Easyfig: a genome comparison visualizer

Summary: Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures

Pragmatic intervention for increasing self-directed exercise behaviour and improving important health outcomes in people with multiple sclerosis : a randomised controlled trial

Background: Exercise programmes that can demonstrate evidence of long-lasting clinical effectiveness are needed forpeople with multiple sclerosis (PwMS). Objective: The objective of this study was to assess the effects of a practically implemented exercise programme onself-directed exercise behaviour and important health outcomes in PwMS to nine months of follow-up. Methods: We conducted a parallel-arm, randomised controlled trial: 120 PwMS (Expanded Disability Status Scale (EDSS) 1.0-6.5) randomised to a three-month exercise intervention plus usual care, or usual care only. Two supervised plus one homeexercisesession (weeks 1-6) were followed by one supervised and two home-exercise sessions (weeks 7-12). Cognitivebehaviouraltechniques promoted long-term exercise behaviour change. Outcomes were blindly assessed at baseline and atthree and nine months after randomisation. The primary outcome was self-reported exercise behaviour (Godin Leisure TimeExercise Questionnaire (GLTEQ)). Secondary outcomes included fatigue and health-related quality of life (HRQoL). Results: The intervention increased self-reported exercise (9.6 points; 95% CI: 2.0 to 17.3 points; p = 0.01) andimproved fatigue (p<0.0001) and many HRQoL domains (p≤0.03) at three months. The improvements in emotionalwell-being (p = 0.01), social function (p = 0.004) and overall quality of life (p = 0.001) were sustained for nine months. Conclusion: This pragmatic approach to implementing exercise increases self-reported exercise behaviour, improves fatigue and leads to a sustained enhancement of HRQoL domains in PwMS

Clinical reasoning and therapeutic approaches of experienced osteopaths

Background: Clinical reasoning refers to the decision-making processes which occur during practice. Over the last thirty years research in the health sciences has explored the clinical reasoning processes of a number of health professions such as medicine, nursing, occupational therapy and physiotherapy. As the osteopathic profession continues to grow, osteopaths are increasingly considered to be important providers of neuromusculoskeletal care. However, there has been minimal research into the clinical reasoning processes and therapeutic approaches used in osteopathy. The aim of this research was to explore the clinical reasoning processes of osteopaths in the UK, and to construct an explanatory theory of clinical reasoning in osteopathy. Methods: A total of 12 UK registered osteopaths participated in this grounded theory study, which was situated in the interpretivist research paradigm. Purposive sampling was used to initially select participants. Subsequent theoretical sampling, which was informed by data analysis, allowed specific participants to be sampled. Data was collected from interviews with 9 participants, which were audio-recorded and transcribed. As the study approached theoretical sufficiency, data collection methods involved non-participant observation and video-recording of 3 further participants during a patient appointment, which was followed by a reflective interview prompted by the video-recording. The constant comparative method was used to code and analyse interview transcripts to construct a substantive theory to explain the therapeutic approaches and clinical reasoning of experienced osteopaths. Findings: Participants took one of three distinct therapeutic approaches, termed; ‘Treater’, ‘Communicator’ or ‘Educator’ which characterised their overarching clinical behaviour. The approaches were developed from participant’s conception of practice which was based on the antecedent conditions of their; educational experiences, professional and clinical experiences, personal values and beliefs, views of health and disease and professional identity. The three therapeutic approaches resulted in varying levels of patient involvement in the clinical reasoning process and consequently different therapeutic outcomes. Participant’s approach to clinical reasoning ranged from ‘practitioner- led’ with a low level of patient involvement; ‘mutual negotiation’ with an equal level of patient involvement; or ‘patient-led’ with a high patient involvement. The process of diagnosis construction involved participants moving between hypothetico-deductive reasoning and pattern recognition and verification. Participants could adapt their therapeutic approach in response to the patient’s preferences, expectations and the patient’s ongoing response. The ability to adapt varied between study participants and was influenced by their conception of practice, working context and time factors

Evidence for a lineage of virulent bacteriophages that target Campylobacter.

