Data Analysis Software Package Research Articles

The CT Scanner Facility at Stellenbosch University: An open access X-ray computed tomography laboratory

The Stellenbosch University CT Scanner Facility is an open access laboratory providing non-destructive X-ray computed tomography (CT) and a high performance image analysis services as part of the Central Analytical Facilities (CAF) of the university. Based in Stellenbosch, South Africa, this facility offers open access to the general user community, including local researchers, companies and also remote users (both local and international, via sample shipment and data transfer). The laboratory hosts two CT instruments, i.e. a micro-CT system, as well as a nano-CT system. A workstation-based Image Analysis Centre is equipped with numerous computers with data analysis software packages, which are to the disposal of the facility users, along with expert supervision, if required. All research disciplines are accommodated at the X-ray CT laboratory, provided that non-destructive analysis will be beneficial. During its first four years, the facility has accommodated more than 400 unique users (33 in 2012; 86 in 2013; 154 in 2014; 140 in 2015; 75 in first half of 2016), with diverse industrial and research applications using X-ray CT as means. This paper summarises the existence of the laboratory’s first four years by way of selected examples, both from published and unpublished projects. In the process a detailed description of the capabilities and facilities available to users is presented.

Rural Customers’ Attitude and Satisfaction towards Honda Two Wheelers and Showroom Services, Tiruvarur

Objectives: A buyer in general compares the performance of the products they bought with their expectation with regard to satisfaction. Firms have to constantly meet the expectations of the buyers by means of their offer which meet and exceed the buyers' expectation. This will ensure firms endurance in the competitive environment which may give them competitive advantage to surpass the rest of the players in the market. Honda is one of the biggest firms in India. They have many models of two wheelers for the customers and also they launch many new models every year. This study deals with the consumer attitude and satisfaction towards Honda two wheelers and services at Honda showroom, Tiruvarur in India. This study was conducted to find out the factors influencing consumer behaviour of Honda two wheelers and the factors influencing consumer behaviour of Honda two wheelers. Methods/Analysis: Primary and secondary data were utilised for this study. 230 two wheeler customers of Honda showroom, Thiruvarur was included for this study. In order to find out the respondents' opinion about awareness about Honda two wheelers, model of Honda, celebrity endorsement, price of Honda, employee behaviour in the showroom and level of services at the showroom structured questionnaire was used. In order to test the structured questionnaire, 20 respondents were used for pilot study. For Data analysis Software package SPSS was used. Statistical techniques like Chi-square test, Factor analysis and percentage analysis were used to analyse the collected data. Findings: From the analysis it is inferred that majority of the customers are highly satisfied with Honda two wheelers and the dealer of Honda motors) in Tiruvarur. Majority of the customers were highly loyal and satisfied (except vehicle provided with the reasonable amount of fuel at the time of delivery) with the service at the showroom. At the time of purchase, customers should be educated towards handling and maintenance of two wheelers and dealers have to ensure the availability of spare parts. Applications/Improvements: This study was conducted in rural area to understand the customer opinion about the Honda two wheelers and showroom experience. Automobile dealers have opportunities to meet the buyers in person and can contact them. In order to understand the buyers' opinion of Honda two wheelers and showroom, dealers have to conduct these kinds of surveys periodically.

The chaotic journey: Recovering from hip fracture in a nursing home

Purpose of the studyTo understand the journey experienced by nursing home residents following hip fracture and impressions of an outreach rehabilitation program offered after their return home. Design and methodsA qualitative investigation was undertaken in parallel with a randomised controlled trial investigating the efficacy and cost utility of providing a hospital outreach rehabilitation program for older nursing home residents who have recently returned from hospital following hip fracture. Family members and nursing home staff of 28 (out of the first 30) participants (14 from intervention and 14 from control) agreed to participate in interviews and focus groups to provide information and perceptions of each person’s journey. NVivo 10 qualitative data analysis software package was used to identify major themes (via open, then axial and finally selective coding). ResultsBoth family members and staff described nursing home residents with dementia as receiving poor post-operative care from hospital staff who seemed unfamiliar with dementia and delirium. Discharge from hospital soon after surgery (median 4.5days) occurred with poor transfer of information. Difficulties with residents’ emotions, pain management and commencing mobilisation seemed more prevalent within usual care group, whereas fewer overall problems were encountered by those with access to a geriatrician and additional therapy. ImplicationsThis research suggests that an integrated care pathway including the hospital stay and first weeks back at nursing homes should be developed. Performance indicators should include carer measures on the quality of the transfer, pain management measures in the first month and return to walking.

