Automation to facilitate optimisation of breast radiotherapy treatments using EPID-basedin vivodosimetry

Objective. To use automation to facilitate the monitoring of each treatment fraction using an electronic portal imaging device (EPID) basedin vivodosimetry (IVD) system, allowing optimisation of breast radiotherapy delivery for individual patients and cohorts.Approach. A suite of in-house software was developed to reduce the number of manual interactions with the commercial IVD system, dosimetry check. An EPID specific pixel sensitivity map facilitated use of the EPID panel away from the central axis. Point dose difference and the change in standard deviation in dose were identified as useful dose metrics, with standard deviation used in preference to gamma in the presence of a systematic dose offset. Automated IVD was completed for 3261 fractions across 704 patients receiving breast radiotherapy.Main results. Multiple opportunities for treatment optimisation were identified for individual patients and across patient cohorts as a result of successful implementation of automated IVD. 5.1% of analysed fractions were out of tolerance with 27.1% of these considered true positives. True positive results were obtained on any fraction of treatment and if IVD had only been completed on the first fraction, 84.4% of true positive results would have been missed. This was made possible due to the automation that saved over 800 h of manual intervention and stored data in an accessible database.Significance. An improved EPID calibration to allow off-axis measurement maximises the number of patients eligible for IVD (36.8% of patients in this study). We also demonstrate the importance in selecting context-specific assessment metrics and how these can lead to a managable false positive rate. We have shown that the use of fully automated IVD facilitates use on every fraction of treatment. This leads to identification of areas for treatment improvement for both individuals and across a patient cohort, expanding the uses of IVD from simply gross error detection towards treatment optimisation.

Using EpiCore to Enable Rapid Verification of Potential Health Threats: Illustrated Use Cases and Summary Statistics

BACKGROUND

The proliferation of digital disease-detection systems has led to an increase in earlier warning signals, which subsequently have resulted in swifter responses to emerging threats. Such highly sensitive systems can also produce weak signals needing additional information for action. The delays in the response to a genuine health threat are often due to the time it takes to verify a health event. It was the delay in outbreak verification that was the main impetus for creating EpiCore.

OBJECTIVE

This paper describes the potential of crowdsourcing information through EpiCore, a network of voluntary human, animal, and environmental health professionals supporting the verification of early warning signals of potential outbreaks and informing risk assessments by monitoring ongoing threats.

METHODS

This paper uses summary statistics to assess whether EpiCore is meeting its goal to accelerate the time to verification of identified potential health events for epidemic and pandemic intelligence purposes from around the world. Data from the EpiCore platform from January 2018 to December 2022 were analyzed to capture request for information response rates and verification rates. Illustrated use cases are provided to describe how EpiCore members provide information to facilitate the verification of early warning signals of potential outbreaks and for the monitoring and risk assessment of ongoing threats through EpiCore and its utilities.

RESULTS

Since its launch in 2016, EpiCore network membership grew to over 3300 individuals during the first 2 years, consisting of professionals in human, animal, and environmental health, spanning 161 countries. The overall EpiCore response rate to requests for information increased by year between 2018 and 2022 from 65.4% to 68.8% with an initial response typically received within 24 hours (in 2022, 94% of responded requests received a first contribution within 24 h). Five illustrated use cases highlight the various uses of EpiCore.

CONCLUSIONS

As the global demand for data to facilitate disease prevention and control continues to grow, it will be crucial for traditional and nontraditional methods of disease surveillance to work together to ensure health threats are captured earlier. EpiCore is an innovative approach that can support health authorities in decision-making when used complementarily with official early detection and verification systems. EpiCore can shorten the time to verification by confirming early detection signals, informing risk-assessment activities, and monitoring ongoing events.

Novel automated antifungal susceptibility testing system for yeasts based on dual-detection algorithm of turbidimetry and colorimetry

Introduction. The increasing prevalence and growing resistance of fungi present a significant peril to public health. There are only four classes of antifungal medicines available today, and few candidates are in clinical trials.Hypothesis/Gap Statement. Rapid and sensitive diagnostic techniques are lacking for most fungal pathogens, and those that do exist are expensive or hard to obtain.Aim. This study aimed to evaluate the feasibility of a novel automated antifungal susceptibility testing system, Fungus AST, in comparison to the broth microdilution method (BMD) recommended by the Clinical and Laboratory Standards Institute (CLSI).Methodology. A total of 101 clinical Candida spp. isolates were collected from the Zengcheng Branch of Nanfang Hospital and subjected to antifungal susceptibility testing. Antifungal susceptibility was assessed using the Fungus AST method and the BMD.Results. In this study, we introduce a novel automated antifungal susceptibility testing system, Fungus AST, which detects the turbidity and/or colour intensity of microdilution wells using a four-wavelength detection technology in real time and is designed to match the growth characteristics of strains over time. Based on our analysis, all reportable ranges of Fungus AST were suitable for clinical fungal isolates in PR China. Within ±twofold dilutions, reproducibility was 100 %. Considering the BMD as a referenced method, ten antifungal agents (anidulafungin, caspofungin, micafungin, fluconazole, voriconazole, posaconazole, itraconazole, amphotericin B, 5-flucytosine and nystatin) showed an essential agreement of >95 %. The category agreement of five antifungal agents (anidulafungin, caspofungin, micafungin, fluconazole and voriconazole) was excellent at >90 %. One Candida albicans isolate and voriconazole showed a major error (ME) (1.7 %), and no other ME or very ME agents were found.Conclusion. Given the above, it can be argued that the utilization of Fungus AST is a discretionary automated approach. More improvements are needed in Fungus AST compared to the BMD system for a wider range of clinical isolates, including different types of fungi.

Periodic verification of results' comparability between several analyzers: experience in the application of the EP31-A-IR guideline

OBJECTIVES

To assess the usefulness of the EP31-A-IR guideline published by the Clinical and Laboratory Standards Institute (CLSI) to perform the periodic verification of results' comparability between several analyzers.

METHODS

Twenty-four biochemistry parameters that could be measured in different analyzers were included: albumin, alkaline phosphatase, alanine aminotransferase, amylase, aspartate aminotransferase, calcium, chloride, C-reactive protein, creatine kinase, creatinine, direct bilirubin, gamma glutamyl transferase, glucose, lactate dehydrogenase, magnesium, phosphate, potassium, sodium, total bilirubin, total cholesterol, total protein, triglycerides, urea and uric acid. In accordance with the EP31-A-IR guideline: (1) Patient samples were selected considering the concentration or activity of interest. (2) Acceptance criteria were established specifically for each concentration or activity level. A quality specification based on biological variation or on state of the art was selected, considering the analytical performance of the available technology. (3) Maximum allowable differences (MAD) between analyzers were calculated. (4) Measurements were performed as stated in appendix B of the guideline. (5) Maximum differences between analyzers were calculated. Results were considered comparable when the maximum difference was less than or equal to the MAD.

RESULTS

For the 24 parameters evaluated, any difference between analyzers exceeded the MAD.

CONCLUSIONS

The EP31-A-IR guideline proved to be useful for periodic verification of results' comparability. However, it must be considered that, to be practicable, it may require to adjust the acceptance criteria in accordance to the analytical performance of the available technology; as well as the number of analytical measurements conforming to the laboratory resources.

Accreditation of analogue quantum simulators

We present an accreditation protocol for analogue, i.e., continuous-time, quantum simulators. For a given simulation task, it provides an upper bound on the variation distance between the probability distributions at the output of an erroneous and error-free analogue quantum simulator. As its overheads are independent of the size and nature of the simulation, the protocol is ready for immediate usage and practical for the long term. It builds on the recent theoretical advances of strongly universal Hamiltonians and quantum accreditation as well as experimental progress toward the realization of programmable hybrid analogue-digital quantum simulators.

Ultrasonography Imaging versus Waveform Capnography in Detecting Endotracheal Tube Placement during Intubation at a Tertiary Hospital

Background

There is continued research to find new faster, highly accurate, easily accessible, and portable methods of confirming endotracheal tube position during intubation. A newer modality for visualizing endotracheal tube location is transtracheal or transcricothyroid ultrasonography. The aim of this study was to see if ultrasound machine can also be routinely used for the confirmation of endotracheal tube position in operating theaters along with capnograph.

Methods

The study was observational and prospective, conducted from January 2017 to July 2017. Study locations were at the Tribhuvan University Teaching Hospital and Manmohan Cardiothoracic Vascular and Transplant Center operating rooms. Sample size taken was 95.

