5,037 results on '"Fully automated"'
Search Results
2. Targeted Next-Generation Sequencing Assay for Direct Detection and Serotyping of Salmonella from Enrichment
- Author
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Andrew Lin, Atul Singh, Adam Allred, Marc Allard, Doug Waltman, Behzad Imanian, Justin H.J. Ng, Yadollah Sanahmadi, and Ramin Khaksar
- Subjects
Fully automated ,Salmonella ,Serotyping ,Targeted Next-Generation Sequencing ,Food processing and manufacture ,TP368-456 ,Nutrition. Foods and food supply ,TX341-641 - Abstract
In this study, an automated, targeted next-generation sequencing (tNGS) assay to detect and serotype Salmonella from sample enrichments was evaluated. The assay generates millions of reads to detect multiple Salmonella-specific genes and serotype-specific alleles, detecting all Salmonella spp. tested to date, and serotyping 62 common Salmonella serotypes. Accuracy was tested on 291 pure reference cultures (251 Salmonella, 40 non-Salmonella), 21 artificially contaminated poultry carcass rinse samples, and 363 naturally contaminated poultry environmental samples. Among the 291 pure reference cultures, the automated tNGS assay resulted in 100% detection accuracy, 100% serotyping accuracy for the claimed serotypes, and 0% false positives. The limit of detection was estimated at 5 × 104 CFU/mL by testing enumerated cultures of strains representative of six serotypes. In cocontamination studies with mixtures of two serotypes (Enteritidis, Typhimurium, Kentucky, Infantis, and Newport) at a 1:1 ratio, tNGS detected both serotypes with 100% accuracy. The assay demonstrated 100% accuracy in artificially contaminated poultry carcass rinse sample enrichments. Targeted NGS was highly effective in detecting Salmonella in samples collected from poultry production facilities. Results demonstrated that tNGS could detect Salmonella and provide accurate serotyping information consistent with conventional serology. These findings highlight the reliable and efficient performance of a fully automated tNGS Salmonella assay in detecting and identifying Salmonella strains in complex matrices, reducing the time to results from 4 to 5 days required by the traditional isolation and serotyping to 10–12 h for tNGS after primary enrichment.
- Published
- 2024
- Full Text
- View/download PDF
3. Machine Retrofitting for Tissue Paper Industry—INTERFOLDER Case
- Author
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Milivojevic, Milos, Bojovic, Bozica, Babic, Vladimir, Djuric, Djordje, Ceccarelli, Marco, Series Editor, Agrawal, Sunil K., Advisory Editor, Corves, Burkhard, Advisory Editor, Glazunov, Victor, Advisory Editor, Hernández, Alfonso, Advisory Editor, Huang, Tian, Advisory Editor, Jauregui Correa, Juan Carlos, Advisory Editor, Takeda, Yukio, Advisory Editor, Rackov, Milan, editor, Mitrović, Radivoje, editor, and Čavić, Maja, editor
- Published
- 2022
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4. High-Throughput and Automated Detection of HLA-B*27 Using the LabTurbo TM AIO System.
- Author
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Chou, Yung-Che and Er, Tze-Kiong
- Subjects
HLA-B27 antigen ,HUMAN DNA ,LIFTING & carrying (Human mechanics) - Abstract
The adoption of an automated system can decrease the hands-on time requirements in a clinical laboratory setting. For the detection of HLA-B*27, implementing a high-throughput and fully automated system has several advantages over using manual methods. Therefore, this study aimed to evaluate automation efficiency for the detection of HLA-B*27. Peripheral blood samples were obtained from 50 participants, and DNA was isolated from these samples. A Pharmigene PG27 detection kit was used for the qualitative detection of HLA-B*27. The performances of the semi-automated and fully automated LabTurbo
TM AIO systems in the detection of HLA-B*27 were compared. The mean absorbance (optical density) values for the MaelstromTM 8 and LabTurboTM AIO systems were found to be 1.88 and 1.9, respectively. The housekeeping gene was amplified and quantified using a real-time PCR assay across all DNA extracts to check the quality of the extracted human DNA. The results were expressed as the cycle threshold (Ct) values for all DNA extracts from both platforms. The mean Ct values for the Roche Cobas z480 and LabTurboTM AIO systems were found to be 22.7 and 20.4, respectively. This study demonstrated that the semi-automated method and the LabTurboTM AIO system yield consistent results for the detection of HLA-B*27. However, compared to the semi-automated method, the LabTurboTM AIO system provides standardized procedures, avoids manual handling, and improves turnaround time. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
5. Effects of a Web-Based Weight Loss Program on the Healthy Eating Index-NVS in Adults with Overweight or Obesity and the Association with Dietary, Anthropometric and Cardiometabolic Variables: A Randomized Controlled Clinical Trial.
- Author
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Kohl, Jan, Brame, Judith, Hauff, Pascal, Wurst, Ramona, Sehlbrede, Matthias, Fichtner, Urs Alexander, Armbruster, Christoph, Tinsel, Iris, Maiwald, Phillip, Farin-Glattacker, Erik, Fuchs, Reinhard, Gollhofer, Albert, and König, Daniel
- Abstract
This randomized, controlled clinical trial examined the impact of a web-based weight loss intervention on diet quality. Furthermore, it was investigated whether corresponding changes in diet quality were associated with changes in measures of cardiovascular risk profile. Individuals with a body mass index (BMI) of 27.5 to 34.9 kg/m
2 and an age of 18 to 65 y were assigned to either an interactive and fully automated web-based weight loss program focusing on dietary energy density (intervention) or a non-interactive web-based weight loss program (control). Examinations were performed at baseline (t0), after the 12-week web-based intervention (t1), and after an additional 6 (t2) and 12 months (t3). Based on a dietary record, the Healthy Eating Index-NVS (HEI-NVS) was calculated and analyzed using a robust linear mixed model. In addition, bootstrapped correlations were performed independently of study group to examine associations between change in HEI-NVS and change in dietary, anthropometric, and cardiometabolic variables. A total of n = 153 participants with a mean BMI of 30.71 kg/m2 (SD 2.13) and an average age of 48.92 y (SD 11.17) were included in the study. HEI-NVS improved significantly in the intervention group from baseline (t0) to t2 (p = 0.003) and to t3 (p = 0.037), whereby the course was significantly different up to t2 (p = 0.013) and not significantly different up to t3 (p = 0.054) compared to the control group. Independent of study group, there was a significant negative association between change in HEI-NVS and dietary energy density. A higher total score in HEI-NVS did not correlate with improvements in cardiovascular risk profile. The interactive and fully automated web-based weight loss program improved diet quality. Independent of study group, changes in HEI-NVS correlated with changes in energy density, but there was no association between improvements in HEI-NVS and improvements in cardiovascular risk profile. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
6. Fully automated quantification of cardiac chamber and function assessment in 2-D echocardiography: clinical feasibility of deep learning-based algorithms.
- Author
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Kim, Sekeun, Park, Hyung-Bok, Jeon, Jaeik, Arsanjani, Reza, Heo, Ran, Lee, Sang-Eun, Moon, Inki, Yoo, Sun Kook, and Chang, Hyuk-Jae
- Abstract
We aimed to compare the segmentation performance of the current prominent deep learning (DL) algorithms with ground-truth segmentations and to validate the reproducibility of the manually created 2D echocardiographic four cardiac chamber ground-truth annotation. Recently emerged DL based fully-automated chamber segmentation and function assessment methods have shown great potential for future application in aiding image acquisition, quantification, and suggestion for diagnosis. However, the performance of current DL algorithms have not previously been compared with each other. In addition, the reproducibility of ground-truth annotations which are the basis of these algorithms have not yet been fully validated. We retrospectively enrolled 500 consecutive patients who underwent transthoracic echocardiogram (TTE) from December 2019 to December 2020. Simple U-net, Res-U-net, and Dense-U-net algorithms were compared for the segmentation performances and clinical indices such as left atrial volume (LAV), left ventricular end diastolic volume (LVEDV), left ventricular end systolic volume (LVESV), LV mass, and ejection fraction (EF) were evaluated. The inter- and intra-observer variability analysis was performed by two expert sonographers for a randomly selected echocardiographic view in 100 patients (apical 2-chamber, apical 4-chamber, and parasternal short axis views). The overall performance of all DL methods was excellent [average dice similarity coefficient (DSC) 0.91 to 0.95 and average Intersection over union (IOU) 0.83 to 0.90], with the exception of LV wall area on PSAX view (average DSC of 0.83, IOU 0.72). In addition, there were no significant difference in clinical indices between ground truth and automated DL measurements. For inter- and intra-observer variability analysis, the overall intra observer reproducibility was excellent: LAV (ICC = 0.995), LVEDV (ICC = 0.996), LVESV (ICC = 0.997), LV mass (ICC = 0.991) and EF (ICC = 0.984). The inter-observer reproducibility was slightly lower as compared to intraobserver agreement: LAV (ICC = 0.976), LVEDV (ICC = 0.982), LVESV (ICC = 0.970), LV mass (ICC = 0.971), and EF (ICC = 0.899). The three current prominent DL-based fully automated methods are able to reliably perform four-chamber segmentation and quantification of clinical indices. Furthermore, we were able to validate the four cardiac chamber ground-truth annotation and demonstrate an overall excellent reproducibility, but still with some degree of inter-observer variability. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
7. High-Throughput and Automated Detection of HLA-B*27 Using the LabTurboTM AIO System
- Author
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Yung-Che Chou and Tze-Kiong Er
- Subjects
semi-automated ,fully automated ,human leukocyte antigen B27 ,Biology (General) ,QH301-705.5 - Abstract
The adoption of an automated system can decrease the hands-on time requirements in a clinical laboratory setting. For the detection of HLA-B*27, implementing a high-throughput and fully automated system has several advantages over using manual methods. Therefore, this study aimed to evaluate automation efficiency for the detection of HLA-B*27. Peripheral blood samples were obtained from 50 participants, and DNA was isolated from these samples. A Pharmigene PG27 detection kit was used for the qualitative detection of HLA-B*27. The performances of the semi-automated and fully automated LabTurboTM AIO systems in the detection of HLA-B*27 were compared. The mean absorbance (optical density) values for the MaelstromTM 8 and LabTurboTM AIO systems were found to be 1.88 and 1.9, respectively. The housekeeping gene was amplified and quantified using a real-time PCR assay across all DNA extracts to check the quality of the extracted human DNA. The results were expressed as the cycle threshold (Ct) values for all DNA extracts from both platforms. The mean Ct values for the Roche Cobas z480 and LabTurboTM AIO systems were found to be 22.7 and 20.4, respectively. This study demonstrated that the semi-automated method and the LabTurboTM AIO system yield consistent results for the detection of HLA-B*27. However, compared to the semi-automated method, the LabTurboTM AIO system provides standardized procedures, avoids manual handling, and improves turnaround time.
