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Search Results: 1 - 10 of 32384 matches for " Peter Simmonds "
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SSE: a nucleotide and amino acid sequence analysis platform
Peter Simmonds
BMC Research Notes , 2012, DOI: 10.1186/1756-0500-5-50
Abstract: A simple sequence editor (SSE) was developed to create an integrated environment where sequences can be aligned, annotated, classified and directly analysed by a number of built-in bioinformatic programs. SSE incorporates a sequence editor for the creation of sequence alignments, a process assisted by integrated CLUSTAL/MUSCLE alignment programs and automated removal of indels. Sequences can be fully annotated and classified into groups and annotated of sequences and sequence groups and access to analytical programs that analyse diversity, recombination and RNA secondary structure. Methods for analysing sequence diversity include measures of divergence and evolutionary distances, identity plots to detect regions of nucleotide or amino acid homology, reconstruction of sequence changes, mono-, di- and higher order nucleotide compositional biases and codon usage.Association Index calculations, GroupScans, Bootscanning and TreeOrder scans perform phylogenetic analyses that reconcile group membership with tree branching orders and provide powerful methods for examining segregation of alleles and detection of recombination events. Phylogeny changes across alignments and scoring of branching order differences between trees using the Robinson-Fould algorithm allow effective visualisation of the sites of recombination events.RNA secondary and tertiary structures play important roles in gene expression and RNA virus replication. For the latter, persistence of infection is additionally associated with pervasive RNA secondary structure throughout viral genomic RNA that modulates interactions with innate cell defences. SSE provides several programs to scan alignments for RNA secondary structure through folding energy thermodynamic calculations and phylogenetic methods (detection of co-variant changes, and structure conservation between divergent sequences). These analyses complement methods based on detection of sequence constraints, such as suppression of synonymous site variab
Cetaceans and Marine Debris: The Great Unknown
Mark Peter Simmonds
Journal of Marine Biology , 2012, DOI: 10.1155/2012/684279
Abstract: Plastics and other marine debris have been found in the gastrointestinal tracts of cetaceans, including instances where large quantities of material have been found that are likely to cause impairment to digestive processes and other examples, where other morbidity and even death have resulted. In some instances, debris may have been ingested as a result of the stranding process and, in others, it may have been ingested when feeding. Those species that are suction or “ram” feeders may be most at risk. There is also evidence of entanglement of cetaceans in marine debris. However, it is usually difficult to distinguish entanglement in active fishing gear from that in lost or discarded gear. The overall significance of the threat from ingested plastics and other debris remains unclear for any population or species of cetaceans, although there are concerns for some taxa, including at the population level, and marine debris in the oceans continues to grow. Further research including the compilation of unpublished material and the investigation of important habitat areas is strongly recommended. 1. Introduction and Background Marine litter has been characterized as an environmental, economic, human health and aesthetic problem, posing a complex and multidimensional challenge with significant implications for the marine environment and human activities all over the world [1]. Much has been written about this pervasive pollution problem in recent years, and there are various international initiatives now striving to address it, including the United Nations Environment Program (UNEP) Global Initiative on Marine Litter. Part of the problem derives from the accumulation and fragmentation of plastics, “one of the most ubiquitous and long-lasting recent changes to the surface of our planet” [2]. In the marine environment, typically 40–80% of the larger categories of marine debris items are plastic. Much of this is packaging, carrier bags, footwear, cigarette lighters and other domestic items and much originates from land, as a recent study in Central and South America showed [3]. Lost or discarded fishing gear can also be important, particularly along continental shelves and remote islands. Thirty-one species of marine mammals have previously been reported to have ingested marine debris [4], and it has been suggested that even small ingested quantities can have large effects [5]. In addition to interference with alimentary processes, another effect could be that the plastics lodged somewhere in the alimentary tract could facilitate the transfer of pollutants into
Photo-Identification Methods Reveal Seasonal and Long-Term Site-Fidelity of Risso’s Dolphins (Grampus griseus) in Shallow Waters (Cardigan Bay, Wales)  [PDF]
Marijke N. de Boer, Josephine Clark, Mardik F. Leopold, Mark P. Simmonds, Peter J. H. Reijnders
Open Journal of Marine Science (OJMS) , 2013, DOI: 10.4236/ojms.2013.32A007
Abstract:

A photo-identification study on Risso’s dolphins was carried out off BardseyIslandinWales(July to September, 1997-2007). Their local abundance was estimated using two different analytical techniques: (1) mark-recapture of well-marked dolphins using a ‘closed-population’ model; and (2) a census technique based on the total number of identified individual dolphins sighted over the study period. The mark-recapture estimates of 121 (left sides; 64 - 178 95% CI; CV 0.24) and 145 dolphins (right sides; 78 - 213 95% CI; CV 0.24) closely matched the census technique estimates (population size of 90 - 151). It was found that the dolphins showed a degree of long-term and seasonal site-fidelity. A first long-distance match was made for Risso’s dolphins (319 km) betweenBardseyIslandandCornwall, confirming they can be wide-ranging animals. This study demonstrates that the combination of systematic and opportunistic photo-ID studies has complementary value as a population assessment tool in generating the first local abundance estimate for Risso’s dolphins inUKwaters. From the conservation perspective, these studies confirm the regular presence of Risso’s dolphins in these waters and the presence of calves shows breeding.BardseyIslandmay be part of a network of localities that are important habitats to this species where it may take advantage of prey abundance in shallow waters. As such, results of this study may provide assistance to include the Risso’s dolphin in future regional conservation strategies including the envisaged marine protected areas.

