semi-automatic detection
Dotaz
Zobrazit nápovědu
In previous RENEB interlaboratory comparisons based on the manual scoring of dicentric chromosomes, a tendency for systematic overestimation for doses > 2.5 Gy was found. However, these exercises included only very few doses in the high dose range, and they were heterogeneous in terms of radiation quality and evaluation mode, and comparable only to a limited extent. Here, this presumed deviation was explored by investigating three doses > 2.5 Gy. Blood samples were irradiated (2.56, 3.41 and 4.54 Gy) using a 60Co source and sent to 14 member laboratories of the RENEB network, which performed the dicentric chromosome assay (manual and/or semi-automatic scoring) and reported dose estimates. Most participants provided estimates that agreed very well with the physical reference doses and all provided dose estimates were in the correct clinical category (> 2 Gy). The previously observed tendency for a systematic bias across all laboratories was not confirmed. However, tendencies for systematic underestimation were detected for dose estimations for reference doses given in terms of absorbed dose to blood and for some participants, a laboratory-specific trend of systematic under- or overestimation was observed. The importance of regularly performed quality checks for a broad dose range became obvious to avoid misinterpretation of results.
AIM: To investigate the feasibility of semiautomatic quantification of mosaic perfusion and the associations between mosaic perfusion on computed tomography (CT; the ratio of hypoperfused parenchyma to the whole lung volume) and haemodynamic parameters through linear regression analysis. MATERIALS AND METHODS: Fifty-eight consecutive patients (mean age 66 years, 28 females) diagnosed with chronic thromboembolic pulmonary hypertension (CTEPH) in General University Hospital, Prague, in 2021 were evaluated retrospectively and underwent both right heart catheterisation and CT pulmonary angiography. The parameters derived from the CT examinations were correlated with the recorded haemodynamic parameters. RESULTS: A method was developed for semiautomatic detection of hypoperfused tissue from CT using widely available software and a statistically significant correlation was found between the proportion of hypoperfused parenchyma and the mean pulmonary artery pressure (mPAP; R2 0.22; p<0.01) and pulmonary vascular resistance (PVR; R2 0.09; p<0.05). CONCLUSIONS: The developed method facilitates the quantification of mosaic perfusion, which is associated with important haemodynamic parameters (mPAP and PVR) in patients with CTEPH.
- MeSH
- chronická nemoc MeSH
- hemodynamika MeSH
- lidé MeSH
- nemoci cév * komplikace MeSH
- perfuze MeSH
- plíce diagnostické zobrazování MeSH
- plicní embolie * komplikace diagnostické zobrazování MeSH
- plicní hypertenze * diagnostické zobrazování MeSH
- retrospektivní studie MeSH
- senioři MeSH
- Check Tag
- lidé MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
After large-scale radiation accidents where many individuals are suspected to be exposed to ionizing radiation, biological and physical retrospective dosimetry assays are important tools to aid clinical decision making by categorizing individuals into unexposed/minimally, moderately or highly exposed groups. Quality-controlled inter-laboratory comparisons of simulated accident scenarios are regularly performed in the frame of the European legal association RENEB (Running the European Network of Biological and Physical retrospective Dosimetry) to optimize international networking and emergency readiness in case of large-scale radiation events. In total 33 laboratories from 22 countries around the world participated in the current RENEB inter-laboratory comparison 2021 for the dicentric chromosome assay. Blood was irradiated in vitro with X rays (240 kVp, 13 mA, ∼75 keV, 1 Gy/min) to simulate an acute, homogeneous whole-body exposure. Three blood samples (no. 1: 0 Gy, no. 2: 1.2 Gy, no. 3: 3.5 Gy) were sent to each participant and the task was to culture samples, to prepare slides and to assess radiation doses based on the observed dicentric yields from 50 manually or 150 semi-automatically scored metaphases (triage mode scoring). Approximately two-thirds of the participants applied calibration curves from irradiations with γ rays and about 1/3 from irradiations with X rays with varying energies. The categorization of the samples in clinically relevant groups corresponding to individuals that were unexposed/minimally (0-1 Gy), moderately (1-2 Gy) or highly exposed (>2 Gy) was successfully performed by all participants for sample no. 1 and no. 3 and by ≥74% for sample no. 2. However, while most participants estimated a dose of exactly 0 Gy for the sham-irradiated sample, the precise dose estimates of the samples irradiated with doses >0 Gy were systematically higher than the corresponding reference doses and showed a median deviation of 0.5 Gy (sample no. 2) and 0.95 Gy (sample no. 3) for manual scoring. By converting doses estimated based on γ-ray calibration curves to X-ray doses of a comparable mean photon energy as used in this exercise, the median deviation decreased to 0.27 Gy (sample no. 2) and 0.6 Gy (sample no. 3). The main aim of biological dosimetry in the case of a large-scale event is the categorization of individuals into clinically relevant groups, to aid clinical decision making. This task was successfully performed by all participants for the 0 Gy and 3.5 Gy samples and by 74% (manual scoring) and 80% (semiautomatic scoring) for the 1.2 Gy sample. Due to the accuracy of the dicentric chromosome assay and the high number of participating laboratories, a systematic shift of the dose estimates could be revealed. Differences in radiation quality (X ray vs. γ ray) between the test samples and the applied dose effect curves can partly explain the systematic shift. There might be several additional reasons for the observed bias (e.g., donor effects, transport, experimental conditions or the irradiation setup) and the analysis of these reasons provides great opportunities for future research. The participation of laboratories from countries around the world gave the opportunity to compare the results on an international level.
BACKGROUND: Manual segmentations of intracranial hemorrhage on non-contrast CT images are the gold-standard in measuring hematoma growth but are prone to rater variability. AIMS: We demonstrate that a convex optimization-based interactive segmentation approach can accurately and reliably measure intracranial hemorrhage growth. METHODS: Baseline and 16-h follow-up head non-contrast CT images of 46 subjects presenting with intracranial hemorrhage were selected randomly from the ANNEXA-4 trial imaging database. Three users semi-automatically segmented intracranial hemorrhage to measure hematoma volume for each timepoint using our proposed method. Segmentation accuracy was quantitatively evaluated compared to manual segmentations by using Dice similarity coefficient, Pearson correlation, and Bland-Altman analysis. Intra- and inter-rater reliability of the Dice similarity coefficient and intracranial hemorrhage volumes and volume change were assessed by the intraclass correlation coefficient and minimum detectable change. RESULTS: Among the three users, the mean Dice similarity coefficient, Pearson correlation, and mean difference ranged from 76.79% to 79.76%, 0.970 to 0.980 (p < 0.001), and -1.5 to -0.4 ml, respectively, for all intracranial hemorrhage segmentations. Inter-rater intraclass correlation coefficients between the three users for Dice similarity coefficient and intracranial hemorrhage volume were 0.846 and 0.962, respectively, and the corresponding minimum detectable change was 2.51 ml. Inter-rater intraclass correlation coefficient for intracranial hemorrhage volume change ranged from 0.915 to 0.958 for each user compared to manual measurements, resulting in an minimum detectable change range of 2.14 to 4.26 ml. CONCLUSIONS: We spatially and volumetrically validate a novel interactive segmentation method for delineating intracranial hemorrhage on head non-contrast CT images. Good spatial overlap, excellent volume correlation, and good repeatability suggest its usefulness for measuring intracranial hemorrhage volume and volume change on non-contrast CT images.
The goal of this research was to design a solution to detect non-reported incidents, especially severe incidents. To achieve this goal, we proposed a method to process electronic medical records and automatically extract clinical notes describing severe incidents. To evaluate the proposed method, we implemented a system and used the system. The system successfully detected a non-reported incident to the safety management department.
Manual and semi-automatic identification of artifacts and unwanted physiological signals in large intracerebral electroencephalographic (iEEG) recordings is time consuming and inaccurate. To date, unsupervised methods to accurately detect iEEG artifacts are not available. This study introduces a novel machine-learning approach for detection of artifacts in iEEG signals in clinically controlled conditions using convolutional neural networks (CNN) and benchmarks the method's performance against expert annotations. The method was trained and tested on data obtained from St Anne's University Hospital (Brno, Czech Republic) and validated on data from Mayo Clinic (Rochester, Minnesota, U.S.A). We show that the proposed technique can be used as a generalized model for iEEG artifact detection. Moreover, a transfer learning process might be used for retraining of the generalized version to form a data-specific model. The generalized model can be efficiently retrained for use with different EEG acquisition systems and noise environments. The generalized and specialized model F1 scores on the testing dataset were 0.81 and 0.96, respectively. The CNN model provides faster, more objective, and more reproducible iEEG artifact detection compared to manual approaches.