Teaching-led research? Exploring the digital agencies of software in qualitative research

This work-in-progress paper explores the intersection of technologies and software with the practices, of qualitative research and qualitative data analysis. Computer aided qualitative data analysis software (CAQDAS) packages such as ATLAS.ti, NVivo and HyperRESEARCH are the focus of competing claims and critiques. We explore the positioning, continuities and disjunctures between manufacturers promoting their software, positioning in teaching and training materials and a range of views in the literature from critical to laudatory, as well as their prevalence in research on networked learning. The pre-eminence and influence of expository writing and paucity of empirical research underscore the relevance and potential contribution of this project, We argue that part of that contribution comes from drawing on insights from science and technology studies (STS) which offer a well-developed vocabulary and set of approaches for exploring the agencies and mediation of technologies in the practices of research.The initial stages of the research project are outlined including online participant recruitment via facebook, methods of screen-share remote interviewing to generate rich data exploring software use, and incorporating accounts of researchers’ practices. Their transformation and mediation to become “data” through different software packages are briefly explored.Drawing on Latour’s model of the two-faced Janus of science with which contrasts “science in the making" with “ready made science” we turn to consider ways in which this project can invert the usual trope of University education as research led, asking instead how a research project could become teaching-led. We briefly explore some of the initial approaches and opportunities this has created for opening up the black-box of research practices and shifting software training methods to engage learners in a process of discovery as “learning in the making” rather than being tasked with stepping through fixed frames of “ready made teaching”.

StrucBreak: A Computational Framework for Structural Break Detection in DNA Sequences.

Damages or breaks in DNA may change the characteristics of genomes and causes various diseases. In this work we construct a system that incorporates the maximum likelihood-based probabilistic formula to assess the number of damages that have occurred in any DNA sequence. This approach has been progressively benchmarked by implementing simulated data sets so that the outcomes can be compared with a ground truth or reference value. At first the sequence data set order is checked through the statistical cumulative sum (STACUMSUM). The verified sequences are then estimated by prior and posterior probability to count the percentages of breaks and mutations. Maximum-likelihood estimation then finds out the exact numbers and positions of breaks and detections. In database manipulation, one factor that decides the orientation and order of the sequence is geometric distance between consecutive sequences. The geometric distance is measured for smooth representation of the genome or DNA sequences. Finally, we compared the performance of our system with DAMBE5: (A Comprehensive Software Package for Data Analysis in Molecular Biology and Evaluation), and in response to time and space complexity, StrucBreak is much faster and consumes much less space due to our algorithmic approaches.

Macromolecular Powder Diffraction: Ready for genuine biological problems.

Knowledge of 3D structures of biological molecules plays a major role in both understanding important processes of life and developing pharmaceuticals. Among several methods available for structure determination, macromolecular X-ray powder diffraction (XRPD) has transformed over the past decade from an impossible dream to a respectable method. XRPD can be employed in biosciences for various purposes such as observing phase transitions, characterizing bulk pharmaceuticals, determining structures via the molecular replacement method, detecting ligands in protein-ligand complexes, as well as combining micro-sized single crystal crystallographic data and powder diffraction data. Studies using synchrotron and laboratory sources in some standard configuration setups are reported in this review, including their respective advantages and disadvantages. Methods presented here provide an alternative, complementary set of tools to resolve structural problems. A variety of already existing software packages for powder diffraction data processing and analysis, some of which have been adapted to large unit cell studies, are briefly described. This review aims to provide necessary elements of theory and current methods, along with practical explanations, available software packages and highlighted case studies.

D.393 - A software package for data registration and analysis in interventional radiology

D.393 - A software package for data registration and analysis in interventional radiology

Quantitative Evaluation of Intensity Inhomogeneity Correction Methods for Structural MR Brain Images

