Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland

Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.

Bioinformatic evaluation of transcriptional regulation of WNT pathway genes with reference to diabetic nephropathy

Objective: Diabetic nephropathy (DN) is a microvascular complication of diabetes. Members of the WNT/ β-catenin pathways have been implicated in interstitial fibrosis and glomerular sclerosis, characteristic hallmarks of DN. These processes are controlled, in part, by transcription factors (TFs), proteins which bind to gene promoter regions attenuating their regulation. We sought to identify predicted cis-acting transcription factor binding sites (TFBS) over-represented within the promoter regions of WNT pathway members compared to genes across the genome.Methods: We assessed the frequency of 62 TFBS motifs from the JASPAR databases on 65 WNT pathway genes. P-values were estimated on the hypergeometric distribution for each TF. Gene expression profiles of enriched motifs were examined from DN-related datasets to assess clinical significance.Results: TFBS motifs transcription factor AP-2 alpha (TFAP2A), myeloid zinc finger 1 (MZF1), and specificity protein 1 (SP1) were significantly enriched within WNT pathway genes (P-values<6.83x10-29, 1.34x10-11 and 3.01x10-6 respectively). MZF1 gene expression was significantly increased in DN in a whole kidney dataset (fold change = 1.16; 16% increase; P = 0.03). TFAP2A gene expression was decreased in an independent dataset (fold change = -1.02; P = 0.03). SP1 was not differentially expressed in any datasets examined.Conclusions: Three TFBS profiles are significantly enriched within the WNT pathway genes examined highlighting the use of in silico analyses for identifying key regulators of this pathway. Modification of TF binding to gene promoter regions involved in DN pathology may limit progression, making refinement of targeted therapeutic strategies possible through clearer delineation of their role.

The use of patient experience survey data by out-of-hours primary care services: a qualitative interview study

Background English National Quality Requirements mandate out-of-hours primary care services to routinely audit patient experience, but do not state how it should be done.

Objectives We explored how providers collect patient feedback data and use it to inform service provision. We also explored staff views on the utility of out-of-hours questions from the English General Practice Patient Survey (GPPS).

Methods A qualitative study was conducted with 31 staff (comprising service managers, general practitioners and administrators) from 11 out-of-hours primary care providers in England, UK. Staff responsible for patient experience audits within their service were sampled and data collected via face-to-face semistructured interviews.

Results Although most providers regularly audited their patients’ experiences by using patient surveys, many participants expressed a strong preference for additional qualitative feedback. Staff provided examples of small changes to service delivery resulting from patient feedback, but service-wide changes were not instigated. Perceptions that patients lacked sufficient understanding of the urgent care system in which out-of-hours primary care services operate were common and a barrier to using feedback to enable change. Participants recognised the value of using patient experience feedback to benchmark services, but perceived weaknesses in the out-of-hours items from the GPPS led them to question the validity of using these data for benchmarking in its current form.

Conclusions The lack of clarity around how out-of-hours providers should audit patient experience hinders the utility of the National Quality Requirements. Although surveys were common, patient feedback data had only a limited role in service change. Data derived from the GPPS may be used to benchmark service providers, but refinement of the out-of-hours items is needed.

Visual outcomes of cataract surgery performed by supervised novice surgeons during training in rural China

