Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

The impact of rehabilitation support services on health-related quality of life for women with breast cancer

As the number of women surviving breast cancer increases, with implications for the health system, research into the physical and psychosocial sequelae of the cancer and its treatment is a priority. This research estimated self-reported health-related quality of life (HRQoL) associated with two rehabilitation interventions for breast cancer survivors, compared to a non-intervention group. Women were selected if they received an early home-based physiotherapy intervention (DAART, n = 36) or a group-based exercise and psychosocial intervention (STRETCH, n = 31). Questionnaires on HRQoL, using the Functional Assessment of Cancer Therapy - Breast Cancer plus Arm Morbidity module, were administered at pre-, post-intervention, 6- and 12-months post-diagnosis. Data on a non-intervention group (n = 208) were available 6- and 12-months post-diagnosis. Comparing pre/post-intervention measures, benefits were evident for functional well-being, including reductions in arm morbidity and upper-body disability for participants completing the DAART service at one-to-two months following diagnosis. In contrast, minimal changes were observed between pre/post-intervention measures for the STRETCH group at approximately 4-months post-diagnosis. Overall, mean HRQoL scores (adjusted for age, chemotherapy, hormone therapy, high blood pressure and occupation type) improved gradually across all groups from 6- to 12-months post-diagnosis, and no prominent differences were found. However, this obscured declining HRQoL scores for 20-40% of women at 12 months post-diagnosis, despite receiving supportive care services. Greater awareness and screening for adjustment problems among breast cancer survivors is required throughout the disease trajectory. Early physiotherapy after surgery has the potential for short-term functional, physical and overall HRQoL benefits.

Meaning-based quality-of-life measurement: A way forward in conceptualizing and measuring client outcomes?

Despite current imperatives to measure client outcomes, social workers have expressed frustration with the ability of traditional forms of quantitative methods to engage with complexity, individuality and meaning. This paper argues that the inclusion of a meaning-based as opposed to a function-based approach to quality of life (QOL) may offer a quantitative means of measurement that is congruent with social-work values and practice.

Quality-of-life in children and adolescents with cystic fibrosis managed in both regional outreach and cystic fibrosis center settings in Queensland

To assess the health-related quality-of-life (HRQOL) of children/adolescents with cystic fibrosis (CF) and compare HRQOL in children managed by cystic fibrosis outreach service (CFOS) with those treated in a cystic fibrosis center (CFC). To compare HRQOL of children with CF in Queensland with previously published HRQOL data from the United States and examine the relationship between HRQOL scores and pulmonary function. Study design: Participants were children/adolescents with CF and their parents managed by the Royal Children’s Hospital Queensland at a CFC or CFOS. Two HRQOL surveys were used: PedsQL™ and Cystic Fibrosis Questionnaire (CFQ). Results: There were 91 CFC and 71 CFOS participants with similar demographics. PedsQL™ total summary score was statistically higher in CFOS, P = .05. There was no significant difference in CFQ scores between groups. Queensland parents reported lower HRQOL for their children compared with US parents (P

Correlation between visual function and visual ability in patients with uveitis

Aim: To investigate the correlation between tests of visual function and perceived visual ability recorded with a quality of life questionnaire for patients with uveitis. Methods: 132 patients with various types of uveitis were studied. High (monocular and binocular) and low (binocular) contrast logMAR letter acuities were recorded using a Bailey-Lovie chart. Contrast sensitivity (binocular) was determined using a Pelli-Robson chart. Vision related quality of life was assessed using the Vision Specific Quality of Life (VQOL) questionnaire. Results: VQOL declined with reduced performance on the following tests: binocular high contrast visual acuity (p = 0.0011), high contrast visual acuity of the better eye (p = 0.0012), contrast sensitivity (p = 0.005), binocular low contrast visual acuity (p = 0.0065), and high contrast visual acuity of the worse eye (p = 0.015). Stepwise multiple regression analysis revealed binocular high contrast visual acuity (p <0.01) to be the only visual function adequate to predict VQOL. The age of the patient was also significantly associated with perceived visual ability (p <0.001). Conclusions: Binocular high contrast visual acuity is a good measure of how uveitis patients perform in real life situations. Vision quality of life is worst in younger patients with poor binocular visual acuity.

