Využití digitální patologie a umělé inteligence v anatomické patologii představuje revoluční krok směrem k modernizaci diagnostických procesů. Digitalizace, postavená zejména na využívání tzv. whole slide imaging, umožňuje vytvářet celoplošné digitální obrazy histologických preparátů, což přináší potenciální benefity v oblasti přesnosti a dostupnosti diagnostiky. Na rozdíl od tradiční mikroskopie poskytuje digitální patologie též možnost telemedicíny a vzdálené konzultace, čímž otevírá nové možnosti spolupráce a sdílení odborných znalostí na národní i mezinárodní úrovni. Implementace digitálního pracovního postupu nicméně vyžaduje rozsáhlé investice do skenerů, softwarových platforem, vysokokapacitních úložišť a IT infrastruktury. Navzdory nemalým nákladům na implementaci však přináší řadu výhod, včetně časových úspor, možnosti centralizace diagnostiky a snížení nákladů na transport vzorků. Tento příspěvek se zaměřuje na praktické aspekty implementace digitální patologie v patologických laboratořích s důrazem na přínosy, rizika a technologické požadavky spojené s digitalizací a diskutuje i zásadní role validace a verifikace celého nového pracovního procesu. Článek představuje digitální patologii jako dynamicky se rozvíjející obor s vysokým potenciálem pro personalizovanou medicínu, zlepšení diagnostické přesnosti a podporu vzdálené spolupráce, čímž reaguje na rostoucí nároky moderní medicíny.

The application of digital pathology and artificial intelligence in anatomical pathology represents a revolutionary step towards the modernization of diagnostic processes. Digitalization, primarily based on creation and subsequent use of whole slide imaging, enables generating of full digital images of histological slides, offering potential benefits in diagnostic accuracy and accessibility. Unlike traditional microscopy, digital pathology also facilitates telemedicine and remote consultation, opening new possibilities for collaboration and sharing of expertise at both national and international levels. However, implementing a digital workflow requires substantial investments in scanners, software platforms, high-capacity storage, and IT infrastructure. Despite considerable costs of implementation, it brings numerous advantages, including time savings, opportunities for centralized diagnostics, and a reduction in sample transport costs. This paper focuses on the practical aspects of implementing digital pathology in pathology laboratories, emphasizing the benefits, risks, and technological requirements associated with digitalized workflows. It also discusses crucial roles of validation and verification, which are essential for ensuring a diagnostic accuracy of digital images compared to conventional microscopy. The article presents digital pathology as a dynamically evolving field with high potential for personalized medicine, improved diagnostic accuracy, and support for remote collaboration, addressing the growing demands of modern medicine.

• MeSH
• lidé MeSH
• patologie * trendy   MeSH
• strojové učení * trendy   MeSH
• telemedicína trendy   MeSH
• Check Tag
• lidé MeSH

The dysplasia grading of Barrett's esophagus (BE), based on the histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue, suffers from high interobserver variability leading to an unsatisfactory prediction of cancer risk. Thus, pre-analytic preservation of biological molecules, which could improve risk prediction in BE enabling molecular and genetic analysis, is needed. We aimed to evaluate such a molecular pre-analytic fixation tool, PAXgene-fixed paraffin-embedded (PFPE) biopsies, and their suitability for histomorphological BE diagnostics in comparison to FFPE. In a ring trial, 9 GI pathologists evaluated 116 digital BE slides of non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinomas (EAC) using virtual microscopy. Overall quality, cytological and histomorphological parameters, dysplasia criteria, and diagnosis were analyzed. PFPE showed better preservation of nuclear details as chromatin and nucleoli, whereas overall quality and histomorphologic parameters as visibility of basal lamina, goblet cells, and presence of artifacts were scored as equal to FFPE. The interobserver reproducibility with regard to the diagnosis was best for NDBE and EAC (κF = 0.72-0.75) and poor for LGD and HGD (κF = 0.13-0.3) in both. In conclusion, our data suggest that PFPE allows equally confident histomorphological diagnosis of BE and EAC, introducing a novel tool for molecular analysis and parallel histomorphological evaluation.