- Published
- 2023
- Full Text
- View/download PDF
8. Fully automated analysis combining [18F]-FET-PET and multiparametric MRI including DSC perfusion and APTw imaging: a promising tool for objective evaluation of glioma progression.
- Author
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Paprottka, K. J., Kleiner, S., Preibisch, C., Kofler, F., Schmidt-Graf, F., Delbridge, C., Bernhardt, D., Combs, S. E., Gempt, J., Meyer, B., Zimmer, C., Menze, B. H., Yakushev, I., Kirschke, J. S., and Wiestler, B.
- Subjects
- *
PERFUSION imaging , *DEEP learning , *GLIOMAS , *MAGNETIC resonance imaging , *POSITRON emission tomography , *IMAGE analysis , *MAGNETIC resonance angiography - Abstract
Purpose: To evaluate diagnostic accuracy of fully automated analysis of multimodal imaging data using [18F]-FET-PET and MRI (including amide proton transfer-weighted (APTw) imaging and dynamic-susceptibility-contrast (DSC) perfusion) in differentiation of tumor progression from treatment-related changes in patients with glioma. Material and methods: At suspected tumor progression, MRI and [18F]-FET-PET data as part of a retrospective analysis of an observational cohort of 66 patients/74 scans (51 glioblastoma and 23 lower-grade-glioma, 8 patients included at two different time points) were automatically segmented into necrosis, FLAIR-hyperintense, and contrast-enhancing areas using an ensemble of deep learning algorithms. In parallel, previous MR exam was processed in a similar way to subtract preexisting tumor areas and focus on progressive tumor only. Within these progressive areas, intensity statistics were automatically extracted from [18F]-FET-PET, APTw, and DSC-derived cerebral-blood-volume (CBV) maps and used to train a Random Forest classifier with threefold cross-validation. To evaluate contribution of the imaging modalities to the classifier's performance, impurity-based importance measures were collected. Classifier performance was compared with radiology reports and interdisciplinary tumor board assessments. Results: In 57/74 cases (77%), tumor progression was confirmed histopathologically (39 cases) or via follow-up imaging (18 cases), while remaining 17 cases were diagnosed as treatment-related changes. The classification accuracy of the Random Forest classifier was 0.86, 95% CI 0.77–0.93 (sensitivity 0.91, 95% CI 0.81–0.97; specificity 0.71, 95% CI 0.44–0.9), significantly above the no-information rate of 0.77 (p = 0.03), and higher compared to an accuracy of 0.82 for MRI (95% CI 0.72–0.9), 0.81 for [18F]-FET-PET (95% CI 0.7–0.89), and 0.81 for expert consensus (95% CI 0.7–0.89), although these differences were not statistically significant (p > 0.1 for all comparisons, McNemar test). [18F]-FET-PET hot-spot volume was single-most important variable, with relevant contribution from all imaging modalities. Conclusion: Automated, joint image analysis of [18F]-FET-PET and advanced MR imaging techniques APTw and DSC perfusion is a promising tool for objective response assessment in gliomas. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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9. Engagement With a Relaxation and Mindfulness Mobile App Among People With Cancer: Exploratory Analysis of Use Data and Self-Reports From a Randomized Controlled Trial.
- Author
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Schläpfer S, Schneider F, Santhanam P, Eicher M, Kowatsch T, Witt CM, and Barth J
- Abstract
Background: Mobile health (mHealth) apps offer unique opportunities to support self-care and behavior change, but poor user engagement limits their effectiveness. This is particularly true for fully automated mHealth apps without any human support. Human support in mHealth apps is associated with better engagement but at the cost of reduced scalability., Objective: This work aimed to (1) describe the theory-informed development of a fully automated relaxation and mindfulness app to reduce distress in people with cancer (CanRelax app 2.0), (2) describe engagement with the app on multiple levels within a fully automated randomized controlled trial over 10 weeks, and (3) examine whether engagement was related to user characteristics., Methods: The CanRelax app 2.0 was developed in iterative processes involving input from people with cancer and relevant experts. The app includes evidence-based relaxation exercises, personalized weekly coaching sessions with a rule-based conversational agent, 39 self-enactable behavior change techniques, a self-monitoring dashboard with gamification elements, highly tailored reminder notifications, an educational video clip, and personalized in-app letters. For the larger study, German-speaking adults diagnosed with cancer within the last 5 years were recruited via the web in Switzerland, Austria, and Germany. Engagement was analyzed in a sample of 100 study participants with multiple measures on a micro level (completed coaching sessions, relaxation exercises practiced with the app, and feedback on the app) and a macro level (relaxation exercises practiced without the app and self-efficacy toward self-set weekly relaxation goals)., Results: In week 10, a total of 62% (62/100) of the participants were actively using the CanRelax app 2.0. No associations were identified between engagement and level of distress at baseline, sex assigned at birth, educational attainment, or age. At the micro level, 71.88% (3520/4897) of all relaxation exercises and 714 coaching sessions were completed in the app, and all participants who provided feedback (52/100, 52%) expressed positive app experiences. At the macro level, 28.12% (1377/4897) of relaxation exercises were completed without the app, and participants' self-efficacy remained stable at a high level. At the same time, participants raised their weekly relaxation goals, which indicates a potential relative increase in self-efficacy., Conclusions: The CanRelax app 2.0 achieved promising engagement even though it provided no human support. Fully automated social components might have compensated for the lack of human involvement and should be investigated further. More than one-quarter (1377/4897, 28.12%) of all relaxation exercises were practiced without the app, highlighting the importance of assessing engagement on multiple levels., (©Sonja Schläpfer, Fabian Schneider, Prabhakaran Santhanam, Manuela Eicher, Tobias Kowatsch, Claudia M Witt, Jürgen Barth. Originally published in JMIR Cancer (https://cancer.jmir.org), 31.05.2024.)
- Published
- 2024
- Full Text
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10. Targeted Next-Generation Sequencing Assay for Direct Detection and Serotyping of Salmonella from Enrichment.
- Author
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Lin A, Singh A, Allred A, Allard M, Waltman D, Imanian B, Ng JHJ, Sanahmadi Y, and Khaksar R
- Subjects
- Animals, Serotyping methods, Serogroup, High-Throughput Nucleotide Sequencing, Salmonella, Poultry
- Abstract
In this study, an automated, targeted next-generation sequencing (tNGS) assay to detect and serotype Salmonella from sample enrichments was evaluated. The assay generates millions of reads to detect multiple Salmonella-specific genes and serotype-specific alleles, detecting all Salmonella spp. tested to date, and serotyping 62 common Salmonella serotypes. Accuracy was tested on 291 pure reference cultures (251 Salmonella, 40 non-Salmonella), 21 artificially contaminated poultry carcass rinse samples, and 363 naturally contaminated poultry environmental samples. Among the 291 pure reference cultures, the automated tNGS assay resulted in 100% detection accuracy, 100% serotyping accuracy for the claimed serotypes, and 0% false positives. The limit of detection was estimated at 5 × 10
4 CFU/mL by testing enumerated cultures of strains representative of six serotypes. In cocontamination studies with mixtures of two serotypes (Enteritidis, Typhimurium, Kentucky, Infantis, and Newport) at a 1:1 ratio, tNGS detected both serotypes with 100% accuracy. The assay demonstrated 100% accuracy in artificially contaminated poultry carcass rinse sample enrichments. Targeted NGS was highly effective in detecting Salmonella in samples collected from poultry production facilities. Results demonstrated that tNGS could detect Salmonella and provide accurate serotyping information consistent with conventional serology. These findings highlight the reliable and efficient performance of a fully automated tNGS Salmonella assay in detecting and identifying Salmonella strains in complex matrices, reducing the time to results from 4 to 5 days required by the traditional isolation and serotyping to 10-12 h for tNGS after primary enrichment., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Ramin Khaksar has patent #11581065 licensed to Clear Labs, Inc. Adam Allred has patent #11581065 licensed to Clear Labs, Inc. Ramin Khaksar has patent #11568958 licensed to Clear Labs, Inc. Adam Allred has patent #11568958 licensed to Clear Labs, Inc. Ramin Khaksar has patent #10246704 licensed to Clear Labs, Inc. Adam Allred has patent #10246704 licensed to Clear Labs, Inc., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2024
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11. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
12. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
13. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
14. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
15. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
16. Automatic Detection of Security Deficiencies and Refactoring Advises for Microservices
- Abstract
The microservice architecture enables organizations to shorten development cycles and deliver cloud-native applications rapidly. However, it also brings security concerns that need to be addressed by developers. Therefore, security testing in microservices becomes even more critical. Recent research papers indicate that security testing of microservices is often neglected for reasons such as lack of time, lack of experience in the security domain, and absence of automated test environments. Even though several security scanning tools exist to detect container, containerized workload management (Kubernetes), and network issues, none individually is sufficient to cover all security problems in microservices. Using multiple scanning tools increases the complexity of analyzing findings and mitigating security vulnerabilities. This paper presents a fully automated test tool suite that can help developers address security issues in microservices and resolve them. It targets to reduce time and effort in security activities by encapsulating open-source scanning tools into one suite and providing improved feedback. The developed security scanning suite is named Pomegranate. To develop Pomegranate, we employed Design Science and conducted our investigation in Ericsson. We have evaluated our tool using a static approach. The evaluation results indicate that the Pomegranate could be helpful to developers by providing simplified and classified outputs for security vulnerabilities in microservices. More than half of the practitioners who give us feedback found Pomegranate helpful in detecting and mitigating security problems in microservices. We conclude that a fully automated test tool suite can help developers to address most security issues in microservices. Based on the findings in this paper, the direction for future work is to conduct a dynamic validation of Pomegranate in a live project. © 2023 IEEE.
