Phyllosticta citricarpa and sister species of global importance to Citrus.

Several Phyllosticta species are known as pathogens of Citrus spp., and are responsible for various disease symptoms including leaf and fruit spots. One of the most important species is P. citricarpa, which causes a foliar and fruit disease called citrus black spot. The Phyllosticta species occurring on citrus can most effectively be distinguished from P. citricarpa by means of multilocus DNA sequence data. Recent studies also demonstrated P. citricarpa to be heterothallic, and reported successful mating in the laboratory. Since the domestication of citrus, different clones of P. citricarpa have escaped Asia to other continents via trade routes, with obvious disease management consequences. This pathogen profile represents a comprehensive literature review of this pathogen and allied taxa associated with citrus, focusing on identification, distribution, genomics, epidemiology and disease management. This review also considers the knowledge emerging from seven genomes of Phyllosticta spp., demonstrating unknown aspects of these species, including their mating behaviour.TaxonomyPhyllosticta citricarpa (McAlpine) Aa, 1973. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Phyllostictaceae, Genus Phyllosticta, Species citricarpa.Host rangeConfirmed on more than 12 Citrus species, Phyllosticta citricarpa has only been found on plant species in the Rutaceae.Disease symptomsP. citricarpa causes diverse symptoms such as hard spot, virulent spot, false melanose and freckle spot on fruit, and necrotic lesions on leaves and twigs.Useful websitesDOE Joint Genome Institute MycoCosm portals for the Phyllosticta capitalensis (https://genome.jgi.doe.gov/Phycap1), P. citriasiana (https://genome.jgi.doe.gov/Phycit1), P. citribraziliensis (https://genome.jgi.doe.gov/Phcit1), P. citrichinaensis (https://genome.jgi.doe.gov/Phcitr1), P. citricarpa (https://genome.jgi.doe.gov/Phycitr1, https://genome.jgi.doe.gov/Phycpc1), P. paracitricarpa (https://genome.jgi.doe.gov/Phy27169) genomes. All available Phyllosticta genomes on MycoCosm can be viewed at https://genome.jgi.doe.gov/Phyllosticta

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

State history and economic development: evidence from six millennia

The presence of a state is one of the most reliable historical predictors of social and economic development. In this article, we complete the coding of an extant indicator of state presence from 3500 BCE forward for almost all but the smallest countries of the world today. We outline a theoretical framework where accumulated state experience increases aggregate productivity in individual countries but where newer or relatively inexperienced states can reach a higher productivity maximum by learning from the experience of older states. The predicted pattern of comparative development is tested in an empirical analysis where we introduce our extended state history variable. Our key finding is that the current level of economic development across countries has a hump-shaped relationship with accumulated state history

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

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

Police performance measurement: an annotated bibliography

This study provides information to assist those involved in performance measurement in police organisations. The strategies used to identify the literature are described. Thematic sections cover; general overviews; methodological issues; performance management in other industries; national, international and cross-national studies; frameworks (e.g. Compstat; the Balanced Scorecard); criticisms (particularly unintended consequences); crime-specific measures; practitioner guides; performance evaluation of individual staff; police department plans and evaluations; annotated bibliographies in related areas, and; other literature. Our discussion offers two conclusions: the measures best aligned with performance are typically more expensive, while most operational data should only provide contextual information; the philosophy of open governance should be pursued to promote transparency, accountability and communication to improve police performance

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