INTRODUCTION: Quantitative wood anatomy is critical for establishing climate reconstruction proxies, understanding tree hydraulics, and quantifying carbon allocation. Its accuracy depends upon the image acquisition methods, which allows for the identification of the number and dimensions of vessels, fibres, and tracheids within a tree ring. Angiosperm wood is analysed with a variety of different image acquisition methods, including surface pictures, wood anatomical micro-sections, or X-ray computed micro-tomography. Despite known advantages and disadvantages, the quantitative impact of method selection on wood anatomical parameters is not well understood. METHODS: In this study, we present a systematic uncertainty analysis of the impact of the image acquisition method on commonly used anatomical parameters. We analysed four wood samples, representing a range of wood porosity, using surface pictures, micro-CT scans, and wood anatomical micro-sections. Inter-annual patterns were analysed and compared between methods from the five most frequently used parameters, namely mean lumen area (MLA), vessel density (VD), number of vessels (VN), mean hydraulic diameter (D h), and relative conductive area (RCA). A novel sectorial approach was applied on the wood samples to obtain intra-annual profiles of the lumen area (A l), specific theoretical hydraulic conductivity (K s), and wood density (ρ). RESULTS: Our quantitative vessel mapping revealed that values obtained for hydraulic wood anatomical parameters are comparable across different methods, supporting the use of easily applicable surface picture methods for ring-porous and specific diffuse-porous tree species. While intra-annual variability is well captured by the different methods across species, wood density (ρ) is overestimated due to the lack of fibre lumen area detection. DISCUSSION: Our study highlights the potential and limitations of different image acquisition methods for extracting wood anatomical parameters. Moreover, we present a standardized workflow for assessing radial tree ring profiles. These findings encourage the compilation of all studies using wood anatomical parameters and further research to refine these methods, ultimately enhancing the accuracy, replication, and spatial representation of wood anatomical studies.

• Klíčová slova
• angiosperms, broad-leaved species, inter-and intra-annual variability, quantitative wood anatomy, radial profile, uncertainty analysis, x-ray CT scanning, xylem porosity,
• Publikační typ
• časopisecké články MeSH

Optimal descriptors calculated with Simplified Molecular Input Line Entry System (SMILES) notation have been used in quantitative structure-property relationships (QSPR) of half-wave potential of N-benzylsalicylthioamides. The QSPR developed is one-variable model based on the optimal descriptors calculated with the Monte Carlo method. The approach has been checked up with three random splits into the training and test sets. Mechanistic interpretations (structural alerts related to the half-wave potential) of the model are discussed.

• Klíčová slova
• CORAL software, Half-wave potential, N-benzylsalicylthioamide, QSPR, SMILES,
• MeSH
• kvantitativní vztahy mezi strukturou a aktivitou * MeSH
• metoda Monte Carlo MeSH
• molekulární struktura MeSH
• thioamidy chemická syntéza   chemie   farmakologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• thioamidy MeSH

Mycobacterium avium paratuberculosis (MAP), etiological agent of paratuberculosis in ruminants, is able to survive extreme conditions like very low pH (stomach), high temperature (pasteurization) or low temperature (refrigerated storage). Cheese, infant powder milk, cream and other milk and dairy products might thus be considered as possible sources of MAP for humans. The aim of this study was to investigate the survival of two MAP field isolates during fermentation of three different types of soured milk products (SMP; yogurt, acidophilus milk and kefir) under laboratory conditions. Pasteurized MAP-free milk was artificially contaminated with 10(6)MAPcells/mL and survival and absolute numbers of MAP were monitored during fermentation (4 or 16 h) and after six weeks of storage at 4°C by culture and quantitative real time PCR (qPCR). Viability of MAP was determined by culture using Herrold's egg yolk medium and Middlebrook 7H10 with antibiotics, supplemented with Mycobactin J and incubated at 37°C for up to 12 weeks. The absolute numbers of MAP were quantified by previously published qPCR assays targeting F57 and IS900 loci in MAP genome. We herein confirm that MAP can survive pH reduction, however, longer exposure to pH below 4 in SMP seems to be critical because it inhibits growth. Therefore, it is suggested that probiotic cultures that can decrease pH below 4 during fermentation could provide better inactivation of MAP in SMP.

• MeSH
• fermentace MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• mléčné výrobky mikrobiologie   MeSH
• mléko mikrobiologie   MeSH
• Mycobacterium avium subsp. paratuberculosis genetika   růst a vývoj   izolace a purifikace   MeSH
• paratuberkulóza mikrobiologie   MeSH
• pasterizace MeSH
• probiotika MeSH
• sýr MeSH
• vysoká teplota MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

This paper is an overview of the most significant and impactful interpretation approaches of quantitative structure-activity relationship (QSAR) models, their development, and application. The evolution of the interpretation paradigm from "model → descriptors → (structure)" to "model → structure" is indicated. The latter makes all models interpretable regardless of machine learning methods or descriptors used for modeling. This opens wide prospects for application of corresponding interpretation approaches to retrieve structure-property relationships captured by any models. Issues of separate approaches are discussed as well as general issues and prospects of QSAR model interpretation.