The correction of intensity non-uniformity (INU) in magnetic resonance (MR) images is extremely important to ensure both within-subject and across-subject reliability. Here we tackled the problem of objectively comparing INU correction techniques for T1-weighted images, which are the most commonly used in structural brain imaging. We focused our investigations on the methods integrated in widely used software packages for MR data analysis: FreeSurfer, BrainVoyager, SPM and FSL. We used simulated data to assess the INU fields reconstructed by those methods for controlled inhomogeneity magnitudes and noise levels. For each method, we evaluated a wide range of input parameters and defined an enhanced configuration associated with best reconstruction performance. By comparing enhanced and default configurations, we found that the former often provide much more accurate results. Accordingly, we used enhanced configurations for a more objective comparison between methods. For different levels of INU magnitude and noise, SPM and FSL, which integrate INU correction with brain segmentation, generally outperformed FreeSurfer and BrainVoyager, whose methods are exclusively dedicated to INU correction. Nonetheless, accurate INU field reconstructions can be obtained with FreeSurfer on images with low noise and with BrainVoyager for slow and smooth inhomogeneity profiles. Our study may prove helpful for an accurate selection of the INU correction method to be used based on the characteristics of actual MR data.Electronic supplementary materialThe online version of this article (doi:10.1007/s12021-015-9277-2) contains supplementary material, which is available to authorized users.

The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.

Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses. Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. mhammell@cshl.edu. Supplementary data are available at Bioinformatics online.

Three-dimensional reciprocal space mapping with a two-dimensional detector as a low-latency tool for investigating the influence of growth parameters on defects in semipolar GaN

A rapid nondestructive defect assessment and quantification method based on X-ray diffraction and three-dimensional reciprocal-space mapping has been established. A fast read-out two-dimensional detector with a high dynamic range of 20 bits, in combination with a powerful data analysis software package, is set up to provide fast feedback to crystal growers with the goal of supporting the development of reduced defect density GaN growth techniques. This would contribute strongly to the improvement of the crystal quality of epitaxial structures and therefore of optoelectronic properties. The method of normalized three-dimensional reciprocal-space mapping is found to be a reliable tool which shows clearly the influence of the parameters of the metal–organic vapour phase epitaxial and hydride vapour phase epitaxial (HVPE) growth methods on the extent of the diffuse scattering streak. This method enables determination of the basal stacking faults and an exploration of the presence of other types of defect such as partial dislocations and prismatic stacking faults. Three-dimensional reciprocal-space mapping is specifically used in the manuscript to determine basal stacking faults quantitatively and to discuss the presence of partial dislocations. This newly developed method has been applied to semipolar GaN structures grown on patterned sapphire substrates (PSSs). The fitting of the diffuse scattering intensity profiles along the stacking fault streaks with simulations based on a Monte Carlo approach has delivered an accurate determination of the basal plane stacking fault density. Three-dimensional reciprocal-space mapping is shown to be a method sensitive to the influence of crystallographic surface orientation on basal stacking fault densities during investigation of semipolar (11{\overline 2}2) GaN grown on an r-plane (1{\overline 1}02) PSS and semipolar (10{\overline 1}1) GaN grown on an n-plane (11{\overline 2}3) PSS. Moreover, the influence of HVPE overgrowth at reduced temperature on the quality of semipolar (11{\overline 2}2) GaN has been studied.

Professional behaviours demonstrated by undergraduate dental students using an incident reporting system.

Critical incident reporting is widely used across healthcare and other sectors for reporting adverse events or behaviours. More recently it has been used in medical education as a means of assessing student professionalism. The aims of this study were to determine the usage of critical incident forms when reporting behaviours related to professionalism demonstrated by undergraduate dental students, and the types of behaviours exhibited. Three types of form could be awarded for highly professional (green), minor unprofessional (yellow) and serious unprofessional (red) behaviours. All forms completed over a two-year period were analysed recording the year of student, type of card and demographic of the member of staff reporting the incident. All text relating to the nature of the incident was entered into a qualitative data analysis software package and analysed thematically. In total, 583 cards were awarded, 55% green, 34% yellow and 11% red. Seventy-four percent of cards were awarded in a clinical environment, with administrative staff using them the most (29%). The overwhelming professional behaviours demonstrated related to altruism. The most common unprofessional behaviours related to a lack of conscientiousness, although a greater range of common unprofessional behaviours were reported. In conclusion, critical incidents forms were widely used for reporting both professional and unprofessional behaviours particularly in clinical environments by a range of staff. Such forms may be a valuable addition to the professionalism assessment portfolio, capturing behaviours not previously reported using traditional methods.

Orthogonalization of regressors in FMRI models.

