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Martin Jones

Publications and source records attributed to Martin Jones.

At least 19 recordsLinked to original sources
PubMed2006

TaxMan: a taxonomic database manager.

BACKGROUND: Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes) can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. RESULTS: TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level) and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. CONCLUSION: TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of both annotation and BLAST similarity, it ensures that all available sequence data can be brought to bear on a phylogenetic problem, but remains fast enough to cope with many thousands of records. By automatically assisting in the selection of the best subset of taxa to address a particular phylogenetic problem, TaxMan greatly speeds up the process of generating multiple sequence alignments for phylogenetic analysis. Our results indicate that an automated phylogenetic workbench can be a useful tool when correctly guided by user knowledge.

Database Management Systems↗
PubMed2006

Phylogenetic relationships of the Wolbachia of nematodes and arthropods.

Wolbachia are well known as bacterial symbionts of arthropods, where they are reproductive parasites, but have also been described from nematode hosts, where the symbiotic interaction has features of mutualism. The majority of arthropod Wolbachia belong to clades A and B, while nematode Wolbachia mostly belong to clades C and D, but these relationships have been based on analysis of a small number of genes. To investigate the evolution and relationships of Wolbachia symbionts we have sequenced over 70 kb of the genome of wOvo, a Wolbachia from the human-parasitic nematode Onchocerca volvulus, and compared the genes identified to orthologues in other sequenced Wolbachia genomes. In comparisons of conserved local synteny, we find that wBm, from the nematode Brugia malayi, and wMel, from Drosophila melanogaster, are more similar to each other than either is to wOvo. Phylogenetic analysis of the protein-coding and ribosomal RNA genes on the sequenced fragments supports reciprocal monophyly of nematode and arthropod Wolbachia. The nematode Wolbachia did not arise from within the A clade of arthropod Wolbachia, and the root of the Wolbachia clade lies between the nematode and arthropod symbionts. Using the wOvo sequence, we identified a lateral transfer event whereby segments of the Wolbachia genome were inserted into the Onchocerca nuclear genome. This event predated the separation of the human parasite O. volvulus from its cattle-parasitic sister species, O. ochengi. The long association between filarial nematodes and Wolbachia symbionts may permit more frequent genetic exchange between their genomes.

Animals↗
PubMed2006

Agricultural health in The Gambia I: Agricultural practices and developments.

This manuscript reports results of our study to characterize the historical developments of agricultural practices in The Gambia and related health risks of farm workers. It surveys the various factors that shape production agriculture in the country and examines the degrees to which hand tools, animal traction, motorized traction and manual labour all contribute to the inherent hazards of farm work. The principal objective of this study is to lay the ground work for detailed research of occupational health hazards in Gambian agriculture; and development of policies and programmes to promote the health of Gambian farmers. The authors of this paper assume the belief that one must first understand the industry and its people before effective policies and programmes can be developed. The study concludes by highlighting the need for the integration of epidemiological investigations in the country's agricultural research programme.

Accidents, Occupational↗
PubMed2006

Agricultural health in The Gambia II: A systematic survey of safety and injuries in production agriculture.

This study was undertaken to provide baseline information on the injuries and health and safety conditions in Gambian agriculture. The objective was to produce information to guide the formulation of an agricultural health and safety policy for the country, future investigations, prevention and surveillance of the adverse health effects in agriculture. A cross-sectional survey of 20 farmers, 20 nurses, and 20 agricultural extension workers was conducted in the Central and Upper River Divisions of The Gambia. The survey was implemented by the means of questionnaires, walk-through survey and hazard checklist. Seventy percent of farms reported an injury during the past year. Major sources and contributing factors for the injuries were characterized. Predisposing factors to the injuries were climatic conditions, working in static positions, bending and twisting and carrying heavy objects. Cuts and lacerations were identified as the commonest injury types and the most common sources were hand tools (hand hoe, cutlass, axe and knife) and animal-powered carts. A workshop for the major stake holders in the country's agriculture was also held to identify problems and possible solutions for health promotion of Gambian farmers.

Agriculture↗
PubMed2005

The impact of a macroalgal mat on benthic biodiversity in Poole Harbour.

Blooms of macroalgal matting are increasingly common within temperate zones and are often comprised of opportunistic species such as Ulva lactuca. Where this algae forms a dense mat, a stressful environment is created in the sediment below, influencing the invertebrate infaunal assemblage. This study was conducted over a six month period during which a dense mat of U. lactuca developed and subsequently dispersed. The algal mat was found to have a significant negative impact on species richness, abundance and biomass of the macroinfauna. However, a faunal community developed within the algal mat which contained several species not previously observed. This community increased the abundance and diversity of the overall invertebrate assemblage. The results are discussed in relation to impacts on the ecosystem as a whole.