The correlation between tests of visual function and perceived visual ability in central field loss patients

Purpose: To investigate the correlation between tests of visual function and perceived visual ability recorded with a 'quality-of-life' questionnaire for patients with central field loss. Method: 12 females and 7 males (mean age = 53.1 years; Range = 23 - 80 years) with subfoveal neovascular membranes underwent a comprehensive assessment of visual function. Tests included unaided distance vision, high and low contrast distance logMAR visual acuity (VA), Pelli-Robson contrast senstivity (at 1m), near logMAR word VA and text reading speed. All tests were done both monocularly and binocularly. The patients also completed a 28 point questionnaire separated into a 'core' section consisting of general questions about perceived visual function and a 'module' section with specific questions on reading function. Results: Step-wise multiple regression analysis was used to determine which visual function tests were correlated with the patients's perceived visual function and to rank them in order of importance. The visual function test that explains most of the variance in both 'core' score (66%0 and the 'module' score (68%) of the questionnaire is low contrast VA in the better eye (P<0.001 in both cases). Further, the module score also accounts for a significant proportion of the variance (P<0.01) of the distance logMAR VA in both the better and worse eye, and the near logMAR in both the better eye and binocularly. Conclusions: The best predictor of both perceived reading ability and of general perceived visual ability in this study is low contrast logMAR VA. The results highlight that distance VA is not the only relevant measure of visual fucntion in relation to a patients's perceived visual performance and should not be considered a determinant of surgical or management success.

Quality performance rating

This Thesis reports on the principles and usefulness of Performance Rating as developed by the writer over a number of years. In Part one a brief analysis is made of the Quality scene and its development up to the present. The need is exposed for Performance Rating as a tool for all areas of management*. At the same time a system of Quality Control is described which the writer has further developed under the title of 'Operator Control'. This system is based on the integration of all Quality control functions with the creative functions required for Quality achievement. The discussions are mainly focussed on the general philosophy of Quality, its creation and control and that part of Operator Control which affects Performance Rating. Whereas it is shown that the combination of Operator Control and Performance Rating is both economically and technically advantageous, Performance Rating can also usefully be applied under inspection control conditions. Part two describes the principles of Area Performance Rating. *The need for, and the advantages of, Performance Rating are particularly demonstrated in Case study No.1. From this a summation expression is derived which gives the key for grouping of areas with similar Performance Rating (P). A model is devised on which the theory is demonstrated. Relevant case studies, carried out in practice in factories are quoted in Part two, Chapter 4, one written by the Quality manager of that particular factory. Particular stress is laid in the final conclusions on management's function in the Quality field and how greatly this function is eased and improved through the introduction of Area Performance Rating.

An investigation of reading ability and visual function with eccentric visual field

This study investigated the detrimental effect of central field loss (CFL) on reading ability and general visual function. The aim was to improve the understanding of reading with eccentric retina in order that reading performances of individuals with CFL may be maximised. To improve visual ability of individuals with CFL, it is important to be able to accurately measure the outcome of any intervention. Various methods for determining visual function were therefore compared with perceived visual performance (as measured with a quality of life questionnaire) before and after surgical removal of choroidal new vessels (CNV) in macular disease patients. The results highlight the importance of low contrast measures (low contrast visual acuity and contrast sensitivity) when investigating perceived reading performance. Reading speed was found to be important for reflecting changes in general visual quality of life. Potential causes for reduced peripheral reading ability were investigated using both normally sighted and CFL subjects. For normally sighted subjects reading eccentrically with rapid serial visual presentation (RSVP) text, the inferior visual field was a better position (in terms of reading speed) for the presentation of the text. The size of the visual span was found to reduce with increasing eccentricity of fixation, providing a potential reason for reduced peripheral reading performances. The investigation of the ability to use context when reading with peripheral retina resulted in conflicting results. Studies in this thesis found both a reduction and no reduction in the ability of the peripheral retina to utilise context compared to the fovea. Individuals with long-term CFL showed no improvement in peripheral reading ability over that found for normally sighted subjects reading at the same eccentricity.

