Data Quality Assessment of Ungated Flow Cytometry Data in High

Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. Methods: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. Results: We found that graphical representations can reveal substantial non-biological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. Conclusions: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.

The role of psychological stress in inflammatory bowel disease: quality assessment of methods of 18 prospective studies and suggestions for future research

BACKGROUND: Enquiries among patients on the one hand and experimental and observational studies on the other suggest an influence of stress on inflammatory bowel diseases (IBD). However, since this influence remains hypothetical, further research is essential. We aimed to devise recommendations for future investigations in IBD by means of scrutinizing previously applied methodology. METHODS: We critically reviewed prospective clinical studies on the effect of psychological stress on IBD. Eligible studies were searched by means of the PubMed electronic library and through checking the bibliographies of located sources. RESULTS: We identified 20 publications resulting from 18 different studies. Sample sizes ranged between 10 and 155 participants. Study designs in terms of patient assessment, control variables, and applied psychometric instruments varied substantially across studies. Methodological strengths and weaknesses were irregularly dispersed. Thirteen studies reported significant relationships between stress and adverse outcomes. CONCLUSIONS: Study designs, including accuracy of outcome assessment and repeated sampling of outcomes (i.e. symptoms, clinical, and endoscopic), depended upon conditions like sample size, participants' compliance, and available resources. Meeting additional criteria of sound methodology, like taking into account covariates of the disease and its course, is strongly recommended to possibly improve study designs in future IBD research.

Image and imaging an emergency department: expense and benefit of different quality assessment methods

Introduction. In this era of high-tech medicine, it is becoming increasingly important to assess patient satisfaction. There are several methods to do so, but these differ greatly in terms of cost, time, and labour and external validity. The aim of this study is to describe and compare the structure and implementation of different methods to assess the satisfaction of patients in an emergency department. Methods. The structure and implementation of the different methods to assess patient satisfaction were evaluated on the basis of a 90-minute standardised interview. Results. We identified a total of six different methods in six different hospitals. The average number of patients assessed was 5012, with a range from 230 (M5) to 20 000 patients (M2). In four methods (M1, M3, M5, and M6), the questionnaire was composed by a specialised external institute. In two methods, the questionnaire was created by the hospital itself (M2, M4).The median response rate was 58.4% (range 9-97.8%). With a reminder, the response rate increased by 60% (M3). Conclusion. The ideal method to assess patient satisfaction in the emergency department setting is to use a patient-based, in-emergency department-based assessment of patient satisfaction, planned and guided by expert personnel.

Quality Assessment and Enhancement Method for high-resolution Fourier-Domain OCT Imaging of Retina Laser Lesions

We present an image quality assessment and enhancement method for high-resolution Fourier-Domain OCT imaging like in sub-threshold retina therapy. A Maximum-Likelihood deconvolution algorithm as well as a histogram-based quality assessment method are evaluated.

Monitoring and data quality assessment of the ATLAS liquid argon calorimeter

The liquid argon calorimeter is a key component of the ATLAS detector installed at the CERN Large Hadron Collider. The primary purpose of this calorimeter is the measurement of electron and photon kinematic properties. It also provides a crucial input for measuring jets and missing transverse momentum. An advanced data monitoring procedure was designed to quickly identify issues that would affect detector performance and ensure that only the best quality data are used for physics analysis. This article presents the validation procedure developed during the 2011 and 2012 LHC data-taking periods, in which more than 98% of the proton-proton luminosity recorded by ATLAS at a centre-of-mass energy of 7–8 TeV had calorimeter data quality suitable for physics analysis.

First international external quality assessment of molecular diagnostics for Mers-CoV

BACKGROUND: Since the discovery of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, diagnostic protocols were quickly published and deployed globally. OBJECTIVES: We set out to assess the quality of MERS-CoV molecular diagnostics worldwide. STUDY DESIGN: Both sensitivity and specificity were assessed using 12 samples containing different viral loads of MERS-CoV or common coronaviruses (OC43, 229E, NL63, HKU1). RESULTS: The panel was sent to more than 106 participants, of which 99 laboratories from 6 continents returned 189 panel results.Scores ranged from 100% (84 laboratories) to 33% (1 laboratory). 15% of respondents reported quantitative results, 61% semi-quantitative (Ct-values or time to positivity) and 24% reported qualitative results. The major specific technique used was real-time RT-PCR using the WHO recommended targets upE, ORF1a and ORF1b. The evaluation confirmed that RT-PCRs targeting the ORF1b are less sensitive, and therefore not advised for primary diagnostics. CONCLUSIONS: The first external quality assessment MERS-CoV panel gives a good insight in molecular diagnostic techniques and their performances for sensitive and specific detection of MERS-CoV RNA globally. Overall, all laboratories were capable of detecting MERS-CoV with some differences in sensitivity. The observation that 8% of laboratories reported false MERS-CoV positive single assay results shows room for improvement, and the importance of using confirmatory targets.