- Published
- 2023
- Full Text
- View/download PDF
17. An Automated Experimentation System for the Touch-Response Quantification of Zebrafish Larvae
- Author
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Vani Tirumalasetty, Daniel Marcato, Ralf Mikut, Ravindra Peravali, Christian Pylatiuk, Naveen Krishna Kanagaraj, Markus Reischl, and Yanke Wang
- Subjects
Computer science ,business.industry ,DATA processing & computer science ,Machine learning ,computer.software_genre ,Fully automated ,Control and Systems Engineering ,Robustness (computer science) ,Zebrafish larvae ,Artificial intelligence ,ddc:004 ,Electrical and Electronic Engineering ,business ,computer - Abstract
Touch-response experimentation in zebrafish helps researchers better understand the link between genetics, drug effects, and behaviors. However, commonly manually conducted experimentation cannot fulfill a high-throughput screening and often delivers low accuracy and lacks reproducibility. Thus, the main aim of this work is to establish a fully automated robot-assisted experimentation system with minimal human participation to conduct the touch-response experimentation with freely swimming zebrafish larvae. Our designed system is able to undertake the role of repeated touch-response experiments at predefined specific location of the larvae in different ages and under different conditions, with high accuracy, robustness, and repeatability, and can also get comparable experimental results. The errors of the detection methods are less than 3 pixels and the offset errors of the touching points are less than 5%. Designed for high-efficiency experimentation, this system will promisingly release a great amount of the burden for the biological operators from touch-response experiments and may also have potential applications in other organisms for touch-evoked response analysis.
- Published
- 2022
18. Fully Automated and Robust Cable Tension Estimation of Wireless Sensor Networks System
- Author
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Min Zhang, Huating He, Gengying Li, and Haiyang Wang
- Subjects
cable tension estimation ,fully automated ,wireless sensor networks ,Chemical technology ,TP1-1185 - Abstract
Accurate estimation of cable tension is crucial for the structural health monitoring of cable-supported structures. Identifying the cable’s force from its vibration data is probably the most widely adopted method of cable tension estimation. According to string theory, the accuracy of estimated cable tension is highly related to identified modal parameters including natural frequencies and frequency order. To alleviate the factors that impact the accuracy of modal parameters when using the peak-picking method in wireless sensor networks, a fully automated and robust identifying method is proposed in this paper. This novel method was implemented on the Xnode wireless sensor system and validated with the data obtained from Jindo Bridge. The experiment results indicate that, through this method, the wireless sensor is able to distinguish the cognizable power spectrum, extract the peaks, eliminate false frequencies and determine frequency orders automatically to estimate cable tension force without any manual intervention or preprocessing. Meanwhile, the results of natural frequencies, corresponding orders and cable tension force obtained from the Xnode system show excellent agreement with the results obtained using the Matlab program method. This demonstrates the effectiveness and reliability of the Xnode estimation system. Furthermore, this method is also appropriate for other high-performance wireless sensor network systems to realize self-identification of cable in long-term monitoring.
- Published
- 2021
- Full Text
- View/download PDF
19. Novel Decision-Making Strategy for Connected and Autonomous Vehicles in Highway On-Ramp Merging
- Author
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Zine El Abidine Kherroubi, Samir Aknine, Rebiha Bacha, Technocentre Renault [Guyancourt], RENAULT, Systèmes Cognitifs et Systèmes Multi-Agents (SyCoSMA), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Université Lumière - Lyon 2 (UL2)
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050210 logistics & transportation ,Artificial neural network ,Computer science ,Mechanical Engineering ,05 social sciences ,Real-time computing ,Computer Science Applications ,Acceleration ,Fully automated ,Work (electrical) ,[INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA] ,0502 economics and business ,Automotive Engineering ,Reinforcement learning ,State (computer science) ,ComputingMilieux_MISCELLANEOUS - Abstract
High-speed highway on-ramp merging is a significant challenge toward realizing fully automated driving (level 4). Connected Autonomous Vehicles (CAVs), that combine communication and autonomous driving technologies, may improve greatly the safety performances when performing highway on-ramp merging. However, even with the emergence of CAVs, some keys constraints should be considered to achieve a safe on-ramp merging. First, human-driven vehicles will still be present on the road, and it may take decades before all the commercialized vehicles will be fully autonomous and connected. Also, onboard vehicle sensors may provide inaccurate or incomplete data due to sensors limitations and blind spots, especially in such critical situations. To resolve these issues, the present work introduces a novel solution that uses an off-board Road-Side Unit (RSU) to realize fully automated highway on-ramp merging for connected and automated vehicles. Our proposed approach is based on an Artificial Neural Network (ANN) to predict drivers' intentions. This prediction is used as an input state to a Deep Reinforcement Learning (DRL) agent that outputs the longitudinal acceleration for the merging vehicle. To achieve this, we first propose a data-driven model that can predict the behavior of the human-driven vehicles in the main highway lane, with 99% accuracy. We use the output of this model as input state to train a Twin Delayed Deep Deterministic Policy Gradients (TD3) agent that learns ``safe'' and ``cooperative'' driving policy to perform highway on-ramp merging. We show that our proposed decision-making strategy improves performance compared to the solutions proposed previously.
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- 2022
20. Representation Learning-Driven Fully Automated Framework for the Inverse Design of Frequency-Selective Surfaces
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Zhao Zhou, Zhaohui Wei, Jian Ren, Yingzeng Yin, Gert Frolund Pedersen, and Ming Shen
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Optimization ,Radiation ,Data models ,Geometry ,fully automated ,Condensed Matter Physics ,Topology ,Metasurfaces ,representation learning ,autoselection ,frequency-selective surface (FSS) ,Training ,inverse design ,Electrical and Electronic Engineering ,Autoevolution - Abstract
Frequency-selective surfaces (FSSs) refer to planar structures that behave with specific electromagnetic (EM) responses within a frequency range and are widely applied in wireless propagation systems. Given the fact that different EM responses correspond to distinguished topologies, conventional inverse design methods of FSSs are usually labor-intensive, as they rely on experienced human engineers to determine the topology and then rationally tune its structures. There have been great attempts using optimization algorithms (e.g., genetic algorithms) or machine learning to automate the second tuning stage after the initial EM topologies are determined by human engineers. However, the first topology selection stage still requires engagements with experienced engineers. This article proposes a fully automated framework for the inverse design of FSSs. We achieved a fully automated inverse design by establishing a machine-friendly mapping flow. The mapping flow derives its continuity and compactness from representation learning, which enables both autoselection of the topology and autoevolution of the unit cell based on the topology. The autoselection stage automatically determines the appropriate topology by compressing the EM constraints through the principal component analysis (PCA) and classifying the topology using the support vector machine (SVM). Afterward, the autoevolution system can efficiently evolve until it yields an optimal unit cell. We developed a self-monitor strategy to control the evolution and maximize the evolution efficiency by adaptively tuning the three modules within the autoevolution system. We validated the presented framework with four FSS designs. The results proved its potential as a highly efficient fully automated tool for the inverse design of FSSs.
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- 2023
21. lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
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Yixiao Gong, Hsuan-Ting Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis, and Aristotelis Tsirigos
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lncRNA ,Comprehensive pipeline ,Data integration ,Fully automated ,Interactive report ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Long non-coding RNAs (lncRNAs) have emerged as a class of factors that are important for regulating development and cancer. Computational prediction of lncRNAs from ultra-deep RNA sequencing has been successful in identifying candidate lncRNAs. However, the complexity of handling and integrating different types of genomics data poses significant challenges to experimental laboratories that lack extensive genomics expertise. Result To address this issue, we have developed lncRNA-screen, a comprehensive pipeline for computationally screening putative lncRNA transcripts over large multimodal datasets. The main objective of this work is to facilitate the computational discovery of lncRNA candidates to be further examined by functional experiments. lncRNA-screen provides a fully automated easy-to-run pipeline which performs data download, RNA-seq alignment, assembly, quality assessment, transcript filtration, novel lncRNA identification, coding potential estimation, expression level quantification, histone mark enrichment profile integration, differential expression analysis, annotation with other type of segmented data (CNVs, SNPs, Hi-C, etc.) and visualization. Importantly, lncRNA-screen generates an interactive report summarizing all interesting lncRNA features including genome browser snapshots and lncRNA-mRNA interactions based on Hi-C data. Conclusion lncRNA-screen provides a comprehensive solution for lncRNA discovery and an intuitive interactive report for identifying promising lncRNA candidates. lncRNA-screen is available as open-source software on GitHub.
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- 2017
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22. Automated segmentation and quantification of aortic calcification at abdominal CT: application of a deep learning-based algorithm to a longitudinal screening cohort.
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Graffy, Peter M., Liu, Jiamin, O'Connor, Stacy, Summers, Ronald M., and Pickhardt, Perry J.