Results

In the study, 11 patients had esophageal intubation out of the 95. The accuracy of both ultrasonography and capnography was found to be 96.84%. For ultrasonography, the sensitivity, specificity, along with positive predictive value and negative predictive value were 97.62%, 90.91%, 98.80%, and 83.33%, respectively, while that for capnography were found to be 96.43%, 100%, 100%, and 78.57%, respectively. The kappa value was calculated to be 0.749, which suggested the degree of agreement of result between the methods to be good. Compared to capnography, ultrasonography was found to be significantly faster for the confirmation of endotracheal tube location by 16.36 s (15.70-17.02) (P = 0.011).

Conclusion

Both waveform capnography and ultrasonography were found to be accurate and reliable in confirming endotracheal tube location. The use of ultrasound during intubation can help confirm endotracheal tube location faster and also aid in precision when used along with capnography. Manual bag ventilations are not necessary when confirming endotracheal tube position by ultrasonography and thus may help in preventing aspiration of gastric contents into the lungs of the patient.

Belgian Recommendations for Analytical Verification and Validation of Immunohistochemical Tests in Laboratories of Anatomic Pathology

Analytical verification and validation of immunohistochemical (IHC) tests and their equipment are common practices for today's anatomic pathology laboratories. Few references or guidelines are available on how this should be performed. The study of Sciensano (the Belgian national competent authority regarding licensing of medical laboratories) performed in 2016, demonstrated a significant interlaboratory variation in validation procedures of IHC tests among Belgian laboratories. These results suggest the unavailability of practical information on the approach to the verification and validation of these tests. The existing Belgian Practice Guideline for the implementation of a quality management system in anatomic pathology laboratories has been reviewed to meet this demand and, in addition, to prepare the laboratories for the EU-IVD revised regulations (IVDR). This paper describes Belgian recommendations for the verification and validation of IHC tests before implementation, for ongoing validation, and for revalidation. For each type of test (according to the IVDR classification and the origin) and its intended use (purpose), it addresses how to perform analytical verification/validation by recommending: (1) the number of cases in the validation set, (2) the performance characteristics to be evaluated, (3) the objective acceptance criteria, (4) the evaluation method for the obtained results, and (5) how and when to revalidate. A literature study and a risk analysis taking into account the majority of variables regarding verification/validation of methods have been performed, resulting in an expert consensus recommendation that is a compromise among achievability, affordability, and patient safety. This new consensus recommendation has been incorporated in the aforementioned ISO 15189:2012-based Practice Guideline.

Correlation of 20 Single-Nucleotide Polymorphisms with Weight and Wool Traits in Alpine Merino Sheep

SNPs associated with important traits of fine-wool sheep that were previously obtained through genome-wide association analysis screening were verified and analyzed. A total of 20 SNPs related to birth weight, bundle strength, cleaning rate, and fiber diameter were screened using whole-genome resequencing, and the SNPshot assay was used to detect and analyze polymorphisms. This study found that, among the 20 SNPs associated with important traits in Alpine Merino sheep, 8 were monomorphic and 12 were polymorphic, of which 6 showed moderate polymorphisms and 6 showed low polymorphisms. The heterozygosity of the 12 polymorphic loci ranged from 0.10 to 0.49, the effective number of alleles ranged from 1.11 to 1.98, and the polymorphic information content ranged from 0.09 to 0.37. The chi-square test showed that only RHPN2:g.42678119T>G and RALYL:g.90030866A>G were in Hardy-Weinberg disequilibrium (p < 0.05); the other loci were in equilibrium (p > 0.05). These SNPs associated with important traits in Alpine Merino sheep provide a theoretical basis for genomic selection and molecular design breeding.

Towards an extensive set of criteria for safety and cyber-security evaluation of cyber-physical systems

Verification and validation (V&V) are complex processes combining different approaches and incorporating many different methods including many activities. System engineers regularly face the question if their V&V activities lead to better products, and having appropriate criteria at hand for evaluation of safety and cybersecurity of the systems would help to answer such a question. Additionally, when there is a demand to improve the quality of an already managed V&V process, there is a struggle over what criteria to use in order to measure the improvement. This paper presents an extensive set of criteria suitable for safety and cybersecurity evaluation of cyberphysical systems. The evaluation criteria are agreed upon by 60 researchers from 32 academic and industrial organizations jointly working in a large-scale European research project on 13 real-world use cases from the domains of automotive, railway, aerospace, agriculture, healthcare, and industrial robotics.

Time Until Proof of Credentials Significantly Decreases With the Use of Blockchain Technology and the Document Management System

Background and objective Physician credentialing and verification in the medical education setting are challenging for the modern workforce. The credentials verification process may be time-consuming and challenging for participants. Blockchain technology is a potential resource for authenticating records with reduced administrative burden and time spent. This study investigates whether the use of blockchain technology reduces the time until verification of a participant's credentials. Methods An anonymous letter designation was assigned to 23 medical students. All students enrolled in, and completed, a course designed and run by the Edward Via College of Osteopathic Medicine at Auburn (VCOM) as part of the routine medical education curriculum. At the completion of the training, a credentials certificate was produced, which showed course completion. The anonymous letter designation was utilized in the creation of the certificates. The letter designations were shared with an anonymous investigator. No student names were shared with the investigator. The investigator posed as an employing/credentialing entity and contacted VCOM to record the time required to verify the credentials certificate indicating course completion. The elapsed time until credentials verification was completed for each student in the current system (CS) was recorded. Subsequently, the credentials certificate was minted as a blockchain-based, non-fungible token (NFT) and uploaded to a document software management system. An investigator again posed as an employing/credentialing entity and utilized this system to verify the credentials of the 23 students in the study using the NFT system. The times elapsed until verification of credentials were recorded as the NFT pathway. Data from the NFT pathway and non-NFT pathway were compiled and reviewed. Results Data were normally distributed per the Andersen-Darling Test. A t-test (Welch's method) was performed. The mean time of 111,214 seconds (30.89 hours or 1.29 days) in the CS varied significantly from the mean time of 14 seconds in the NFT blockchain system (p<0.01). The standard deviation of 56,568 seconds in CS varied significantly from 9.9178 seconds in the NFT blockchain (p<0.01).  Conclusions The NFT/blockchain system reduces the mean time until the credential verification is completed and reduces the variance seen in time until credentialing is completed. The NFT/blockchain system may significantly bring down the administrative burden and time spent in the credentialing process.

Microbiological hazards associated with the use of water in the post-harvest handling and processing operations of fresh and frozen fruits, vegetables and herbs (ffFVHs). Part 1 (outbreak data analysis, literature review and stakeholder questionnaire)

The contamination of water used in post-harvest handling and processing operations of fresh and frozen fruit, vegetables and herbs (ffFVHs) is a global concern. The most relevant microbial hazards associated with this water are: Listeria monocytogenes, Salmonella spp., human pathogenic Escherichia coli and enteric viruses, which have been linked to multiple outbreaks associated with ffFVHs in the European Union (EU). Contamination (i.e. the accumulation of microbiological hazards) of the process water during post-harvest handling and processing operations is affected by several factors including: the type and contamination of the FVHs being processed, duration of the operation and transfer of microorganisms from the product to the water and vice versa, etc. For food business operators (FBOp), it is important to maintain the microbiological quality of the process water to assure the safety of ffFVHs. Good manufacturing practices (GMP) and good hygienic practices (GHP) related to a water management plan and the implementation of a water management system are critical to maintain the microbiological quality of the process water. Identified hygienic practices include technical maintenance of infrastructure, training of staff and cooling of post-harvest process water. Intervention strategies (e.g. use of water disinfection treatments and water replenishment) have been suggested to maintain the microbiological quality of process water. Chlorine-based disinfectants and peroxyacetic acid have been reported as common water disinfection treatments. However, given current practices in the EU, evidence of their efficacy under industrial conditions is only available for chlorine-based disinfectants. The use of water disinfection treatments must be undertaken following an appropriate water management strategy including validation, operational monitoring and verification. During operational monitoring, real-time information on process parameters related to the process and product, as well as the water and water disinfection treatment(s) are necessary. More specific guidance for FBOp on the validation, operational monitoring and verification is needed.

Multicentre verification of haematology laboratory blood collection tubes during a global blood collection tube shortage

INTRODUCTION

Verification of blood collection tubes is essential for clinical laboratories. The aim of this study was to assess performance of candidate tubes from four alternative suppliers for routine diagnostic haematology testing during an impending global shortage of blood collection tubes.