Fabrication of high quality optical coherence tomography (OCT) calibration artefacts using femtosecond inscription

Optical coherence tomography (OCT) is a non-invasive three-dimensional imaging system that is capable of producing high resolution in-vivo images. OCT is approved for use in clinical trials in Japan, USA and Europe. For OCT to be used effectively in a clinical diagnosis, a method of standardisation is required to assess the performance across different systems. This standardisation can be implemented using highly accurate and reproducible artefacts for calibration at both installation and throughout the lifetime of a system. Femtosecond lasers can write highly reproducible and highly localised micro-structured calibration artefacts within a transparent media. We report on the fabrication of high quality OCT calibration artefacts in fused silica using a femtosecond laser. The calibration artefacts were written in fused silica due to its high purity and ability to withstand high energy femtosecond pulses. An Amplitude Systemes s-Pulse Yb:YAG femtosecond laser with an operating wavelength of 1026 nm was used to inscribe three dimensional patterns within the highly optically transmissive substrate. Four unique artefacts have been designed to measure a wide variety of parameters, including the points spread function (PSF), modulation transfer function (MTF), sensitivity, distortion and resolution - key parameters which define the performance of the OCT. The calibration artefacts have been characterised using an optical microscope and tested on a swept source OCT. The results demonstrate that the femtosecond laser inscribed artefacts have the potential of quantitatively and qualitatively validating the performance of any OCT system.

The impact of privatisation and regulation on the water and sewerage industry in England and Wales:a translog cost function approach

After the ten Regional Water Authorities (RWAs) of England and Wales were privatized in November 1989, the successor Water and Sewerage Companies (WASCs) faced a new regulatory regime that was designed to promote economic efficiency while simultaneously improving drinking water and environmental quality. As legally mandated quality improvements necessitated a costly capital investment programme, the industry's economic regulator, the Office of Water Services (Ofwat), implemented a retail price index (RPI)+K pricing system, which was designed to compensate the WASCs for their capital investment programme while also encouraging gains in economic efficiency. In order to analyse jointly the impact of privatization, as well as the impact of increasingly stringent economic and environmental regulation on the WASCs' economic performance, this paper estimates a translog multiple output cost function model for the period 1985–1999. Given the significant costs associated with water quality improvements, the model is augmented to include the impact of drinking water quality and environmental quality on total costs. The model is then employed to determine the extent of scale and scope economies in the water and sewerage industry, as well as the impact of privatization and economic regulation on economic efficiency.

GEO Label – quality information interrogation tool for geospatial datasets:towards effective visualization of quality metadata

Although the importance of dataset fitness-for-use evaluation and intercomparison is widely recognised within the GIS community, no practical tools have yet been developed to support such interrogation. GeoViQua aims to develop a GEO label which will visually summarise and allow interrogation of key informational aspects of geospatial datasets upon which users rely when selecting datasets for use. The proposed GEO label will be integrated in the Global Earth Observation System of Systems (GEOSS) and will be used as a value and trust indicator for datasets accessible through the GEO Portal. As envisioned, the GEO label will act as a decision support mechanism for dataset selection and thereby hopefully improve user recognition of the quality of datasets. To date we have conducted 3 user studies to (1) identify the informational aspects of geospatial datasets upon which users rely when assessing dataset quality and trustworthiness, (2) elicit initial user views on a GEO label and its potential role and (3), evaluate prototype label visualisations. Our first study revealed that, when evaluating quality of data, users consider 8 facets: dataset producer information; producer comments on dataset quality; dataset compliance with international standards; community advice; dataset ratings; links to dataset citations; expert value judgements; and quantitative quality information. Our second study confirmed the relevance of these facets in terms of the community-perceived function that a GEO label should fulfil: users and producers of geospatial data supported the concept of a GEO label that provides a drill-down interrogation facility covering all 8 informational aspects. Consequently, we developed three prototype label visualisations and evaluated their comparative effectiveness and user preference via a third user study to arrive at a final graphical GEO label representation. When integrated in the GEOSS, an individual GEO label will be provided for each dataset in the GEOSS clearinghouse (or other data portals and clearinghouses) based on its available quality information. Producer and feedback metadata documents are being used to dynamically assess information availability and generate the GEO labels. The producer metadata document can either be a standard ISO compliant metadata record supplied with the dataset, or an extended version of a GeoViQua-derived metadata record, and is used to assess the availability of a producer profile, producer comments, compliance with standards, citations and quantitative quality information. GeoViQua is also currently developing a feedback server to collect and encode (as metadata records) user and producer feedback on datasets; these metadata records will be used to assess the availability of user comments, ratings, expert reviews and user-supplied citations for a dataset. The GEO label will provide drill-down functionality which will allow a user to navigate to a GEO label page offering detailed quality information for its associated dataset. At this stage, we are developing the GEO label service that will be used to provide GEO labels on demand based on supplied metadata records. In this presentation, we will provide a comprehensive overview of the GEO label development process, with specific emphasis on the GEO label implementation and integration into the GEOSS.