The occurrence of collinearity in fMRI-based GLMs (general linear models) may reduce power or produce unreliable parameter estimates. It is commonly believed that orthogonalizing collinear regressors in the model will solve this problem, and some software packages apply automatic orthogonalization. However, the effects of orthogonalization on the interpretation of the resulting parameter estimates is widely unappreciated or misunderstood. Here we discuss the nature and causes of collinearity in fMRI models, with a focus on the appropriate uses of orthogonalization. Special attention is given to how the two popular fMRI data analysis software packages, SPM and FSL, handle orthogonalization, and pitfalls that may be encountered in their usage. Strategies are discussed for reducing collinearity in fMRI designs and addressing their effects when they occur.

Maximum sustainable yield of Greater lizardfish Saurida tumbil fishery in Pakistan using the CEDA and ASPIC packages

The catch and effort data analysis (CEDA) and ASPIC (a stock assessment production model incorporating covariates) computer software packages were used to estimate the maximum sustainable yield (MSY) from the catch and effort data of Greater lizardfish Saurida tumbil fishery of Pakistan from 1986 to 2009. In CEDA three surplus production models of Fox, Schaefer and Pella-Tomlinson were used. Here initial proportion (IP) of 0.5 was used because the starting catch was roughly 50% of the maximum catch. With IP = 0.5, the estimated MSY from Fox model were 20.59 mt and 38.16 mt for normal and log-normal error assumptions, while the MSY from Schaefer and Pella-Tomlinson were 60.40, 60.40 and 60.40 mt, for normal, log-normal and gamma error assumptions respectively. The MSY values from Schaefer and Pella-Tomlinson models of three error assumptions were the same. The R2 values from those three models were above 0.6. When IP = 0.5, the MSY values estimated from ASPIC from Fox were 132 mt, and from logistic model were 69.4 mt, with R2 value above 0.8. Therefore we suggest the MSY of S. tumbil fishery from Pakistan to be 60–70 mt, which is higher than the latest catch, thus we would recommend that the fishing efforts for this fishery may be kept at the current level.

Impact of a short biostatistics course on knowledge and performance of postgraduate scholars: Implications for training of African doctors and biomedical researchers.

This study was designed to evaluate the impact of a short biostatistics course on knowledge and performance of statistical analysis by biomedical researchers in Africa. It is recognized that knowledge of biostatistics is essential for understanding and interpretation of modern scientific literature and active participation in the global research enterprise. Unfortunately, it has been observed that basic education of African scholars may be deficient in applied mathematics including biostatistics. Forty university affiliated biomedical researchers from South Africa volunteered for a 4-day short-course where participants were exposed to lectures on descriptive and inferential biostatistics and practical training on using a statistical software package for data analysis. A quantitative questionnaire was used to evaluate participants' statistical knowledge and performance pre- and post-course. Changes in knowledge and performance were measured using objective and subjective criteria. Data from completed questionnaires were captured and analyzed using Statistical Package for Social Sciences. Participants' pre- and post-course data were compared using nonparametric Wilcoxon signed ranks tests for nonnormally distributed variables. A P < 0.05 was considered statistically significant. Baseline testing of statistical knowledge showed a median score of 0, with 75th percentile at 28.6%, and a maximum score of 71.4%. Postcourse evaluation revealed improvement in participants' core knowledge with the median score increasing to 28.5%; and the 75th percentile score to 85.7%; signifying improved understanding of statistical concepts and ability to carry out data analyses. This study just showed poor baseline knowledge of biostatistics among postgraduate scholars and health science researchers in this cohort and highlights the potential benefits of short-courses in biostatistics to improve the knowledge and skills of biomedical researchers and scholars in Africa.

Breast Cancer , Breast Self - Examination Knowledge among Female High School Students in Riyadh City

Breast cancer (BC) is the most prevalent form of cancer in the Kingdom of Saudi Arabia, accounting for 11% of all female cancers. It is considered to be a progressive disease with a poor prognosis if detected late. The low level of knowledge and practice of breast self-examination is an important method of prevention. The study was aimed at assessing the knowledge of breast cancer and practice of Breast Self-Examination (BSE) among female secondary school students in Riyadh city. Material & Methods : A cross-sectional descriptive correlation design was used in this study. A representative probability sample was recruited (Sample Size = 917 Students). A selfadministered questionnaire was prepared by the researcher. It consists of four parts. Data was analyzed using the SPSS software package (version 16) for data entry and analysis. Results: The results of the study indicated that none of the secondary school students had an excellent knowledge regarding breast cancer; 98.8% of the participants had a fair level of knowledge about breast cancer. The mass media was the most common source of information about breast cancer. The majority of participants did not perform breast self-examination 80.8%; only 3.4% perform (BSE) on monthly basis. There was a statistically significant relation between level of breast cancer knowledge and secondary school type, nationality, family history of breast cancer and secondary school levels but there was no significant relation between knowledge of breast cancer and age groups, marital status and family income level. Logistic regression analysis revealed that a negative family history of breast cancer was a significant predictor for lower scores on the level of knowledge of breast cancer. However, age group, family history of breast cancer were significant predictors of performance of breast self-examination. Conclusions : This study revealed that most of the female secondary school students in Riyadh, Saudi Arabia had very low knowledge about breast cancer. We recommended developing a health educational program about breast cancer for students, teachers and the community, to raise awareness.