METHODS

A multicentre verification study was performed in Cape Town, South Africa. Blood from 300 healthy volunteers was collected into K2 EDTA and sodium citrate tubes of BD Vacutainer® comparator tubes and one of four candidate tubes (Vacucare, Vacuette®, V-TUBE™ and Vacutest®). A technical verification was performed, which included tube physical properties and safety. Routine haematology testing was performed for clinical verification.

RESULTS

Vacucare tubes did not have a fill-line indicator, Vacuette® tubes had external blood contamination on the caps post-venesection and Vacutest® tubes had hard rubber stoppers. K2 EDTA tubes of Vacuette®, Vacucare and Vacutest® performed similarly to the comparator. Unacceptable constant bias was seen for PT in Vacucare (95% CI -2.38 to -0.10), Vacutest® (95% CI -1.91 to -0.49) and Vacuette® (95% CI 0.10-1.84) tubes and for aPTT in Vacuette® (95% CI 0.22-2.00) and V-TUBE™ (95% CI -2.88 to -0.44). Unacceptable %bias was seen for aPTT in Vacucare (95% CI 2.78-4.59) and Vacutest® tubes (95% CI 2.53-3.82; desirable ±2.30), and in V-TUBE™ for mean cell volume (95% CI 1.15-1.47, desirable ±0.95%) and mean cell haemoglobin concentration (95% CI -1.65 to -0.93, desirable ±0.43%).

CONCLUSION

Blood collection tubes introduce variability to routine haematology results. We recommend that laboratories use one brand of tube. Verification of new candidate tubes should be performed to ensure consistency and reliable reporting of results.

veRification: an R Shiny application for laboratory method verification and validation

OBJECTIVES

According to international standards, clinical laboratories are required to verify the performance of assays prior to their implementation in routine practice. This typically involves the assessment of the assay's imprecision and trueness vs. appropriate targets. The analysis of these data is typically performed using frequentist statistical methods and often requires the use of closed source, proprietary software. The motivation for this paper was therefore to develop an open-source, freely available software capable of performing Bayesian analysis of verification data.

METHODS

The veRification application presented here was developed with the freely available R statistical computing environment, using the Shiny application framework. The codebase is fully open-source and is available as an R package on GitHub.

RESULTS

The developed application allows the user to analyze imprecision, trueness against external quality assurance, trueness against reference material, method comparison, and diagnostic performance data within a fully Bayesian framework (with frequentist methods also being available for some analyses).

CONCLUSIONS

Bayesian methods can have a steep learning curve and thus the work presented here aims to make Bayesian analyses of clinical laboratory data more accessible. Moreover, the development of the application and seeks to encourage the dissemination of open-source software within the community and provides a framework through which Shiny applications can be developed, shared, and iterated upon.

Analytical evaluation and quality assessment of the ARKRAY ADAMS A1c Lite HA-8380V for HbA1c

INTRODUCTION

ARKRAY ADAMS A1c Lite HA-8380V is a fully automated high- performance liquid chromatography system for the measurement of HbA1c. We aimed to evaluate its analytical performance using the Variant Mode.

METHODS

Carry-over, linearity, imprecision, trueness, interferences and comparison against ARKRAY ADAMS A1c HA-8180V and HA-8180T analyzers were studied.

RESULTS

Total CVs 0.93% (IFCC units), 0.63% (NGSP units) at low concentration and 1.01% (IFCC) 0.74% (NGSP), at high concentration. Mean difference with the target values was -0.44 mmol/mol (IFCC) -0.04% (NGSP). Carry-over, linearity and method comparison were excellent.The results were not affected in the range of total Hb 39-199 g/L, labile fraction 5.7%, carbamylated Hb 9.1% nor acetylated Hb 7.8%, effect of common variants was negligible.

CONCLUSIONS

the analyzer demonstrated very good analytical performances, according to the consensus criteria established for HbA1c; it is adequate for laboratories with medium-low workloads.

The value of RPS15 and MRPS27 in ischemic stroke

Ischemic stroke is caused by insufficient blood supply to the brain. It has acute onset, often disturbance of consciousness, and high mortality and disability rate. However, relationship between ribosomal proteins (RP)-S15 and mitochondrial ribosomal proteins (MRP)-S27 and ischemic stroke remains unclear. The ischemic stroke datasets GSE22255, GSE16561, and GSE199435 were downloaded from gene expression omnibus generated by GPL6883, GPL11154, and GPL570. Differentially expressed genes (DEGs) were screened, and the construction and analysis of protein-protein interaction network, functional enrichment analysis and gene set enrichment analysis were performed. The gene expression heat map was drawn. Comparative toxicogenomics database analysis were performed to find the disease most related to core gene. TargetScan screened miRNAs that regulated central DEGs. Five hundred DEGs were identified. According to gene ontology analysis, they were mainly enriched in leukocyte activation, myoid cell activation involved in immune response, cell membrane, mitochondria, secretory vesicles, catalytic activity, enzyme binding, ribonucleic acid binding, splicing. Gene set enrichment analysis showed that the enrichment items are similar to the enrichment items of differentially expressed genes. And 20 core genes were obtained. Comparative toxicogenomics database analysis showed that 6 genes (RPS15, RPS2, RPS3, MRPS27, POLR2A, MRPS26) were found to be associated with chemical and drug-induced liver injury, necrosis, delayed prenatal exposure, nephropathy, hepatomegaly and tumor. RPS15 and MRPS27 are the core genes of ischemic stroke and play an important role in ischemic stroke.

Implementing laboratory automation for next-generation sequencing: benefits and challenges for library preparation

In the wake of COVID-19, the importance of next-generation sequencing (NGS) for diagnostic testing and surveillance-based screening has never been more evident. Considering this, continued investment is critical to ensure more public health laboratories can adopt these advanced molecular technologies. However, many facilities may face potential barriers such as limited staff available to routinely prepare, test, and analyze samples, lack of expertise or experience in sequencing, difficulties in assay standardization, and an inability to handle throughput within expected turnaround times. Workflow automation provides an opportunity to overcome many of these challenges. By identifying these types of sustainable solutions, laboratories can begin to utilize more advanced molecular-based approaches for routine testing. Nevertheless, the introduction of automation, while valuable, does not come without its own challenges. This perspective article aims to highlight the benefits and difficulties of implementing laboratory automation used for sequencing. We discuss strategies for implementation, including things to consider when selecting instrumentation, how to approach validations, staff training, and troubleshooting.

Basics of laboratory statistics

The strict monitoring of examinations and evaluation of newer methods or instruments is a daily routine in clinical laboratory. The automated analyzers accumulate an enormous amount of data from patients' examinations and quality control procedures. This laboratory data is meaningless if it does not generate the information that we can extend to the population of our interest. In an analytical work, the most important operation is the comparison of data, to quantify accuracy and precision and to generate meaningful explanation for clinician and patients queries. Most of the information needed in the regular laboratory work can be obtained with the use of simple convenient statistical tools. This article describes the basics of laboratory statistics, the knowledge of which answers about the application of quality control in laboratory, accuracy and diagnostic power of our examinations, variability in reports, comparison of different methods and derivation of a biological reference interval for an analyte.

Application of Wireless Magnetic Sensors in the Urban Environment and Their Accuracy Verification

In a smart city, sensors are essential elements-the source of up-to-date traffic information. This article deals with magnetic sensors connected to wireless sensor networks (WSNs). They have a low investment cost, a long lifetime, and easy installation. However, it is still necessary to disturb the road surface locally during their installation. All road lanes to and from the city center of Žilina have sensors that send data at five-minute intervals. They send up-to-date information about the traffic flow's intensity, speed, and composition. The LoRa network ensures the data transmission, but in the event of failure, the 4G/LTE modem realizes the backup transmission. The disadvantage of this application of sensors is their accuracy. The research task was to compare the outputs from the WSN with a traffic survey. The appropriate method for the traffic survey on the selected road profile is a video recording and speed measurement using the Sierzega radar. The results show distorted values, mainly for short intervals. The most accurate output from magnetic sensors is the number of vehicles. On the other hand, traffic flow composition and speed measurement are relatively inaccurate because it is not easy to identify vehicles based on dynamic length. Another problem with sensors is frequent communication outages, which cause an accumulation of values after the outage ends. The secondary objective of the paper is to describe the traffic sensor network and its publicly accessible database. In the end, there are several proposals for data usage.

