605 research outputs found

    Development and Application of Comparative Gene Co-expression Network Methods in Brachypodium distachyon

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    Gene discovery and characterization is a long and labor-intensive process. Gene co-expression network analysis is a long-standing powerful approach that can strongly enrich signals within gene expression datasets to predict genes critical for many cellular functions. Leveraging this approach with a large number of transcriptome datasets does not yield a concomitant increase in network granularity. Independently generated datasets that describe gene expression in various tissues, developmental stages, times of day, and environments can carry conflicting co-expression signals. The gene expression responses of the model C3 grass Brachypodium distachyon to abiotic stress is characterized by a co-expression-based analysis, identifying 22 modules of genes, annotated with putative DNA regulatory elements and functional terms. A great deal of co-expression elasticity is found among the genes characterized therein. An algorithm, dGCNA, designed to determine statistically significant changes in gene-gene co-expression relationships is presented. The algorithm is demonstrated on the very well-characterized circadian system of Arabidopsis thaliana, and identifies potential strong signals of molecular interactions between a specific transcription factor and putative target gene loci. Lastly, this network comparison approach based on edge-wise similarities is demonstrated on many pairwise comparisons of independent microarray datasets, to demonstrate the utility of fine-grained network comparison, rather than amassing as large a dataset as possible. This approach identifies a set of 182 gene loci which are differentially expressed under drought stress, change their co-expression strongly under loss of thermocycles or high-salinity stress, and are associated with cell-cycle and DNA replication functions. This set of genes provides excellent candidates for the generation of rhythmic growth under thermocycles in Brachypodium distachyon

    The Effect of Physical Weight and Stimulus Spatial Location on Lexical Decision: Implications for Embodied Cognition

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    Traditional models of cognition within cognitive psychology have utilised dualistic perspectives and largely ignored the roles of the motor systems and bodily experiences. More recent embodied approaches have sought to combat this dualism by incorporating the motor systems and bodily experiences into their perspectives. Recent research has highlighted the role of bodily experiences in shaping cognition (Proffitt, 2006; Jostmann et al., 2009), how language comprehension can be embodied and grounded in physical experiences (Glenberg and Kaschak, 2002; Zwaan and Yaxley, 2003) and also how stimulus spatial location can influence responses (Meteyard et al., 2008; Dunn et al., 2014). The present study aimed to explore those areas and provide empirical evidence in support as well as explore a gap in current research. The literature search indicated an abundance of embodied system research but a lack of research looking at possible interactions between the systems, it was this gap that was explored within the present study. Utilising a lexical decision task and methods similar to that of Proffitt (2006) three experiments were conducted. A total of 64 participants underwent standard and spatial lexical decision tasks. Three experiments were conducted exploring the bodily effect of weight, stimulus spatial effect and interactions between embodied systems.Results from the three experiments displayed a lack of support for past research regarding the effect of the bodily experience of weight. Results also displayed a main effect of word type leading to the indication that the comprehension of the word/non-word letter strings affected task performance. Analysis of results proposed that a cohesion effect between embodied systems facilitated task performance. It was concluded that further research is needed in order to fully understand the possibility of dominance or cohesion effects within an embodied perspective

    The Development of an Average, Anatomically Based, Young Adult, GRIN Eye Model

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    The purpose of this thesis is to describe the development of an anatomically based, young adult eye model, which includes a crystalline lens with a gradient refractive index (GRIN). This model will then be used to investigate the effect of laser refractive surgery. The first step in this process involved developing a symmetrical eye model that was found to be a better predictor of empirical longitudinal spherical aberration than any previous model. Myopia was simulated by either a purely axial or refractive technique. While these models were found to be good predictors of the spherical aberration measured in young adults, they did not predict the total amount of high-order aberrations. The techniques used to simulate a single type of myopia caused the myopic models to become anatomically inaccurate. To improve the eye models a biconic surface was used to quantify the anterior corneal shape as a function of myopia. A method to describe the refractive error and biconic shape parameters in Jackson Cross Cylinder terms was implemented to determine correlations. Results indicate that a biconic accurately models the average shape of the anterior corneal surface as a function of myopia. Adopting the biconic model for the anterior corneal surface and adding average misalignments of the ocular components transformed the models from symmetrical to asymmetrical. Refractive error was now simulated by the anatomically accurate changes in both the anterior corneal shape and axial length. The asymmetrical aberrations resulted from the misalignment of the ocular components and provided a good prediction of average empirical aberrations but underestimated the aberrations of individual subjects. Photorefractive keratectomy, a form of laser refractive surgery, was simulated by theoretically calculated and by empirically measured changes in the shape of the anterior corneal surface. Applying the change in anterior corneal shape to the asymmetrical models was used to develop postoperative models. Changes in corneal shape and model aberrations attributed to theoretical calculations do not match empirical observations. The prediction of increased high-order aberrations in postoperative models based on empirically measured changes in the anterior corneal topography was similar to clinical results. Average anatomically based, GRIN eye models have been developed that accurately predict the average aberrations of emmetropic and myopic young adults. These models underestimate the asymmetrical and total high-order aberrations that have been measured in individual subjects but are still useful for investigating the average effects of procedures like refractive surgery