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- *
CALCIFICATION , *IMAGE reconstruction algorithms , *CLINICAL indications , *RISK assessment , *ALGORITHMS - Abstract
Objective: To investigate an automated aortic calcium segmentation and scoring tool at abdominal CT in an adult screening cohort. Methods: Using instance segmentation with convolutional neural networks (Mask R-CNN), a fully automated vascular calcification algorithm was applied to a data set of 9914 non-contrast CT scans from 9032 consecutive asymptomatic adults (mean age, 57.5 ± 7.8 years; 4467 M/5447F) undergoing colonography screening. Follow-up scans were performed in a subset of 866 individuals (mean interval, 5.4 years). Automated abdominal aortic calcium volume, mass, and Agatston score were assessed. In addition, comparison was made with a separate validated semi-automated approach in a subset of 812 cases. Results: Mean values were significantly higher in males for Agatston score (924.2 ± 2066.2 vs. 564.2 ± 1484.2, p < 0.001), aortic calcium mass (222.2 ± 526.0 mg vs. 144.5 ± 405.4 mg, p < 0.001) and volume (699.4 ± 1552.4 ml vs. 426.9 ± 1115.5 HU, p < 0.001). Overall age-specific Agatston scores increased an average of 10%/year for the entire cohort; males had a larger Agatston score increase between the ages of 40 to 60 than females (91.2% vs. 75.1%, p < 0.001) and had significantly higher mean Agatston scores between ages 50 and 80 (p < 0.001). For the 812-scan subset with both automated and semi-automated methods, median difference in Agatston score was 66.4 with an r2 agreement value of 0.84. Among the 866-patient cohort with longitudinal follow-up, the average Agatston score change was 524.1 ± 1317.5 (median 130.9), reflecting a mean increase of 25.5% (median 73.6%). Conclusion: This robust, fully automated abdominal aortic calcification scoring tool allows for both individualized and population-based assessment. Such data could be automatically derived at non-contrast abdominal CT, regardless of the study indication, allowing for opportunistic assessment of cardiovascular risk. [ABSTRACT FROM AUTHOR]
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- 2019
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23. Comparison of safety and kinematic patterns of automated vehicles turning left in interaction with oncoming manually driven vehicles
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Adrian Sonka, Florian Krauns, Mandy Dotzauer, Marek Junghans, and Michael Böhm
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Computer science ,trajectory data analysis ,Transportation ,Kinematics ,Management, Monitoring, Policy and Law ,conditionally tolerable left turn ,Automotive engineering ,Acceleration ,traffic safety ,Fully automated ,Turning behaviour ,automated driving ,Automotive Engineering ,Use case ,road user behaviour ,Queue ,Applied Psychology ,Intersection (aeronautics) ,Civil and Structural Engineering ,Road user - Abstract
Highly and fully automated driving has been under development for the past two decades in order to increase comfort, efficiency, and traffic safety. Particularly in the latter domain, experts agree on automated driving, especially in case of automated vehicles (AV) with SAE level 4 or higher, having the most promising effects. Automated driving is expected to decrease the number of seriously injured or even killed road users to zero (Vision Zero). However, automated driving is still in an early stage of development and many AV tend to drive very carefully to avoid crashes. So, the goal is to make driving more efficient while maintaining the highest level of safety. In the project “Digitaler Knoten 4.0” cooperative automated driving was assessed regarding efficiency and safety aspects. One of the use cases investigated was turning left with oncoming traffic at an urban intersection as this situation represents one of the most complex situations in urban areas yielding to crashes with—in many cases—serious consequences for the involved road users. At the Application Platform Intelligent Mobility (AIM) Research Intersection in Braunschweig, Germany, an SAE level 3 AV was turning left interacting with oncoming manually driven vehicles (MV). The performance of the AV was compared to MV executing the same manoeuvre. The recorded video-based trajectories of the respective AV as well as MV were analysed regarding the influence of situational factors (e.g. position of the vehicle in the queue and gap acceptance) and kinematic factors (e.g. speed and acceleration) on traffic safety. The similarities and differences between this specific AV and MV were identified yielding insight for further developing algorithms for more efficient driving while maintaining the same traffic safety level. For instance, it appears that the AV shows a very conservative left turning behaviour leading to very safe PET distributions in comparison to left turning MV.
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- 2022
24. Rapid Fabrication of a Pumpless PDMS Microfluidic Device Using CO2 Laser Micromachining for Automated Formation of Monodisperse Water-in-Oil Droplets
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Masahiko Hashimoto, Masaya Nakatani, and Shotaro Okayama
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chemistry.chemical_compound ,Surface micromachining ,Fabrication ,Co2 laser ,Polydimethylsiloxane ,Fully automated ,Chemistry ,Microfluidics ,Dispersity ,Nanotechnology ,General Chemistry ,Water in oil - Abstract
To form monodisperse water-in-oil droplets in a fully automated fashion, we fabricated a pumpless microfluidic device consisting of top and bottom polydimethylsiloxane slabs. All microstructures re...
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- 2022
25. Nationwide external quality assessment of SARS-CoV-2 nucleic acid amplification tests in Japan
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Mend-Amar Ravzanaaadii, Yasumasa Akai, Satomi Asai, Akira Seki, Hiromitsu Tazawa, Hayato Miyachi, and Hidehumi Kakizoe
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Microbiology (medical) ,medicine.medical_specialty ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Infectious and parasitic diseases ,RC109-216 ,Sensitivity and Specificity ,Article ,Japan ,External quality assessment ,diagnostics ,medicine ,Humans ,Nucleic Acid Amplification Tests ,molecular ,Sample handling ,SARS-CoV-2 ,business.industry ,Public health ,COVID-19 ,General Medicine ,external quality assessment ,Infectious Diseases ,Fully automated ,Emergency medicine ,business ,Nucleic Acid Amplification Techniques - Abstract
Objectives We conducted a nationwide external quality assessment (EQA) study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid amplification testing in Japan. Methods A total of 563 public health and private sector laboratories participated. The EQA samples comprised 6 RNA and full-process controls. Results The overall agreements were 99.3% and 97.9% for the RNA and full-process controls, respectively. A total of 530/563 (94.1%) laboratories reported correct results; public health laboratories had the highest accuracy. Thirty-three laboratories reported at least one incorrect result (26 laboratories of medical facilities, 5 commercial laboratories, 1 public health laboratory, and 1 other). Sixteen laboratories of medical facilities that used a fully automated assay system failed to detect the presence of the full-process control, due to inherent insufficiency in the limit of detection (LOD). Other causes of incorrect results included failure to ensure the LOD (n = 13), error in result judging or reporting (n = 3), and error in sample handling (n = 1). Conclusions Performance was mostly dependent on the laboratory category and assay evaluation, particularly the LOD. Guidance should be developed based on these results, particularly in the phase of new entry into laboratory services for SARS-CoV-2.
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- 2022
26. Luminescence Analysis of PV-Module Soiling in Germany
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Bernd Doll, Christoph J. Brabec, Johannes Hepp, Ian Marius Peters, Claudia Buerhop-Lutz, Stefan Langner, Karen Forberich, and J. Hauch
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Fully automated ,Photovoltaic system ,Environmental science ,Dirt ,Electrical and Electronic Engineering ,Condensed Matter Physics ,Luminescence ,Electronic, Optical and Magnetic Materials ,Remote sensing ,Pv power - Abstract
Energy losses of photovoltaic (PV) plants because of soiling are a problem in all regions, including Germany. Soft soiling, caused by a uniform dust film, is shading a PV module and is reducing yield depending on the thickness of the debris layer. Hard soiling, caused by agglomerations of dust or dirt, only covers parts of a PV module, and it causes local shading. A spot check of modules from different PV power plants in Germany revealed a power reduction because of soft- and hard soiling of up to 6%. Determination of soiling type and amount is a prerequisite for decisions about cleaning and for optimizing yield. In this article, we show that luminescence imaging can be used to detect and characterize soiling and quantify losses. For this purpose, we compare luminescence images before and after cleaning and we show that soiling becomes detectable and power losses quantifiable from difference images. We also show that the impact of hard soiling can be quantified from a single photoluminescence (PL) image. This technique may enable a fully automated quantification of power losses because of hard soiling in PV- modules and strings in the future.
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- 2022
27. Fully Automated Deep Learning Tool for Sarcopenia Assessment on CT: L1 Versus L3 Vertebral Level Muscle Measurements for Opportunistic Prediction of Adverse Clinical Outcomes
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Perry J. Pickhardt, Peter M Graffy, Ryan Zea, Ronald M. Summers, Alberto A Perez, and John Garrett
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Male ,Sarcopenia ,medicine.medical_specialty ,Vertebral level ,MEDLINE ,Risk Assessment ,Article ,Deep Learning ,Physical medicine and rehabilitation ,Predictive Value of Tests ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,Muscle, Skeletal ,Opportunistic screening ,Retrospective Studies ,business.industry ,Reproducibility of Results ,Skeletal muscle ,General Medicine ,Middle Aged ,musculoskeletal system ,medicine.disease ,Spine ,body regions ,medicine.anatomical_structure ,Fully automated ,Radiographic Image Interpretation, Computer-Assisted ,Female ,Tomography, X-Ray Computed ,business ,human activities ,Follow-Up Studies - Abstract
BACKGROUND. Sarcopenia is associated with adverse clinical outcomes. CT-based skeletal muscle measurements for sarcopenia assessment are most commonly performed at the L3 vertebral level. OBJECTIVE. The purpose of this article is to compare the utility of fully automated deep learning CT-based muscle quantitation at the L1 versus L3 level for predicting future hip fractures and death. METHODS. This retrospective study included 9223 asymptomatic adults (mean age, 57 ± 8 [SD] years; 4071 men, 5152 women) who underwent unenhanced low-dose abdominal CT. A previously validated fully automated deep learning tool was used to assess muscle for myosteatosis (by mean attenuation) and myopenia (by cross-sectional area) at the L1 and L3 levels. Performance for predicting hip fractures and death was compared between L1 and L3 measures. Performance for predicting hip fractures and death was also evaluated using the established clinical risk scores from the fracture risk assessment tool (FRAX) and Framingham risk score (FRS), respectively. RESULTS. Median clinical follow-up interval after CT was 8.8 years (interquartile range, 5.1–11.6 years), yielding hip fractures and death in 219 (2.4%) and 549 (6.0%) patients, respectively. L1-level and L3-level muscle attenuation measurements were not different in 2-, 5-, or 10-year AUC for hip fracture (p = .18–.98) or death (p = .19–.95). For hip fracture, 5-year AUCs for L1-level muscle attenuation, L3-level muscle attenuation, and FRAX score were 0.717, 0.709, and 0.708, respectively. For death, 5-year AUCs for L1-level muscle attenuation, L3-level muscle attenuation, and FRS were 0.737, 0.721, and 0.688, respectively. Lowest quartile hazard ratios (HRs) for hip fracture were 2.20 (L1 attenuation), 2.45 (L3 attenuation), and 2.53 (FRAX score), and for death were 3.25 (L1 attenuation), 3.58 (L3 attenuation), and 2.82 (FRS). CT-based muscle cross-sectional area measurements at L1 and L3 were less predictive for hip fracture and death (5-year AUC ≤ 0.571; HR ≤ 1.56). CONCLUSION. Automated CT-based measurements of muscle attenuation for myosteatosis at the L1 level compare favorably with previously established L3-level measurements and clinical risk scores for predicting hip fracture and death. Assessment for myopenia was less predictive of outcomes at both levels. CLINICAL IMPACT. Alternative use of the L1 rather than L3 level for CT-based muscle measurements allows sarcopenia assessment using both chest and abdominal CT scans, greatly increasing the potential yield of opportunistic CT screening.