• MeSH
• kvantitativní vztahy mezi strukturou a aktivitou * MeSH
• strojové učení MeSH
• teoretické modely * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Disruption of the blood-brain barrier (BBB) is a key feature of various brain disorders. To assess its integrity a parametrization of dynamic magnetic resonance imaging (DCE MRI) with a contrast agent (CA) is broadly used. Parametrization can be done quantitatively or semi-quantitatively. Quantitative methods directly describe BBB permeability but exhibit several drawbacks such as high computation demands, reproducibility issues, or low robustness. Semi-quantitative methods are fast to compute, simply mathematically described, and robust, however, they do not describe the status of BBB directly but only as a variation of CA concentration in measured tissue. Our goal was to elucidate differences between five semi-quantitative parameters: maximal intensity (Imax), normalized permeability index (NPI), and difference in DCE values between three timepoints: baseline, 5 min, and 15 min (delta5-0, delta15-0, delta15-5) and two quantitative parameters: transfer constant (Ktrans) and an extravascular fraction (Ve). For the purpose of comparison, we analyzed DCE data of four patients 12-15 days after the stroke with visible CA enhancement. Calculated parameters showed abnormalities spatially corresponding with the ischemic lesion, however, findings in individual parameters morphometrically differed. Ktrans and Ve were highly correlated. Delta5-0 and delta15-0 were prominent in regions with rapid CA enhancement and highly correlated with Ktrans. Abnormalities in delta15-5 and NPI were more homogenous with less variable values, smoother borders, and less detail than Ktrans. Moreover, only delta15-5 and NPI were able to distinguish vessels from extravascular space. Our comparison provides important knowledge for understanding and interpreting parameters derived from DCE MRI by both quantitative and semi-quantitative methods.

• MeSH
• hematoencefalická bariéra * diagnostické zobrazování   MeSH
• kontrastní látky MeSH
• lidé MeSH
• magnetická rezonanční tomografie metody   MeSH
• nemoci mozku * MeSH
• reprodukovatelnost výsledků MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kontrastní látky MeSH

Lysosomes are the terminal end of catabolic pathways in the cell, as well as signaling centers performing important functions such as the recycling of macromolecules, organelles, and nutrient adaptation. The importance of lysosomes in human health is supported by the fact that the deficiency of most lysosomal genes causes monogenic diseases called as a group Lysosomal Storage Diseases (LSDs). A common phenotypic hallmark of LSDs is the expansion of the lysosomal compartment that can be detected by using conventional imaging methods based on immunofluorescence protocols or overexpression of tagged lysosomal proteins. These methods require the alteration of the cellular architecture (i.e., due to fixation methods), can alter the behavior of cells (i.e., by the overexpression of proteins), and require sample preparation and the accurate selection of compatible fluorescent markers in relation to the type of analysis, therefore limiting the possibility of characterizing cellular status with simplicity. Therefore, a quantitative and label-free methodology, such as Quantitative Phase Imaging through Digital Holographic (QPI-DH), for the microscopic imaging of lysosomes in health and disease conditions may represent an important advance to study and effectively diagnose the presence of lysosomal storage in human disease. Here we proof the effectiveness of the QPI-DH method in accomplishing the detection of the lysosomal compartment using mouse embryonic fibroblasts (MEFs) derived from a Mucopolysaccharidosis type III-A (MSP-IIIA) mouse model, and comparing them with wild-type (WT) MEFs. We found that it is possible to identify label-free biomarkers able to supply a first pre-screening of the two populations, thus showing that QPI-DH can be a suitable candidate to surpass fluorescent drawbacks in the detection of lysosomes dysfunction. An appropriate numerical procedure was developed for detecting and evaluate such cellular substructures from in vitro cells cultures. Results reported in this study are encouraging about the further development of the proposed QPI-DH approach for such type of investigations about LSDs.

• Klíčová slova
• digital holography, intracellular specificity, label‐free imaging, lysosomal storage diseases, lysosomes, quantitative phase imaging,
• MeSH
• fibroblasty metabolismus   patologie   MeSH
• kvantitativní fázové zobrazování MeSH
• lidé MeSH
• lyzozomální nemoci z ukládání metabolismus   patologie   genetika   diagnóza   MeSH
• lyzozomy * metabolismus   MeSH
• mukopolysacharidóza III metabolismus   patologie   genetika   MeSH
• myši MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

JBI offers a suite of critical appraisal instruments that are freely available to systematic reviewers and researchers investigating the methodological limitations of primary research studies. The JBI instruments are designed to be study-specific and are presented as questions in a checklist. The JBI instruments have existed in a checklist-style format for approximately 20 years; however, as the field of research synthesis expands, many of the tools offered by JBI have become outdated. The JBI critical appraisal tools for quantitative studies (eg, randomized controlled trials, quasi-experimental studies) must be updated to reflect the current methodologies in this field. Cognizant of this and the recent developments in risk-of-bias science, the JBI Effectiveness Methodology Group was tasked with updating the current quantitative critical appraisal instruments. This paper details the methods and rationale that the JBI Effectiveness Methodology Group followed when updating the JBI critical appraisal instruments for quantitative study designs. We detail the key changes made to the tools and highlight how these changes reflect current methodological developments in this field.

• MeSH
• lidé MeSH
• výzkumný projekt * MeSH
• zkreslení výsledků (epidemiologie) MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BCR-ABL1 molecular detection using quantitative PCR (qPCR) methods is the golden standard of chronic myeloid leukemia (CML) monitoring. However, due to variable sensitivity of qPCR assays across laboratories, alternative methods are tested. Digital PCR (dPCR) has been suggested as a robust and reproducible option. Here we present a comparison of droplet dPCR with routinely used reverse-transcription qPCR (RT-qPCR) and automated GeneXpert systems. Detection limit of dPCR was above 3 BCR-ABL1 copies, although due to background amplification the resulting sensitivity was 0.01% BCR-ABL1 (MR4.0). Nevertheless, in comparison with GeneXpert, dPCR categorized more than 50% of the patients into different MR groups, showing a potential for improved BCR-ABL1 detection.

• Klíčová slova
• BCR-ABL1 monitoring, CML, chronic myeloid leukemia, Chronic myeloid leukemia, Digital PCR, EAC, Europe Against Cancer, FPR, false positivity rate, GeneXpert BCR-ABL Monitor assay, IS, international scale, LOB, limit of blank, LOD, limit of detection, MR, molecular response, NTC, no template control, RT-qPCR, RT-qPCR, reverse-transcription quantitative PCR, TKI, tyrosine kinase inhibitors, cDNA, complementary DNA, dPCR, digital PCR, pDNA, plasmid DNA, qPCR, quantitative PCR,
• Publikační typ
• časopisecké články MeSH

Quantitative Real-Time Polymerase Chain Reaction, better known as qPCR, is the most sensitive and specific technique we have for the detection of nucleic acids. Even though it has been around for more than 30 years and is preferred in research applications, it has yet to win broad acceptance in routine practice. This requires a means to unambiguously assess the performance of specific qPCR analyses. Here we present methods to determine the limit of detection (LoD) and the limit of quantification (LoQ) as applicable to qPCR. These are based on standard statistical methods as recommended by regulatory bodies adapted to qPCR and complemented with a novel approach to estimate the precision of LoD.

• Klíčová slova
• Data analysis, GenEx software, Limit of detection, Limit of quantification, LoD, LoQ, MIQE, Quality control, Real-time PCR, Replicates, Standardization, qPCR,
• Publikační typ
• časopisecké články MeSH

In the current study, the sensitivity and specificity of methods of HER2 status detection were studied in 55 patients presenting with gastric/gastroesophageal junction carcinoma (30 intestinal and 25 diffuse), in small biopsy (endoscopy; n=33) and resection specimens (n=22). The primary objective of the present study was to compare various methods for the assessment of HER2 status, with regards to the sensitivity and specificity of each method, as well as their concordance. In all cases, the status of HER2 was determined using immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), silver in situ hybridization (SISH), and quantitative polymerase chain reaction (qPCR). The concordance rate between IHC and ISH was 100% for IHC 0 and 3+. The concordance rate for IHC 1+ was 100% between IHC and SISH, and 92.9% between IHC and FISH. The concordance rate among different FISH methods was 100%, between FISH and SISH it was 96.2%, and between qPCR and ISH methods it was 88.5%. Thus, the results demonstrate that different in situ hybridization methods are comparable and that none were superior. Furthermore, the IHC and FISH methods were found to be comparable and the concordance rate was particularly good. qPCR analysis correlated well with the other methods and appears to be a possible alternative tool for detection of the HER2 status. However, the concordance rate of qPCR with other methods was identified to be lower in the diffuse carcinoma group of endoscopy biopsy specimens; therefore investigation of further cases is required.

• MeSH
• adenokarcinom diagnóza   metabolismus   MeSH
• diagnostické techniky molekulární MeSH
• dospělí MeSH
• gastroezofageální junkce patologie   MeSH
• hybridizace in situ fluorescenční MeSH
• imunohistochemie MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádory žaludku diagnóza   metabolismus   MeSH
• receptor erbB-2 genetika   metabolismus   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• ERBB2 protein, human MeSH Prohlížeč
• receptor erbB-2 MeSH