    Investigation of a glucosyltransferase that recognises abscisic acid

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    EThOS - Electronic Theses Online ServiceGBUnited Kingdo

    Racismo e SaĂșde: um corpus crescente de evidĂȘncia internacional

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    Este artigo resenha um crescente corpus de investigação empĂ­rica, o qual indica que o racismo, em suas variantes institucional e interpessoal, persiste nas sociedades contemporĂąneas racializadas de todo o mundo, e pode ter impactos adversos importantes sobre a saĂșde. ApĂłs um breve apanhado das desigualdades Ă©tnico-raciais na saĂșde da população, em vĂĄrios contextos nacionais, o artigo concentra-se na pesquisa empĂ­rica sobre a natureza e persistĂȘncia do racismo e as mĂșltiplas maneiras em que esse pode impactar negativamente a saĂșde de grupos Ă©tnico-raciais nĂŁo dominantes e estigmatizados. Primeiramente, atravĂ©s de polĂ­ticas e prĂĄticas que limitam o acesso a recursos e oportunidades na sociedade, o racismo institucional produz consequĂȘncias patogĂȘnicas, por restringir a mobilidade social, e criar diferenciaçÔes raciais no status socioeconĂŽmico e nas condiçÔes de vida e trabalho, prejudiciais ao bem-estar. Em segundo lugar, o racismo cultural, no Ăąmbito da sociedade, provoca e sustenta o racismo institucional e interpessoal, criando um ambiente polĂ­tico hostil a polĂ­ticas igualitĂĄrias. No nĂ­vel individual, estereĂłtipos negativos, sustentados pelo racismo cultural, fomentam respostas psicolĂłgicas prejudiciais Ă  saĂșde, tais como a “ameaça de estereĂłtipo” e o racismo internalizado. Terceiro, a experiĂȘncia subjetiva de discriminação racial Ă© um tipo de experiĂȘncia de vida estressante, mas historicamente negligenciado na literatura, que pode levar a mudanças adversas nas condiçÔes de saĂșde e a padrĂ”es alterados de comportamento que aumentam os riscos Ă  saĂșde.

    Subtractive NCE-MRA: Improved background suppression using robust regression-based weighted subtraction.

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    PURPOSE: To correct the intensity difference of static background signal between bright blood images and dark blood images in subtractive non-contrast-enhanced MR angiography using robust regression, thereby improving static background signal suppression on subtracted angiograms. METHODS: Robust regression (RR), using iteratively reweighted least squares, is used to calculate the regression coefficient of background tissues from a scatter plot showing the voxel intensity of bright blood images versus dark blood images. The weighting function is based on either the Euclidean distance from the estimated regression line or the deviation angle. Results from RR using the deviation angle (RRDA), conventional RR using the Euclidean distance, and ordinary leastsquares regression were compared with reference values determined manually by two observers. Performance was evaluated over studies using different sequences, including 36 thoracic flow-sensitive dephasing data sets, 13 iliac flow-sensitive dephasing data sets, and 26 femoral fresh blood imaging data sets. RESULTS: RR deviation angle achieved robust and accurate performance in all types of images, with small bias, small mean absolute error, and high-correlation coefficients with reference values. Background tissues, such as muscle, veins, and bladder, were suppressed while the vascular signal was preserved. Euclidean distance gave good performance for thoracic and iliac flow-sensitive dephasing, but could not suppress background tissues in femoral fresh blood imaging. Ordinary least squares regression was sensitive to outliers and overestimated regression coefficients in thoracic flow-sensitive dephasing. CONCLUSION: Weighted subtraction using RR was able to acquire the regression coefficients of background signal and improve background suppression of subtractive non-contrast-enhanced MR angiography techniques. RR deviation angle has the most robust and accurate overall performance among three regression methods

    Quantitative BOLD imaging at 3T: Temporal changes in hepatocellular carcinoma and fibrosis following oxygen challenge.

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    PURPOSE: To evaluate the utility of oxygen challenge and report on temporal changes in blood oxygenation level-dependent (BOLD) contrast in normal liver, hepatocellular carcinoma (HCC) and background fibrosis. MATERIALS AND METHODS: Eleven volunteers (nine male and two female, mean age 33.5, range 27-41 years) and 10 patients (nine male and one female, mean age 68.9, range 56-87 years) with hepatocellular carcinoma on a background of diffuse liver disease were recruited. Imaging was performed on a 3T system using a multiphase, multiecho, fast gradient echo sequence. Oxygen was administered via a Hudson mask after 2 minutes of free-breathing. Paired t-tests were performed to determine if the mean pre- and post-O2 differences were statistically significant. RESULTS: In patients with liver fibrosis (n = 8) the change in T2* following O2 administration was elevated (0.88 ± 0.582 msec, range 0.03-1.69 msec) and the difference was significant (P = 0.004). The magnitude of the BOLD response in patients with HCC (n = 10) was larger, however the response was more variable (1.07 ± 1.458 msec, range -0.93-3.26 msec), and the difference was borderline significant (P = 0.046). The BOLD response in the volunteer cohort was not significant (P = 0.121, 0.59 ± 1.162 msec, range -0.81-2.44 msec). CONCLUSION: This work demonstrates that the BOLD response following oxygen challenge within cirrhotic liver is consistent with a breakdown in vascular autoregulatory mechanisms. Similarly, the elevated BOLD response within HCC is consistent with the abnormal capillary vasculature within tumors and the arterialization of the blood supply. Our results suggest that oxygen challenge may prove a viable BOLD contrast mechanism in the liver. J. Magn. Reson. Imaging 2016;44:739-744.This study was supported by the Addenbrooke’s Charitable Trust, Cambridge’s Experimental Cancer Medicine Centre and a NIHR comprehensive Biomedical Research Centre award to Cambridge University Hospitals NHS Foundation Trust in partnership with the University of Cambridge.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/jmri.2518

    What is a Paraconsistent Logic?

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    Paraconsistent logics are logical systems that reject the classical principle, usually dubbed Explosion, that a contradiction implies everything. However, the received view about paraconsistency focuses only the inferential version of Explosion, which is concerned with formulae, thereby overlooking other possible accounts. In this paper, we propose to focus, additionally, on a meta-inferential version of Explosion, i.e. which is concerned with inferences or sequents. In doing so, we will offer a new characterization of paraconsistency by means of which a logic is paraconsistent if it invalidates either the inferential or the meta-inferential notion of Explosion. We show the non-triviality of this criterion by discussing a number of logics. On the one hand, logics which validate and invalidate both versions of Explosion, such as classical logic and Asenjo–Priest’s 3-valued logic LP. On the other hand, logics which validate one version of Explosion but not the other, such as the substructural logics TS and ST, introduced by Malinowski and Cobreros, EgrĂ©, Ripley and van Rooij, which are obtained via Malinowski’s and Frankowski’s q- and p-matrices, respectively

    Amniotic fluid volume: Rapid MR-based assessment at 28-32 weeks gestation

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    Objectives: This work evaluates rapid magnetic resonance projection hydrography (PH) based amniotic fluid volume (AFV) estimates against established routine ultrasound single deepest vertical pocket (SDVP) and amniotic fluid index (AFI) measurements, in utero, at 28-32 weeks gestation. Manual multi-section planimetry (MSP) based measurement of AFV is used as a proxy reference standard. Methods: 35 women with a healthy singleton pregnancy (20-41 years) attending routine antenatal ultrasound were recruited. SDVP and AFI were measured using ultrasound, with same day MRI assessing AFV with PH and MSP. The relationships between the respective techniques were assessed using linear regression analysis and Bland-Altman method comparison statistics. Results: When comparing estimated AFV, a highly significant relationship was observed between PH and the reference standard MSP (R2=0.802, p<0.001). For the US measurements, SDVP measurement related most closely to amniotic fluid volume, (R2=0.470, p<0.001), with AFI demonstrating a weaker relationship (R2=0.208, p=0.007). Conclusion: This study shows that rapid MRI based PH measurement is a better predictor of AFV, relating more closely to our proxy standard than established US techniques. Although larger validation studies across a range of gestational ages are required this approach could form part of MR fetal assessment, particularly where poly or oligohydramnios is suspected.This study was supported by the National Institute of Health Research, Cambridge Biomedical Research Centre. The authors also acknowledge the support of Addenbrooke’s Charitable Trust and thank the participants for their contribution to the study.This is the author accepted manuscript. The final version is available from Springer via http://dx.doi.org/10.1007/s00330-015-4179-
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