Novel Positive-Sense, Single-Stranded RNA (+ssRNA) Virus with Di-Cistronic Genome from Intestinal Content of Freshwater Carp (Cyprinus carpio)
ákos Boros, Péter Pankovics, Peter Simmonds, Gábor Reuter
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0029145
Abstract: A novel positive-sense, single-stranded RNA (+ssRNA) virus (Halastavi árva RNA virus, HalV; JN000306) with di-cistronic genome organization was serendipitously identified in intestinal contents of freshwater carps (Cyprinus carpio) fished by line-fishing from fishpond “L?rinte halastó” located in Veszprém County, Hungary. The complete nucleotide (nt) sequence of the genomic RNA is 9565 nt in length and contains two long - non-in-frame - open reading frames (ORFs), which are separated by an intergenic region. The ORF1 (replicase) is preceded by an untranslated sequence of 827 nt, while an untranslated region of 139 nt follows the ORF2 (capsid proteins). The deduced amino acid (aa) sequences of the ORFs showed only low (less than 32%) and partial similarity to the non-structural (2C-like helicase, 3C-like cystein protease and 3D-like RNA dependent RNA polymerase) and structural proteins (VP2/VP4/VP3) of virus families in Picornavirales especially to members of the viruses with dicistronic genome. Halastavi árva RNA virus is present in intestinal contents of omnivorous freshwater carps but the origin and the host species of this virus remains unknown. The unique viral sequence and the actual position indicate that Halastavi árva RNA virus seems to be the first member of a new di-cistronic ssRNA virus. Further studies are required to investigate the specific host species (and spectrum), ecology and role of Halastavi árva RNA virus in the nature.
A Scalable Architecture Supporting QoS Guarantees Using Traffic Engineering and Policy Based Routing in the Internet  [PDF]
Priyadarsi NANDA, Andrew SIMMONDS
Int'l J. of Communications, Network and System Sciences (IJCNS) , 2009, DOI: 10.4236/ijcns.2009.27065
Abstract: The study of Quality of Service (QoS) has become of great importance since the Internet is used to support a wide variety of new services and applications with its legacy structure. Current Internet architecture is based on the Best Effort (BE) model, which attempts to deliver all traffic as soon as possible within the limits of its abilities, but without any guarantee about throughput, delay, packet loss, etc. We develop a three-layer policy based architecture which can be deployed to control network resources intelligently and support QoS sensi-tive applications such as real-time voice and video streams along with standard applications in the Internet. In order to achieve selected QoS parameter values (e.g. loss, delay and PDV) within the bounds set through SLAs for high priority voice traffic in the Internet, we used traffic engineering techniques and policy based routing supported by Border Gateway Protocol (BGP). Use of prototype and simulations validates function-ality of our architecture.
