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It has been reported that the aberrant DNA methylation may result in copy number variations (CNVs), and the CNVs may alter the levels of DNA methylation. Whole genome bisulfite sequencing (WGBS) is able to generate the sequencing data of DNAs, and shows the potential ability to detect CNVs. However, the evaluations and performances on the detections of CNVs using WGBS data is still unclear. In this study, five software with different strategies for CNV detections, e.g., BreakDancer, cn.mops, CNVnator, DELLY and Pindel, were selected to explore and benchmark the performances of CNV detections with WGBS data. Based on the real (2.62 billion reads) and simulated (12.35 billion reads) WGBS data of humans, we calculated the number, precision, recall, relative ability, memory usage, and running time of CNV detections by 150 times, and tried to figure out the optimal strategy for CNV detections with WGBS data. Based on the real WGBS data, Pindel detected the most deletions and duplications, CNVnator detected the deletions with the highest precision, cn.mops detected the duplications with the highest precision, Pindel detected the deletions with the highest recall, and cn.mops detected the duplications with the highest recall. Based on the simulated WGBS data, BreakDancer detected the most deletions, and cn.mops detected the most duplications. The CNVnator showed the highest precision and recall for both deletions and duplications. In real and simulated WGBS data, the ability of CNVnator to detect CNVs was likely to overtake that in the whole genome sequencing data. Additionally, DELLY and BreakDancer displayed the lowest peak of memory usage and the lest CPU runtime, while CNVnator expressed the highest peak of memory usage and the most CPU runtime. Taken together, CNVnator and cn.mops showed the excellent performances of CNV detections with WGBS data. These results suggested that it was feasible to detect CNVs using WGBS data, and provided the useful information to further investigate both CNVs and DNA methylation using WGBS data alone.

Infection clusters of multidrug-resistant bacteria increase mortality and entail expensive infection control measures. Whereas whole-genome sequencing (WGS) is the current gold standard to confirm infection clusters, PCR-based assays targeting cluster-specific signatures, such as single nucleotide polymorphisms (SNPs) derived from WGS data, are more suitable to initially screen for cluster isolates within large sample sizes. Here, we evaluated four software tools (SeqSphere + , RUCS, Gegenees, and Find Differential Primers) regarding their efficiency to find SNPs within WGS data sets that were specific for two bacterial monospecies infection clusters but were absent from a WGS reference data set comprising several hundred diverse genotypes of the same bacterial species. Cluster-specific SNPs were subsequently used to establish a probe-based real-time PCR screening assay for in vitro differentiation between cluster and noncluster isolates. SeqSphere + and RUCS found 2 and 24 SNPs for clusters 1 and 14 and 24 SNPs for cluster 2, respectively. However, some signatures detected by RUCS were not cluster specific. Interestingly, all SNPs identified by SeqSphere + were also detected by RUCS. In contrast, analyses with the remaining tools either resulted in no SNPs (with Find Differential Primers) or failed (Gegenees). Design of six cluster-specific real-time PCR assays enabled reliable cluster screening in vitro . Our evaluation revealed that SeqSphere + and RUCS identified cluster-specific SNPs that could be used for large-scale screening in surveillance samples via real-time PCR, thereby complementing WGS efforts. This faster and simplified approach for the surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians. IMPORTANCE Infection clusters of multidrug-resistant bacteria threaten medical facilities worldwide and cause immense health care costs. In recent years, whole-genome sequencing (WGS) has been increasingly applied to detect and to further control bacterial clusters. However, as WGS is still expensive and time-consuming, its exclusive application for screening and confirmation of bacterial infection clusters contributes to high costs and enhanced turnaround times, which many hospitals cannot afford. Therefore, there is need for alternative methods that can enable further surveillance of bacterial clusters that are initially detected by WGS in a faster and more cost-efficient way. Here, we established a system based on real-time PCR that enables rapid large-scale sample screening for bacterial cluster isolates within 7 days after the initial detection of an infection cluster, thereby complementing WGS efforts. This faster and simplified surveillance of bacterial clusters will improve infection control measures and will enhance protection of patients and physicians.

Objectives: The number of electronic prescriptions (ePrescriptions) grows steadily in Belgium as in other European countries. In the future, Belgium wants to dematerialize the ePrescription flow, removing all paper trails. A quality check of the digital content and implementation of national ePrescription guidelines in the field was conducted, comparing the content at both prescription and pharmacy side., Methods: An explanatory mixed-methods design was applied. In a first phase, potential problems (warning flags) were identified by consulting stakeholders. Secondly, the warning flags were validated to problems (errors) in a random set of ePrescriptions collected in April 2019. In a third phase, explanatory interviews were held with various stakeholders in order to find explanations and to identify the initiators of these errors., Results: In the first phase, 15 warning flags were identified to evaluate the quality of an ePrescription. In the second phase, a random selection of 11,798 ePrescriptions was validated. The most prevalent errors found, were the digital construction of the messages (18.88%), combined with lots of necessarily deemed substitutions by the pharmacist (3.39%) not following what was prescribed originally. In the third phase, stakeholders indicated that software of the prescriber and the use of inconsistent databases between prescriber and pharmacy can often be seen as the cause and initiator of these problems., Conclusions: Use of authentic medication databases and well-designed software systems have the potential to solve ePrescription problems. Focus should go to prevention instead of detection.

