JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

Development of a new tool for assessing health-related quality of life in patients with primary hyperparathyroidism.

BACKGROUND Several studies in recent years have evaluated Health Related Quality of Life (HRQoL) of patients with primary hyperparathyroidism (PHPT). No disease specific questionnaires are available to assess the impact of the disease. The aim of this research is to describe the development of a new disease specific Quality of Life (QoL) questionnaire for use specifically with PHPT patients. METHODS A conceptual model was developed describing the impact of the disease and its symptoms on QoL domains. A literature review was conducted to identify the most relevant domains. A focus group with experts was used to validate the domains; 24 patients were also interviewed to complement the information from the patient's perspective. A content analysis of the interviews was performed to identify items related with the impact of the disease, leading to PHPQoL-V.1 which was presented to a sample of 67 patients. Reliability was assessed by Cronbach's coefficient alpha and item-total score correlations. Validity was assessed by a factor analysis performed to determine the number of domains. Rasch analysis was carried out in order to refine the questionnaire items. RESULTS 259 items were extracted from the interviews that were subsequently reduced to 34 items. Cronbach's coefficient alpha was 0.92. The factor analysis extracted two domains (physical and emotional). After Rasch analysis the questionnaire PHPQoL-V.2 kept 16 items (9 physical and 7 emotional). The questionnaire was developed in a Spanish population and the final version was translated to English through translation and back-translation. CONCLUSION The first disease specific HRQoL questionnaire for PHPT patients (PHPQoL-16) has been developed. Validation studies designed to assess measurement properties of this tool are currently underway.

Quality of life after pulmonary embolism: validation of the French version of the PEmb-QoL questionnaire.

Background The PEmb-QoL is a validated 40-item questionnaire to quantify health-related quality of life in patients having experienced pulmonary embolism (PE). It covers six health dimensions: frequency of complaints, activities of daily living limitations, work-related problems, social limitations, intensity of complaints, and emotional complaints. Originally developed in Dutch and English, we sought to prospectively validate the psychometric properties of a French version of the PEmb-QoL.MethodsWe performed a forward and backward translation of the English version of the PEmb-QoL into French. French-speaking consecutive adult patients with an acute, objectively confirmed PE admitted to the emergency department of a Swiss university hospital between 08/2009 and 09/2011 were recruited telephonically. We used standard psychometric tests and criteria to evaluate the acceptability, reliability, and validity of the French version of the PEmb-QoL. We also performed an exploratory factor analysis.ResultsOverall, 102 patients were enrolled in the study. The French version of the PEmb-QoL showed good reliability (internal consistency, item¿total and inter-item correlations), reproducibility (test-retest reliability), and validity (convergent, discriminant) in French-speaking patients with PE. The exploratory factor analysis suggested three underlying dimensions: limitations in daily activity (items 4b-m, 5a-d), symptoms (items 1a-h and 7), and emotional complaints (items 9a-f and j).ConclusionWe successfully validated the French version of the PEmb-QoL questionnaire in patients with PE. Our results show that the PEmb-QoL is a valuable tool for assessing health-related quality of life after PE in French-speaking patients.

Validation of the Mini Nutritional Assessment short-form (MNA-SF): a practical tool for identification of nutritional status.

OBJECTIVE: To validate a revision of the Mini Nutritional Assessment short-form (MNA(R)-SF) against the full MNA, a standard tool for nutritional evaluation. METHODS: A literature search identified studies that used the MNA for nutritional screening in geriatric patients. The contacted authors submitted original datasets that were merged into a single database. Various combinations of the questions on the current MNA-SF were tested using this database through combination analysis and ROC based derivation of classification thresholds. RESULTS: Twenty-seven datasets (n=6257 participants) were initially processed from which twelve were used in the current analysis on a sample of 2032 study participants (mean age 82.3y) with complete information on all MNA items. The original MNA-SF was a combination of six questions from the full MNA. A revised MNA-SF included calf circumference (CC) substituted for BMI performed equally well. A revised three-category scoring classification for this revised MNA-SF, using BMI and/or CC, had good sensitivity compared to the full MNA. CONCLUSION: The newly revised MNA-SF is a valid nutritional screening tool applicable to geriatric health care professionals with the option of using CC when BMI cannot be calculated. This revised MNA-SF increases the applicability of this rapid screening tool in clinical practice through the inclusion of a "malnourished" category.

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.