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- 2022
28. Fully Automated Electrically Controlled Tunable Broadband Interferometric Dielectric Spectroscopy for Aqueous Solutions
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Xiue Bao, Bart Nauwelaers, Ilja Ocket, Dominique Schreurs, Pawel Barmuta, Meng Zhang, Juncheng Bao, and Tomislav Markovic
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Interferometry ,Radiation ,Aqueous solution ,Materials science ,Fully automated ,business.industry ,Broadband ,Optoelectronics ,Electrical and Electronic Engineering ,Condensed Matter Physics ,business ,Dielectric spectroscopy - Published
- 2022
29. A Comparison between a Two-Dimensional Liquid Chromatography System and a Traditional QuEChERS-LC Method with Regard to Matrix Removal and Matrix Effects in Pesticide Analysis Using Time-of-Flight Mass Spectrometry
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Sascha Rohn, Nina Meyburg, Sandra Muehlwald, and Nadja Buchner
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Analyte ,Chromatography ,Chemistry ,Electrospray ionization ,Chemical polarity ,Pesticide Residues ,General Chemistry ,Pesticide ,Quechers ,Matrix (chemical analysis) ,Fully automated ,Tandem Mass Spectrometry ,Pesticides ,Time-of-flight mass spectrometry ,General Agricultural and Biological Sciences ,Chromatography, Liquid - Abstract
In this study, a fully automated two-dimensional liquid chromatography (2D-LC) system was used for the investigation of the clean-up effect and was compared with a traditional Quick Easy Cheap Effective Rugged and Safe (QuEChERS) liquid chromatography (LC) method. The focus of those investigations was on negative electrospray ionization (ESI) mode. For that purpose, matrix fingerprinting profiles were created. The results allowed a comparison of both methods regarding the estimation of the number and the polarity of detected compounds. Moreover, the results of the present study were compared with the results generated in positive ESI mode (presented in a previous study). Furthermore, the two methods were compared with regard to matrix effects (ME) of 321 analytes in positive ESI mode and 96 analytes in negative ESI mode. In general, fewer compounds could be detected when 2D-LC and/or the negative ESI mode was used. Especially, very polar compounds with m/z values >1000 could be separated and could not be detected anymore when 2D-LC was applied. Furthermore, the best results were obtained for most analytes when 2D-LC was used, although the extent of ME seemed to be higher with 2D-LC.
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- 2021
30. Prediction of genetic alterations from gastric cancer histopathology images using a fully automated deep learning approach
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Ahwon Lee, Hyun-Jong Jang, In Hye Song, Sung Hak Lee, and Jun Kang
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medicine.medical_specialty ,Pathology ,Staining and Labeling ,Formalin-fixed paraffin-embedded ,business.industry ,Deep learning ,Gastroenterology ,Cancer ,General Medicine ,Basic Study ,Genes, p53 ,medicine.disease ,Deep Learning ,Fully automated ,Stomach Neoplasms ,Mutation ,Humans ,Digital pathology ,Medicine ,Histopathology ,Artificial intelligence ,Gastric cancer ,business - Abstract
BACKGROUND Studies correlating specific genetic mutations and treatment response are ongoing to establish an effective treatment strategy for gastric cancer (GC). To facilitate this research, a cost- and time-effective method to analyze the mutational status is necessary. Deep learning (DL) has been successfully applied to analyze hematoxylin and eosin (H and E)-stained tissue slide images. AIM To test the feasibility of DL-based classifiers for the frequently occurring mutations from the H and E-stained GC tissue whole slide images (WSIs). METHODS From the GC dataset of The Cancer Genome Atlas (TCGA-STAD), wild-type/mutation classifiers for CDH1, ERBB2, KRAS, PIK3CA, and TP53 genes were trained on 360 × 360-pixel patches of tissue images. RESULTS The area under the curve (AUC) for the receiver operating characteristic (ROC) curves ranged from 0.727 to 0.862 for the TCGA frozen WSIs and 0.661 to 0.858 for the TCGA formalin-fixed paraffin-embedded (FFPE) WSIs. The performance of the classifier can be improved by adding new FFPE WSI training dataset from our institute. The classifiers trained for mutation prediction in colorectal cancer completely failed to predict the mutational status in GC, indicating that DL-based mutation classifiers are incompatible between different cancers. CONCLUSION This study concluded that DL could predict genetic mutations in H and E-stained tissue slides when they are trained with appropriate tissue data.
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- 2021
31. Deep learning-based fully automated Z-axis coverage range definition from scout scans to eliminate overscanning in chest CT imaging
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Saleh Sandoughdaran, Yazdan Salimi, Masoumeh Pakbin, Amirhossein Sanaat, Hossein Arabi, Abdollah Saberi Manesh, Habib Zaidi, Azadeh Akhavanallaf, Isaac Shiri, Dariush Askari, Zahra Mansouri, and Ehsan Sharifipour
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Chest ct ,R895-920 ,ddc:616.0757 ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,Medical physics. Medical radiology. Nuclear medicine ,0302 clinical medicine ,Sørensen–Dice coefficient ,Range (statistics) ,Overscanning ,Medicine ,Radiology, Nuclear Medicine and imaging ,Neuroradiology ,business.industry ,Radiation dose ,Ultrasound ,Deep learning ,3. Good health ,ddc:616.8 ,Fully automated ,030220 oncology & carcinogenesis ,Absorbed dose ,Original Article ,Chest imaging ,business ,Nuclear medicine ,CT - Abstract
Background Despite the prevalence of chest CT in the clinic, concerns about unoptimized protocols delivering high radiation doses to patients still remain. This study aimed to assess the additional radiation dose associated with overscanning in chest CT and to develop an automated deep learning-assisted scan range selection technique to reduce radiation dose to patients. Results A significant overscanning range (31 ± 24) mm was observed in clinical setting for over 95% of the cases. The average Dice coefficient for lung segmentation was 0.96 and 0.97 for anterior–posterior (AP) and lateral projections, respectively. By considering the exact lung coverage as the ground truth, and AP and lateral projections as input, The DL-based approach resulted in errors of 0.08 ± 1.46 and − 1.5 ± 4.1 mm in superior and inferior directions, respectively. In contrast, the error on external scout views was − 0.7 ± 4.08 and 0.01 ± 14.97 mm for superior and inferior directions, respectively.The ED reduction achieved by automated scan range selection was 21% in the test group. The evaluation of a large multi-centric chest CT dataset revealed unnecessary ED of more than 2 mSv per scan and 67% increase in the thyroid absorbed dose. Conclusion The proposed DL-based solution outperformed previous automatic methods with acceptable accuracy, even in complicated and challenging cases. The generizability of the model was demonstrated by fine-tuning the model on AP scout views and achieving acceptable results. The method can reduce the unoptimized dose to patients by exclunding unnecessary organs from field of view.
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- 2021
32. Gamifying Software Engineering Tools to Motivate Computer Science Students to Start and Finish Programming Assignments Earlier
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Gina Sprint, Tristan Call, and Erik Fox
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Unit testing ,business.industry ,Computer science ,Best practice ,Control (management) ,Data structure ,Education ,Test (assessment) ,Fully automated ,ComputingMilieux_COMPUTERSANDEDUCATION ,Learning Management ,Electrical and Electronic Engineering ,Software engineering ,business - Abstract
Contribution: Research has shown that computer science (CS) students who start programming assignments (PAs) early generally receive higher grades. This article presents and evaluates a gamification approach that utilizes software engineering tools to motivate CS students to start and finish PAs earlier. Background: CS can be difficult to learn because students often struggle with errors and how to properly test their code. For these reasons, it is essential that students start their PAs early. Furthermore, software engineering tools, such as version control and unit testing, are increasingly important for students to learn early in their career. Intended Outcomes: This gamification approach aims to motivate CS students to start and complete PAs earlier, as well as instill software engineering best practices. Application Design: To motivate students to start and finish assignments early, an open-source gamification system called the Leaderboard was developed. Using gamified points, the Leaderboard rewards students who pass PA unit tests well before the assignment is due. The system is fully automated using Github Classroom, a build server, and the Moodle learning management system. Findings: Results indicate students who used the Leaderboard did not start assignments significantly earlier; however, they finished assignments earlier, committed code more frequently, and passed more unit tests. The students found the Leaderboard to be motivating and passing unit tests was exciting for them.
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- 2021
33. Learning-based fully automated prediction of lumbar disc degeneration progression with specified clinical parameters and preliminary validation
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Xihe Kuang, Marcus Kin Long Lai, Teng Zhang, Jason Pui Yin Cheung, Fengdong Zhao, Zhaomin Zheng, Dino Samartzis, Jaro Karppinen, Honghan Wu, and Kenneth M.C. Cheung
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medicine.medical_specialty ,business.industry ,Pipeline (computing) ,Lumbar disc degeneration ,Region detection ,Lumbar ,Fully automated ,medicine ,Orthopedics and Sports Medicine ,Surgery ,Learning based ,Radiology ,business ,Grading (tumors) - Abstract
Lumbar disc degeneration (LDD) may be related to aging, biomechanical and genetic factors. Despite the extensive work on understanding its etiology, there is currently no automated tool for accurate prediction of its progression. We aim to establish a novel deep learning-based pipeline to predict the progression of LDD-related findings using lumbar MRIs. We utilized our dataset with MRIs acquired from 1,343 individual participants (taken at the baseline and the 5-year follow-up timepoint), and progression assessments (the Schneiderman score, disc bulging, and Pfirrmann grading) that were labelled by spine specialists with over ten years clinical experience. Our new pipeline was realized by integrating the MRI-SegFlow and the Visual Geometry Group-Medium (VGG-M) for automated disc region detection and LDD progression prediction correspondingly. The LDD progression was quantified by comparing the Schneiderman score, disc bulging and Pfirrmann grading at the baseline and at follow-up. A fivefold cross-validation was conducted to assess the predictive performance of the new pipeline. Our pipeline achieved very good performances on the LDD progression prediction, with high progression prediction accuracy of the Schneiderman score (Accuracy: 90.2 ± 0.9%), disc bulging (Accuracy: 90.4% ± 1.1%), and Pfirrmann grading (Accuracy: 89.9% ± 2.1%). This is the first attempt of using deep learning to predict LDD progression on a large dataset with 5-year follow-up. Requiring no human interference, our pipeline can potentially achieve similar predictive performances in new settings with minimal efforts.