BACKGROUND: Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. RESULTS: Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (> or = 96%) with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM) genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. CONCLUSIONS: Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host. Genetic conservation has been shown to extend to other Campylobacter bacteriophages, forming a highly conserved lineage of bacteriophages that predate upon campylobacters and indicating that highly adapted bacteriophage genomes can be stable over prolonged periods of time

Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins

Legionella pneumophila is a ubiquitous inhabitant of environmental water reservoirs. The bacteria infect a wide variety of protozoa and, after accidental inhalation, human alveolar macrophages, which can lead to severe pneumonia. The capability to thrive in phagocytic hosts is dependent on the Dot/Icm type IV secretion system (T4SS), which translocates multiple effector proteins into the host cell. In this study, we determined the draft genome sequence of L. pneumophila strain 130b (Wadsworth). We found that the 130b genome encodes a unique set of T4SSs, namely, the Dot/Icm T4SS, a Trb-1-like T4SS, and two Lvh T4SS gene clusters. Sequence analysis substantiated that a core set of 107 Dot/Icm T4SS effectors was conserved among the sequenced L. pneumophila strains Philadelphia-1, Lens, Paris, Corby, Alcoy, and 130b. We also identified new effector candidates and validated the translocation of 10 novel Dot/Icm T4SS effectors that are not present in L. pneumophila strain Philadelphia-1. We examined the prevalence of the new effector genes among 87 environmental and clinical L. pneumophila isolates. Five of the new effectors were identified in 34 to 62% of the isolates, while less than 15% of the strains tested positive for the other five genes. Collectively, our data show that the core set of conserved Dot/Icm T4SS effector proteins is supplemented by a variable repertoire of accessory effectors that may partly account for differences in the virulences and prevalences of particular L. pneumophila strains. Copyright © 2010, American Society for Microbiology. All Rights Reserved

A qualitative grounded theory study of the conceptions of clinical practice in osteopathy – A continuum from technical rationality to professional artistry

How practitioners conceive clinical practice influences many aspects of their clinical work including how they view knowledge, clinical decision-making, and their actions. Osteopaths have relied upon the philosophical and theoretical foundations upon which the profession was built to guide clinical practice. However, it is currently unknown how osteopaths conceive clinical practice, and how these conceptions develop and influence their clinical work. This paper reports the conceptions of practice of experienced osteopaths in the UK. A constructivist grounded theory approach was taken in this study. The constant comparative method of analysis was used to code and analyse data. Purposive sampling was employed to initially select participants. Subsequent theoretical sampling, informed by data analysis, allowed specific participants to be sampled. Data collection methods involved semi-structured interviews and non-participant observation of practitioners during a patient appointment, which was video-recorded and followed by a video-prompted reflective interview. Participants' conception of practice lay on a continuum, from technical rationality to professional artistry and the development of which was influenced by their educational experience, view of health and disease, epistemology of practice knowledge, theory-practice relationship and their perceived therapeutic role. The findings from this study provide the first theoretical insight of osteopaths' conceptions of clinical practice and the factors which influence such conceptions

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

<p>Abstract</p> <p>Background</p> <p>Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image.</p> <p>Results</p> <p>BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically.</p> <p>Conclusions</p> <p>There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at <url>http://sourceforge.net/projects/brig/</url>.</p

Participant recruitment into a randomised controlled trial of exercise therapy for people with multiple sclerosis

The success of a clinical trial is often dependant on whether recruitment targets can be met in the required time frame. Despite an increase in research into the benefits of exercise in people with multiple sclerosis (PwMS), no trial has reported detailed data on effective recruitment strategies for large-scale randomised controlled trials. The main purpose of this report is to provide a detailed outline of recruitment strategies, rates and estimated costs in the Exercise Intervention for Multiple Sclerosis (ExIMS) trial to identify best practices for future trials involving multiple sclerosis (MS) patient recruitment