Patient and Caregiver Perspectives of Factors Associated with Adherence to and Satisfaction with Iron Chelation Therapy

BackgroundAdherence to iron chelation therapy (ICT) is critical in patients with transfusion dependent anemias (TDA) (e.g., sickle cell disease [SCD], thalassemia), myelodysplastic syndromes (MDS), aplastic anemia, and myelofibrosis (MF). One of the biggest challenges is poor adherence to therapy, which in turn could cause tissue damage in vital organs such as the heart, liver, and endocrine organs, leading to end-organ dysfunction and eventually organ failure. Some causes of poor adherence to ICT therapy in the literature include inconvenience and palatability issues. The literature also suggests that satisfaction with medication impacts adherence to medication regimens, and that satisfaction is an umbrella term for specific components such as convenience, and efficacy. There is limited information on the factors that influence adherence with ICT, however, from the patient and caregiver perspective.AimThe objective of this study was to explore the factors that influence adherence with ICT from the perspective of patients and caregivers of patients through qualitative research.MethodsSemi-structured interviews including an open-ended component were conducted to elicit subjects’ (patients with TDA, MDS, aplastic anemia, or MF or caregivers thereof) experiences with ICT. Institutional Review Board approval was granted and subjects were screened by clinicians to meet pre-defined inclusion and exclusion criteria. Audio recordings of the interviews were transcribed and a code book that contained definitions of all codes was developed through a consensus process. Transcripts were coded and data were analyzed using Atlas ti, a qualitative data analysis software package. Several concepts related to adherence and satisfaction were identified.ResultsFour interviewers conducted 11 patient and 10 caregiver interviews in 6 US cities. The children of the caregivers were not interviewed as they were below the age of nine. Eight of the eleven patients were male and three were female, aged 14 to 81 years (mean=43). Nine of the ten caregivers were female, aged 35 to 65 years (mean=48). Six of the ten children of caregivers were female and four were male, with a mean age of 8.9 years (range 1.56-16.81 years). Conditions across pediatric and adult patients included: MDS (n=3), SCD (n=13), thalassemia (n=3), MF (n=1), and aplastic anemia (n=1). Reported reasons for adherence included perceived effect on health and longevity, support from clinicians and caregivers, and an established routine for taking their treatment. Reported reasons for non-adherence included palatability related issues of taste and aftertaste, texture of the ICT formulation, solubility, side effects such as GI symptoms, and mealtime restrictions. Caregivers reported better adherence if their children had a better understanding of treatment benefit, which usually “gets better as the child gets older”; physician involvement in explaining the importance of ICT; and patients witnessing the decrease in their iron levels. Caregivers indicated that if they were satisfied with the efficacy of the ICT, their children were more likely to adhere to their medications. Coping mechanisms included modifying how the medicine was taken to change or mask the taste, aftertaste, or texture and “dose splitting” during the day.ConclusionsFactors associated with adherence and non-adherence to ICT and satisfaction with current therapies identified by patients and caregivers of patients provide information and insight for clinicians to provide optimal treatment with ICT and gain better adherence. These factors can be used to develop measures of adherence, palatability, GI symptoms, and satisfaction with ICT and design interventions to improve adherence to ICT. DisclosuresBal:Novartis Pharmaceutical Corporation: Employment, Equity Ownership. Cote:Novartis Pharmaceutical Corporation: Employment, Equity Ownership. Lasch:Pharmerit International: Employment, Research Funding. Huang:Novartis Pharmaceutical Corporation: Employment, Equity Ownership.

The association between dental and periodontal diseases and sickle cell disease. A pilot case-control study.