• MeSH
• adenokarcinom * diagnóza   genetika   patologie   MeSH
• Barrettův syndrom * diagnóza   patologie   MeSH
• fixace tkání MeSH
• hyperplazie MeSH
• lidé MeSH
• nádory jícnu * diagnóza   patologie   MeSH
• prekancerózy * patologie   MeSH
• progrese nemoci MeSH
• reprodukovatelnost výsledků MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• klinická studie MeSH

Automatic detection and segmentation of biological objects in 2D and 3D image data is central for countless biomedical research questions to be answered. While many existing computational methods are used to reduce manual labeling time, there is still a huge demand for further quality improvements of automated solutions. In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility to biomedical data is largely unexplored. Here we introduce EmbedSeg, an embedding-based instance segmentation method designed to segment instances of desired objects visible in 2D or 3D biomedical image data. We apply our method to four 2D and seven 3D benchmark datasets, showing that we either match or outperform existing state-of-the-art methods. While the 2D datasets and three of the 3D datasets are well known, we have created the required training data for four new 3D datasets, which we make publicly available online. Next to performance, also usability is important for a method to be useful. Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. We believe that this renders EmbedSeg accessible to virtually everyone who requires high-quality instance segmentations in 2D or 3D biomedical image data.

• MeSH
• algoritmy * MeSH
• lidé MeSH
• mikroskopie * metody   MeSH
• počítačové zpracování obrazu metody   MeSH
• zobrazování trojrozměrné metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

With the development of light microscopy, it is becoming increasingly easy to obtain detailed multicolor fluorescence volumetric data. The need for their appropriate visualization has become an integral part of fluorescence imaging. Virtual reality (VR) technology provides a new way of visualizing multidimensional image data or models so that the entire 3D structure can be intuitively observed, together with different object features or details on or within the object. With the need for imaging advanced volumetric data, demands for the control of virtual object properties are increasing; this happens especially for multicolor objects obtained by fluorescent microscopy. Existing solutions with universal VR controllers or software-based controllers with the need to define sufficient space for the user to manipulate data in VR are not usable in many practical applications. Therefore, we developed a custom gesture-based VR control system with a custom controller connected to the FluoRender visualization environment. A multitouch sensor disk was used for this purpose. Our control system may be a good choice for easier and more comfortable manipulation of virtual objects and their properties, especially using confocal microscopy, which is the most widely used technique for acquiring volumetric fluorescence data so far.

• MeSH
• gesta * MeSH
• konfokální mikroskopie MeSH
• software MeSH
• virtuální realita * MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: There are only sporadic references in literature regarding general medicine and dentistry student´s preparedness for Histology, study resources and how students might use them in the era of virtual microscopy. METHODS: A structured questionnaire was used to evaluate students´ opinion, with 192 students of general medicine and 82 students of dentistry responding. RESULTS: The dentistry students evaluate their previous knowledge of basic high school disciplines as less helpful when compared to their general medicine colleagues, but this difference diminishes during the first year of medical school studies. Students of dentistry display a better orientation in the amount of study resources (electronic vs printed) and also the ways of their use (practical vs theoretical preparation). The main problems surfacing in the study of Histology have been: the lack of time due to the high demands of Anatomy, problems with correct identification of structures in specimens and correct orientation in a large number of available study resources. Students indicate that they would appreciate the introduction of interactive exercise tests to verify practical and theoretical knowledge. CONCLUSION: We revealed significant differences between students of general medicine and dentistry in terms of student´s preparedness and learning habits. According to our findings, it is still necessary to further develop teaching methods utilising virtual microscopy, taking into account the needs of both general medicine and dental school students.

