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Search Results: 1 - 10 of 4195 matches for " Tim Yates "
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An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data
Micha? J Okoniewski, Tim Yates, Sian Dibben, Crispin J Miller
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-5-r79
Abstract: Alternative splicing has been implicated in a wide range of human diseases, including neuropathological conditions such as Alzheimer's disease, cystic fibrosis, those involving growth and developmental defects, and many human cancers [1,2]. It is involved in diverse cellular processes, including apoptosis, invasion, angiogenesis and differentiation [1], and can impact on both the efficacy and the toxicology of drugs [3].Given that 40% to 60% of all human genes, corresponding to approximately 70% of all multi-exon genes, are predicted to be alternatively spliced [4,5], the prospect of being able to investigate coordinated changes in gene expression at the level of individual isoforms is of significant interest. Recently, a new generation of microarrays has been designed with substantially higher probe densities than were previously available, allowing probes to be targeted at individual exons and gene expression to be monitored at much finer granularities than before. The Affymetrix Exon 1.0 ST array, for example, has approximately 5.5 million features, corresponding to approximately 1.4 million probesets, targeting approximately 1.2 million individual exons. The aim was to design an array that interrogated every single known and predicted exon in the human genome.While such arrays offer great promise, they also pose major challenges for data analysis. Figure 1, for example, shows the transcript and exon structure for the 5' end of the oestrogen receptor (ESR1) gene accompanied by Affymetrix probeset target locations. The gene is represented by probesets targeting known exons, introns, putative exons, the untranslated regions (UTRs) and genomic sequences, both up- and downstream of the predicted gene. This level of coverage poses two problems: first, it must be possible to present and interpret such data for each individual gene of interest. Second, if analysis is to be pursued systematically (rather than simply by selecting genes based on prior knowledge), technique
Summary of current knowledge of the size and spatial distribution of the horse population within Great Britain
Lisa A Boden, Tim DH Parkin, Julia Yates, Dominic Mellor, Rowland R Kao
BMC Veterinary Research , 2012, DOI: 10.1186/1746-6148-8-43
Abstract: A conservative estimate for the accurately geo-located NED horse population within GB is approximately 840,000 horses. This is likely to be an underestimate because of the exclusion of horses due to age or location criteria. In both datasets, horse density was higher in England and Wales than in Scotland. The high density of horses located in urban areas as indicated in the NED is consistent with previous reports indicating that owner location cannot always be viewed as a direct substitute for horse location. Otherwise, at a regional resolution, there are few differences between the datasets. There are inevitable biases in the stakeholder data, and leisure horses that are unaffiliated to major stakeholders are not included in these data. Despite this, the similarity in distributions of these datasets is re-assuring, suggesting that there are few regional biases in the NED.Our analyses suggest that stakeholder data could be used to monitor possible changes in horse demographics. Given such changes in horse demographics and the advantages of stakeholder data (which include annual updates and accurate horse location), it may be appropriate to use these data for future disease modelling in conjunction with, if not in place of the NED.Understanding how an infectious disease might spread through a population and how then to control that spread requires knowing both the size of the susceptible population at risk and, and how frequently individuals in a population come into contact with one another. In the case of disease spread at a national scale, this requires knowledge of the spatial distribution of the susceptible population, as this will inform 'local' spread that transmits simply as a result of geographical proximity, and can be used to parameterise 'network-based' spread, such as can occur via livestock movements. Great Britain (GB) needs to prepare for a potential equine infectious disease epidemic due to the recent incursion of Bluetongue virus (BTV) from North Af
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, Crispin J Miller
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-282
Abstract: We found a high degree of correspondence between the two platforms in terms of exon-level fold changes and detection. For example, over 80% of exons detected as expressed in RNA-Seq were also detected on the Exon array, and 91% of exons flagged as changing from Absent to Present on at least one platform had fold-changes in the same direction. The greatest detection correspondence was seen when the read count threshold at which to flag exons Absent in the SOLiD data was set to t<1 suggesting that the background error rate is extremely low in RNA-Seq. We also found RNA-Seq more sensitive to detecting differentially expressed exons than the Exon array, reflecting the wider dynamic range achievable on the SOLiD platform. In addition, we find significant evidence of novel protein coding regions outside known exons, 93% of which map to Exon array probesets, and are able to infer the presence of thousands of novel