To assess the outcomes of cataract surgery performed by novice surgeons during training in a rural programme. Design: Retrospective study. Participants: Three hundred thirty-four patients operated by two trainees under supervision at rural Chinese county hospitals. Methods: Two trainees performed surgeries under supervision. Visual acuity, refraction and examinations were carried out 3 months postoperatively. Main Outcome Measures: Postoperative uncorrected visual acuity, pinhole visual acuity, causes of visual impairment (postoperative uncorrected visual acuity<6/18) Results: Among 518 operated patients, 426 (82.2%) could be contacted and 334 (64.4% of operated patients) completed the examinations. The mean age was 74.1±8.8 years and 62.9% were women. Postoperative uncorrected visual acuity was available in 372 eyes. Among them, uncorrected visual acuity was ≥6/18 in 278 eyes (74.7%) and <6/60 in 60 eyes (16.1%), and 323 eyes (86.8%) had pinhole visual acuity≥6/18 and 38 eyes (10.2%) had pinhole visual acuity<6/60. Main causes of visual impairment were uncorrected refractive error (63.9%) and comorbid eye disease (24.5%). Comorbid eye diseases associated with pinhole visual acuity<6/60 (n=23, 6.2%) included glaucoma, other optic nerve atrophy, vitreous haemorrhage and retinal detachment. Conclusions: The findings suggest that hands-on training remains safe and effective even when not implemented in centralized training centres. Further refinement of the training protocol, providing postoperative refractive services and more accurate preoperative intraocular lens calculations, can help optimize outcomes. © 2012 The Authors Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.

Species distribution models reveal apparent competitive and facilitative effects of a dominant species on the distribution of tundra plants

Abiotic factors are considered strong drivers of species distribution and assemblages. Yet these spatial patterns are also influenced by biotic interactions. Accounting for competitors or facilitators may improve both the fit and the predictive power of species distribution models (SDMs). We investigated the influence of a dominant species, Empetrum nigrum ssp. hermaphroditum, on the distribution of 34 subordinate species in the tundra of northern Norway. We related SDM parameters of those subordinate species to their functional traits and their co-occurrence patterns with E. hermaphroditum across three spatial scales. By combining both approaches, we sought to understand whether these species may be limited by competitive interactions and/or benefit from habitat conditions created by the dominant species. The model fit and predictive power increased for most species when the frequency of occurrence of E. hermaphroditum was included in the SDMs as a predictor. The largest increase was found for species that 1) co-occur most of the time with E. hermaphroditum, both at large (i.e. 750 m) and small spatial scale (i.e. 2 m) or co-occur with E. hermaphroditum at large scale but not at small scale and 2) have particularly low or high leaf dry matter content (LDMC). Species that do not co-occur with E. hermaphroditum at the smallest scale are generally palatable herbaceous species with low LDMC, thus showing a weak ability to tolerate resource depletion that is directly or indirectly induced by E. hermaphroditum. Species with high LDMC, showing a better aptitude to face resource depletion and grazing, are often found in the proximity of E. hermaphroditum. Our results are consistent with previous findings that both competition and facilitation structure plant distribution and assemblages in the Arctic tundra. The functional and co-occurrence approaches used were complementary and provided a deeper understanding of the observed patterns by refinement of the pool of potential direct and indirect ecological effects of E. hermaphroditum on the distribution of subordinate species. Our correlative study would benefit being complemented by experimental approaches.

Modularity of auditory spatial representations

Abstract : Auditory spatial functions are of crucial importance in everyday life. Determining the origin of sound sources in space plays a key role in a variety of tasks including orientation of attention, disentangling of complex acoustic patterns reaching our ears in noisy environments. Following brain damage, auditory spatial processing can be disrupted, resulting in severe handicaps. Complaints of patients with sound localization deficits include the inability to locate their crying child or being over-loaded by sounds in crowded public places. Yet, the brain bears a large capacity for reorganization following damage and/or learning. This phenomenon is referred as plasticity and is believed to underlie post-lesional functional recovery as well as learning-induced improvement. The aim of this thesis was to investigate the organization and plasticity of different aspects of auditory spatial functions. Overall, we report the outcomes of three studies: In the study entitled "Learning-induced plasticity in auditory spatial representations" (Spierer et al., 2007b), we focused on the neurophysiological and behavioral changes induced by auditory spatial training in healthy subjects. We found that relatively brief auditory spatial discrimination training improves performance and modifies the cortical representation of the trained sound locations, suggesting that cortical auditory representations of space are dynamic and subject to rapid reorganization. In the same study, we tested the generalization and persistence of training effects over time, as these are two determining factors in the development of neurorehabilitative intervention. In "The path to success in auditory spatial discrimination" (Spierer et al., 2007c), we investigated the neurophysiological correlates of successful spatial discrimination and contribute to the modeling of the anatomo-functional organization of auditory spatial processing in healthy subjects. We showed that discrimination accuracy depends on superior temporal plane (STP) activity in response to the first sound of a pair of stimuli. Our data support a model wherein refinement of spatial representations occurs within the STP and that interactions with parietal structures allow for transformations into coordinate frames that are required for higher-order computations including absolute localization of sound sources. In "Extinction of auditory stimuli in hemineglect: space versus ear" (Spierer et al., 2007a), we investigated auditory attentional deficits in brain-damaged patients. This work provides insight into the auditory neglect syndrome and its relation with neglect symptoms within the visual modality. Apart from contributing to a basic understanding of the cortical mechanisms underlying auditory spatial functions, the outcomes of the studies also contribute to develop neurorehabilitation strategies, which are currently being tested in clinical populations.