Analytical verification of the Dymind D7-CRP automated analyser

Introduction

The aim of this study was to perform a verification of the Dymind D7-CRP automated analyser and compare it with established analysers.

Materials and methods

Analytical verification included estimation of repeatability, between run precision, within-laboratory precision, and bias in control samples with low, normal and high levels. The acceptance criteria for analytical verification were defined using the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) 2019 Biological Variation Database. Method comparison between the Dymind D7-CRP and the Sysmex XN1000 for haematological parameters and the Dymind D7-CRP and the Beckman Coulter AU680 for CRP values was performed on 40 patient samples.

Results

Analytical verification criteria were adequately met with the exception of monocyte count for repeatability and within-laboratory precision (13.4% and 11.5%, respectively, acceptance criteria 10.1%) and measurement uncertainty (23.0, acceptance criteria 20.0%) at low level, eosinophil count for BIAS at the low level (37.7%, acceptance criteria 25.2%), basophil count (BAS) for BIAS at the high level (14.2%, acceptance criteria 10.9%), and mean platelet volume (MPV) for repeatability (4.2% and 6.8%), between run precision (2.2% and 4.7%), within-laboratory precision (4.0% and 7.3%) (acceptance criteria 1.7%), and measurement uncertainty (8.0 and 14.6%, acceptance criteria 3.4%) at both the low and high concentrations. Method comparison showed no clinically significant constant or proportional differences for all parameters except BAS and MPV.

Conclusion

The analytical verification of the Dymind D7-CRP showed adequate analytical characteristics. The Dymind D7-CRP can be used interchangeably with the Sysmex XN-1000 for all parameters tested, except BAS and MPV, and with the Beckman Coulter AU-680 for the determination of CRP.

Structured Verification of Machine Learning Models in Industrial Settings

The use of machine learning (ML) allows us to automate and scale the decision-making processes. The key to this automation is the development of ML models that generalize training data toward unseen data. Such models can become extremely versatile and powerful, which makes democratization of artificial intelligence (AI) possible, that is, providing ML to non-ML experts such as software engineers or domain experts. Typically, automated ML (AutoML) is being referred to as a key step toward it. However, from our perspective, we believe that democratization of the verification process of ML systems is a larger and even more crucial challenge to achieve the democratization of AI. Currently, the process of ensuring that an ML model works as intended is unstructured. It is largely based on experience and domain knowledge that cannot be automated. The current approaches such as cross-validation or explainable AI are not enough to overcome the real challenges and are discussed extensively in this article. Arguing toward structured verification approaches, we discuss a set of guidelines to verify models, code, and data in each step of the ML lifecycle. These guidelines can help to reliably measure and select an optimal solution, besides minimizing the risk of bugs and undesired behavior in edge-cases.

A verified and validated moving domain computational fluid dynamics solver with applications to cardiovascular flows

Computational fluid dynamics (CFD) in combination with patient-specific medical images has been used to correlate flow phenotypes with disease initiation, progression and outcome, in search of a prospective clinical tool. A large number of CFD software packages are available, but are typically based on rigid domains and low-order finite volume methods, and are often implemented in massive low-level C++ libraries. Furthermore, only a handful of solvers have been appropriately verified and validated for their intended use. Our goal was to develop, verify and validate an open-source CFD solver for moving domains, with applications to cardiovascular flows. The solver is an extension of the CFD solver Oasis, which is based on the finite element method and implemented using the FEniCS open source framework. The new solver, named OasisMove, extends Oasis by expressing the Navier-Stokes equations in the arbitrary Lagrangian-Eulerian formulation, which is suitable for handling moving domains. For code verification we used the method of manufactured solutions for a moving 2D vortex problem, and for validation we compared our results against existing high-resolution simulations and laboratory experiments for two moving domain problems of varying complexity. Verification results showed that the L 2 error followed the theoretical convergence rates. The temporal accuracy was second-order, while the spatial accuracy was second- and third-order using ℙ 1 / ℙ 1 and ℙ 2 / ℙ 1 finite elements, respectively. Validation results showed good agreement with existing benchmark results, by reproducing lift and drag coefficients with less than 1% error, and demonstrating the solver's ability to capture vortex patterns in transitional and turbulent-like flow regimes. In conclusion, we have shown that OasisMove is an open-source, accurate and reliable solver for cardiovascular flows in moving domains.

The Analytical and Clinical Validity of the pfSTEP Digital Biomarker of the Susceptibility/Risk of Declining Physical Function in Community-Dwelling Older Adults

Measures of stepping volume and rate are common outputs from wearable devices, such as accelerometers. It has been proposed that biomedical technologies, including accelerometers and their algorithms, should undergo rigorous verification as well as analytical and clinical validation to demonstrate that they are fit for purpose. The aim of this study was to use the V3 framework to assess the analytical and clinical validity of a wrist-worn measurement system of stepping volume and rate, formed by the GENEActiv accelerometer and GENEAcount step counting algorithm. The analytical validity was assessed by measuring the level of agreement between the wrist-worn system and a thigh-worn system (activPAL), the reference measure. The clinical validity was assessed by establishing the prospective association between the changes in stepping volume and rate with changes in physical function (SPPB score). The agreement of the thigh-worn reference system and the wrist-worn system was excellent for total daily steps (CCC = 0.88, 95% CI 0.83-0.91) and moderate for walking steps and faster-paced walking steps (CCC = 0.61, 95% CI 0.53-0.68 and 0.55, 95% CI 0.46-0.64, respectively). A higher number of total steps and faster paced-walking steps was consistently associated with better physical function. After 24 months, an increase of 1000 daily faster-paced walking steps was associated with a clinically meaningful increase in physical function (0.53 SPPB score, 95% CI 0.32-0.74). We have validated a digital susceptibility/risk biomarker-pfSTEP-that identifies an associated risk of low physical function in community-dwelling older adults using a wrist-worn accelerometer and its accompanying open-source step counting algorithm.

Predicting children's real-ear-to-coupler differences based on tympanometric data

OBJECTIVE

Paediatric hearing-aid verification relies on measures of output obtained from the ear canal or in a coupler with the child's real-ear-to-coupler difference (RECD). Measured RECD cannot always be completed in children, leading to fitting inaccuracies. Audiologists often have tympanometry data that characterises the child's ear-canal acoustics. The goal of this study was to determine if tympanometry can be used to improve predictions of measured RECD.

DESIGN

A retrospective analysis of RECD and admittance, tympanometric peak pressure, and equivalent ear-canal volume from 226 Hz tympanometry collected as part of a longitudinal study of children with hearing loss were modelled with Bayesian hierarchical regression.

STUDY SAMPLE

Two-hundred sixty-six children with mild-to-severe hearing loss contributed data.

RESULTS

Age-based average RECD models were within 3 dB of measured RECD values in 54% of cases with normal middle ear status and 50.6% of cases with abnormal middle ear status. Immittance-predicted RECD were within 3 dB in 69.6% of cases with normal middle ear status and 74.4% of cases with abnormal middle ear status.

CONCLUSION

Immittance-predicted RECD was more accurate than age-based average RECD, particularly in children with abnormal middle ear status. The findings suggest that 226 Hz tympanometry could be used clinically to improve predictions of measured RECD when it cannot be measured.

Verifiable biology

The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological systems. In particular, formal verification, complementary approach to standard computational techniques such as simulation, is used to validate the system correctness and obtain critical information about system behaviour. In this study, we survey the most frequently used computational modelling approaches and formal verification techniques for computational biology. We compare a number of verification tools and software suites used to analyse biological systems and biochemical networks, and to verify a wide range of biological properties. For users who have no expertise in formal verification, we present a novel methodology that allows them to easily apply formal verification techniques to analyse their biological or biochemical system of interest.

Application and Development of QKD-Based Quantum Secure Communication

Quantum key distribution (QKD) protocols have unique advantages of enabling symmetric key sharing with information-theoretic security (ITS) between remote locations, which ensure the long-term security even in the era of quantum computation. QKD-based quantum secure communication (QSC) enhancing the security of key generation and update rate of keys, which could be integrated with a variety of cryptographic applications and communication protocols, has become one of the important solutions to improve information security. In recent years, the research on QKD has been active and productive, the performance of novel protocol systems has been improved significantly, and the feasibility of satellite-based QKD has been experimentally verified. QKD network construction, application exploration, and standardization have been carried out in China as well as other countries and regions around the world. Although QKD-based QSC applications and industrialization are still in the initial stage, the research and exploration momentum is positive and more achievements could be expected in the future.