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- 2021
34. Validation of the Applied Biosystems RapidHIT ID instrument and ACE GlobalFiler Express sample cartridge
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Kapema Bupe Kapema, Jennifer Churchill Cihlar, and Bruce Budowle
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Reproducibility ,Rapid DNA ,Computer science ,Sample (material) ,Buccal swab ,Reproducibility of Results ,ACE cartridge ,DNA ,Repeatability ,STR ,computer.software_genre ,DNA Fingerprinting ,Pathology and Forensic Medicine ,Cartridge ,SWGDAM ,Fully automated ,Rapid dna ,Validation ,Humans ,Original Article ,Data mining ,computer ,Software ,Analysis method ,Microsatellite Repeats - Abstract
Rapid DNA platforms are fully automated systems capable of processing DNA from biological samples and interpreting the results in approximately 90 minutes with minimal human intervention. With a greater reliance on the system than on the analyst, validation data are especially needed to define the performance and limitations of commercially available Rapid DNA systems. Thus, validation studies of a Rapid DNA workflow consisting of the Applied Biosystems RapidHIT ID Instrument and RapidLINK software with a focus on the ACE GlobalFiler Express Sample Cartridge and reference buccal swabs were performed in accordance with Scientific Working Group on DNA Analysis Methods Validation Guidelines. These validation studies included assessments of sensitivity, contamination, concordance, reproducibility and repeatability, stability, inhibition, mixtures, sample reprocessing, precision, and first-pass success rate. Overall, the current Applied Biosystems RapidHIT ID Instrument with the ACE GlobalFiler Express sample cartridge was found to be a reliable tool for generation of STR profiles from reference-type buccal swabs. Supplementary Information The online version contains supplementary material available at 10.1007/s00414-021-02722-9.
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- 2021
35. Fully automated glioma tumour segmentation using anatomical symmetry plane detection in multimodal brain MRI
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Zeynab Barzegar and Mansour Jamzad
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business.industry ,Computer science ,Plane (geometry) ,Computer applications to medicine. Medical informatics ,R858-859.7 ,medicine.disease ,Tumour segmentation ,QA76.75-76.765 ,Nuclear magnetic resonance ,Fully automated ,Glioma ,medicine ,Brain mri ,Computer Vision and Pattern Recognition ,Artificial intelligence ,Computer software ,Symmetry (geometry) ,business ,Software - Abstract
Automatic brain abnormality detection is a major challenge in medical image processing. Manual lesion delineation techniques are susceptible to subjective errors, and therefore, computer aided preliminary screening of a lesion is necessary. This study introduces an efficient and automated algorithm based on the symmetry of the brain structures in the two hemispheres for brain tumour segmentation using multimodal brain magnetic resonoce imaging. Symmetry is a vital clue for determining intensity‐based lesion difference in the two hemispheres of brain. A reliable method is proposed for extracting the cancerous region in order to improve the speed and accuracy of brain tumour segmentation. First, a symmetry plane is detected and then through features extracted from both sides of the brain, a similarity measure for comparing the hemisphere is defined. The cancerous region is extracted using similarity measurement, and the accuracy is improved using postprocessing operation. This algorithm is evaluated against the BRATS datasets including high‐ and low‐grade glioma brain tumours. The performance indices are calculated and comparative analysis is implemented as well. Experimental results demonstrate accuracy close to manual lesion demarcation with performance indices.
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- 2021
36. Toward High-Throughput Artificial Intelligence-Based Segmentation in Oncological PET Imaging
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Arman Rahmim, Abhinav K. Jha, Fereshteh Yousefirizi, Julia Brosch-Lenz, and Babak Saboury
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ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,FOS: Physical sciences ,Convolutional neural network ,GeneralLiterature_MISCELLANEOUS ,030218 nuclear medicine & medical imaging ,Limited access ,03 medical and health sciences ,0302 clinical medicine ,Artificial Intelligence ,Medical imaging ,Humans ,Medicine ,Radiology, Nuclear Medicine and imaging ,Segmentation ,Throughput (business) ,Radiation ,business.industry ,General Medicine ,Pet imaging ,Physics - Medical Physics ,ComputingMethodologies_PATTERNRECOGNITION ,Workflow ,Fully automated ,Positron-Emission Tomography ,030220 oncology & carcinogenesis ,Medical Physics (physics.med-ph) ,Neural Networks, Computer ,Artificial intelligence ,business - Abstract
Artificial intelligence (AI) techniques for image-based segmentation have garnered much attention in recent years. Convolutional neural networks (CNNs) have shown impressive results and potential towards fully automated segmentation in medical imaging, and particularly PET imaging. To cope with the limited access to annotated data needed in supervised AI methods, given tedious and prone-to-error manual delineations, semi-supervised and unsupervised AI techniques have also been explored for segmentation of tumors or normal organs in single and bi-modality scans. This work provides a review of existing AI techniques for segmentation tasks and the evaluation criteria for translational AI-based segmentation efforts towards routine adoption in clinical workflows., Comment: This manuscript has been accepted for publication in PET Clinics, Volume 16, Issue 4, 2021
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- 2021
37. PERFORMANCE EVALUATION OF NUCLEATED RED BLOOD CELL (NRBC) COUNT USING A FULLY AUTOMATED HAEMATOLOGY ANALYZER VERSUS MANUAL COUNTING
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Usman Tahir Swati, Tanweer Ahmed, Nasir Uddin, Helen Mary Robert, Muhammad Ashraf, and Asad Mahmood
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bland-altman plot ,medicine.medical_specialty ,Spectrum analyzer ,Medicine (General) ,Hematology ,business.industry ,Nucleated Red Blood Cell ,nucleated rbc count ,Peripheral blood ,R5-920 ,Fully automated ,Internal medicine ,Linear regression ,automated haematology analyzer ,medicine ,Medicine ,Bland–Altman plot ,Nuclear medicine ,business ,Whole blood - Abstract
Objective: To evaluate the performance of Nucleated RBC (NRBC) Count using a fully automated haematology analyzer versus manual counting. Study Design: Cross-Sectional Study. Place and Duration of Study: Department of Hematology, Armed Forces Institute of Pathology, from Sep 2019-Jun 2020. Methodology: Routine fresh whole blood samples were run on Sysmex XN-3000 automated haematology analyzer and 384 samples with results of ≥0.1% Nucleated red blood cells were included in this study. Manual NRBC counting was carried out twice on Leishman-stained peripheral blood smears from all 384 samples. Comparison between manual and automated nucleated red blood cell counting methods was statistically analyzed through linear regression analysis & coefficient correlation. The degree of agreement between two methods was analyzed through Bland-Altman plot. Finally, concordance between the two methods was also analyzed at 5 different ranges of nucleated red blood cells. Results: Linear regression analysis revealed a (r2) value of 0.97. Regression equation was calculated as XN = 0.76MC ± 1.28, with 95% limits of agreement between ± 40.42% and -24.47%. A mean bias of 7.97% was demonstrated through Bland-Altman plot. Concordance analysis revealed a concordance rate of 93.74% (360/384). Nucleated red blood cell counting between two methods were more concordant when nucleated red blood cell counts were
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- 2021
38. Evaluation of the correlation between the access SARS‐CoV‐2 IgM and IgG II antibody tests with the SARS‐CoV‐2 surrogate virus neutralization test
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Kazuo Imai, Katsumi Kubota, Shigefumi Maesaki, Ai Fukada, Masaru Matsuoka, Momoko Sato, Shinichi Takeuchi, Tomohito Takada, Norihito Tarumoto, Yutaro Kitagawa, Sakiko Noguchi, and Takuya Maeda
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Adult ,Male ,IgM ,neutralization antibody ,Coronavirus disease 2019 (COVID-19) ,IgG ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Virus Neutralization ,Antibodies, Viral ,Sensitivity and Specificity ,Neutralization ,SARS‐CoV‐2 ,COVID‐19 ,Neutralization Tests ,Virology ,Medicine ,Humans ,Research Articles ,Aged ,Aged, 80 and over ,Immunoassay ,biology ,business.industry ,SARS-CoV-2 ,COVID-19 ,Middle Aged ,Antibodies, Neutralizing ,Vaccination ,Infectious Diseases ,Fully automated ,Immunoglobulin M ,Immunoglobulin G ,Humoral immunity ,biology.protein ,Female ,Antibody ,business ,Research Article - Abstract
Fully automated immunoassays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies that are strongly correlated with neutralization antibodies (nAbs) are clinically important because they enable assessment of humoral immunity after infection and vaccination. Access SARS-CoV-2 IgM and IgG II antibody tests are semi-quantitative, fully automated immunoassays that detect anti-receptor-binding domain (RBD) antibodies and might reflect nAb levels in coronavirus disease 2019 (COVID-19). However, no studies have investigated the clinical utility of these tests in association with nAbs to date. To evaluate the clinical utility of Access SARS-CoV-2 IgM and IgG II antibody tests and their correlation with the SARS-CoV-2 surrogate virus neutralization test (sVNT) that measures nAbs in patients with COVID-19. We analyzed 54 convalescent serum samples from COVID-19 patients and 89 serum samples from non-COVID-19 patients. The presence of anti-RBD antibodies was detected by Access SARS-CoV-2 IgM and IgG II antibody tests, while nAbs were measured by sVNT. The sensitivity and specificity of sVNT were 94.4% and 98.9%, respectively. There were strong positive correlations between the inhibition values of sVNT and the results of the Access SARS-CoV-2 IgM (R = 0.95, R2 = 0.90, p < 0.001) and IgG II antibody tests (R = 0.96, R2 = 0.92, p < 0.001). In terms of the presence of nAbs, the sensitivity and specificity were 98.1% and 98.9% in the IgM assay, and 100.0% and 100.0% in the IgG II assay, respectively. The Access SARS-CoV-2 IgM and IgG II antibody tests showed high sensitivity and specificity for the detection of nAbs in COVID-19 patients and might be alternatives for measuring nAbs. This article is protected by copyright. All rights reserved.