Effect of medications with anti-cholinergic properties on cognitive function, delirium, physical function and mortality:a systematic review

Objectives: to determine the effect of drugs with anti-cholinergic properties on relevant health outcomes.Design: electronic published and unpublished literature/trial registries were systematically reviewed. Studies evaluating medications with anti-cholinergic activity on cognitive function, delirium, physical function or mortality were eligible.Results: forty-six studies including 60,944 participants were included. Seventy-seven percent of included studies evaluating cognitive function (n = 33) reported a significant decline in cognitive ability with increasing anti-cholinergic load (P < 0.05). Four of five included studies reported no association with delirium and increasing anti-cholinergic drug load (P > 0.05). Five of the eight included studies reported a decline in physical function in users of anti-cholinergics (P < 0.05). Three of nine studies evaluating mortality reported that the use of drugs with anti-cholinergic properties was associated with a trend towards increased mortality, but this was not statistically significant. The methodological quality of the evidence-base ranged from poor to very good.Conclusion: medicines with anti-cholinergic properties have a significant adverse effect on cognitive and physical function, but limited evidence exists for delirium or mortality outcomes. © The Author 2014. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved.

Dimensioning of Telecommunication Network Based on Quality of Services Demand and Detailed Behaviour of Users

The aim of this paper is to be determined the network capacity (number of necessary internal switching lines) based on detailed users’ behaviour and demanded quality of service parameters in an overall telecommunication system. We consider detailed conceptual and its corresponded analytical traffic model of telecommunication system with (virtual) circuit switching, in stationary state with generalized input flow, repeated calls, limited number of homogeneous terminals and losses due to abandoned and interrupted dialing, blocked and interrupted switching, not available intent terminal, blocked and abandoned ringing (absent called user) and abandoned conversation. We propose an analytical - numerical solution for finding the number of internal switching lines and values of the some basic traffic parameters as a function of telecommunication system state. These parameters are requisite for maintenance demand level of network quality of service (QoS). Dependencies, based on the numericalanalytical results are shown graphically. For proposed conceptual and its corresponding analytical model a network dimensioning task (NDT) is formulated, solvability of the NDT and the necessary conditions for analytical solution are researched as well. It is proposed a rule (algorithm) and computer program for calculation of the corresponded number of the internal switching lines, as well as corresponded values of traffic parameters, making the management of QoS easily.

On the Quality of Decision Functions in Pattern Recognition

The problem of decision functions quality in pattern recognition is considered. An overview of the approaches to the solution of this problem is given. Within the Bayesian framework, we suggest an approach based on the Bayesian interval estimates of quality on a finite set of events.

Optical quality for keratoconic eyes with conventional RGP lens and simulated, customised contact lens corrections:a comparison

Purpose: To compare monochromatic aberrations of keratoconic eyes when uncorrected, corrected with spherically-powered RGP (rigid gas-permeable) contact lenses and corrected using simulations of customised soft contact lenses for different magnitudes of rotation (up to 15°) and translation (up to 1mm) from their ideal position. Methods: The ocular aberrations of examples of mild, moderate and severe keratoconic eyes were measured when uncorrected and when wearing their habitual RGP lenses. Residual aberrations and point-spread functions of each eye were simulated using an ideal, customised soft contact lens (designed to neutralise higher-order aberrations, HOA) were calculated as a function of the angle of rotation of the lens from its ideal orientation, and its horizontal and vertical translation. Results: In agreement with the results of other authors, the RGP lenses markedly reduced both lower-order aberrations and HOA for all three patients. When compared with the RGP lens corrections, the customised lens simulations only provided optical improvements if their movements were constrained within limits which appear to be difficult to achieve with current technologies. Conclusions: At the present time, customised contact lens corrections appear likely to offer, at best, only minor optical improvements over RGP lenses for patients with keratoconus. If made in soft materials, however, these lenses may be preferred by patients in term of comfort. © 2012 The College of Optometrists.