Analysis of Variance↗
PubMed2005

Quetiapine monotherapy for mania associated with bipolar disorder: combined analysis of two international, double-blind, randomised, placebo-controlled studies.

OBJECTIVE: To evaluate the efficacy and safety of quetiapine monotherapy for mania in bipolar disorder by an a priori defined combined analysis of data from two placebo-controlled studies. METHOD: The intent-to-treat (ITT) populations from two studies of patients with DSM-IV bipolar I disorder, manic episode, randomised to 12 weeks of double-blind treatment with quetiapine (up to 800 mg/day) or placebo were combined. The primary efficacy endpoint was change in Young Mania Rating Scale (YMRS) score from baseline to Day 21. Secondary endpoints included change from baseline in YMRS to Day 84, YMRS response and remission rates and change from baseline to Days 21 and 84 in the Montgomery-Asberg Depression Rating Scale (MADRS), Clinical Global Impressions (CGI), Clinical Global Impressions-Bipolar (CGI-BP) and the Positive and Negative Syndrome Scale (PANSS). These endpoints were analysed as continuous variables, using an analysis of covariance (ANCOVA), with the baseline as covariate. In order to account for any difference in response between studies, the analyses were stratified by study as a fixed effect, and centre as a random effect. The Cochran-Mantel-Haenszel test was used to analyse binary variables. A chi square test was used to compare the frequency of adverse events between the treatment groups. RESULTS: The combined analysis included a total of 403 patients from two quetiapine monotherapy studies in patients with bipolar I disorder. A significant improvement in YMRS score was observed from Day 4 (p = 0.021) onward in the quetiapine group compared with placebo. The treatment advantage of quetiapine over placebo continued to increase to Day 21 (p < 0.001) and Day 84 (p < 0.001). Significantly more quetiapine-treated than placebo-treated patients achieved a response (p < 0.001). The average quetiapine dose in responders was approximately 600 mg daily. Of adverse events occurring in > or = 5% of patients, quetiapine-treated patients had a significantly greater incidence versus placebo of somnolence (16.3% vs. 4.0%), dry mouth (15.8% vs. 3%), weight gain (9.1% vs. 1.5%) and dizziness (6.7% vs. 2.5%). CONCLUSIONS: The data from this combined analysis support the results from the individual studies and indicate that quetiapine monotherapy is effective across a broad range of mood symptoms, fast-acting and well tolerated in the treatment of mania.

Adolescent↗
PubMed2005

A randomized, double-blind, placebo-controlled efficacy and safety study of quetiapine or lithium as monotherapy for mania in bipolar disorder.

OBJECTIVE: To evaluate the efficacy and tolerability of quetiapine monotherapy versus placebo for the treatment of mania associated with bipolar disorder. METHOD: In an international, multicenter, double-blind, parallel-group, 12-week study, patients with a DSM-IV diagnosis of bipolar I disorder (manic episode) were randomly assigned to treatment with quetiapine (flexibly dosed up to 800 mg/day), placebo, or lithium. The primary efficacy measure was change from baseline in Young Mania Rating Scale (YMRS) score at day 21. Data were gathered from April 2001 to May 2002. RESULTS: More patients in the quetiapine (72/107) and lithium (67/98) groups completed the study compared with the placebo group (35/97). Improvement (reduction) in YMRS score was significantly greater for quetiapine than placebo at day 7 (-8.03 vs. -4.89; p < .01), and the difference between groups continued to increase over time to day 21 (-14.6 vs. -6.7; p < .001) and to endpoint at day 84 (-20.3 vs. -9.0; p < .001). Significantly more quetiapine patients compared with placebo patients fulfilled YMRS response criteria at day 21 (53.3% vs. 27.4%; p < .001) and at day 84 (72.0% vs. 41.1%; p < .001). Quetiapine was also superior to placebo in efficacy at day 21 and day 84 by all secondary measures. Lithium-treated patients improved significantly compared with placebo patients and similarly to quetiapine-treated patients on the primary efficacy measure. The most common adverse events for quetiapine were dry mouth, somnolence, and weight gain, while lithium was associated with tremor and insomnia. The quetiapine and placebo groups had similar, low levels of extrapyramidal symptom-related adverse events. CONCLUSIONS: Quetiapine demonstrated superior efficacy to placebo in patients with bipolar mania and was well tolerated.

Adolescent↗
PubMed2004

Two-stage grafting of flexor tendons: results after mobilisation by controlled early active movement.

We present the results of two-stage flexor tendon grafting to the hand followed by early active mobilisation. Twenty-six digits from 22 patients were assessed over a 10-year period between 1991 and 2001. Using the LaSalle and Strickland assessment for surgical outcome, we found that 20 digits (77%) achieved excellent or good results. Two ruptured (8%) and one developed adhesions (4%). We think that our results are achieved through meticulous attention to surgical technique with the use of mid-lateral incisions for surgical access, strong bony fixation of the graft that allows a good interface between tendon and distal phalanx, and a closely supervised early active mobilisation regimen after the repair.