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- 2021
39. Wireless sensing system for the welfare of sewer labourers
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V.D. Ambeth Kumar, D. Elangovan, G. Gokul, J. Praveen Samuel, and V.D. Ashok Kumar
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gas sensors ,wireless sensor networks ,biomedical measurement ,personnel ,health hazards ,industrial accidents ,wireless sensing system ,sewer labourer welfare ,environmental pollution monitoring ,toxic chemicals ,toxic gases ,microcontroller ,internet of things ,hazardous gases ,heart beats ,pulse detector ,alert warning message ,health center ,first aid ,fully automated ,quick response time ,Medical technology ,R855-855.5 - Abstract
There is a growing demand for the environmental pollution monitoring and control systems. In the view of ever increasing sources of toxic chemicals, these systems should have the facilities to detect and calibrate the source quickly. Toxic gases are the ones that cause health impact but humans are being exposed to it in various situations. These gases have to be monitored such that increase in the normal level of them could be known and proper precaution measures can be undertaken. So, an embedded system is designed using a microcontroller with internet of things, for the purpose of detecting and monitoring the hazardous gas leakage, which aids in the evasion of endangering of human lives. The hazardous gases can be sensed and displayed each and every second, in proximity to one more sensor for tracking heart beats which help to monitor the condition of the sewer labourers. If both the gases along with a pulse detector exceeds the normal level then an alarm is generated immediately and also an alert warning message can be sent to the authorised administrator and as well to the nearest health center to make the sewer labourers feel comfortable with necessary first aid and possibilities with the treatment in the case of emergency. Once the message is received by the health center, they enforce their team with necessary first aid to the current location to save the sewer labourer. Once this system is established for a particular user this will completely become fully automated and does not need any other additional people for monitoring and alerting purpose. It has an advantage over the manual method in offering quick response time and accurate detection of an emergency.
- Published
- 2018
- Full Text
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40. Machine Retrofitting for Tissue Paper Industry—INTERFOLDER Case
- Abstract
This paper is a presentation of applied design knowledge as well as practical experience in mechanical engineering and industrial automation in order to retrofit machines. The main goal is to offer affordable solution for automated log transfer and at the same time extend the life of those tissue paper converting machines that are already in operation. We exhibit practically tested solutions for a module for sheet counting and log separation that can be mounted onto existing semi-automated machine. The digital prototype e.g. CAD model is generated for a preliminary module design. Rapid prototyping is used to refine delicate geometry of moving segment before tangible manufacturing. By machine retrofitting we attain a fully automated production that consequently increased efficiency of the line by elimination of the log manual transfer operation. Also, data collection from built-in sensors and analysis provide optimization of the overall equipment effectiveness. Additionally, retrofitting includes repairs, replacements and adjustments of electrical and pneumatic systems, implementation of software for controlling that adapts machine for conformity marking and for regulations.
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- 2022
41. Fully automated noncoplanar radiation therapy treatment planning
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Lei Xing, Yong Yang, and Charles Huang
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Organs at Risk ,business.industry ,Computer science ,Radiotherapy Planning, Computer-Assisted ,medicine.medical_treatment ,FOS: Physical sciences ,Radiotherapy Dosage ,General Medicine ,Beam angle ,Modular design ,Physics - Medical Physics ,Multi-objective optimization ,Radiation therapy ,Fully automated ,Histogram ,medicine ,Medical Physics (physics.med-ph) ,Radiotherapy, Intensity-Modulated ,Radiometry ,business ,Projection (set theory) ,Radiation treatment planning ,Algorithm - Abstract
Noncoplanar radiation therapy treatment planning has the potential to improve dosimetric quality as compared to traditional coplanar techniques. Likewise, automated treatment planning algorithms can reduce a planner's active treatment planning time and remove inter-planner variability. To address the limitations of traditional treatment planning, we have been developing a suite of algorithms called station parameter optimized radiation therapy (SPORT). Within the SPORT suite of algorithms, we propose a method called NC-POPS to produce noncoplanar (NC) plans using the fully automated Pareto Optimal Projection Search (POPS) algorithm. Our NC-POPS algorithm extends the original POPS algorithm to the noncoplanar setting with potential applications to both IMRT and VMAT. The proposed algorithm consists of two main parts: 1) noncoplanar beam angle optimization (BAO) and 2) fully automated inverse planning using the POPS algorithm. We evaluate the performance of NC-POPS by comparing between various noncoplanar and coplanar configurations. To evaluate plan quality, we compute the homogeneity index (HI), conformity index (CI), and dose-volume histogram (DVH) statistics for various organs-at-risk (OARs). As compared to the evaluated coplanar baseline methods, the proposed NC-POPS method achieves significantly better OAR sparing, comparable or better dose conformity, and similar dose homogeneity. Our proposed NC-POPS algorithm provides a modular approach for fully automated treatment planning of noncoplanar IMRT cases with the potential to substantially improve treatment planning workflow and plan quality.
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- 2021
42. A Novel Thyroglobulin Immunoassay Using the Specimen-Pretreatment Process Improves the Accuracy of Thyroglobulin Measurements in Anti-Thyroglobulin Positive Specimens
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Shintaro Yagi, Sho Narita, Katsumi Aoyagi, Kitamura Yoshiyuki, and Yu Kuroda
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Immunoassay ,Detection limit ,Chromatography ,medicine.diagnostic_test ,Chemistry ,medicine.medical_treatment ,Autoantibody ,General Medicine ,Thyroglobulin ,law.invention ,Fully automated ,law ,medicine ,Humans ,Thyroid Neoplasms ,Anti thyroglobulin ,Autoantibodies ,Tumor marker ,Chemiluminescence - Abstract
Background Recently, second-generation thyroglobulin (Tg) sandwich immunoassays have been used in clinical laboratories to measure the serum Tg levels, which is a tumor marker used to monitor postoperative patients with differentiated thyroid cancers. However, these immunoassays are often subject to Tg autoantibody (TgAb) interference. TgAb interference is inevitable for almost all Tg immunoassays, resulting in unreliable Tg measurement values of TgAb-positive samples. Methods To address TgAb interference, we have developed a novel immunoassay based on a fully automated chemiluminescent enzyme immunoassay system using the effective specimen-pretreatment process to inactivate TgAb in blood and evaluated its assay performance. Results The developed assay was traceable to BCR457 IRMM reference material with a limit of quantification of 0.03 ng/mL. The pretreatment process inactivated almost all TgAb in specimens and allowed accurate Tg measurements in TgAb-positive samples in which TgAb interference was observed using the immunoassays. Size-exclusion chromatography analysis of immunoreactive Tg molecule in a TgAb-positive serum verified disruption of the Tg–TgAb immune complex by the pretreatment process. Good correlation of Tg values in TgAb-negative specimens was observed between the new Tg immunoassay and the second-generation sandwich immunoassays. However, there were numerous discrepant samples on bias plots between the new Tg immunoassay and the second-generation sandwich immunoassays for TgAb-positive specimens. Conclusions This study indicates the new Tg immunoassay with the specimen-pretreatment process is both robust and free from interference by TgAb. Thus, this novel assay is superior to second-generation sandwich immunoassays and gives accurate Tg concentrations even for TgAb-positive cases.
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- 2021
43. Fully Automated Placental Volume Quantification From <scp>3D</scp> Ultrasound for Prediction of Small‐for‐Gestational‐Age Infants
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James C. Gee, Natalie Yushkevich, Jiancong Wang, Ipek Oguz, Paul A. Yushkevich, Shobhana Parameshwaran, Baris U. Oguz, Alison M. Pouch, and Nadav Schwartz
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Placenta ,Pipeline (computing) ,Gestational Age ,Ultrasonography, Prenatal ,Article ,Pregnancy ,Placental volume ,medicine ,Humans ,Radiology, Nuclear Medicine and imaging ,3D ultrasound ,Segmentation ,Radiological and Ultrasound Technology ,medicine.diagnostic_test ,business.industry ,Infant, Newborn ,Obstetrics and Gynecology ,General Medicine ,Patient counseling ,medicine.disease ,Pregnancy Trimester, First ,Fully automated ,Infant, Small for Gestational Age ,Small for gestational age ,Female ,Test performance ,Nuclear medicine ,business - Abstract
OBJECTIVES: Early placental volume (PV) has been associated with small-for-gestational-age infants born under the 10(th)/5(th) centiles (SGA10/SGA5). Manual or semi-automated PV quantification from 3DUS is time-intensive, limiting its incorporation into clinical care. We devised a novel convolutional neural network (CNN) pipeline for fully-automated placenta segmentation from 3DUS images, exploring the association between the calculated PV and SGA. METHODS: 3DUS volumes obtained from singleton pregnancies at 11–14 weeks’ gestation were automatically segmented by our CNN pipeline trained and tested on 99/25 images, combining two 2D and one 3D models with downsampling/upsampling architecture. The PVs derived from the automated segmentations (PV(CNN)) were used to train multi-variable logistic-regression classifiers for SGA10/SGA5. The test performance for predicting SGA was compared to PVs obtained via the semi-automated VOCAL (GE-Healthcare) method (PV(VOCAL)). RESULTS: We included 442 subjects with 37 (8.4%) and 18 (4.1%) SGA10/SGA5 infants, respectively. Our segmentation pipeline achieved a mean Dice score of 0.88 on an independent test-set. Adjusted models including PV(CNN) or PV(VOCAL) were similarly predictive of SGA10 (AUCs: PV(CNN)=0.780, PV(VOCAL)=0.768). The addition of PV(CNN) to a clinical model without any PV included (AUC=0.725) yielded statistically significant improvement in AUC (P
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- 2021
44. Automated, Multistep Continuous‐Flow Synthesis of 2,6‐Dideoxy and 3‐Amino‐2,3,6‐trideoxy Monosaccharide Building Blocks
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Ashley E. DeYong, Alexander Zsikla, Clay S. Bennett, Tu-Anh V Nguyen, Olivea Vasquez, Subbarao Yalamanchili, John Florek, Nicola L. B. Pohl, and Gavin Stamper
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chemistry.chemical_classification ,business.industry ,Continuous flow ,Chemistry ,Monosaccharides ,Amino Sugars ,General Chemistry ,Flow chemistry ,General Medicine ,Modular design ,Automation ,Combinatorial chemistry ,Catalysis ,Article ,chemistry.chemical_compound ,Fully automated ,Deoxy Sugars ,Monosaccharide ,Organic synthesis ,business - Abstract
An automated continuous flow system capable of producing protected deoxy-sugar donors from commercial material is described. Four 2,6-dideoxy and two 3-amino-2,3,6-trideoxy sugars with orthogonal protecting groups were synthesized in 11-32 % overall yields in 74-131.5 minutes of total reaction time. Several of the reactions were able to be concatenated into a continuous process, avoiding the need for chromatographic purification of intermediates. The modular nature of the experimental setup allowed for reaction streams to be split into different lines for the parallel synthesis of multiple donors. Further, the continuous flow processes were fully automated and described through the design of an open-source Python-controlled automation platform.
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- 2021
45. Underlying dimensions of benefit and risk perception and their effects on people’s acceptance of conditionally/fully automated vehicles
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Yukari Jessica Tham, Takaaki Hashimoto, and Kaori Karasawa
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business.industry ,Emerging technologies ,media_common.quotation_subject ,Applied psychology ,Transportation ,Intention to use ,Usability ,Development ,Risk perception ,Harm ,Fully automated ,Perception ,business ,Psychology ,Practical implications ,Civil and Structural Engineering ,media_common - Abstract
Automated vehicles (AVs) have garnered increasing attention since they have the potential to dramatically reshape our lives in the near future. At the same time, people are concerned about various risks associated with the new technologies. Thus, people’s attitudes toward AVs pose a major challenge to the wider adoption of them. Previous studies examined the effect of benefit/risk perception on people’s acceptance of AVs, but they did not address the multidimensionality of benefit/risk perception. We conducted a survey (n = 840) to reveal the underlying dimensions of how people construe the benefits and risks of conditionally/fully automated vehicles. Our results showed that there were two dimensions underlying benefit perception (i.e., the perception that AVs would increase convenience and reduce harm) and three dimensions underlying risk perception (i.e., the perception of risk to physical safety and comfort, cybersecurity, and ease of use). The perception that AVs would reduce harm positively impacted people’s intention to use both fully automated vehicles and conditionally automated vehicles. The perception that AVs would increase convenience and the perception that AVs would pose a risk to ease of use had a positive and negative effect, respectively, on intention to use fully automated vehicles. This study makes theoretical contributions by questioning the assumption that benefit/risk perception is a one-dimensional factor that impacts people’s acceptance of AVs. This study also has practical implications as it suggests an effective method for automobile manufacturers and policymakers to communicate with the public regarding the new technologies and diffuse them safely.
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- 2021
46. A fully automated inpatient transport system
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David E. Katz, Joseph Mendlovic, and Eli Gargir
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0206 medical engineering ,Biomedical Engineering ,Biophysics ,Pilot Projects ,Health Informatics ,Bioengineering ,02 engineering and technology ,Case review ,Tertiary care ,Patient identification ,Biomaterials ,03 medical and health sciences ,Patient safety ,0302 clinical medicine ,Electronic Health Records ,Humans ,Medicine ,Unmeasured confounding ,Retrospective Studies ,Inpatients ,business.industry ,Electronic medical record ,medicine.disease ,020601 biomedical engineering ,Fully automated ,Medical emergency ,Emergency Service, Hospital ,business ,030217 neurology & neurosurgery ,Transport system ,Information Systems - Abstract
BACKGROUND: The transport of the inpatients to and from locations inside the hospital can vary in complexity depending on the patient location, status, and logistical needs. Most transport systems have not developed at the same speed as other medically related technologies. We conducted a pilot study of a new automated transport system for patients within the hospital. METHODS: Our innovative system was introduced in January 2020. We present a retrospective case review of all in-patient transport request during April 15, 2020 through May 30, 2020 at the Shaare Zedek Medical Center, Jerusalem, Israel. The system is fully automated and works via smartphone and electronic medical record integration. Transfer requests are processed on the basis of priority, proximity, and availably. RESULTS: During the study period there were 15, 581 transfer requests. Mean times to hospital destinations ranged from 9:25 to 28:02 minutes. Overall, mean times were quicker for emergency and surgical services. Trip times by priority code were likely influence by unmeasured confounders. There were no reported patient identification adverse events. Peak requests occurred during 0900-1500, and at the beginning of the week. CONCLUSION: Our automated in-patient transfer system appears to be efficient, safe, well received, and capable of servicing our large tertiary care medical center. Future controlled studies are needed to assess efficacy, adverse events, and clinical outcomes.
- Published
- 2021
47. Preventive strategy of flatfoot deformity using fully automated procedure
- Author
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Arnold Baca, Toh Yen Pang, Peter Dabnichki, Che-Wei Hu, and Canh Toan Nguyen
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Orthotic Devices ,Preventive strategy ,Foot ,Computer science ,business.industry ,Finite Element Analysis ,Biomedical Engineering ,Biophysics ,Walking ,Sitting ,Flatfoot ,Automation ,Finite element method ,Parametric design ,Fully automated ,Humans ,Arch ,business ,Engineering design process ,Simulation - Abstract
A non-invasive, no radiation, out-of-hospital automated system is proposed to identify low arch integrated in the design and manufacturing of personalized orthoses using parametric modelling. The aim of the design process is to integrate assistive technology with assessment and prevent low arch progressing to a more serious case - flatfoot. In the automated procedure, we developed an assessment method including reliable thresholds of foot type classification and test protocol to reduce interferences due to preceding activities, an automation to translate scanned data into parametric design for orthotic customization, finite element model evaluating effectiveness of the personalized design, and a personalized comparative test to evaluate the long-term improvement of foot arch shape. Our low arch threshold established by subject-specific 3D models reduced the misclassification rate from 55%, as previously reported to 6.9%. Individuals who engaged in sedentary activity (i.e. sitting) had the greater change in arch height compared to active activity (i.e. standing and walking), which is more likely to affect the obtained measure. Therefore, a test protocol now states that participants are not allowed to sit over 100 min prior the measurement to reduce such interference. We have proposed and tested an automated algorithm to translate scanned data including seven foot's parameters into customised parametric design of the insert. The method decreases the required time of orthotic computer-aided design from over 3 h to less than 2 min. A finite element analysis procedure was additionally developed to assess the performance of geometries and material of designed orthotic based on the distribution of plantar pressure and internal stress. The personalized comparative assessment based on midfoot contact area was carried out periodically for follow-up and the orthotic could be re-designed if necessary. The proposed automated procedure develops a pre-screening system to distinguish low arch and provide preventatives before it becomes symptomatic. Furthermore, non-symptom flatfoot can be detected at early stages and referred to medics for further diagnosis or treatment.
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- 2021
48. Fully Automated Unattended Data Collection and Remote Interactive Data Collection at the Photon Factory Macromolecular Crystallography Beamlines
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Yusuke Yamada
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Photon ,Data collection ,Fully automated ,Computer science ,Computer graphics (images) ,Macromolecular crystallography ,Factory (object-oriented programming) - Published
- 2021
49. Automated Object Detection, Mapping, and Assessment of Roadside Clear Zones Using Lidar Data
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Bruno Arantes de Achilles Mello, Maged Gouda, and Karim El-Basyouny
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050210 logistics & transportation ,Light detection ,Mechanical Engineering ,05 social sciences ,0211 other engineering and technologies ,Alberta canada ,Ranging ,02 engineering and technology ,Object detection ,Edge detection ,Lidar ,Fully automated ,11. Sustainability ,021105 building & construction ,0502 economics and business ,Environmental science ,Lidar data ,Civil and Structural Engineering ,Remote sensing - Abstract
This paper proposes a fully automated approach to map and assess roadside clearance parameters using mobile Light Detection and Ranging (lidar) data on rural highways. Compared with traditional manual surveying methods, lidar data could provide a more efficient and cost-effective source to extract roadside information. This study proposes a novel voxel-based raycasting approach focused primarily on automating roadside mapping and assessment. First, the scanning vehicle trajectory is extracted. Pavement surface points are then detected, and a method is proposed to extract pavement edge trajectories. Once pavement edges are extracted, guardrails were identified using a conical frustum emitted from the edge trajectory points. Target points and flexion points are then generated and located on the roadside, and a voxel-based raycasting approach is used to search for roadside obstacles and query their locations. Finally, roadside slopes and embankment heights were mapped at specific intervals, and roadside design guidelines and requirements were automatically checked against the mapping results. Noncompliant locations with substandard conditions were automatically queried. The method was tested on four highway segments in Alberta, Canada. The accuracy of the edge detection reached up to 98.5%. Furthermore, the method proved to be accurate in object detection, being able to detect all obstructions on the roadside in each tested segment. The proposed method can help transportation authorities automatically map and inventory roadside clearance parameters. Moreover, the safety performance of existing road infrastructure can be studied using collected information and crash data to support decision making on road maintenance and upgrades.
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- 2021
50. A fully automated Dobson sun spectrophotometer for total column ozone and Umkehr measurements
- Author
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Eliane Maillard Barras, Herbert Schill, René Stübi, Jörg Klausen, and Alexander Haefele
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Atmospheric Science ,Dobson ozone spectrophotometer ,Ozone ,010504 meteorology & atmospheric sciences ,business.industry ,TA715-787 ,Environmental engineering ,TA170-171 ,01 natural sciences ,Automation ,Column (database) ,Automated control ,chemistry.chemical_compound ,Data acquisition ,Earthwork. Foundations ,Fully automated ,chemistry ,Environmental science ,business ,0105 earth and related environmental sciences ,Remote sensing ,Ozone column - Abstract
The longest ozone column measurement series are based on the Dobson sun spectrophotometers developed in the 1920s by Prof. G. B. W. Dobson. These ingenious and robustly designed instruments still constitute an important part of the global network presently. However, the Dobson sun spectrophotometer requires manual operation, which has led to the discontinuation of its use at many stations, thus disrupting long-term records of observation. To overcome this problem, MeteoSwiss developed a fully automated version of the Dobson spectrophotometer. The description of the data acquisition and automated control of the instrument is presented here with some technical details. The results of different tests performed regularly to assess the instrument's good working conditions are illustrated and discussed. Compared to manual operation, automation results in a higher number of daily measurements with lower random error and additional housekeeping information to characterize the measuring conditions. The automated Dobson instrument allows for continuous observation of the ozone column with a resolution of ∼ 1 DU under clear-sky conditions.
- Published
- 2021
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