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Search Results: 1 - 10 of 300858 matches for " Keith J Edwards "
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Cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth
Mark O Winfield, Chungui Lu, Ian D Wilson, Jane A Coghill, Keith J Edwards
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-55
Abstract: We observed novel responses of several genes thought to be of major importance in vernalisation-induced phase transition, and identified several MADS-box genes that might play an important role in the onset of flowering. In addition, we saw responses in genes of the Gibberellin pathway that would indicate that this pathway also has some role to play in phase transition.Phase transition in wheat is more complex than previously reported, and there is evidence that day-length has an influence on genes that were once thought to respond exclusively to an extended period of cold.In plants, the timing of the change from vegetative to reproductive growth is critical for successful reproduction, and must occur when both internal and external conditions are appropriate. The environmental cues of day-length and temperature have a strong influence on flowering, and the ability to perceive and respond to these cues is controlled through the photoperiod and vernalisation pathways, respectively [1].Wheat (Triticum aestivum L.) is normally a long-day plant, flowering in spring and early summer when days are lengthening [2]. Additionally, wheat cultivars can be broadly divided into two categories, winter or spring, according to whether they require an extended period of cold to become competent to flower. In winter varieties, change from vegetative to reproductive phase is promoted by exposure to low temperatures (3°C – 8°C) for 4–6 weeks. These varieties are planted in the autumn so that seedlings are exposed to the cold of winter and so become competent to flower. However, they only become committed to flower as days lengthen in the spring. In addition to these two external factors, different wheat varieties can be distinguished by the intrinsic rate at which they tend to pass from floral induction to heading. This tendency is referred to as earliness per se [3].In Arabidopsis, the genetic factors underpinning phase change have been well-characterised [4-6]. Four major genetic pat
Kronecker Product Linear Exponent AR(1) Correlation Structures for Multivariate Repeated Measures
Sean L. Simpson, Lloyd J. Edwards, Martin A. Styner, Keith E. Muller
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088864
Abstract: Longitudinal imaging studies have moved to the forefront of medical research due to their ability to characterize spatio-temporal features of biological structures across the lifespan. Credible models of the correlations in longitudinal imaging require two or more pattern components. Valid inference requires enough flexibility of the correlation model to allow reasonable fidelity to the true pattern. On the other hand, the existence of computable estimates demands a parsimonious parameterization of the correlation structure. For many one-dimensional spatial or temporal arrays, the linear exponent autoregressive (LEAR) correlation structure meets these two opposing goals in one model. The LEAR structure is a flexible two-parameter correlation model that applies to situations in which the within-subject correlation decreases exponentially in time or space. It allows for an attenuation or acceleration of the exponential decay rate imposed by the commonly used continuous-time AR(1) structure. We propose the Kronecker product LEAR correlation structure for multivariate repeated measures data in which the correlation between measurements for a given subject is induced by two factors (e.g., spatial and temporal dependence). Excellent analytic and numerical properties make the Kronecker product LEAR model a valuable addition to the suite of parsimonious correlation structures for multivariate repeated measures data. Longitudinal medical imaging data of caudate morphology in schizophrenia illustrates the appeal of the Kronecker product LEAR correlation structure.
Bogoliubov approach to superfluidity of atoms in an optical lattice
Ana Maria Rey,Keith Burnett,Robert Roth,Mark Edwards,Carl J. Williams,Charles W. Clark
Physics , 2002, DOI: 10.1088/0953-4075/36/5/304
Abstract: We use the Bogoliubov theory of atoms in an optical lattice to study the approach to the Mott-insulator transition. We derive an explicit expression for the superfluid density based on the rigidity of the system under phase variations. This enables us to explore the connection between the quantum depletion of the condensate and the quasi-momentum distribution on the one hand and the superfluid fraction on the other. The approach to the insulator phase may be characterized through the filling of the band by quantum depletion, which should be directly observable via the matter wave interference patterns. We complement these findings by self-consistent Hartree-Fock-Bogoliubov-Popov calculations for one-dimensional lattices including the effects of a parabolic trapping potential.
Kronecker product linear exponent AR(1) correlation structures and separability tests for multivariate repeated measures
Sean L. Simpson,Lloyd J. Edwards,Martin A. Styner,Keith E. Muller
Statistics , 2010,
Abstract: Longitudinal imaging studies have moved to the forefront of medical research due to their ability to characterize spatio-temporal features of biological structures across the lifespan. Credible models of the correlations in longitudinal imaging require two or more pattern components. Valid inference requires enough flexibility of the correlation model to allow reasonable fidelity to the true pattern. On the other hand, the existence of computable estimates demands a parsimonious parameterization of the correlation structure. For many one-dimensional spatial or temporal arrays, the linear exponent autoregressive (LEAR) correlation structure meets these two opposing goals in one model. The LEAR structure is a flexible two-parameter correlation model that applies in situations in which the within-subject correlation decreases exponentially in time or space. It allows for an attenuation or acceleration of the exponential decay rate imposed by the commonly used continuous-time AR(1) structure. Here we propose the Kronecker product LEAR correlation structure for multivariate repeated measures data in which the correlation between measurements for a given subject is induced by two factors. We also provide a scientifically informed approach to assessing the adequacy of a Kronecker product LEAR model and a general unstructured Kronecker product model. The approach provides useful guidance for high dimension, low sample size data that preclude using standard likelihood based tests. Longitudinal medical imaging data of caudate morphology in schizophrenia illustrates the appeal of the Kronecker product LEAR correlation structure.