SUMMARY: We present a tool designed for visualization of large-scale genetic and genomic data exemplified by results from genome-wide association studies. This software provides an integrated framework to facilitate the interpretation of SNP association studies in genomic context. Gene annotations can be retrieved from Ensembl, linkage disequilibrium data downloaded from HapMap and custom data imported in BED or WIG format. AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets. AVAILABILITY: The Java code for AssociationViewer is distributed under the GNU General Public Licence and has been tested on Microsoft Windows XP, MacOSX and GNU/Linux operating systems. It is available from the SourceForge repository. This also includes Java webstart, documentation and example datafiles.

Evaluation de la satisfaction des infirmiers(-ères): développement et validation d'un nouvel outil d'analyse [Evaluation of satisfaction of nurses: development and validation of a new analysis tool]

A new device for the analyses of nurses' satisfaction has been developed and validated on two types of general and intensive treatments at the University Hospital in Vaudois, Switzerland. A questionnaire has been elaborated for identifying the variables linked with characteristics of the nurse's work, as well as personal variables of the employer which could have an influence on the level of satisfaction. In identifying the sources of satisfaction and dissatisfaction, it has been possible to propose recommendations and corrective measures in order to improve the level of global satisfaction of the nursing team.

Translation and validation of the Ten-Item-Personality Inventory into spanish and catalan

In response to an increasing need for ever-shorter personality instruments, Gosling, Rentfrow, and Swann (2003) developed the Ten-Item-Personality Inventory (TIPI), which measures the dimensions of the Five Factor Model (FFM) using 10 items (two for each dimension) and can be administered in about one minute. In two studies and using a multi-judge (self and observer) and multi-instrument design, we develop Spanish (Castilian) and Catalan versions of the TIPI and evaluate them in terms of internal consistency, test-retest reliability, convergent, discriminant, and content validity, as well as self-observer correlations. Test-retest correlations were strong, and convergence with the NEO-PI-R factors was significant. There were also strong correlations between observer ratings and the participants’ self-ratings. Despite some inconsistencies with respect to the Agreeableness scale, the Catalan translation and both translations into Spanish of the original TIPI demonstrated sufficient psychometric properties to warrant use as a Five Factor personality measure when the use of longer instruments is not convenient or possible. Furthermore, as the first translation of a brief standard Big Five Instrument into Catalan, this work should facilitate future research on personality in the Catalan-speaking population.

Automatic acquisition of Named Entities for Rule-Based Machine Translation

This paper proposes to enrich RBMTdictionaries with Named Entities(NEs) automatically acquired fromWikipedia. The method is appliedto the Apertium English-Spanishsystem and its performance comparedto that of Apertium with and withouthandtagged NEs. The system withautomatic NEs outperforms the onewithout NEs, while results vary whencompared to a system with handtaggedNEs (results are comparable forSpanish to English but slightly worstfor English to Spanish). Apart fromthat, adding automatic NEs contributesto decreasing the amount of unknownterms by more than 10%.

Maca - a configurable tool to integrate Polish morphological data

There are a number of morphological analysers for Polish. Most of these, however, are non-free resources. What is more, different analysers employ different tagsets and tokenisation strategies. This situation calls for a simpleand universal framework to join different sources of morphological information, including the existing resources as well as user-provided dictionaries. We present such a configurable framework that allows to write simple configuration files that define tokenisation strategies and the behaviour of morphologicalanalysers, including simple tagset conversion.

Validation of the spiritual distress assessment tool in older hospitalized patients.