Use of quality assessment tools in systematic reviews was varied and inconsistent

OBJECTIVES To assess the use of quality assessment tools among a cross-section of systematic reviews (SRs) and to further evaluate whether quality was used as a parameter in the decision to include primary studies within subsequent meta-analysis. STUDY DESIGN AND SETTING We searched PubMed for SRs (interventional, observational, and diagnostic) published in Core Clinical Journals between January 1 and March 31, 2014. RESULTS Three hundred nine SRs were identified. Quality assessment was undertaken in 222 (71.8%) with isolated use of the Cochrane risk of bias tool (26.1%, n = 58) and the Newcastle-Ottawa Scale (15.3%, n = 34) most common. A threshold level of primary study quality for subsequent meta-analysis was used in 12.9% (40 of 309) of reviews. Overall, fifty-four combinations of quality assessment tools were identified with a similar preponderance of tools used among observational and interventional reviews. Multiple tools were used in 11.7% (n = 36) of SRs overall. CONCLUSION We found that quality assessment tools were used in a majority of SRs; however, a threshold level of quality for meta-analysis was stipulated in just 12.9% (n = 40). This cross-sectional analysis provides further evidence of the need for more active or intuitive editorial processes to enhance the reporting of SRs.

Quality assessment in radiation oncology

Oncologic specialty societies and multidisciplinary collaborative groups have dedicated considerable effort to developing evidence-based quality indicators (QIs) to facilitate quality improvement, accreditation, benchmarking, reimbursement, maintenance of certification, and regulatory reporting. In particular, radiation oncology as a field has a long history of organized quality assessment efforts, and continues to work toward developing consensus quality standards in the face of continually evolving technologies and standards of care. The present report provides a comprehensive review of the current state of quality assessment in radiation oncology, with an emphasis on recent quality improvement efforts. Specifically, this report aims to highlight implications of the healthcare quality movement for radiation oncology and review existing efforts to define and measure quality in the field, with particular focus on dimensions of quality that are specific to radiation oncology within the "big picture" of oncologic quality improvement efforts.^

Quality assessment by region in spot images fused by means dual-tree complex wavelet transform

This work is motivated in providing and evaluating a fusion algorithm of remotely sensed images, i.e. the fusion of a high spatial resolution panchromatic image with a multi-spectral image (also known as pansharpening) using the dual-tree complex wavelet transform (DT-CWT), an effective approach for conducting an analytic and oversampled wavelet transform to reduce aliasing, and in turn reduce shift dependence of the wavelet transform. The proposed scheme includes the definition of a model to establish how information will be extracted from the PAN band and how that information will be injected into the MS bands with low spatial resolution. The approach was applied to Spot 5 images where there are bands falling outside PAN’s spectrum. We propose an optional step in the quality evaluation protocol, which is to study the quality of the merger by regions, where each region represents a specific feature of the image. The results show that DT-CWT based approach offers good spatial quality while retaining the spectral information of original images, case SPOT 5. The additional step facilitates the identification of the most affected regions by the fusion process.

Using Provenance for Quality Assessment and Repair in Linked Open Data

As the number of data sources publishing their data on the Web of Data is growing, we are experiencing an immense growth of the Linked Open Data cloud. The lack of control on the published sources, which could be untrustworthy or unreliable, along with their dynamic nature that often invalidates links and causes conflicts or other discrepancies, could lead to poor quality data. In order to judge data quality, a number of quality indicators have been proposed, coupled with quality metrics that quantify the “quality level” of a dataset. In addition to the above, some approaches address how to improve the quality of the datasets through a repair process that focuses on how to correct invalidities caused by constraint violations by either removing or adding triples. In this paper we argue that provenance is a critical factor that should be taken into account during repairs to ensure that the most reliable data is kept. Based on this idea, we propose quality metrics that take into account provenance and evaluate their applicability as repair guidelines in a particular data fusion setting.