Adolescent↗
PubMed2004

Prevalence and diagnosis of migraine in patients consulting their physician with a complaint of headache: data from the Landmark Study.

CONTEXT: Headache experts have suggested that to improve the recognition of migraine, patients with a stable pattern of episodic, disabling headache and a normal physical exam should be considered to have migraine in the absence of contradictory evidence. The premise upon which this approach is based-that is, that episodic, recurrent primary headache in the clinic is usually migraine-has not been evaluated in prospective clinical studies. OBJECTIVES: To (1) evaluate the diagnoses of patients consulting their physician with primary episodic headache and (2) compare clinic diagnoses and patient self-diagnoses with International Headache Society (IHS) headache diagnoses assigned on the basis of longitudinal data from patient diaries. DESIGN: Prospective, open-label study. During the screening visit, patients self-reported a headache diagnosis and then were assigned a headache diagnosis by their physician following his or her customary practice. Patients with a new physician diagnosis of migraine or nonmigraine primary headache were given diaries to record headache symptoms for up to 3 months or 6 attacks. Members of an expert panel, unaware of the clinic diagnosis, used diary data to assign a headache diagnosis to each attack and to each patient. SETTING: One hundred twenty-eight (128) practices in 15 countries including the United States. PATIENTS: A total of 1203 male and female patients between 18 and 65 years of age who consulted their physician with headache as a primary or secondary complaint. RESULTS: Overall, 94% of patients with a physician diagnosis of nonmigraine primary headache or a new clinic diagnosis of migraine had IHS-defined migraine (76%) or probable migraine (migrainous) (18%) headache on the basis of longitudinal diary data. A new clinic diagnosis of migraine was almost always correct: 98% of patients with a clinic diagnosis of migraine had IHS-defined migraine (87% of patients) or probable migraine (11% of patients) headache on the basis of longitudinal diary data. On the other hand, review of diaries of patients with a clinic diagnosis of nonmigraine revealed that 82% of these patients had IHS-defined migraine (48%) or probable migraine (34%) headache. Altogether, one in four patients (25%) with IHS-defined migraine according to longitudinal diary data did not receive a clinic diagnosis of migraine. CONCLUSIONS: These findings support the diagnostic approach of considering episodic, disabling primary headaches with an otherwise normal physical exam to be migraine in the absence of contradictory evidence. If in doubt of diagnosis or when assigning a nonmigraine diagnosis, strong consideration should be given to the use of a diary to confirm primary headache diagnosis.

Adolescent↗
PubMed2003

Immunohistochemical endothelial localisation--a novel method of vessel delineation in tendon tissue.

The mechanism of tendon healing is still not fully understood. A dual source of nutrition for the tendon is important at times of injury either from synovial-type fluid bathing the tendon or its own blood supply. In addition, neovascularisation occurs at the site of injury from the time of the insult. The aim of this study was to develop a method of precise endothelial localisation in archived paraffin tendon sections, therefore facilitating the study of the healing of tendons within different species. The sections had to retain a high degree of cytoarchitecture and the stain be of enough contrast to allow quantitative assessment of tendon vascularity in different sites and different species. Endothelial staining was produced using an antibody to the endothelial cell surface marker CD-31 (Dako, Cambridge, UK). The signal was intensified using the Catalytic Signal Amplification kit (Dako). It resulted in a dark brown staining of the tendon endothelium, which was in sufficient contrast to allow automated image analysis.

Animals↗
PubMed2003

Undiagnosed HIV in women attending a sexual health clinic for non-barrier methods of contraception. Two case studies.

Approximately one-third of human immunodeficiency virus (HIV) cases in the UK remain undiagnosed. More than half of new diagnoses in the last 2 years have been acquired through heterosexual sexual intercourse. Two cases of women with identified risk factors for HIV infection, who presented for contraception and were later found to be HIV-positive, are described. It is suggested that providers of contraception are well placed to identify clients at high risk of HIV and to recommend HIV testing.

AIDS Serodiagnosis↗
PubMed2003

Bacterial STIs.

The three most common bacterial sexually transmitted infections--chlamydia, gonorrhoea and syphilis--and are now more common than viral STIs in the UK.

Anti-Bacterial Agents↗
PubMedDate not supplied

Prevention and control of infection in non-acute healthcare settings.

This article discusses the main principles of infection prevention and control in non-acute healthcare settings. It explores the use of a set of ten tools developed by the Infection Control Nurses Association (ICNA) to audit infection prevention and control, using the standard statements and criteria within the tools as a checklist. The results of the audit of facilities, commodities and practice using the ICNA audit tools will help staff to identify areas of best practice and areas where improvements are needed to enhance patient care.

Benchmarking↗