Inhibition of apoptosis through AKT-mTOR pathway in ovarian cancer and renal cancer

OBJECTIVE

Ovarian cancer and renal cancer are malignant tumors; however, the relationship between TTK Protein Kinase (TTK), AKT-mTOR pathway and ovarian cancer, renal cancer remains unclear.

METHODS

Download GSE36668 and GSE69428 from Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was performed. Created protein-protein interaction (PPI) network. Used Gene Ontology analysis (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional enrichment analysis. Gene Set Enrichment Analysis (GSEA) analysis and survival analysis were performed. Created animal model for western blot analysis. Gene Expression Profiling Interactive Analysis (GEPIA) was performed to explore the role of TTK on the overall survival of renal cancer.

RESULTS

GO showed that DEGs were enriched in anion and small molecule binding, and DNA methylation. KEGG analysis presented that they mostly enriched in cholesterol metabolism, type 1 diabetes, sphingolipid metabolism, ABC transporters, etc., TTK, mTOR, p-mTOR, AKT, p-AKT, 4EBP1, p-4EBP1 and Bcl-2 are highly expressed in ovarian cancer, Bax, Caspase3 are lowly expressed in ovarian cancer, cell apoptosis is inhibited, leading to deterioration of ovarian cancer. Furthermore, the TTK was not only the hub biomarker of ovarian cancer, but also one significant hub gene of renal cancer, and its expression was up-regulated in the renal cancer. Compared with the renal cancer patients with low expression of TTK, the patients with high expression of TTK have the poor overall survival (P = 0.0021).

CONCLUSION

TTK inhibits apoptosis through AKT-mTOR pathway, worsening ovarian cancer. And TTK was also one significant hub biomarker of renal cancer.

Phosphonylated tyrosine and lysine residues as biomarkers of local exposure of human hair to the organophosphorus nerve agents sarin and VX

We herein present for the first time a micro liquid chromatography-electrospray ionization high-resolution tandem-mass spectrometry (μLC-ESI MS/HR MS) procedure to detect phosphonylated tyrosine (Tyr) and lysine (Lys) residues obtained from human hair exposed to organophosphorus nerve agents (OPNA). In general, toxic OPNA react with endogenous blood proteins causing the formation of adducts representing well-known targets for biomedical analysis to prove exposure. In contrast, no protein-derived biomarker has been introduced so far to document local exposure of hair. Accordingly, we developed and characterized a μLC-ESI MS/HR MS method for the analysis of scalp hair exposed to OPNA in vitro. Type I and Type II keratin from hair was dissolved during lysis, precipitated and subjected to pronase-catalyzed hydrolysis yielding single adducted Lys and in a much higher amount Tyr residues. Exposure to sarin caused the adduction of an isopropyl methylphosphonic acid moiety and exposure to VX yielded adducts of ethyl methylphosphonic acid, well suited as biomarkers of exposure. These were of appropriate stability in the autosampler for 24 h. The biomarker yield obtained from hair of six individuals as well as from hair of six different parts of the body of one individual (armpit, beard, leg, arm, scalp, and pubic) differed reasonably indicating the variable individual protein composition and structure of hair. Exposed hair stored at ambient temperature for 9 weeks with contact to air and daylight showed stability of all adducts and therefore their suitability for verification of exposure.

Leveraging Multiple Distinct EEG Training Sessions for Improvement of Spectral-Based Biometric Verification Results

Most studies on EEG-based biometry recognition report results based on signal databases, with a limited number of recorded EEG sessions using the same single EEG recording for both training and testing a proposed model. However, the EEG signal is highly vulnerable to interferences, electrode placement, and temporary conditions, which can lead to overestimated assessments of the considered methods. Our study examined how different numbers of distinct recording sessions used as training sessions would affect EEG-based verification. We analyzed the original data from 29 participants with 20 distinct recorded sessions each, as well as 23 additional impostors with only one session each. We applied raw coefficients of power spectral density estimate, and the coefficients of power spectral density estimate converted to the decibel scale, as the input to a shallow neural network. Our study showed that the variance introduced by multiple recording sessions affects sensitivity. We also showed that increasing the number of sessions above eight did not improve the results under our conditions. For 15 training sessions, the achieved accuracy was 96.7 ± 4.2%, and for eight training sessions and 12 test sessions, it was 94.9 ± 4.6%. For 15 training sessions, the rate of successful impostor attacks over all attack attempts was 3.1 ± 2.2%, but this number was not significantly different from using six recording sessions for training. Our findings indicate the need to include data from multiple recording sessions in EEG-based recognition for training, and that increasing the number of test sessions did not significantly affect the obtained results. Although the presented results are for the resting-state, they may serve as a baseline for other paradigms.

Trusted Operation of Cyber-Physical Processes Based on Assessment of the System's State and Operating Mode

We consider the trusted operation of cyber-physical processes based on an assessment of the system's state and operating mode and present a method for detecting anomalies in the behavior of a cyber-physical system (CPS) based on the analysis of the data transmitted by its sensory subsystem. Probability theory and mathematical statistics are used to process and normalize the data in order to determine whether or not the system is in the correct operating mode and control process state. To describe the mode-specific control processes of a CPS, the paradigm of using cyber-physical parameters is taken as a basis, as it is the feature that most clearly reflects the system's interaction with physical processes. In this study, two metrics were taken as a sign of an anomaly: the probability of falling into the sensor values' confidence interval and parameter change monitoring. These two metrics, as well as the current mode evaluation, produce a final probability function for our trust in the CPS's currently executing control process, which is, in turn, determined by the operating mode of the system. Based on the results of this trust assessment, it is possible to draw a conclusion about the processing state in which the system is operating. If the score is higher than 0.6, it means the system is in a trusted state. If the score is equal to 0.6, it means the system is in an uncertain state. If the trust score tends towards zero, then the system can be interpreted as unstable or under stress due to a system failure or deliberate attack. Through a case study using cyber-attack data for an unmanned aerial vehicle (UAV), it was found that the method works well. When we were evaluating the normal flight mode, there were no false positive anomaly estimates. When we were evaluating the UAV's state during an attack, a deviation and an untrusted state were detected. This method can be used to implement software solutions aimed at detecting system faults and cyber-attacks, and thus make decisions about the presence of malfunctions in the operation of a CPS, thereby minimizing the amount of knowledge and initial data about the system.

A clinical study comparing polymer and gold fiducials for prostate cancer radiotherapy

Introduction

Image guidance with gold fiducials improves outcomes of prostate radiotherapy. However, gold produces artefact on CT imaging, interfering with contouring and verification. The purpose of this study was to compare polymer to standard gold fiducials using radiotherapy imaging modalities to assess the visibility and artefact.

Methods

Twenty eight patients with locally advanced prostate cancer were enrolled, half had three polymer fiducials implanted into the prostate and half underwent insertion of gold fiducials. Patients were imaged with CT, T2 weighted MRI, cone-beam CT (CBCT) and planar KV images. Fiducials were scored for visibility and assessed for CT artefact in surrounding prostate tissue. The artefact was quantified from Hounsfield number histograms and separated into percentile ranges and proportion of voxels in HU normal tissue range of a 2cm sphere surrounding the fiducial.

Results

Gold and polymer fiducials were sufficiently visible for CT and CBCT verification. The gold fiducials could be visualized well on KV planar imaging; however, the polymer markers were obscured by pelvic bones. Neither polymer nor gold fiducials could be visualized on MRI. The polymer fiducial produced less artefact than gold on CT, having less voxel spread for the HU percentile ranges and a greater proportion of voxels in the normal tissue range.

Conclusions

Polymer fiducials are a more suitable fiducial than gold for CT/CBCT in prostate cancer radiotherapy, demonstrating minimal artefact and good visibility on CT. However, they were not well seen on MRI or KV imaging and thus not suitable for co-registration or planar KV verification.

Pediatric reference interval verification for 17 specialized immunoassays and cancer markers on the Abbott Alinity i system in the CALIPER cohort of healthy children and adolescents

OBJECTIVES

Clinical laboratory investigation of autoimmune, metabolic, and oncologic disorders in children and adolescents relies on appropriateness of reference intervals (RIs). The Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) previously established comprehensive pediatric RIs for specialized immunoassays on the Abbott ARCHITECT system. Herein, we aim to verify performance on new Alinity i assays by evaluating sera collected from healthy children as per Clinical and Laboratory Standards Institute (CLSI) EP-28A3C guidelines.