Exercise therapy for the management of osteoarthritis of the hip joint: a systematic review
Peter J McNair, Marion A Simmonds, Mark G Boocock, Peter J Larmer
Arthritis Research & Therapy , 2009, DOI: 10.1186/ar2743
Abstract: A systematic literature search of 14 electronic databases was undertaken to identify interventions that used exercise therapy as a treatment modality for hip osteoarthritis. The quality of each article was critically appraised and graded according to standardized methodologic approaches. A 'pattern-of-evidence' approach was used to determine the overall level of evidence in support of exercise-therapy interventions for treating hip osteoarthritis.More than 4,000 articles were identified, of which 338 were considered suitable for abstract review. Of these, only 6 intervention studies met the inclusion criteria. Few well-designed studies specifically investigated the use of exercise-therapy management on hip-joint osteoarthritis. Insufficient evidence was found to suggest that exercise therapy can be an effective short-term management approach for reducing pain levels, improving joint function and the quality of life.Limited information was available on which conclusions regarding the efficacy of exercise could be clearly based. No studies met the level of exercise recommended for individuals with osteoarthritis. High-quality trials are needed, and further consideration should be given to establishing the optimal exercises and exposure levels necessary for achieving long-term gains in the management of osteoarthritis of the hip.Osteoarthritis (OA) is a major problem in modern society. In Western populations, the estimated prevalence for hip-joint OA is between 1% and 11% [1,2]. Treatments are typically directed at the management of symptoms, such as pain relief and improving function, with exercise therapy being commonly used as a treatment modality.Recently, a Physical Activity Guidelines Advisory Committee report to the U.S. Department of Health and Human Services [3] provided guidelines concerning physical activity for those individuals with disabilities. This report made specific mention of exercise for those with OA, and the guidelines recommended that adults sho
Molecular Epidemiology and Evolution of Human Respiratory Syncytial Virus and Human Metapneumovirus
Eleanor R. Gaunt,Rogier R. Jansen,Yong Poovorawan,Kate E. Templeton,Geoffrey L. Toms,Peter Simmonds
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0017427
Abstract: Human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV) are ubiquitous respiratory pathogens of the Pneumovirinae subfamily of the Paramyxoviridae. Two major surface antigens are expressed by both viruses; the highly conserved fusion (F) protein, and the extremely diverse attachment (G) glycoprotein. Both viruses comprise two genetic groups, A and B. Circulation frequencies of the two genetic groups fluctuate for both viruses, giving rise to frequently observed switching of the predominantly circulating group. Nucleotide sequence data for the F and G gene regions of HRSV and HMPV variants from the UK, the Netherlands, Bangkok and data available from Genbank were used to identify clades of both viruses. Several contemporary circulating clades of HRSV and HMPV were identified by phylogenetic reconstructions. The molecular epidemiology and evolutionary dynamics of clades were modelled in parallel. Times of origin were determined and positively selected sites were identified. Sustained circulation of contemporary clades of both viruses for decades and their global dissemination demonstrated that switching of the predominant genetic group did not arise through the emergence of novel lineages each respiratory season, but through the fluctuating circulation frequencies of pre-existing lineages which undergo proliferative and eclipse phases. An abundance of sites were identified as positively selected within the G protein but not the F protein of both viruses. For HRSV, these were discordant with previously identified residues under selection, suggesting the virus can evade immune responses by generating diversity at multiple sites within linear epitopes. For both viruses, different sites were identified as positively selected between genetic groups.
Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH): study protocol
Diana Eccles, Sue Gerty, Peter Simmonds, Victoria Hammond, Sarah Ennis, Douglas G Altman, the POSH steering group
BMC Cancer , 2007, DOI: 10.1186/1471-2407-7-160
Abstract: The study is a prospective cohort study recruiting 3,000 women aged 40 years or younger at breast cancer diagnosis; the recruiting period covers 1st June 2001 to 31st December 2007. Written informed consent is obtained at study entry. Family history and known epidemiological risk data are collected by questionnaire. Clinical information about diagnosis, treatment and clinical course is collected and blood is stored. Follow up data are collected annually after the first year. An additional recruitment category includes women aged 41 to 50 years who are found to be BRCA1 or BRCA2 gene carriers and were diagnosed with their first breast cancer during the study recruiting period.Power estimates were based on 10% of the cohort carrying a BRCA1 gene mutation. Preliminary BRCA1 and BRCA2 mutation analysis in a pilot set of study participants confirms we should have 97% power to detect a difference of 10% in event rates between gene carriers and sporadic young onset cases. Most of the recruited patients (>80%) receive an anthracycline containing adjuvant chemotherapy regimen making planned analyses more straightforward.Less than 5% of breast cancers diagnosed in the UK are diagnosed in women aged 40 years or younger although there is a rapid increase in the incidence from about 35 years of age[1].Published retrospective studies suggest that early age at onset of breast cancer (below 35 years) is a poor prognosis factor; high grade and oestrogen receptor (ER) negative tumours appear to be more frequent in younger women[2,3]. Breast cancer arising due to a high penetrance genetic predisposition gene such as BRCA1 or BRCA2 occurs at younger average age than breast cancer in the general population and a higher proportion of young onset cases will have a genetic predisposition than breast cancer cases in general. Family history is still the most important indicator of an underlying inherited predisposition [4]. However BRCA1 and BRCA2 may account for less than 40% of all familia
The Influence of Topographic and Dynamic Cyclic Variables on the Distribution of Small Cetaceans in a Shallow Coastal System
Marijke N. de Boer, Mark P. Simmonds, Peter J. H. Reijnders, Geert Aarts
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086331
Abstract: The influence of topographic and temporal variables on cetacean distribution at a fine-scale is still poorly understood. To study the spatial and temporal distribution of harbour porpoise Phocoena phocoena and the poorly known Risso’s dolphin Grampus griseus we carried out land-based observations from Bardsey Island (Wales, UK) in summer (2001–2007). Using Kernel analysis and Generalized Additive Models it was shown that porpoises and Risso’s appeared to be linked to topographic and dynamic cyclic variables with both species using different core areas (dolphins to the West and porpoises to the East off Bardsey). Depth, slope and aspect and a low variation in current speed (for Risso’s) were important in explaining the patchy distributions for both species. The prime temporal conditions in these shallow coastal systems were related to the tidal cycle (Low Water Slack and the flood phase), lunar cycle (a few days following the neap tidal phase), diel cycle (afternoons) and seasonal cycle (peaking in August) but differed between species on a temporary but predictable basis. The measure of tidal stratification was shown to be important. Coastal waters generally show a stronger stratification particularly during neap tides upon which the phytoplankton biomass at the surface rises reaching its maximum about 2–3 days after neap tide. It appeared that porpoises occurred in those areas where stratification is maximised and Risso’s preferred more mixed waters. This fine-scale study provided a temporal insight into spatial distribution of two species that single studies conducted over broader scales (tens or hundreds of kilometers) do not achieve. Understanding which topographic and cyclic variables drive the patchy distribution of porpoises and Risso’s in a Headland/Island system may form the initial basis for identifying potentially critical habitats for these species.
Sequencing of the Hepatitis C Virus: A Systematic Review
Brendan Jacka, Francois Lamoury, Peter Simmonds, Gregory J. Dore, Jason Grebely, Tanya Applegate
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0067073
Abstract: Since the identification of hepatitis C virus (HCV), viral sequencing has been important in understanding HCV classification, epidemiology, evolution, transmission clustering, treatment response and natural history. The length and diversity of the HCV genome has resulted in analysis of certain regions of the virus, however there has been little standardisation of protocols. This systematic review was undertaken to map the location and frequency of sequencing on the HCV genome in peer reviewed publications, with the aim to produce a database of sequencing primers and amplicons to inform future research. Medline and Scopus databases were searched for English language publications based on keyword/MeSH terms related to sequence analysis (9 terms) or HCV (3 terms), plus “primer” as a general search term. Exclusion criteria included non-HCV research, review articles, duplicate records, and incomplete description of HCV sequencing methods. The PCR primer locations of accepted publications were noted, and purpose of sequencing was determined. A total of 450 studies were accepted from the 2099 identified, with 629 HCV sequencing amplicons identified and mapped on the HCV genome. The most commonly sequenced region was the HVR-1 region, often utilised for studies of natural history, clustering/transmission, evolution and treatment response. Studies related to genotyping/classification or epidemiology of HCV genotype generally targeted the 5′UTR, Core and NS5B regions, while treatment response/resistance was assessed mainly in the NS3–NS5B region with emphasis on the Interferon sensitivity determining region (ISDR) region of NS5A. While the sequencing of HCV is generally constricted to certain regions of the HCV genome there is little consistency in the positioning of sequencing primers, with the exception of a few highly referenced manuscripts. This study demonstrates the heterogeneity of HCV sequencing, providing a comprehensive database of previously published primer sets to be utilised in future sequencing studies.
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