High definition video quality assessment metric built upon full reference ratios

Métrica de calidad de video de alta definición construida a partir de ratios de referencia completa. La medida de calidad de video, en inglés Visual Quality Assessment (VQA), es uno de los mayores retos por solucionar en el entorno multimedia. La calidad de vídeo tiene un impacto altísimo en la percepción del usuario final (consumidor) de los servicios sustentados en la provisión de contenidos multimedia y, por tanto, factor clave en la valoración del nuevo paradigma denominado Calidad de la Experiencia, en inglés Quality of Experience (QoE). Los modelos de medida de calidad de vídeo se pueden agrupar en varias ramas según la base técnica que sustenta el sistema de medida, destacando en importancia los que emplean modelos psicovisuales orientados a reproducir las características del sistema visual humano, en inglés Human Visual System, del que toman sus siglas HVS, y los que, por el contrario, optan por una aproximación ingenieril en la que el cálculo de calidad está basado en la extracción de parámetros intrínsecos de la imagen y su comparación. A pesar de los avances recogidos en este campo en los últimos años, la investigación en métricas de calidad de vídeo, tanto en presencia de referencia (los modelos denominados de referencia completa), como en presencia de parte de ella (modelos de referencia reducida) e incluso los que trabajan en ausencia de la misma (denominados sin referencia), tiene un amplio camino de mejora y objetivos por alcanzar. Dentro de ellos, la medida de señales de alta definición, especialmente las utilizadas en las primeras etapas de la cadena de valor que son de muy alta calidad, son de especial interés por su influencia en la calidad final del servicio y no existen modelos fiables de medida en la actualidad. Esta tesis doctoral presenta un modelo de medida de calidad de referencia completa que hemos llamado PARMENIA (PArallel Ratios MEtric from iNtrInsic features Analysis), basado en la ponderación de cuatro ratios de calidad calculados a partir de características intrínsecas de la imagen. Son: El Ratio de Fidelidad, calculado mediante el gradiente morfológico o gradiente de Beucher. El Ratio de Similitud Visual, calculado mediante los puntos visualmente significativos de la imagen a través de filtrados locales de contraste. El Ratio de Nitidez, que procede de la extracción del estadístico de textura de Haralick contraste. El Ratio de Complejidad, obtenido de la definición de homogeneidad del conjunto de estadísticos de textura de Haralick PARMENIA presenta como novedad la utilización de la morfología matemática y estadísticos de Haralick como base de una métrica de medida de calidad, pues esas técnicas han estado tradicionalmente más ligadas a la teledetección y la segmentación de objetos. Además, la aproximación de la métrica como un conjunto ponderado de ratios es igualmente novedosa debido a que se alimenta de modelos de similitud estructural y otros más clásicos, basados en la perceptibilidad del error generado por la degradación de la señal asociada a la compresión. PARMENIA presenta resultados con una altísima correlación con las valoraciones MOS procedentes de las pruebas subjetivas a usuarios que se han realizado para la validación de la misma. El corpus de trabajo seleccionado procede de conjuntos de secuencias validados internacionalmente, de modo que los resultados aportados sean de la máxima calidad y el máximo rigor posible. La metodología de trabajo seguida ha consistido en la generación de un conjunto de secuencias de prueba de distintas calidades a través de la codificación con distintos escalones de cuantificación, la obtención de las valoraciones subjetivas de las mismas a través de pruebas subjetivas de calidad (basadas en la recomendación de la Unión Internacional de Telecomunicaciones BT.500), y la validación mediante el cálculo de la correlación de PARMENIA con estos valores subjetivos, cuantificada a través del coeficiente de correlación de Pearson. Una vez realizada la validación de los ratios y optimizada su influencia en la medida final y su alta correlación con la percepción, se ha realizado una segunda revisión sobre secuencias del hdtv test dataset 1 del Grupo de Expertos de Calidad de Vídeo (VQEG, Video Quality Expert Group) mostrando los resultados obtenidos sus claras ventajas. Abstract Visual Quality Assessment has been so far one of the most intriguing challenges on the media environment. Progressive evolution towards higher resolutions while increasing the quality needed (e.g. high definition and better image quality) aims to redefine models for quality measuring. Given the growing interest in multimedia services delivery, perceptual quality measurement has become a very active area of research. First, in this work, a classification of objective video quality metrics based on their underlying methodologies and approaches for measuring video quality has been introduced to sum up the state of the art. Then, this doctoral thesis describes an enhanced solution for full reference objective quality measurement based on mathematical morphology, texture features and visual similarity information that provides a normalized metric that we have called PARMENIA (PArallel Ratios MEtric from iNtrInsic features Analysis), with a high correlated MOS score. The PARMENIA metric is based on the pooling of different quality ratios that are obtained from three different approaches: Beucher’s gradient, local contrast filtering, and contrast and homogeneity Haralick’s texture features. The metric performance is excellent, and improves the current state of the art by providing a wide dynamic range that make easier to discriminate between very close quality coded sequences, especially for very high bit rates whose quality, currently, is transparent for quality metrics. PARMENIA introduces a degree of novelty against other working metrics: on the one hand, exploits the structural information variation to build the metric’s kernel, but complements the measure with texture information and a ratio of visual meaningful points that is closer to typical error sensitivity based approaches. We would like to point out that PARMENIA approach is the only metric built upon full reference ratios, and using mathematical morphology and texture features (typically used in segmentation) for quality assessment. On the other hand, it gets results with a wide dynamic range that allows measuring the quality of high definition sequences from bit rates of hundreds of Megabits (Mbps) down to typical distribution rates (5-6 Mbps), even streaming rates (1- 2 Mbps). Thus, a direct correlation between PARMENIA and MOS scores are easily constructed. PARMENIA may further enhance the number of available choices in objective quality measurement, especially for very high quality HD materials. All this results come from validation that has been achieved through internationally validated datasets on which subjective tests based on ITU-T BT.500 methodology have been carried out. Pearson correlation coefficient has been calculated to verify the accuracy of PARMENIA and its reliability.

Automatic 3DTV Quality Assessment Based On Depth Perception Analysis

Quality assessment is a key factor for stereoscopic 3D video content as some observers are affected by visual discomfort in the eye when viewing 3D video, especially when combining positive and negative parallax with fast motion. In this paper, we propose techniques to assess objective quality related to motion and depth maps, which facilitate depth perception analysis. Subjective tests were carried out in order to understand the source of the problem. Motion is an important feature affecting 3D experience but also often the cause of visual discomfort. The automatic algorithm developed tries to quantify the impact on viewer experience when common cases of discomfort occur, such as high-motion sequences, scene changes with abrupt parallax changes, or complete absence of stereoscopy, with a goal of preventing the viewer from having a bad stereoscopic experience.

A quality assessment system for fresh fruits in hypermarkets and fruit trading centres.

When the fresh fruit reaches the final markets from the suppliers, its quality is not always as good as it should, either because it has been mishandled during transportation or because it lacks an adequate quality control at the producer level, before being shipped. This is why it is necessary for the final markets to establish their own quality assessment system if they want to ensure to their customers the quality they want to sell. In this work, a system to control fruit quality at the last level of the distribution channel has been designed. The system combines rapid control techniques with laboratory equipment and statistical sampling protocols, to obtain a dynamic, objective process, which can substitute advantageously the quality control inspections carried out visually by human experts at the reception platform of most hypermarkets. Portable measuring equipment have been chosen (firmness tester, temperature and humidity sensors...) as well as easy-to-use laboratory equipment (texturometer, colorimeter, refractometer..,) combining them to control the most important fruit quality parameters (firmness, colour, sugars, acids). A complete computer network has been designed to control all the processes and store the collected data in real time, and to perform the computations. The sampling methods have been also defined to guarantee the confidence of the results. Some of the advantages of a quality assessment system as the proposed one are: the minimisation of human subjectivity, the ability to use modern measuring techniques, and the possibility of using it also as a supplier's quality control system. It can be also a way to clarify the quality limits of fruits among members of the commercial channel, as well as the first step in the standardisation of quality control procedures.

Storabelity of melon for different ripeness stages at harvest. Selection of instrumental procedures for quality assessment.

The consumption of melon (Cucumis melo L.) has been, until several years ago, regional, seasonal and without commercial interest. Recent commercial changes and world wide transportation have changed this situation. Melons from 3 different ripeness stages at harvest and 7 cold storage periods have been analysed by destructive and non destructive tests. Chemical, physical, mechanical (non destructive impact, compression, skin puncture and Magness- Taylor) and sensory tests were carried out in order to select the best test to assess quality and to determine the optimal ripeness stage at harvest. Analysis of variance and Principal Component Analysis were performed to study the data. The mechanical properties based on non-destructive Impact and Compression can be used to monitor cold storage evolution. They can also be used at harvest to segregate the highest ripeness stage (41 days after anthesis DAA) in relation to less ripe stages (34 and 28 DAA).Only 34 and 41 DAA reach a sensory evaluation above 50 in a scale from 0-100.