• MeSH
• histologie * výchova   MeSH
• lidé MeSH
• školy stomatologické * MeSH
• studenti MeSH
• studium stomatologie MeSH
• učení MeSH
• zvyky MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes pathological pulmonary symptoms. Most efforts to develop vaccines and drugs against this virus target the spike glycoprotein, particularly its S1 subunit, which is recognised by angiotensin-converting enzyme 2. Here we use the in-house developed tool CaverDock to perform virtual screening against spike glycoprotein using a cryogenic electron microscopy structure (PDB-ID: 6VXX) and the representative structures of five most populated clusters from a previously published molecular dynamics simulation. The dataset of ligands was obtained from the ZINC database and consists of drugs approved for clinical use worldwide. Trajectories for the passage of individual drugs through the tunnel of the spike glycoprotein homotrimer, their binding energies within the tunnel, and the duration of their contacts with the trimer's three subunits were computed for the full dataset. Multivariate statistical methods were then used to establish structure-activity relationships and select top candidate for movement inhibition. This new protocol for the rapid screening of globally approved drugs (4359 ligands) in a multi-state protein structure (6 states) showed high robustness in the rate of finished calculations. The protocol is universal and can be applied to any target protein with an experimental tertiary structure containing protein tunnels or channels. The protocol will be implemented in the next version of CaverWeb (https://loschmidt.chemi.muni.cz/caverweb/) to make it accessible to the wider scientific community.

• Publikační typ
• časopisecké články MeSH

BACKGROUND AND AIMS: Patients after endoscopic treatment of Barrett's esophagus (BE) related neoplasia (BORN) should enter endoscopic surveillance with biopsies to detect persistent or recurrent neoplasia or intestinal metaplasia (IM). Probe-based confocal laser endomicroscopy (pCLE) serves as a virtual biopsy and could replace standard biopsies. However, the role of pCLE in patients after endoscopic treatment of BORN has not been systematically assessed. The aim of this study was to compare pCLE with biopsies in detecting persistent/recurrent IM/neoplasia. METHODS: A single center, prospective and pathologist-blinded study was performed. Patients after endoscopic treatment of BORN (endoscopic resection or dissection, radiofrequency ablation) underwent surveillance endoscopy with pCLE followed by biopsies. RESULTS: A total of 56 patients were enrolled: initial diagnoses were low-grade dysplasia (LGD) in 24 patients (43%), high-grade dysplasia (HGD) in 12 patients (21%) and early adenocarcinoma (EAC) in 20 patients (36%). Only one patient (2%) experienced recurrent neoplasia (LGD), which was diagnosed by pCLE only. Twenty patients (35.7%) experienced persistent/recurrent IM, diagnosed by both pCLE and biopsies in 17 patients (17/30, 85%) and by pCLE only in 3 pts (3/30, 15%). Sensitivity, specificity, positive and negative predictive values to diagnose recurrent/persistent IM did not differ significantly between pCLE and biopsies; diagnostic accuracy was 100% (95%CI 93.6-100) for pCLE and 94.6 (95%CI 85.1-98.9%) for biopsies, p=0.25. In patients with IM detected by both tested methods, pCLE detected significantly more goblet cells (median 43 per patient) than biopsies (median 12 per patient), p=0.01. CONCLUSION: pCLE is at least as effective as standard biopsies in the detection of persistent/recurrent IM after endoscopic treatment of BORN.

• MeSH
• Barrettův syndrom patologie   chirurgie   MeSH
• biopsie MeSH
• časové faktory MeSH
• dospělí MeSH
• ezofagektomie * škodlivé účinky   MeSH
• ezofágoskopie * škodlivé účinky   MeSH
• konfokální mikroskopie * MeSH
• lidé středního věku MeSH
• lidé MeSH
• lokální recidiva nádoru * MeSH
• nádory jícnu patologie   chirurgie   MeSH
• prediktivní hodnota testů MeSH
• prospektivní studie MeSH
• radiofrekvenční ablace * MeSH
• reprodukovatelnost výsledků MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• stupeň nádoru MeSH
• výsledek terapie 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
• srovnávací studie MeSH