ObjectiveThis is a pilot case-control study conducted to investigate the prevalence of dental caries and periodontal disease and examine the possible association between oral health deterioration and SCD severity in a sample of Saudi SCD patients residing in the city of Al-Qatif, Eastern Province, Saudi Arabia.Materials and methodsDental examination to determine the Decayed, Missing and Filled Teeth index (DMFT), Community Periodontal Index (CPI), and plaque index system were recorded for 33 SCD patients and 33 age and sex-matched controls in the Al-Qatif Central Hospital, Qatif, Saudi Arabia. Self-administered surveys used to assess socio-economic status; oral health behaviors for both SCD patients and controls were recorded. In addition, the disease severity index was established for all patients with SCD. SPSS data analysis software package version 18.0 was used for statistical analysis. Numerical variables were described as mean with a standard deviation.ResultsDecayed teeth were significantly more in individuals with ages ranging from 18 to 38 years with SCD compared to the control group (p = 0.036) due to oral hygiene negligence. The mean number of filled teeth was significantly lower in individuals with SCD when compared to the control group (p = 0.015) due to the lack of appropriate and timely treatment reflected in the survey responses of SCD patients as 15.2% only taking oral care during hospitalization. There were differences between the cases and controls in the known caries risk factors such as income level, flossing, and brushing habit. The DMFT, CPI, and plaque index systems did not differ significantly between the SCD patients and the control group.ConclusionData suggest that patients with SCD have increased susceptibility to dental caries, with a higher prevalence of tooth decay and lower prevalence of filled teeth. Known caries risk factors influenced oral health more markedly than did factors related to SCD.

Adaptive and robust statistical methods for processing near-field scanning microwave microscopy images.

Near-field scanning microwave microscopy offers great potential to facilitate characterization, development and modeling of materials. By acquiring microwave images at multiple frequencies and amplitudes (along with the other modalities) one can study material and device physics at different lateral and depth scales. Images are typically noisy and contaminated by artifacts that can vary from scan line to scan line and planar-like trends due to sample tilt errors. Here, we level images based on an estimate of a smooth 2-d trend determined with a robust implementation of a local regression method. In this robust approach, features and outliers which are not due to the trend are automatically downweighted. We denoise images with the Adaptive Weights Smoothing method. This method smooths out additive noise while preserving edge-like features in images. We demonstrate the feasibility of our methods on topography images and microwave |S11| images. For one challenging test case, we demonstrate that our method outperforms alternative methods from the scanning probe microscopy data analysis software package Gwyddion. Our methods should be useful for massive image data sets where manual selection of landmarks or image subsets by a user is impractical.

Nurses’ perspectives regarding the disclosure of errors to patients: A qualitative study

BackgroundThere is often a mismatch between patients’ desire to be informed about errors and clinical reality. In closing the “disclosure gap” an understanding of the views of all members of the healthcare team regarding errors and their disclosure to patients is needed. However, international research on nurses’ views regarding this issue is currently limited. ObjectivesExplore nurses’ attitudes and experiences concerning disclosing errors to patients and perceived barriers to disclosure. DesignInductive, exploratory study employing semi-structured interviews with participants, followed by conventional content analysis in which investigators read and discussed transcribed data to identify important themes. SettingsNursing departments from hospitals in two German-speaking cantons in Switzerland. ParticipantsPurposive sample of 18 nurses from a range of fields, positions in organisational hierarchy, work experience, hospitals, and religious perspectives. MethodsData were collected via individual, face-to-face interviews using a researcher–developed semi-structured interview guide. Interviews were transcribed in German and analysed using the qualitative data analysis software package Atlas-Ti (Berlin) and conventional content analysis. The most illustrative quotes were translated into English. ResultsNurses generally thought that patients should be informed about every error, but only a very few nurses actually reported disclosing errors in practice. Indeed, many nurses reported that most errors are not disclosed to the patient. Nurses identified a number of barriers to error disclosure that have already been reported in the literature among all clinicians, such as legal consequences and the fear of losing patients’ trust. However, nurses in this study more frequently reported personal characteristics and a lack of guidance from the organisation as barriers to disclosure. Both issues suggest the need for a systematic institutional approach to error disclosure in which the decision to inform the patient stems from within the organisation and is not shouldered by individual nurses alone. ConclusionsOur study suggests that hospitals need to do more to support and train nurses in relation to error disclosure. Such measures as hospitals establishing a disclosure support system, providing background disclosure education, ensuring that disclosure coaching is available at all times, and providing emotional support for all parties involved, would likely go a long way to address the barriers identified by nurses.