ABSTRACT:¦BACKGROUND: The Spiritual Distress Assessment Tool (SDAT) is a 5-item instrument developed to assess unmet spiritual needs in hospitalized elderly patients and to determine the presence of spiritual distress. The objective of this study was to investigate the SDAT psychometric properties.¦METHODS: This cross-sectional study was performed in a Geriatric Rehabilitation Unit. Patients (N = 203), aged 65 years and over with Mini Mental State Exam score ≥ 20, were consecutively enrolled over a 6-month period. Data on health, functional, cognitive, affective and spiritual status were collected upon admission. Interviews using the SDAT (score from 0 to 15, higher scores indicating higher distress) were conducted by a trained chaplain. Factor analysis, measures of internal consistency (inter-item and item-to-total correlations, Cronbach α), and reliability (intra-rater and inter-rater) were performed. Criterion-related validity was assessed using the Functional Assessment of Chronic Illness Therapy-Spiritual well-being (FACIT-Sp) and the question "Are you at peace?" as criterion-standard. Concurrent and predictive validity were assessed using the Geriatric Depression Scale (GDS), occurrence of a family meeting, hospital length of stay (LOS) and destination at discharge.¦RESULTS: SDAT scores ranged from 1 to 11 (mean 5.6 ± 2.4). Overall, 65.0% (132/203) of the patients reported some spiritual distress on SDAT total score and 22.2% (45/203) reported at least one severe unmet spiritual need. A two-factor solution explained 60% of the variance. Inter-item correlations ranged from 0.11 to 0.41 (eight out of ten with P < 0.05). Item-to-total correlations ranged from 0.57 to 0.66 (all P < 0.001). Cronbach α was acceptable (0.60). Intra-rater and inter-rater reliabilities were high (Intraclass Correlation Coefficients ranging from 0.87 to 0.96). SDAT correlated significantly with the FACIT-Sp, "Are you at peace?", GDS (Rho -0.45, -0.33, and 0.43, respectively, all P < .001), and LOS (Rho 0.15, P = .03). Compared with patients showing no severely unmet spiritual need, patients with at least one severe unmet spiritual need had higher odds of occurrence of a family meeting (adjOR 4.7, 95%CI 1.4-16.3, P = .02) and were more often discharged to a nursing home (13.3% vs 3.8%; P = .027).¦CONCLUSIONS: SDAT has acceptable psychometrics properties and appears to be a valid and reliable instrument to assess spiritual distress in elderly hospitalized patients.

An open source browser-based software tool for graph drawing and visualisation

In this research work we searched for open source libraries which supports graph drawing and visualisation and can run in a browser. Subsequent these libraries were evaluated to find out which one is the best for this task. The result was the d3.js is that library which has the greatest functionality, flexibility and customisability. Afterwards we developed an open source software tool where d3.js was included and which was written in JavaScript so that it can run browser-based.

Western blotting as a tool for the serodiagnosis of farmer's lung disease: validation with Lichtheimia corymbifera protein extracts.

Electrosyneresis and double diffusion are immunoprecipitation techniques commonly used in the serological diagnosis of Farmer's lung disease (FLD). These techniques are reliable but lack standardization. The aim of this study was to evaluate Western blotting for the serodiagnosis of FLD. We carried out Western blotting with an antigenic extract of Lichtheimia corymbifera, an important aetiological agent of the disease. The membranes were probed with sera from 21 patients with FLD and 21 healthy exposed controls to examine the IgG antibody responses against purified somatic antigens. Given the low prevalence of the disease, 21 patients could be considered as a relevant series. Four bands were significantly more frequently represented in membranes probed with FLD sera (bands at 27.7, 40.5, 44.0 and 50.5 kDa) than those probed with control sera. We assessed the diagnostic value of different criteria alone or in combination. The diagnostic accuracy of the test was highest with the inclusion of at least two of the following criteria: at least five bands on the strip and the presence of one band at 40.5 or 44.0 kDa. Sensitivity, specificity and positive and negative predictive values were all 81%, and the odds ratio was 18.06. Inclusion of bands of high intensity diminished rather than improved the diagnostic value of the test. We concluded that Western blotting is a valuable technique for the serodiagnosis of FLD. The industrial production of ready-to-use membranes would enable the routine use of this technique in laboratories, and provide reliable and standardized diagnostic results within a few hours.

Benchmarked Quality Measurement Process in a Software Validation Process

Jatkuva laadunmittaus osana ohjelmistoprosessia on yleistynyt ohjelmistoyritysten keskuudessa viime vuosien aikana. ISO 9001:2000 -laatustandardi vaatii yrityksiltä tuotteiden ja prosessien laadun mittaamista ja seuraamista. Laadun mittareiden valinta on haastava tehtävä. Yritykset luulevat usein mittaavansa laatua, vaikka ne todellisuudessa mittaavatkin ohjelmistojen eri ominaisuuksia kuten kokoa tai monimutkaisuutta. Tässä diplomityössä kehitetään ohjelmistojen validointiprosessiin vertailuun perustuva laadunmittausprosessi ohjelmistotuotteiden laadun arviointiin, mittaamiseen ja seurantaan. Laatumittarit valitaan ennalta määriteltyjen kriteereiden mukaisesti, ja niille asetetaan tavoitearvot vertailuanalyysistä saatujen tulosten perusteella. Laadunmittausprosessin lisäksi työssä annetaan suositus prosessin käyttöönotosta ja käytöstä osana yrityksen toimintaa, mikä mahdollistaa jatkuvan seurannan sekä kehityksen tulevaisuudessa.