METHODS

Precision, linearity, and method comparison experiments were completed for 17 specialized Alinity immunoassays, including cancer antigens, autoimmune peptides, and hormones. Sera collected from healthy children and adolescents (birth-18 years, n=100) were evaluated. CLSI-based verification was completed using previously established CALIPER RIs for ARCHITECT assays as the reference.

RESULTS

Of 17 specialized immunoassays assays, only anti-cyclic citrullinated peptides (anti-CCP) did not meet acceptable verification criterion (i.e., ≥90% of results within ARCHITECT reference CI). Anti-thyroglobulin, anti-thyroid peroxidase, and carcinoembryonic antigen did not require age-specific consideration beyond one year of age, with 63, 91, and 80% of samples equalling the limit of detection, respectively. Estimates were separated by sex for relevant assays (e.g., sex hormone binding globulin, total and free prostate specific antigen).

CONCLUSIONS

Findings support transferability of pediatric RIs on ARCHITECT system to the Alinity system for 16 specialized immunoassays in the CALIPER cohort and will be a useful resource for pediatric clinical laboratories using Alinity assays. Further work is needed to establish evidence-based interpretative recommendations for anti-CCP and continue to evaluate pediatric RI acceptability for newly available assay technologies.

Verification, Evaluation, and Validation: Which, How & Why, in Medical Augmented Reality System Design

This paper presents a discussion about the fundamental principles of Analysis of Augmented and Virtual Reality (AR/VR) Systems for Medical Imaging and Computer-Assisted Interventions. The three key concepts of Analysis (Verification, Evaluation, and Validation) are introduced, illustrated with examples of systems using AR/VR, and defined. The concepts of system specifications, measurement accuracy, uncertainty, and observer variability are defined and related to the analysis principles. The concepts are illustrated with examples of AR/VR working systems.

Listening Preferences of New Adult Hearing Aid Users: A Registered, Double-Blind, Randomized, Mixed-Methods Clinical Trial of Initial Versus Real-Ear Fit

Hearing aid verification with real-ear measurement (REM) is recommended in clinical practice. Improvements, over time, in accuracy of manufacturers' initial fit mean the benefit of routine REM for new adult users is unclear. This registered, double-blinded, randomized, mixed-methods clinical trial aimed to (i) determine whether new adult hearing aid users prefer initial or real-ear fit and (ii) investigate the reasons for preferences. New adult hearing aid users (n = 45) were each fitted with two programs: the initial fit and real-ear fit, both with adjustments based on immediate feedback from the patient. Participants were asked to complete daily paired-comparisons of the two programs with a magnitude estimation of the preference, one for each of clarity/comfort in quiet/noise as well as overall preference. The results revealed gain adjustment requests were low in number and small in magnitude. Deviation from NAL-NL2 targets (after adjustment for a 65 dB SPL input) was close to zero, except at high frequencies where real-ear fits were around 3 dB closer to target. There was no difference in clarity ratings between programs, but comfort ratings favored initial fit. Overall, 10 participants (22%) expressed a preference for real-ear fit. Reasons for preference were primarily based on comfort with the initial fit and clarity with real-ear fit. It may be acceptable to fit new adult users with mild-to-moderate hearing loss without the need for REMs, if the primary outcome of interest is user preference. It remains to be seen if the findings generalize to other fitting software, other outcome measures and more severe hearing loss.

Design of a temperature-feedback controlled automated magnetic hyperthermia therapy device

Introduction

Magnetic hyperthermia therapy (MHT) is a minimally invasive adjuvant therapy capable of damaging tumors using magnetic nanoparticles exposed radiofrequency alternating magnetic fields. One of the challenges of MHT is thermal dose control and excessive heating in superficial tissues from off target eddy current heating.

Methods

We report the development of a control system to maintain target temperature during MHT with an automatic safety shutoff feature in adherence to FDA Design Control Guidance. A proportional-integral-derivative (PID) control algorithm was designed and implemented in NI LabVIEW^®. A standard reference material copper wire was used as the heat source to verify the controller performance in gel phantom experiments. Coupled electromagnetic thermal finite element analysis simulations were used to identify the initial controller gains.

Results

Results showed that the PID controller successfully achieved the target temperature control despite significant perturbations.

Discussion and Conclusion

Feasibility of PID control algorithm to improve efficacy and safety of MHT was demonstrated.

Awareness and attitude toward oocyte cryopreservation for non-medical reasons: a study on women candidates for social egg freezing

PURPOSE

The present study was to investigate awareness and attitudes toward female fertility and aging, desire for a child and motherhood, and oocyte freezing for non-medical reasons among women candidates for Social Egg Freezing (SEF).

MATERIALS AND METHODS

This was a cross-sectional study on all 216 women who sought oocyte cryopreservation for nonmedical reasons at Royan Institute. A 24-item self-administered questionnaire measured knowledge and attitudes to SEF. Responses were as yes/no or a 4-point Likert scale.

RESULTS

Only 40% of participants accurately indicated that having a sexual partner does not help to preserve their fertility. A quarter of women correctly recalled chance of pregnancy with unprotected intercourse during a period of a year, for women 20 to 40 years old. Only one-third of respondents accurately identified the age-related fertility decline at 35-39 years. Only 6.9% correctly mentioned the low chance of pregnancy after egg freezing at 35 years old. Almost a third of women knew that the age range of 31-35 years is the right age to freeze an egg with the highest chance of pregnancy. Aging and health of offspring were most influential in women's decisions on SEF.

CONCLUSION

In conclusion, there was significant gaps in knowledge about age-related fertility decline, and egg cryopreservation conditions and its complications. It is crucial to impart to these women a better knowledge about fertility and a realistic picture about SEF, especially on the number of high-quality retrieved mature oocytes and live birth rates depend on women's age.

Method evaluation in the clinical laboratory

Method evaluation is one of the critical components of the quality system that ensures the ongoing quality of a clinical laboratory. As part of implementing new methods or reviewing best practices, the peer-reviewed published literature is often searched for guidance. From the outset, Clinical Chemistry and Laboratory Medicine (CCLM) has a rich history of publishing methods relevant to clinical laboratory medicine. An insight into submissions, from editors' and reviewers' experiences, shows that authors still struggle with method evaluation, particularly the appropriate requirements for validation in clinical laboratory medicine. Here, we consider through a series of discussion points an overview of the status, challenges, and needs of method evaluation from the perspective of clinical laboratory medicine. We identify six key high-level aspects of clinical laboratory method evaluation that potentially lead to inconsistency. 1. Standardisation of terminology, 2. Selection of analytical performance specifications, 3. Experimental design of method evaluation, 4. Sample requirements of method evaluation, 5. Statistical assessment and interpretation of method evaluation data, and 6. Reporting of method evaluation data. Each of these areas requires considerable work to harmonise the practice of method evaluation in laboratory medicine, including more empirical studies to be incorporated into guidance documents that are relevant to clinical laboratories and are freely and widely available. To further close the loop, educational activities and fostering professional collaborations are essential to promote and improve the practice of method evaluation procedures.

Accommodating population differences when validating risk prediction models

Validation of risk prediction models in independent data provides a more rigorous assessment of model performance than internal assessment, for example, done by cross-validation in the data used for model development. However, several differences between the populations that gave rise to the training and the validation data can lead to seemingly poor performance of a risk model. In this paper we formalize the notions of "similarity" or "relatedness" of the training and validation data, and define reproducibility and transportability. We address the impact of different distributions of model predictors and differences in verifying the disease status or outcome on measures of calibration, accuracy and discrimination of a model. When individual level information from both the training and validation data sets is available, we propose and study weighted versions of the validation metrics that adjust for differences in the risk factor distributions and in outcome verification between the training and validation data to provide a more comprehensive assessment of model performance. We provide conditions on the risk model and the populations that gave rise to the training and validation data that ensure a model's reproducibility or transportability, and show how to check these conditions using weighted and unweighted performance measures. We illustrate the method by developing and validating a model that predicts the risk of developing prostate cancer using data from two large prostate cancer screening trials.

Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER

Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.