transcripts through the detection of previously unreported exon-exon junctions.By focusing on exon-level expression, we present the most fine-grained comparison between RNA-Seq and microarrays to date. Overall, our study demonstrates that data from a SOLiD RNA-Seq experiment are sufficient to generate results comparable to those produced from Affymetrix Exon arrays, even using only a single replicate from each platform, and when presented with a large genome.Massively Parallel Nucleotide Sequencing (MPNS) allows the rapid generation of gigabases of sequence data at a relatively low cost per residue. A variety of platforms exist, but all rely on the generation of a large number of relatively short sequences, known as 'tags' or 'reads' that can then be aligned to a target database, or assembled de novo into contiguous sequences. In many MPNS experiments, it is possible to treat the set of reads generated during a sequencing run as an unbiased sampling of the total nucleotide complement of the cells, making it possible to use the number of reads aligning to a given
Development of a 'toolkit' to identify medical students at risk of failure to thrive on the course: an exploratory retrospective case study
Janet Yates
BMC Medical Education , 2011, DOI: 10.1186/1472-6920-11-95
Abstract: The study group was drawn from five successive cohorts. Students who had experienced difficulties were identified in any of four ways: from Minutes of the Academic Progress Committee; by scanning examination lists at key stages (end of the first two years, and finals at the end of the clinical course); from lists of students flagged to the Postgraduate Deanery as in need of extra monitoring or support; and from progress files of those who had left the course prematurely. Relevant data were extracted from each student's course progress file into a customised database.1188 students were admitted over the five years. 162 (14%) were identified for the study, 75 of whom had failed to complete the course by October 2010. In the 87 who did graduate, a combination of markers in Years 1 and 2 identified over half of those who would subsequently have the most severe problems throughout the course. This 'toolkit' comprised failure of 3 or more examinations per year, an overall average of <50%, health or social difficulties, failure to complete Hepatitis B vaccination on time, and remarks noted about poor attitude or behaviour.A simple toolkit of academic and non-academic markers could be used routinely to help identify potential strugglers at an early stage, enabling additional support and guidance to be given to these students.Every year, a small number of undergraduate students at the University of Nottingham Medical School fail to make satisfactory progress on the course. Some have problems at all stages, others have sporadic difficulties, and a proportion fail to graduate at all, either leaving voluntarily or having their course terminated. In an earlier study we found that 10-15% of the annual intake were affected to some degree [1]. There is often a combination of causative factors, including difficulty in coping with the academic workload, health problems, and social issues such as not settling at university or having adverse personal or family circumstances. Some stude
When did they leave, and why? A retrospective case study of attrition on the Nottingham undergraduate medical course
Janet Yates
BMC Medical Education , 2012, DOI: 10.1186/1472-6920-12-43
Abstract: Relevant data on admission and course progress were extracted manually from the archived files of students who had failed to graduate from five recent consecutive cohorts (entry in 2000–2004 inclusive), using a customised Access database. Discrete categories of information were supplemented with free text entries.1188 students registered over the five-year entry period and 73 (6%) failed to graduate. The highest rates of attrition (46/1188, 4%) occurred during the first two years (largely preclinical studies), with 34 students leaving voluntarily, including 11 within the first semester, and 12 having their courses terminated for academic failure. Seventeen left at the end of the third year (Honours course plus early clinical practice) and the remaining ten during the final two clinical years. The reasons for attrition were not always clear-cut and often involved a mixture of academic, personal, social and health factors, especially mental health problems.The causes of attrition are complex. A small number of students with clear academic failure might require individual educational interventions for remediation. However, this could have substantial resource implications for the Faculty. Mental health problems predominate in late course attrition and may have been undisclosed for some time. The introduction of a structured exit interview may provide further insight, especially for those students who leave suddenly and unexpectedly early in the course.
Análise de uma experiência de rota??o
Yates, Frank;
Bragantia , 1952, DOI: 10.1590/S0006-87051952000300001
Abstract: the paper describes the methods which should be followed when analysing a rotation experiment containing rotations of different length in which all phases of each rotation are not represented, and in which consequently the mean yields for the different rotations of a particular crop are liable to be affected by annual variations in the yield of that crop. constants are fitted by the method of least squares, the arithmetical method of successive approximation first described by stevens being used. the estimation of the errors to which the estimates are subject is considered in detail.
Novel oral anticoagulants for stroke prevention in atrial fibrillation: a focus on the older patient
Yates SW
International Journal of General Medicine , 2013, DOI: http://dx.doi.org/10.2147/IJGM.S39379
Abstract: vel oral anticoagulants for stroke prevention in atrial fibrillation: a focus on the older patient Review (18) Total Article Views Authors: Yates SW Published Date March 2013 Volume 2013:6 Pages 167 - 180 DOI: http://dx.doi.org/10.2147/IJGM.S39379 Received: 20 October 2012 Accepted: 03 December 2012 Published: 21 March 2013 Scott W Yates Center for Executive Medicine, Plano, TX, USA Abstract: Atrial fibrillation (AF) is a common arrhythmia that is associated with an increased risk of stroke, particularly in the elderly. Traditionally, a vitamin K antagonist such as warfarin is prescribed for stroke prevention. Warfarin is effective at lowering stroke risk but has several limitations due to food restrictions, drug interactions, and a narrow therapeutic window. Various novel oral anticoagulants (NOACs) are available or under development to provide alternative treatment options. This article reviews the efficacy and safety of three NOACs (dabigatran etexilate, rivaroxaban, and apixaban) in addition to warfarin and aspirin, for prevention of stroke in patients with AF, focusing on the elderly population. Results of clinical trials demonstrate that the efficacy of NOACs for stroke prevention in patients with AF is as good as or better than that of warfarin. The NOACs are also associated with an equivalent or lower risk of bleeding. Regardless of the medication chosen, older patients with AF must be treated cautiously due to an increased risk of stroke and bleeding, as well as potential challenges related to drug interactions and monitoring requirements. NOACs may be suitable alternatives to warfarin for stroke prevention in older patients due to several advantages, including a faster onset of action, few drug or food interactions, and no requirement for regular monitoring. However, dose adjustments may be required for certain patients, such as those with severe renal impairment or in the setting of drug interactions.
Novel oral anticoagulants for stroke prevention in atrial fibrillation: a focus on the older patient
Yates SW
International Journal of General Medicine , 2013,
Abstract: Scott W YatesCenter for Executive Medicine, Plano, TX, USAAbstract: Atrial fibrillation (AF) is a common arrhythmia that is associated with an increased risk of stroke, particularly in the elderly. Traditionally, a vitamin K antagonist such as warfarin is prescribed for stroke prevention. Warfarin is effective at lowering stroke risk but has several limitations due to food restrictions, drug interactions, and a narrow therapeutic window. Various novel oral anticoagulants (NOACs) are available or under development to provide alternative treatment options. This article reviews the efficacy and safety of three NOACs (dabigatran etexilate, rivaroxaban, and apixaban) in addition to warfarin and aspirin, for prevention of stroke in patients with AF, focusing on the elderly population. Results of clinical trials demonstrate that the efficacy of NOACs for stroke prevention in patients with AF is as good as or better than that of warfarin. The NOACs are also associated with an equivalent or lower risk of bleeding. Regardless of the medication chosen, older patients with AF must be treated cautiously due to an increased risk of stroke and bleeding, as well as potential challenges related to drug interactions and monitoring requirements. NOACs may be suitable alternatives to warfarin for stroke prevention in older patients due to several advantages, including a faster onset of action, few drug or food interactions, and no requirement for regular monitoring. However, dose adjustments may be required for certain patients, such as those with severe renal impairment or in the setting of drug interactions.Keywords: aspirin, warfarin, dabigatran etexilate, rivaroxaban, apixaban
Neuropsychological impairment in alcoholic cirrhosis: correlates and effects on One-year outcome
Yates William
Annals of General Psychiatry , 2006, DOI: 10.1186/1744-859x-5-s1-s247
Abstract:
Continuous Enrolment: Heresies, Headaches and Heartaches
Lynda Yates
English Language Teaching , 2008, DOI: 10.5539/elt.v1n2p8
Abstract: In this paper I report on a research project designed to address the question of how the policy of continuous enrolment has been working in practice in the AMEP (Adult Migrant English Program), the national English language program offered to newly-arrived migrants to Australia. Managers, teachers and learners from around Australia were interviewed individually or in focus groups to ascertain their views on the policy and its management. The literature on continuous enrolment has focused almost exclusively on adult education in North America, and has generally found little positive support for the policy among teachers. The results of this study indicate that the potential benefits to students in the context of the AMEP may outweigh the considerable disruption to classes it causes. In two of the three participating centres, the students were overall very positive about starting class immediately, and many teachers also appreciated these benefits for students and were developing strategies to minimize the negative effects. Similarly, while the managers generally recognized the organizational and pedagogical headaches that the policy caused, they appreciated the flexibility it gave them to open and manage classes according to local conditions. I argue that these more sympathetic views are a product of the unique context and history of the AMEP as a nationally-supported on-arrivals program, but that positive measures are nevertheless necessary in order to address the issues caused by continuous enrolment.
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