The aim of this study is to build an evaluation framework for the user-centric testing of the Data Curation Tool. The tool was developed in the scope of the FAIR4Health project to make health data FAIR by transforming them from legacy formats into a Common Data Model based on HL7 FHIR. The end user evaluation framework was built by following a methodology inspired from the Delphi method. We applied a series of questionnaires to a group of experts not only in different roles and skills, but also from various parts of Europe. Overall, 26 questions were formulated for 16 participants. The results showed that the users are satisfied with the capabilities and performance of the tool. The feedbacks were considered as recommendations for technical improvement and fed back into the software development cycle of the Data Curation Tool.

Emotional facial expressions can inform researchers about an individual's emotional state. Recent technological advances open up new avenues to automatic Facial Expression Recognition (FER). Based on machine learning, such technology can tremendously increase the amount of processed data. FER is now easily accessible and has been validated for the classification of standardized prototypical facial expressions. However, applicability to more naturalistic facial expressions still remains uncertain. Hence, we test and compare performance of three different FER systems (Azure Face API, Microsoft; Face++, Megvii Technology; FaceReader, Noldus Information Technology) with human emotion recognition (A) for standardized posed facial expressions (from prototypical inventories) and (B) for non-standardized acted facial expressions (extracted from emotional movie scenes). For the standardized images, all three systems classify basic emotions accurately (FaceReader is most accurate) and they are mostly on par with human raters. For the non-standardized stimuli, performance drops remarkably for all three systems, but Azure still performs similarly to humans. In addition, all systems and humans alike tend to misclassify some of the non-standardized emotional facial expressions as neutral. In sum, emotion recognition by automated facial expression recognition can be an attractive alternative to human emotion recognition for standardized and non-standardized emotional facial expressions. However, we also found limitations in accuracy for specific facial expressions; clearly there is need for thorough empirical evaluation to guide future developments in computer vision of emotional facial expressions., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Küntzler, Höfling and Alpers.)

Epidemics and emerging infectious diseases are becoming an increasing threat to global populations-challenging public health practitioners, decision makers and researchers to plan, prepare, identify and respond to outbreaks in near real-timeframes. The aim of this research is to evaluate the range of public domain and freely available software epidemic modelling tools. Twenty freely utilisable software tools underwent assessment of software usability, utility and key functionalities. Stochastic and agent based tools were found to be highly flexible, adaptable, had high utility and many features, but low usability. Deterministic tools were highly usable with average to good levels of utility., (Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.)

Rationale and Objectives: This study aims to compare the speed and accuracy of three different software packages in segmenting the liver and the spleen., Materials and Methods: The three software packages are Advantage Workstation Solutions (AWS), Claron Technology (Claron) Liver Segmentor, and Vitrea Core Fx (Vitrea). The dataset consisted of abdominal computed tomography scans of 30 patients obtained from the portal venous phase. All but two of the patients had a cancer diagnosis. The livers of 14 patients and the spleens of 24 patients were reported as normal; the remaining livers and spleens contained one or more abnormalities. The initial segmentation times and volumes were recorded in Claron and Vitrea as these created automatic segmentations. The total segmentation times and volumes following corrections were recorded. The livers and spleens were segmented separately by two radiologists who used all three packages. Accuracy was assessed by comparing volumes measured using fully manual segmentation on the AWS., Results: Claron could not segment the spleen in four subjects for the first reader and in two subjects for the second reader. The final mean segmentation times for the liver for both readers were 6.5 and 5.5 minutes for AWS, 4.4 and 3.6 minutes for Claron, and 5.1 and 4.2 minutes for Vitrea. The final mean segmentation times for the spleen were 2.7 and 2.1 minutes for AWS, 2.1 and 1.4 minutes for Claron, and 1.8 and 1.2 minutes for Vitrea. No statistically significant difference was found between the organ volumes measured by the two readers when using Vitrea. The mean differences between the initial and final segmentation volumes ranged from -1.2% to 0.4% for the liver and from -4.0% to 9.8% for the spleen. The mean differences between the automated liver segmentation volumes and the AWS volumes were 2.5%-2.9% for Claron and 4.9%-6.6% for Vitrea. The mean differences between the automated splenic segmentation volumes and the AWS volumes were 5.0%-6.2% for Claron and 10.6%-12.0% for Vitrea., Conclusions: Both automated packages (Claron and Vitrea) measured liver and spleen volumes that were accurate and quick before manual correction. Volumes for the liver were more accurate than those for the spleen, perhaps due to the much smaller splenic volumes compared to those of the liver. For both liver and spleen, manual corrections were time consuming and for most subjects did not significantly change the volume measurement., (Copyright © 2017. Published by Elsevier Inc.)