Two triphosphate tunnel metalloenzymes from apple exhibit adenylyl cyclase activity

Adenylyl cyclase (AC) is the key catalytic enzyme for the synthesis of 3',5'-cyclic adenosine monophosphate. Various ACs have been identified in microorganisms and mammals, but studies on plant ACs are still limited. No AC in woody plants has been reported until now. Based on the information on HpAC1, three enzymes were screened out from the woody fruit tree apple, and two of them (MdTTM1 and MdTTM2) were verified and confirmed to display AC activity. Interestingly, in the apple genome, these two genes were annotated as triphosphate tunnel metalloenzymes (TTMs) which were widely found in three superkingdoms of life with multiple substrate specificities and enzymatic activities, especially triphosphate hydrolase. In addition, the predicted structures of these two proteins were parallel, especially of the catalytic tunnel, including conserved domains, motifs, and folded structures. Their tertiary structures exhibited classic TTM properties, like the characteristic EXEXK motif and β-stranded anti-parallel tunnel capable of coordinating divalent cations. Moreover, MdTTM2 and HpAC1 displayed powerful hydrolase activity to triphosphate and restricted AC activity. All of these findings showed that MdTTMs had hydrolysis and AC activity, which could provide new solid evidence for AC distribution in woody plants as well as insights into the relationship between ACs and TTMs.

Observational Verification of the Cumulative Resilience Screening Index (CRSI) Using Hurricanes, Inland Floods, and Wildfires From 2016 to 2019

Users can apply three processes to develop confidence in decision-making tools like models and indices-validation, verification, and observation. The utility of the Cumulative Resilience Screening Index (CRSI) was demonstrated by combining the processes of verification and observation using real-world natural hazard events (i.e., hurricanes, inland flooding, and wildfires). The ability of CRSI to determine the counties most vulnerable to hazards and least likely to recover quickly from natural hazards is demonstrated using these natural hazard events from outside the original index construction data set. Using Hurricane Harvey and Hurricane Michael, the counties in Texas and Florida/Georgia, respectively, experiencing the most damage and the most extended recovery intervals were determined accurately. Similarly, the most vulnerable and least recoverable counties were correctly identified as those associated with the Great Louisiana Flood of 2016. Finally, three different types of wildfires in California were examined to determine the likelihood of recovery and the strength of pre-event planning. All models and indices developed for use by decision-makers should consider undertaking this verification or a similar validation operation to enhance user confidence.

PLK1 as one novel target for the poor prognosis of bladder cancer: An observational study

Bladder cancer (BC) is one of the most common male malignant tumors and the most common urological tumor. However, the molecular mechanism and role of PLK1 on bladder cancer were unclear. Therefore, the study aims to explore the potential part of the overall survival of bladder cancer through bioinformatics analysis. GSE121711 and GSE130598, from the Gene Expression Omnibus database. The GEO2R screened differently expressed genes, and DAVID and Metascape were used for functional annotation. The cytoHubba made hub genes identification and expression. A total of 50 BC participants were recruited. After surgery, 50 BC tumor samples from BC patients and 50 adjacent standard bladder tissue samples were obtained. The RT-qPCR assay was performed to verify the expression of hub genes. The Kaplan-Meier Plotter analyzed the effect of hub gene expression for overall survival of BC. The compulsory module of Molecular Complex Detection tool analysis was shown, which included CDK1, TTK, AURKB, MELK, PLK1, and BUB1. And the six hub genes were up-regulated in the BC compared with the normal tissues. The relative expression levels of CDK1, TTK, AURKB, MELK, PLK1, and BUB1 were significantly higher in BC samples compared with the regular kidney tissue groups. The result demonstrated that CDK1, TTK, AURKB, MELK, PLK1, and BUB1 might be considered biomarkers for BC. Overall survival analysis showed that BC patients with high expression level of PLK1 had poorer overall survival times than those with low expression level (P < .05). The expression levels of CDK1, TTK, AURKB, MELK, and BUB1 was not related to the overall survival of BC patients (P > .05). The PLK1 gene might provide new ideas and evidence for bladder cancer research.

Model Checking Autonomous Components within Electric Power Systems Specified by Interpreted Petri Nets

Autonomous components within electric power systems can be successfully specified by interpreted Petri nets. Such a formal specification makes it possible to check some basic properties of the models, such as determinism or deadlock freedom. In this paper, it is shown how these models can also be formally verified against some behavioral user-defined properties that relate to the safety or liveness of a designed system. The requirements are written as temporal logic formulas. The rule-based logical model is used to support the verification process. An interpreted Petri net is first written as an abstract logical model, and then automatically transformed into a verifiable model that is supplemented by appropriate properties for checking. Formal verification is then performed with the nuXmv model checker. Thanks to this the initial specification of autonomous components can be formally verified and any design errors can be identified at an early stage of system development. An electric energy storage (EES) is presented as an application system for the provision of a system service for stabilizing the power of renewable energy sources (RES) or highly variable loads. The control algorithm of EES in the form of an interpreted Petri net is then written as a rule-based logical model and transformed into a verifiable model, allowing automatic checking of user-defined requirements.

Verification and Comparison of Qualitative Serological Assays for Anti-SARS-COV-2 IgM and IgG Antibodies Detection

Background

Due to their wide application in the SARS-CoV-2 pandemic, we verified and compared three qualitative serological methods in order to select the most optimal that will best serve its purpose under laboratory conditions.

Methods

We assessed the diagnostic characteristics of two automated serological methods (Roche Elecsys^® Anti-SARS-CoV-2 and Abbott SARS-CoV-2 IgG) and a POCT test (Colloidal Gold Method SARS-CoV-2 IgM/IgG Antibody Assay Kit). In the process of verification, analytical precision was also assessed for the automated assays.

Results

Diagnostic characteristics were determined by measuring antibodies against SARS-CoV-2 in 91 RT-PCR-negative and 60 RT-PCR-positive samples. The POCT test gave the highest number of false positive cases (8.61%). Roche Elecsys^® Anti-SARS-CoV-2 gave only 2.65% false positivity and showed the highest diagnostic sensitivity of 98.33% (95% CI: 91.06-99.96), while Abbott SARS-CoV-2 IgG method showed 100.00% (95% CI: 96.03-100.00) diagnostic specificity and an almost perfect agreement with Roche Elecsys^® Anti-SARS-CoV-2. When assessing the precision of the automated methods, we observed some variability in the positive control samples, but the values did not affect clinical interpretation.

Conclusion

Both automated methods demonstrate superior diagnostic characteristics compared to the Colloidal Gold Method, and this POCT test is not considered as an appropriate choice for routine testing. The two automated methods showed low variability without altering the results and their interpretation.

Self-expandable stent for thrombus removal modeling: Solid or beam finite elements?

BACKGROUND

The performance of self-expandable stents is being increasingly studied by means of finite-element analysis. As for peripheral stents, transcatheter valves and stent-grafts, there are numerous computational studies for setting up a proper model, this information is missing for stent-retrievers used in the procedure of thrombus removal in cerebral arteries. It is well known that the selection of the appropriate finite-element dimensions (topology) and formulations (typology) is a fundamental step to set up accurate and reliable computational simulations. In this context, a thorough verification analysis is here proposed, aimed at investigating how the different element typologies and topologies - available to model a stent-retriever - affect simulation results.

METHOD

Hexahedral and beam element formulations were analyzed first individually by virtually replicating a crimping test on the device, and then by replicating the thrombectomy procedure aiming at removing a thrombus from a cerebral vessel. In particular, three discretization refinements for each element type and different element formulations including both full and reduced integration were investigated and compared in terms of the resultant radial force of the stent and the stress field generated in the thrombus.

RESULTS

The sensitivity analysis on the element formulation performed with the crimping simulations allowed the identification of the optimal setting for each element family. Both setting lead to similar results in terms of stent performance in the virtual thrombectomy and should be used in future studies simulating the mechanical thrombectomy with stent-retrievers.

CONCLUSIONS

The carried out virtual thrombectomy procedures confirmed that the beam element formulation results were sufficiently accurate to model the radial force and the performance of the stent-retriever during the procedure. For different self-expandable stents, hexahedral formulation could be essential in stress analysis.

Impact of EEG Frequency Bands and Data Separation on the Performance of Person Verification Employing Neural Networks

The paper is devoted to the study of EEG-based people verification. Analyzed solutions employed shallow artificial neural networks using spectral EEG features as input representation. We investigated the impact of the features derived from different frequency bands and their combination on verification results. Moreover, we studied the influence of a number of hidden neurons in a neural network. The datasets used in the analysis consisted of signals recorded during resting state from 29 healthy adult participants performed on different days, 20 EEG sessions for each of the participants. We presented two different scenarios of training and testing processes. In the first scenario, we used different parts of each recording session to create the training and testing datasets, and in the second one, training and testing datasets originated from different recording sessions. Among single frequency bands, the best outcomes were obtained for the beta frequency band (mean accuracy of 91 and 89% for the first and second scenarios, respectively). Adding the spectral features from more frequency bands to the beta band features improved results (95.7 and 93.1%). The findings showed that there is not enough evidence that the results are different between networks using different numbers of hidden neurons. Additionally, we included results for the attack of 23 external impostors whose recordings were not used earlier in training or testing the neural network in both scenarios. Another significant finding of our study shows worse sensitivity results in the second scenario. This outcome indicates that most of the studies presenting verification or identification results based on the first scenario (dominating in the current literature) are overestimated when it comes to practical applications.

YouTube as a source of information on carbon monoxide poisoning: a content-quality analysis

OBJECTIVES

The variety of clinical presentation on the topic of carbon monoxide (CO) intoxication ranges from slight headache to coma or death. YouTube allows patients to search not only for entertainment but also medical advice. Therefore, the aim of this study was to evaluate the content and quality of YouTube videos concerning CO poisoning as a source of knowledge for non-medical audience.

MATERIAL AND METHODS

On the December 8, 2020 a YouTube search was conducted for the following phrases: "carbon monoxide poisoning," "carbon monoxide symptoms," "CO poisoning," "carbon monoxide asphyxiation," "carbon monoxide intoxication" using the "incognito mode" and without attachment to Google Account. The search results were set as: "default" in the YouTube browser. The first 50 results were taken into consideration. Two raters, a specialist in emergency medicine and a specialist in clinical toxicology rated videos with Quality Criteria for Consumer Health Information (DISCERN), Global Quality Score (GQS) and Journal of the American Medical Association (JAMA). "VidIQ Vision for YouTube" plug-in was used.

RESULTS

Ninety-five videos were included. The interclass coefficient for DISCERN, GQS and JAMA scores were: 0.8, 0.74 and 0.62 reaching good and moderate reliability. The mean DISCERN/GQS/JAMA was 28.1 (SD 7.9), 2.5 (SD 0.8) and 1.1 (SD 0.7) respectively. Higher DISCERN/GQS/JAMA had videos providing information on: exposure time, treatment options, hyperbaric chamber indications as well as physician speaker (p < 0.05). Video Power Index was higher when the video contained animations and presented patients own history of CO exposure but not influenced the DISCERN/ GQS/JAMA scores. Videos providing misleading information had a higher like ratio.

CONCLUSIONS

The overall video quality was poor indicating inappropriate educational and informative value for patients who search information about carbon monoxide poisoning. Int J Occup Med Environ Health. 2022;35(3):285-95.

NAL-NL2 Prescriptive Targets for Bone Conduction Devices With an Adaptation to Device Constraints in the Low Frequencies

OBJECTIVES

To study the effectivity of a transformed NAL non-linear version 2 (NAL-NL2) gain prescription for percutaneous bone conduction devices (BCDs) and to investigate how to take into account output constraints for the lower frequencies.

DESIGN

The NAL-NL2 prescription was converted to a bone conduction prescription rule. Adaptations were needed, as this converted rule prescribes more output at low frequencies than the device delivers. Three adaptations with different audibility and compression were compared. Setting 1 (S1, "optimal audibility") had most audibility due to adapted frequency-dependent compression, setting 2 (S2, "moderate audibility") had moderate output reduction below 1 kHz, and setting 3 (S3, "reduced audibility, least distortion") had most output reduction. Eighteen experienced BCD users rated their relative sound quality in paired comparisons for different sounds (own voice, mixed voices, traffic noise, and music). In addition speech intelligibility in quiet and noise were assessed.

RESULTS

The relative sound quality rating for the adapted prescriptions varied between the stimuli: more low-frequency sound was preferred for music (S1 over S3), and less low-frequency sound was preferred for the own voice (S2 and S3 over S1). No differences in quality rating were found for mixed voices or traffic noise. Speech intelligibility in quiet scores at 45 dB SPL was significantly lower for S3 than for S1. Speech intelligibility in noise was significantly reduced in all settings and S3 yielded significantly better speech intelligibility in noise than S1.

CONCLUSIONS

With a moderate gain reduction for low frequencies to comply with device constraints the transformed NAL-NL2 prescription was found suitable for fitting BCDs. Perceived sound quality depended on the gain settings, but also on the sound spectra and how the sound was appreciated. A moderate gain reduction below 1 kHz seems to be the optimal adaptation as it has a neutral or positive relative sound quality for all stimuli without negative effects on Speech intelligibility. The NAL-NL2-BC prescribed a sufficient amount of gain, as indicated by the speech tests.

Comparison between polynomial regression and weighted least squares regression analysis for verification of analytical measurement range

OBJECTIVES

Recently, the linearity evaluation protocol by the Clinical & Laboratory Standards Institute (CLSI) has been revised from EP6-A to EP6-ED2, with the statistical method of interpreting linearity evaluation data being changed from polynomial regression to weighted least squares linear regression (WLS). We analyzed and compared the analytical measurement range (AMR) verification results according to the present and prior linearity evaluation guidelines.

METHODS

The verification of AMR of clinical chemistry tests was performed using five samples with two replicates in three different laboratories. After analyzing the same evaluation data in each laboratory by the polynomial regression analysis and WLS methods, results were compared to determine whether linearity was verified across the five sample concentrations. In addition, whether the 90% confidence interval of deviation from linearity by WLS was included in the allowable deviation from linearity (ADL) was compared.

RESULTS

A linearity of 42.3-56.8% of the chemistry items was verified by polynomial regression analysis in three laboratories. For analysis of the same data by WLS, a linearity of 63.5-78.3% of the test items was verified where the deviation from linearity of all five samples was within the ADL criteria, and the cases where the 90% confidence interval of all deviation from linearity overlapped the ADL was 78.8-91.3%.

CONCLUSIONS

Interpreting AMR verification data by the WLS method according to the newly revised CLSI document EP6-ED2 could reduce laboratory workload, enabling efficient laboratory practice.

A novel method for objective in-situ measurement of audibility in bone conduction hearing devices - a pilot study using a skin drive BCD

OBJECTIVE

Objective measurement of audibility (verification) using bone conduction devices (BCDs) has long remained an elusive problem for BCDs. For air conduction hearing aids there are well-defined and often used objective methods, and the aim of this study is to develop an objective method for BCDs.

DESIGN

In a novel setup for audibility measurements of bone-anchored hearing aid (BAHA) attached via a soft band, we used a skin microphone (SM) on the forehead measuring in-situ sound field thresholds, maximum power output (MPO) and international speech test signal (ISTS) responses.

STUDY SAMPLE

Five normal-hearing persons.

RESULT

Using the electrical output of SM it was possible to objectively measure the audibility of a skin drive BCD, presented as an eSPL-o-gram showing thresholds, MPO and ISTS response. Normalised eSPL-o-gram was verified against corresponding FL-o-grams (corresponding force levels from skull simulator and artificial mastoid (AM)).

CONCLUSION

The proposed method with the SM can be used for objective measurements of the audibility of any BCDs based on thresholds, MPO and speech response allowing for direct comparisons of hearing and BCD output on the same graph using an eSPL-o-gram. After normalisation to hearing thresholds, the audibility can be assessed without the need for complicated calibration procedures.

A multi-laboratory assessment of lupus anticoagulant assays performed on the ACL TOP 50 family for harmonized testing in a large laboratory network

Introduction

Lupus anticoagulant (LA) testing is commonly performed within hemostasis laboratories, and the ACL TOP 50 family of instruments represent a new “single platform” of hemostasis instrumentation. Our aim was to evaluate these instruments and manufacturer reagents or alternatives for utility in LA testing.

Methods

Comparative evaluations of LA testing using newly installed ACL TOPs 550 and 750 as well as comparative assessments with existing “reference,” predominantly Stago, instrumentation, and reagents. Evaluations comprised both dilute Russell viper venom time (dRVVT) and activated partial thromboplastin time (APTT)‐based assays. Establishment of normal reference ranges (NRR).

Results

The HemosIL dRVVT‐based assays showed good comparability with the existing Stago reference method (R > 0.9) and could be considered as verified as fit for purpose. A variety of APTT assays was additionally evaluated for LA utility, and we identified from the assessment good utility of a non‐Werfen solution in Hyphen BioMed Cephen reagents. NRR were established based on ≥120 normal individual plasma samples.

Conclusion

This evaluation of LA reagents on ACL TOP 50 Family instruments identified overall acceptable performance of both dRVVT (Werfen solution) and APTT (non‐Werfen solution) to enable harmonization of LA testing in our large network.