Feasibility and clinical outcomes when using practice guidelines for evaluation of fever in returning travelers and migrants : a validation study.

BACKGROUND: Practice guidelines for examining febrile patients presenting upon returning from the tropics were developed to assist primary care physicians in decision making. Because of the low level of evidence available in this field, there was a need to validate them and assess their feasibility in the context they have been designed for. OBJECTIVES: The objectives of the study were to (1) evaluate physicians' adherence to recommendations; (2) investigate reasons for non-adherence; and (3) ensure good clinical outcome of patients, the ultimate goal being to improve the quality of the guidelines, in particular to tailor them for the needs of the target audience and population. METHODS: Physicians consulting the guidelines on the Internet (www.fevertravel.ch) were invited to participate in the study. Navigation through the decision chart was automatically recorded, including diagnostic tests performed, initial and final diagnoses, and clinical outcomes. The reasons for non-adherence were investigated and qualitative feedback was collected. RESULTS: A total of 539 physician/patient pairs were included in this study. Full adherence to guidelines was observed in 29% of the cases. Figure-specific adherence rate was 54.8%. The main reasons for non-adherence were as follows: no repetition of malaria tests (111/352) and no presumptive antibiotic treatment for febrile diarrhea (64/153) or abdominal pain without leukocytosis (46/101). Overall, 20% of diversions from guidelines were considered reasonable because there was an alternative presumptive diagnosis or the symptoms were mild, which means that the corrected adherence rate per case was 40.6% and corrected adherence per figure was 61.7%. No death was recorded and all complications could be attributed to the underlying illness rather than to adherence to guidelines. CONCLUSIONS: These guidelines proved to be feasible, useful, and leading to good clinical outcomes. Almost one third of physicians strictly adhered to the guidelines. Other physicians used the guidelines not to forget specific diagnoses but finally diverged from the proposed attitudes. These diversions should be scrutinized for further refinement of the guidelines to better fit to physician and patient needs.

The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halide molecules /

TITLE: The normal co-ordinate analysis, vibrational spectra and theoretical infrared intensities of some thiocarbonyl halides. AUTHOR: J. L. Brema SUPERVISOR: Dr. D. C. Moule NUMBER OF PAGES: 89 ABSTRACT: The vibrational assignment of the five-in-plane fundamental modes of CSClBr has been made on the basis of infrared gas phase and liquid Raman spectral analyses to supplement our earlier vibrational studies. Even though the one out-of-plane fundamental was not observed spectroscopically an attempt has been made to predict its frequency. The vibrational spectra contained impurity bands and the CSClBr assignment was made only after a thorough analysis of the impurities themselves. A normal co-ordinate analysis calculation was performed assuming a Urey-Bradley force field. This calculation yielded the fundamental frequencies in good agreement with those observed after refinement of the originally transferred force constants. The theoretical frequencies are the eigenvalues of the secular equation and the calculation also gave the corresponding eigenvectors in the form of the very important LLj matrix. The [l] matrix is the transfoirmation between internal co-ordinates and normal co-ordinates and it is essential for Franck-Condon calculations on electronically excited molecules and for infrared Integrated band intensity studies. Using a self-consistent molecular orbital calculation termed "complete neglect of differential overlap" (CNDO/2) , theoretical values of equilibrium bond lengths and angleswere calcuted for a series of carbonyl and thlocarbonyl molecules. From these calculations valence force field force constants were also determined but with limited success. With the CNIX)/2 method theoretical dipole moment derivatives with respect to symmetrized internal co-ordinates were calculated and the results should be useful in a correlation with experimentally determined values.