Cíl studie: Poškození DNA vlivem celkové anestezie (CA) je popsáno použitím různých metod. Publikace porovnávající vliv rozdílných anesteziologických technik nebyly v dostupné odborné literatuře nalezeny. Primárním cílem práce bylo ověřit proveditelnost metody. Sekundárním cílem bylo vyvrátit hypotézu, že neuraxiální anestezie (SAB) poškozuje DNA stejně jako CA v pilotní studii. Typ studie: Prospektivní nerandomizovaná monocentrická observační pilotní studie.Typ pracoviště: Fakultní nemocnice.Materiál a metoda: Pacienti (n = 34) podstupující ortopedicko-traumatologický výkon na dolní končetině byli rozděleni do dvou skupin: skupina CA a skupina SAB. U všech zařazených pacientů byl po podepsání informovaného souhlasu proveden odběr krve před operací a do 24 hodin po operaci. Poškození lymfocytární DNA bylo vyšetřeno metodou comet assay, která umí kvantitativně detekovat poškození nukleární DNA. Pomocí specifických enzymů lze stanovit poškození DNA způsobené oxidací bází. Výsledky comet assay byly dále hodnoceny semiautomaticky programem Lucia (Laboratory Imaging, CZ) ve fluorescenční mikroskopii, která umožňuje kvantifikaci oxidovaných bází DNA a zlomů jednošroubovicové DNA. Pro porovnání výsledků v obou skupinách byl použit Wilcoxonův test na hladině statistické významnosti pro p = 0,05. Výsledky: Skupinu CA tvořilo 19 pacientů, skupinu SAB 15 pacientů. Ve skupině CA bylo nalezeno statisticky významně vyšší poškození DNA ve srovnání s předoperačními hodnotami, u pacientů skupiny SAB byly zaznamenány statisticky nevýznamné rozdíly v poškození DNA před a po operaci. Závěr: Metoda comet assay se ukázala jako použitelná pro kvantifikaci změn DNA u pacientů po chirurgickém výkonu v anestezii. Výsledky poukazují na možný vztah mezi anesteziologickou technikou a změnami DNA asociovanými s operačním traumatem a/nebo anestezií. Zvolená metoda přináší reprodukovatelné výsledky s potenciálem jejího využití ve výzkumu vlivu anestezie na změny DNA a otevírá cestu k testování protektivních konceptů směřujících k minimalizaci poškození DNA v důsledku anestezie a operačního traumatu.
Objective: DNA damage due to general anesthesia (GA) has been described by various methods. Comparisons of different anesthesia techniques has not been found in the available literature. The primary aim of the study was to test the feasibility of the method. The secondary aim was to disprove the hypothesis that neuraxial anesthesia damages DNA just as much as GA in a pilot study. Design: Prospective, non-randomized, monocentric, observational pilot study. Setting: University Hospital. Materials and methods: Patients (n = 34) undergoing orthopedic/traumatological lower limb surgery were divided into two groups: general anesthesia (GA group) and subarachnoid anesthesia (SAB group). In all enrolled patients, after informed consent was obtained, blood was taken before surgery and within 24 hours after the surgery. Lymphocyte DNA damage was assessed by comet assay, which can quantitatively detect damage to nuclear DNA. Using specific enzymes, oxidative DNA damage can be detected. Comet assay results are evaluated semi-automatically by Lucia software (Laboratory Imaging, CZ) in fluorescence microscopy, which allows quantification of oxidized DNA bases and single stranded DNA breaks. The Wilcoxon test at the statistical significance level of p = 0.05 was used to compare the results between both groups. Results: The GA group consisted of 19 patients, the SAB group of 15 patients. There was a significantly higher DNA damage in the GA group compared to their preoperative values. Non-significant differences in DNA damage were observed in the SAB group. Conclusion: We proved the feasibility of the comet assay method in quantification of DNA damage in patients after anesthesia and surgery. The results point at the possible relationship between the anesthesia technique and DNA changes associated with surgery and/or anesthesia. The chosen method brings reproducible results with a potential for its use in the investigation of the effects of anesthesia on DNA, and opens the way for testing protective concepts aimed at minimizing DNA damage due to surgical trauma and anesthesia.
- Klíčová slova
- neuraxiální anestezie,
- MeSH
- celková anestezie * škodlivé účinky MeSH
- klinická studie jako téma MeSH
- lidé MeSH
- poškození DNA * MeSH
- Check Tag
- lidé MeSH
Extracellular vesicles (EVs) function as important conveyers of information between cells and thus can be exploited as drug delivery systems or disease biomarkers. Transmission electron microscopy (TEM) remains the gold standard method for visualisation of EVs, however the analysis of individual EVs in TEM images is time-consuming if performed manually. Therefore, we present here a software tool for computer-assisted evaluation of EVs in TEM images. TEM ExosomeAnalyzer detects EVs based on their shape and edge contrast criteria and subsequently analyses their size and roundness. The software tool is compatible with common negative staining protocols and isolation methods used in the field of EV research; even with challenging TEM images (EVs both lighter and darker than the background, images containing artefacts or precipitated stain, etc.). If the fully-automatic analysis fails to produce correct results, users can promptly adjust the detected seeds of EVs as well as their boundaries manually. The performance of our tool was evaluated for three different modes with variable levels of human interaction, using two datasets with various heterogeneity. The semi-automatic mode analyses EVs with high success rate in the homogenous dataset (F1 score 0.9094, Jaccard coefficient 0.8218) as well as in the highly heterogeneous dataset containing EVs isolated from cell culture medium and patient samples (F1 score 0.7619, Jaccard coefficient 0.7553). Moreover, the extracted size distribution profiles of EVs isolated from malignant ascites of ovarian cancer patients overlap with those derived by cryo-EM and are comparable to NTA- and TRPS-derived data. In summary, TEM ExosomeAnalyzer is an easy-to-use software tool for evaluation of many types of vesicular microparticles and is available at http://cbia.fi.muni.cz/exosome-analyzer free of charge for non-commercial and research purposes. The web page contains also detailed description how to use the software tool including a video tutorial.
- Publikační typ
- časopisecké články MeSH
The present paper aims to test performances of semi-automatic tools for mesh-to-mesh processing while assessing sex and ancestry in documented human crania. The studied sample of 80 human crania, which originated in two documented Brazilian collections (São Paulo, Brazil) was digitized using photogrammetry and laser scanning. 3D cranial morphology was quantified by computing inter-mesh dissimilarity measures using in-house freeware FIDENTIS Analyst (www.fidentis.com). Numerical outputs were further processed using Discriminant Function Analysis and Canonical Variant Analysis in order to classify models into sex and ancestry groups. In addition, cranial morphology was described by a set of 37 landmarks, processed by a Procrustes analysis and confronted with the inter-mesh comparison. Patterns of sexual dimorphism and ancestral group-specific variation were interpreted using average meshes and further emphasized by employing advanced visualization graphics. The mesh-to-mesh processing was capable to detect shape differences related to sex and ancestry. The highest accuracy levels for sex determination were obtained for meshes representing the facial skeleton and the supraorbital region. For both, analysis correctly assigned 82.5% of the crania. Ancestry-related differences were manifested primarily in the global cranial features (observed accuracy rates reaching 63%). The advanced visualization tools provided a highly informative insight into sexual dimorphism and ancestry-related variation. While in the current state the technique cannot be considered suitable for being implemented into the everyday forensic practice, the extent of automatization proved to be perspective, especially for assessing skeletal features that cannot be properly quantified using discrete variables.
- MeSH
- dospělí MeSH
- lebka anatomie a histologie MeSH
- lidé MeSH
- soudní antropologie * MeSH
- určení pohlaví podle kostry metody MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Brazílie MeSH
Acute leukemia is a disease pathologically manifested at both genomic and proteomic levels. Molecular genetic technologies are currently widely used in clinical research. In contrast, sensitive and high-throughput proteomic techniques for performing protein analyses in patient samples are still lacking. Here, we used a technology based on size exclusion chromatography followed by immunoprecipitation of target proteins with an antibody bead array (Size Exclusion Chromatography-Microsphere-based Affinity Proteomics, SEC-MAP) to detect hundreds of proteins from a single sample. In addition, we developed semi-automatic bioinformatics tools to adapt this technology for high-content proteomic screening of pediatric acute leukemia patients.To confirm the utility of SEC-MAP in leukemia immunophenotyping, we tested 31 leukemia diagnostic markers in parallel by SEC-MAP and flow cytometry. We identified 28 antibodies suitable for both techniques. Eighteen of them provided excellent quantitative correlation between SEC-MAP and flow cytometry (p< 0.05). Next, SEC-MAP was applied to examine 57 diagnostic samples from patients with acute leukemia. In this assay, we used 632 different antibodies and detected 501 targets. Of those, 47 targets were differentially expressed between at least two of the three acute leukemia subgroups. The CD markers correlated with immunophenotypic categories as expected. From non-CD markers, we found DBN1, PAX5, or PTK2 overexpressed in B-cell precursor acute lymphoblastic leukemias, LAT, SH2D1A, or STAT5A overexpressed in T-cell acute lymphoblastic leukemias, and HCK, GLUD1, or SYK overexpressed in acute myeloid leukemias. In addition, OPAL1 overexpression corresponded to ETV6-RUNX1 chromosomal translocation.In summary, we demonstrated that SEC-MAP technology is a powerful tool for detecting hundreds of proteins in clinical samples obtained from pediatric acute leukemia patients. It provides information about protein size and reveals differences in protein expression between particular leukemia subgroups. Forty-seven of SEC-MAP identified targets were validated by other conventional method in this study.
- MeSH
- akutní lymfatická leukemie diagnóza imunologie metabolismus MeSH
- diferenciální diagnóza MeSH
- dítě MeSH
- gelová chromatografie metody MeSH
- imunofenotypizace metody MeSH
- imunoprecipitace MeSH
- kojenec MeSH
- laboratorní automatizace MeSH
- lidé MeSH
- mladiství MeSH
- nádorové buněčné linie MeSH
- předškolní dítě MeSH
- proteomika metody MeSH
- protilátky farmakologie MeSH
- regulace genové exprese u leukemie MeSH
- Check Tag
- dítě MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- předškolní dítě MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