System Utilization and Changes in Implemented Information Systems: A Case Study
H. Keith Edwards
IAENG International Journal of Computer Science , 2007,
Abstract:
Improvement in symptoms and signs in the forefoot of patients with rheumatoid arthritis treated with anti-TNF therapy
Catherine J Bowen, Christopher J Edwards, Lindsey Hooper, Keith Dewbury, Madeleine Sampson, Sally Sawyer, Jane Burridge, Nigel K Arden
Journal of Foot and Ankle Research , 2010, DOI: 10.1186/1757-1146-3-10
Abstract: Consecutive RA patients starting anti-TNF therapy (infliximab, etanercept, adalimumab) were assessed for presence of synovial hypertrophy and synovitis in the 2nd and 5th metatarso-phalangeal (MTP) joints and plantar forefoot bursal hypertrophy before and 12 weeks after therapy. Tender MTP joints and swollen bursae were established clinically by an experienced podiatrist and ultrasound (US) images were acquired and interpreted by a radiologist. Assessment of patient reported disease impact on the foot was performed using the Manchester Foot Pain and Disability Index (MFPDI).31 patients (24 female, 7 male) with RA (12 seronegative, 19 seropositive) completed the study: mean age 59.6 (SD 10.1) years, disease duration 11.1 (SD 10.5) years, and previous number of Disease Modifying Anti Rheumatic Drugs 3.0 (1.6). Significant differences after therapy were found for Erythrocyte Sedimentation Rate (t = 4.014, p < 0.001), C-reactive protein (t = 3.889, p = 0.001), 28 joint Disease Activity Score (t = 3.712, p = 0.0001), Visual Analog Scale (t = 2.735, p = 0.011) and Manchester Foot Pain and Disability Index (t = 3.712, p = 0.001).Presence of MTP joint synovial hypertrophy on US was noted in 67.5% of joints at baseline and 54.8% of joints at twelve weeks. Presence of plantar forefoot bursal hypertrophy on US was noted in 83.3% of feet at baseline and 75% at twelve weeks. Although there was a trend for reduction in observed presence of person specific forefoot pathology, when the frequencies were analysed (McNemar) this was not significant.Significant improvements were seen in patient reported foot pain and disability 12 weeks after commencing TNF inhibition in RA, but this may not be enough time to detect changes in forefoot pathology.Tumour Necrosis Factor (TNF) inhibition is known to be an effective way of reducing synovial hypertrophy and preventing erosions in patients who have rheumatoid arthritis (RA) [1,2]. Unfortunately studies to date have tended to focus on the han
Musculoskeletal ultrasound imaging of the plantar forefoot in patients with rheumatoid arthritis: inter-observer agreement between a podiatrist and a radiologist
Catherine J Bowen, Keith Dewbury, Madeline Sampson, Sally Sawyer, Jane Burridge, Christopher J Edwards, Nigel K Arden
Journal of Foot and Ankle Research , 2008, DOI: 10.1186/1757-1146-1-5
Abstract: A consecutive sample of thirty-two patients with rheumatoid arthritis was assessed for presence of synovitis, erosions and bursitis within the forefoot using MSUS. All MSUS assessments were performed independently on the same day by a podiatrist and one of two Consultant Radiologists experienced in MSUS.Moderate agreement on image acquisition and interpretation was achieved for bursitis (kappa 0.522; p < 0.01) and erosions (kappa 0.636; p < 0.01) and fair agreement for synovitis (kappa 0.216; p < 0.05) during the primary assessments. Following a further training session, substantial agreement (kappa 0.702) between the two investigators was recorded. The sensitivity of the podiatrist using MSUS was 82.4% for detection of bursitis, 83.0% for detection of erosion and 84.0% for detection of synovitis. Specificity of the podiatrist using MSUS was 88.9% for detection of bursitis, 80.7% for detection of erosion and 35.9% for detection of synovitis.This study demonstrated good inter-observer agreement between a podiatrist and radiologist on MSUS assessment of the forefoot, particularly for bursitis and erosions, in patients with rheumatoid arthritis. There is scope to further evaluate and consider the role of podiatrists in the MSUS imaging of the foot following appropriate training and also in the development of reliable protocols for MSUS assessment of the foot.As technology has improved, clinical expertise in performing musculoskeletal ultrasound (MSUS) has also advanced dramatically [1,2]. The advantages of ultrasound imaging over conventional radiography, computed tomography, radioisotope scan and MRI (Magnetic Resonance Imaging) are reported as being that it is: painless, does not use ionising radiation, less expensive, can be performed real time, needs no special environment and is clinically readily accessible [1].There have been a number of studies that have utilised MSUS to diagnose specific soft tissue foot pain in healthy volunteers [3-5] and soft tissue problem
Impacts of Intensive Logging on the Trophic Organisation of Ant Communities in a Biodiversity Hotspot
Paul Woodcock, David P. Edwards, Rob J. Newton, Chey Vun Khen, Simon H. Bottrell, Keith C. Hamer
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060756