Úvod: Histopatologická diagnostika indeterminovaných biliárních stenóz a pankreatických lézí má svá úskalí, např. nedostatečnou kvalitu vzorků tkáně odebraných při ERCP (kartáčkový stěr), cholangioskopii (biopsie) nebo endosonografii (EUS, punkční cytologie − FNAB). Konfokální laserová endomikroskopie (CLE) umožňuje virtuální histopatologickou diagnostiku a mohla by nahradit nebo zpřesnit standardní diagnostiku biliárních a pankreatických lézí. Cílem prospektivní pilotní studie bylo jednak srovnat výtěžnost standardní histopatologické diagnózy s CLE u pacientů, kteří byli indikováni k cholangioskopii nebo k EUS vyšetření pankreatu. Dalším cílem bylo zhodnotit finanční náročnost metody. Metody: Zařazení pacienti nejprve podstoupili CLE (buď s cholangioskopií, nebo s EUS) a následně byl proveden odběr tkáně. Histopatologická diagnostika na základě CLE byla srovnána se standardní histopatologickou diagnózou. U cholangioskopie byla CLE sonda zavedena skrze pracovní kanál cholangioskopu, v případě EUS byla CLE sonda zavedena skrze punkční jehlu. Výsledky: Do studie bylo zařazeno celkem 23 pacientů (12 žen, průměrný věk 61 let), 13 pacientů podstoupilo cholangioskopii, 10 pacientů EUS pankreatu. Cholangioskopie: U cholangioskopie CLE diagnostikovala všechny 4 maligní striktury (histologie pouze dvě, u 2 pacientů byly biopsie nevýtěžné). Shoda mezi standardní diagnostikou a CLE byla dosažena v 85 %. EUS: CLE i FNAB správně diagnostikovaly všechny (n=3) karcinomy pankreatu. Ostatní premaligní i benigní léze byly správně diagnostikovány oběma metodami. CLE je finančně náročnější oproti FNAB, je však cenově srovnatelná s tkáňovou analýzou při digitální cholangioskopii. Závěr: CLE je spolehlivou metodou poskytující histopatologickou diagnózu u pacientů s biliárními či pankreatickými lézemi, která by mohla zlepšit výtěžnost nebo i nahradit standardní histopatologickou diagnostiku.

Introduction: An accurate histopathological diagnosis of indeterminate biliary strictures and pancreatic lesions is challenging because of insufficient quality of tissue specimen taken during ERCP (brush cytology), cholangioscopy (biopsies) or endosonography (EUS, FNAB). Confocal laser endomicroscopy (CLE) allows virtual histopathological diagnosis with the potential to either replace or increase the diagnostic yield of standard histopathological diagnosis in patients presenting with biliary strictures and pancreatic lesions. The aims of our prospective pilot study were to: 1. Assess the diagnostic yield of standard histopathology compared to CLE in patients referred for cholangioscopy or for EUS of the pancreas; 2. Evaluate the cost of CLE in these indications. Methods: CLE was performed (during cholangioscopy or EUS), followed by standard tissue sampling. CLE-based diagnosis was compared with standard histopathology/cytology. CLE probe was introduced through the working channel of the cholangioscope or through the FNAB needle. Results: A total of 23 patients were enrolled (12 women, mean age 61 years); 13 patients underwent cholangioscopy and 10 patients underwent EUS. Cholangioscopy: CLE diagnosed correctly all 4 malignant strictures (histology 2 of them only as 2 patients had insufficient quality of the tissue specimen). Agreement between standard histopathology and CLE was achieved in 85 %. EUS: All 3 cases of pancreatic cancer were correctly diagnosed by both CLE and FNAB. All remaining (premalignant and benign) lesions were also correctly diagnosed by both methods. The cost of CLE examination is higher compared to FNAB but comparable with tissue sampling during digital cholangioscopy. Conclusion: CLE demonstrated sufficient diagnostic accuracy in patients with indeterminate biliary strictures or pancreatic lesions and, therefore, might improve diagnostic accuracy or even replace standard histopathology in these indications.