A classroom-based investigation of reciprocal teaching at the grade seven level

This study assessed the effectiveness of a reciprocal teaching program as a method of teaching reading comprehension, using narrative text material in a t.ypical grade seven classroom. In order to determine the effectiveness of the reciprocal teaching program, this method was compared to two other reading instruction approaches that, unlike rcciprocal teaching, did not include social interaction components. Two intact grade scven classes, and a grade seven teacher, participated in this study. Students were appropriately assigned to three treatment groups by reading achievement level as determined from a norm-referenced test. Training proceeded for a five week intervention period during regularly scheduled English periods. Throughout the program curriculum-based tests were administered. These tests were designed to assess comprehension in two distinct ways; namely, character analysis components as they relate to narrative text, and strategy use components as they contribute to student understanding of narrative and expository text. Pre, post, and maintenance tests were administered to measure overall training effects. Moreover, during intervention, training probes were administered in the last period of each week to evaluate treatment group performance. AU curriculum-based tests were coded and comparisons of pre, post, maintenance tests and training probes were presented in graph form. Results showed that the reciprocal group achieved some improvement in reading comprehension scores in the strategy use component of the tests. No improvements were observed for the character analysis components of the curriculum-based tests and the norm-referenced tests. At pre and post intervention, interviews requiring students to respond to questions that addressed metacomprehension awareness of study strategies were administered. The intelviews were coded and comparisons were made between the two intelVicws. No significant improvements were observed regarding student awareness of ten identified study strategies . This study indicated that reciprocal teaching is a viable approach that can be utilized to help students acquire more effective comprehension strategies. However, the maximum utility of the technique when administered to a population of grade seven students performing at average to above average levels of reading achievement has yet to be determined. In order to explore this issue, the refinement of training materials and curriculum-based measurements need to be explored. As well, this study revealed that reciprocal teaching placed heavier demands on the classroom teacher when compared to other reading instruction methods. This may suggest that innovative and intensive teacher training techniques are required before it is feasible to use this method in the classroom.

Experiential learning instruments : an examination of the concept of the instrumental approach in experiential learning

Experiential Learning Instruments (ELls) are employed to modify the leamer's apprehension and / or comprehension in experiential learning situations, thereby improving the efficiency and effectiveness of those modalities in the learning process. They involve the learner in reciprocally interactive and determining transactions with his/her environment. Experiential Learning Instruments are used to keep experiential learning a process rather than an object. Their use is aimed at the continual refinement of the learner's knowledge and skill. Learning happens as the leamer's awareness, directed by the use of Ells, comes to experience, monitor and then use experiential feedback from living situations in a way that facilitates knmvledge/skill acquisition, self-correction and refinement. The thesis examined the literature relevant to the establishing of a theoretical experiential learning framework within which ELls can be understood. This framework included the concept that some learnings have intrinsic value-knowledge of necessary information-while others have instrumental value-knowledge of how to learn. The Kolb Learning Cycle and Kolb's six characteristics of experiential learning were used in analyzing three ELls from different fields of learning-saxophone tone production, body building and interpersonal communications. The ELls were examined to determine their learning objectives and how they work using experiential learning situations. It was noted that ELls do not transmit information but assist the learner in attending to and comprehending aspects of personal experience. Their function is to telescope the experiential learning process.

