender as a predictor of smoking cessation.</p> <p>Results</p> <p>At the one-year follow-up, the six-month continuous abstinence quit rate was 9.4% in men and 8.5% in women (p = 0.400). The logistic mixed-effects regression model showed that women did not have a higher odds of being an ex-smoker than men after the analysis was adjusted for confounders (OR adjusted = 0.9, 95% CI = 0.7-1.2).</p> <p>Conclusions</p> <p>Gender does not appear to be a predictor of smoking cessation at the one-year follow-up in individuals presenting at Primary Care Centers.</p> <p>ClinicalTrials.gov Identifier</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT00125905">NCT00125905</a>.</p