The domain of biobanking has gone through many stages and as a result there are a wide range of commercial and open source software solutions available. The utilization of these software tools requires different levels of domain and technical skills for installation, configuration and ultimate us of these biobank software tools. To compound this complexity the biobanking community are required to work together in order to share knowledge and jointly build solutions to underpin the research infrastructure. We have evaluated the available tools, described them in a catalogue (BiobankApps) and made a selection of tools available to biobanks in a reference toolbox (BIBBOX) that are use-case driven. In the BiobankApps tool catalogue, both commercial and open source software solutions related to the biobanking domain are included, classified and evaluated. The evaluation covers: 1) "user review" by an authenticated user 2) domain expert: quick analysis by BBMRI members and 3) domain expert: detailed analysis and test installation with real world data. The evaluation is paired with a survey across the more "advanced" (from a technology perspective) biobanks to investigate what tools are currently used and summarises known benefits/drawbacks of the respective packages. In the second step we recommend tools for specific use cases, and install, configure and connect these in the BIBBOX framework. This service also builds on the existing work in the United Kingdom in seeking to establish the motivations for different stakeholders to become involved and therefore assisting in prioritising the use-cases based on the level of need and support within the research community. All tools associated to a use-case are available as BIBBOX applications (technically this is achieved by docker containers), which are integrated in the BIBBOX framework with central identification and user management. In future work we plan to share the acquired knowledge with other networks, develop an Application Programmable Interface (API) for the exchange of metadata with other tool catalogues and work on an ontology for the evaluation of biobank software.

Accurate sampling of cancer suspicious locations is critical in targeted prostate biopsy, but can be complicated by the motion of the prostate. We present an open-source software for intra-procedural tracking of the prostate and biopsy targets using deformable image registration. The software is implemented in 3D Slicer and is intended for clinical users. We evaluated accuracy, computation time and sensitivity to initialization, and compared implementations that use different versions of the Insight Segmentation Toolkit (ITK). Our retrospective evaluation used data from 25 in-bore MRI-guided prostate biopsy cases (343 registrations total). Prostate Dice similarity coefficient improved on average by 0.17 (p < 0.0001, range 0.02-0.48). Registration was not sensitive to operator variability. Computation time decreased significantly for the implementation using the latest version of ITK. In conclusion, we presented a fully functional open-source tool that is ready for prospective evaluation during clinical MRI-guided prostate biopsy interventions.

Nowadays, we live in the "data era" where the use of statistical or data analysis software is inevitable, in any research field. This means that the choice of the right software tool or platform is a strategic issue for a research department. Nevertheless, in many cases decision makers do not pay the right attention to a comprehensive and appropriate evaluation of what the market offers. Indeed, the choice still depends on few factors like, for instance, researcher's personal inclination, e.g., which software have been used at the university or is already known. This is not wrong in principle, but in some cases it's not enough at all and might lead to a "dead end" situation, typically after months or years of investments already done on the wrong software. This article, far from being a full and complete guide to statistical software evaluation, aims to illustrate some key points of the decision process and introduce an extended range of factors which can help to undertake the right choice, at least in potential. There is not enough literature about that topic, most of the time underestimated, both in the traditional literature and even in the so called "gray literature", even if some documents or short pages can be found online. Anyhow, it seems there is not a common and known standpoint about the process of software evaluation from the final user perspective. We suggests a multi-factor analysis leading to an evaluation matrix tool, to be intended as a flexible and customizable tool, aimed to provide a clearer picture of the software alternatives available, not in abstract but related to the researcher's own context and needs. This method is a result of about twenty years of experience of the author in the field of evaluating and using technical-computing software and partially arises from a research made about such topics as part of a project funded by European Commission under the Lifelong Learning Programme 2011.

This paper presents a comprehensive method for evaluating intrusion detection systems (IDSs). It integrates and extends ROC (receiver operating characteristic) and cost analysis methods to provide an expected cost metric. Results are given for determining the optimal operation of an IDS based on this expected cost metric. Results are given for the operation of a single IDS and for a combination of two IDSs. The method is illustrated for: 1) determining the best operating point for a single and double IDS based on the costs of mistakes and the hostility of the operating environment as represented in the prior probability of intrusion and 2) evaluating single and double IDSs on the basis of expected cost. A method is also described for representing a compound IDS as an equivalent single IDS. Results are presented from the point of view of a system administrator, but they apply equally to designers of IDSs.