Synthesis of unnatural analogues of pancratistatin and narciclasine

Described herein is the chemoenzymatic synthesis of several different types of unnatural analogues of Amaryllidaceae constituents. Development and refinement of existing and design and execution of new approaches towards the synthesis of C-1 analogues of pancratistatin and A-ring heterocyclic analogues of narciclasine are discussed. Evaluation of the new analogues as cancer growth inhibitory agents is also described

Patent pools and competition law : an examination of the enforcement strategies of competition authorities

"Mémoire présenté à la Faculté des études supérieures en vue de l'obtention du grade de maîtrise en droit, option recherche"

Design and Control of an Anthropomorphic Robotic Finger with Multi-point Tactile Sensation

The goal of this research is to develop the prototype of a tactile sensing platform for anthropomorphic manipulation research. We investigate this problem through the fabrication and simple control of a planar 2-DOF robotic finger inspired by anatomic consistency, self-containment, and adaptability. The robot is equipped with a tactile sensor array based on optical transducer technology whereby localized changes in light intensity within an illuminated foam substrate correspond to the distribution and magnitude of forces applied to the sensor surface plane. The integration of tactile perception is a key component in realizing robotic systems which organically interact with the world. Such natural behavior is characterized by compliant performance that can initiate internal, and respond to external, force application in a dynamic environment. However, most of the current manipulators that support some form of haptic feedback either solely derive proprioceptive sensation or only limit tactile sensors to the mechanical fingertips. These constraints are due to the technological challenges involved in high resolution, multi-point tactile perception. In this work, however, we take the opposite approach, emphasizing the role of full-finger tactile feedback in the refinement of manual capabilities. To this end, we propose and implement a control framework for sensorimotor coordination analogous to infant-level grasping and fixturing reflexes. This thesis details the mechanisms used to achieve these sensory, actuation, and control objectives, along with the design philosophies and biological influences behind them. The results of behavioral experiments with a simple tactilely-modulated control scheme are also described. The hope is to integrate the modular finger into an %engineered analog of the human hand with a complete haptic system.

A high-order arbitrarily unstructured finite-volume model of the global atmosphere: tests solving the shallow-water equations

Simulations of the global atmosphere for weather and climate forecasting require fast and accurate solutions and so operational models use high-order finite differences on regular structured grids. This precludes the use of local refinement; techniques allowing local refinement are either expensive (eg. high-order finite element techniques) or have reduced accuracy at changes in resolution (eg. unstructured finite-volume with linear differencing). We present solutions of the shallow-water equations for westerly flow over a mid-latitude mountain from a finite-volume model written using OpenFOAM. A second/third-order accurate differencing scheme is applied on arbitrarily unstructured meshes made up of various shapes and refinement patterns. The results are as accurate as equivalent resolution spectral methods. Using lower order differencing reduces accuracy at a refinement pattern which allows errors from refinement of the mountain to accumulate and reduces the global accuracy over a 15 day simulation. We have therefore introduced a scheme which fits a 2D cubic polynomial approximately on a stencil around each cell. Using this scheme means that refinement of the mountain improves the accuracy after a 15 day simulation. This is a more severe test of local mesh refinement for global simulations than has been presented but a realistic test if these techniques are to be used operationally. These efficient, high-order schemes may make it possible for local mesh refinement to be used by weather and climate forecast models.

Vibrational energy levels of water

Several quartic force fields and a full sextic anharmonic force field for H,O have been determined from high-quality ab initio calculations, the highest at the aug-cc-pVQZ CCSD(T) level of theory. These force fields have been used to determine vibrational excited state band origins up to 15 000 cm - ’ above the zero-point level, using both a perturbation-resonancea pproach and a variational approach. An optimisedq uartic force field hasb eeno btained by least squares refinement of our best ab initio results to fit the observed overtone levels of 5 symmetrically substituted isotopomers of water (Hi60, Hi70, HisO, D,O, and T,O) with an rms error of less than 10 cm-‘, using the perturbation-resonancem odel for the vibrational calculation. Predicatel east squaresr efinement was usedt o provide a loose constraint of the refined force field to the ab initio results. The results obtained prove the viability of the perturbation-resonancem odel for usei n larger molecular systemsa nd also highlight someo f its weaknesse