Abstract: Trophic organisation defines the flow of energy through ecosystems and is a key component of community structure. Widespread and intensifying anthropogenic disturbance threatens to disrupt trophic organisation by altering species composition and relative abundances and by driving shifts in the trophic ecology of species that persist in disturbed ecosystems. We examined how intensive disturbance caused by selective logging affects trophic organisation in the biodiversity hotspot of Sabah, Borneo. Using stable nitrogen isotopes, we quantified the positions in the food web of 159 leaf-litter ant species in unlogged and logged rainforest and tested four predictions: (i) there is a negative relationship between the trophic position of a species in unlogged forest and its change in abundance following logging, (ii) the trophic positions of species are altered by logging, (iii) disturbance alters the frequency distribution of trophic positions within the ant assemblage, and (iv) disturbance reduces food chain length. We found that ant abundance was 30% lower in logged forest than in unlogged forest but changes in abundance of individual species were not related to trophic position, providing no support for prediction (i). However, trophic positions of individual species were significantly higher in logged forest, supporting prediction (ii). Consequently, the frequency distribution of trophic positions differed significantly between unlogged and logged forest, supporting prediction (iii), and food chains were 0.2 trophic levels longer in logged forest, the opposite of prediction (iv). Our results demonstrate that disturbance can alter trophic organisation even without trophically-biased changes in community composition. Nonetheless, the absence of any reduction in food chain length in logged forest suggests that species-rich arthropod food webs do not experience trophic downgrading or a related collapse in trophic organisation despite the disturbance caused by logging. These food webs appear able to bend without breaking in the face of some forms of anthropogenic disturbance.
Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription
Rebecca L Poole, Gary LA Barker, Kay Werner, Gaia F Biggi, Jane Coghill, J George Gibbings, Simon Berry, Jim M Dunwell, Keith J Edwards
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-475
Abstract: Examination of 71,930 Long SAGE tags generated from six libraries derived from two wheat genotypes grown under two different conditions suggested that SAGE is a reliable and reproducible technique for use in studying the hexaploid wheat transcriptome. However, our results also showed that in poorly annotated and/or poorly sequenced genomes, such as hexaploid wheat, considerably more information can be extracted from SAGE data by carrying out a systematic analysis of both perfect and "fuzzy" (partially matched) tags. This detailed analysis of the SAGE data shows first that while there is evidence of alternative polyadenylation this appears to occur exclusively within the 3' untranslated regions. Secondly, we found no strong evidence for widespread alternative splicing in the developing wheat grain transcriptome. However, analysis of our SAGE data shows that antisense transcripts are probably widespread within the transcriptome and appear to be derived from numerous locations within the genome. Examination of antisense transcripts showing sequence similarity to the Puroindoline a and Puroindoline b genes suggests that such antisense transcripts might have a role in the regulation of gene expression.Our results indicate that the detailed analysis of transcriptome data, such as SAGE tags, is essential to understand fully the factors that regulate gene expression and that such analysis of the wheat grain transcriptome reveals that antisense transcripts maybe widespread and hence probably play a significant role in the regulation of gene expression during grain development.With cereals constituting more than 60% of the world's dietary intake, the bread wheat Triticum aestivum is one of the most important crops in world agriculture [1,2]. Despite the high yields achieved in Europe there is still a real need to generate improved cultivars, as yield and flour quality can be dramatically affected by the environment. This need has become even greater in recent years with tight
Delineation of the Innate and Adaptive T-Cell Immune Outcome in the Human Host in Response to Campylobacter jejuni Infection
Lindsey A. Edwards,Kiran Nistala,Dominic C. Mills,Holly N. Stephenson,Matthias Zilbauer,Brendan W. Wren,Nick Dorrell,Keith J. Lindley,Lucy R. Wedderburn,Mona Bajaj-Elliott
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015398
Abstract: Campylobacter jejuni is the most prevalent cause of bacterial gastroenteritis worldwide. Despite the significant health burden this infection presents, molecular understanding of C. jejuni-mediated disease pathogenesis remains poorly defined. Here, we report the characterisation of the early, innate immune response to C. jejuni using an ex-vivo human gut model of infection. Secondly, impact of bacterial-driven dendritic cell activation on T-cell mediated immunity was also sought.
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