• Klíčová slova
• biliární striktura, cystické léze pankreatu,
• MeSH
• konfokální mikroskopie metody   MeSH
• lidé MeSH
• nemoci slinivky břišní * diagnóza   MeSH
• nemoci žlučových cest * diagnóza   MeSH
• prospektivní studie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH

Histone deacetylase 6 (HDAC6) is a multidomain cytosolic enzyme having tubulin deacetylase activity that has been unequivocally assigned to the second of the tandem catalytic domains. However, virtually no information exists on the contribution of other HDAC6 domains on tubulin recognition. Here, using recombinant protein expression, site-directed mutagenesis, fluorimetric and biochemical assays, microscale thermophoresis, and total internal reflection fluorescence microscopy, we identified the N-terminal, disordered region of HDAC6 as a microtubule-binding domain and functionally characterized it to the single-molecule level. We show that the microtubule-binding motif spans two positively charged patches comprising residues Lys-32 to Lys-58. We found that HDAC6-microtubule interactions are entirely independent of the catalytic domains and are mediated by ionic interactions with the negatively charged microtubule surface. Importantly, a crosstalk between the microtubule-binding domain and the deacetylase domain was critical for recognition and efficient deacetylation of free tubulin dimers both in vitro and in vivo Overall, our results reveal that recognition of substrates by HDAC6 is more complex than previously appreciated and that domains outside the tandem catalytic core are essential for proficient substrate deacetylation.

• MeSH
• acetylace MeSH
• histondeacetylasa 6 metabolismus   MeSH
• katalytická doména MeSH
• lidé MeSH
• mikrotubuly metabolismus   MeSH
• proteinové domény fyziologie   MeSH
• sekvence aminokyselin MeSH
• substrátová specifita MeSH
• tubulin metabolismus   MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Chromosome pairing in meiosis usually starts in the vicinity of the telomere attachment to the nuclear membrane and congregation of telomeres in the leptotene bouquet is believed responsible for bringing homologue pairs together. In a heterozygote for an inversion of a rye (Secale cereale L.) chromosome arm in wheat, a distal segment of the normal homologue is capable of chiasmate pairing with its counterpart in the inverted arm, located near the centromere. Using 3D imaging confocal microscopy, we observed that some telomeres failed to be incorporated into the bouquet and occupied various positions throughout the entire volume of the nucleus, including the centromere pole. Rye telomeres appeared ca. 21 times more likely to fail to be included in the telomere bouquet than wheat telomeres. The frequency of the out-of-bouquet rye telomere position in leptotene was virtually identical to the frequency of telomeres deviating from Rabl's orientation in the nuclei of somatic cells, and was similar to the frequency of synapsis of the normal and inverted chromosome arms, but lower than the MI pairing frequency of segments of these two arms normally positioned across the volume of the nucleus. Out-of-position placement of the rye telomeres may be responsible for reduced MI pairing of rye chromosomes in hybrids with wheat and their disproportionate contribution to aneuploidy, but appears responsible for initiating chiasmate pairing of distantly positioned segments of homology in an inversion heterozygote.

• MeSH
• buněčné jádro genetika   ultrastruktura   MeSH
• centromera chemie   ultrastruktura   MeSH
• chiméra genetika   MeSH
• chromozomální inverze * MeSH
• chromozomy rostlin chemie   ultrastruktura   MeSH
• druhová specificita MeSH
• heterozygot MeSH
• hybridizace in situ fluorescenční MeSH
• konfokální mikroskopie MeSH
• párování chromozomů MeSH
• počítačové zpracování obrazu statistika a číselné údaje   MeSH
• profáze meiózy I * MeSH
• pšenice genetika   ultrastruktura   MeSH
• rostlinné buňky metabolismus   ultrastruktura   MeSH
• telomery chemie   ultrastruktura   MeSH
• žito genetika   ultrastruktura   MeSH
• zobrazování trojrozměrné metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH