Handcrafted Histological Transformer (H2T): Unsupervised representation of whole slide images.

Diagnostic, prognostic and therapeutic decision-making of cancer in pathology clinics can now be carried out based on analysis of multi-gigapixel tissue images, also known as whole-slide images (WSIs). Recently, deep convolutional neural networks (CNNs) have been proposed to derive unsupervised WSI representations; these are attractive as they rely less on expert annotation which is cumbersome. However, a major trade-off is that higher predictive power generally comes at the cost of interpretability, posing a challenge to their clinical use where transparency in decision-making is generally expected. To address this challenge, we present a handcrafted framework based on deep CNN for constructing holistic WSI-level representations. Building on recent findings about the internal working of the Transformer in the domain of natural language processing, we break down its processes and handcraft them into a more transparent framework that we term as the Handcrafted Histological Transformer or H2T. Based on our experiments involving various datasets consisting of a total of 10,042 WSIs, the results demonstrate that H2T based holistic WSI-level representations offer competitive performance compared to recent state-of-the-art methods and can be readily utilized for various downstream analysis tasks. Finally, our results demonstrate that the H2T framework can be up to 14 times faster than the Transformer models.

Protein arginine methyltransferase 3 promotes glycolysis and hepatocellular carcinoma growth by enhancing arginine methylation of lactate dehydrogenase A.

BACKGROUND: Protein arginine methylation has emerged a pivotal role in cancer progression. However, the role of protein arginine methyltransferase 3 (PRMT3) in hepatocellular carcinoma (HCC) remains unknown. METHODS: The expression pattern of PRMT3 in HCC was analysed using quantitative real-time-polymerase chain reaction (qRT-PCR), Western blotting and immunohistochemistry assays. Loss- and gain-of-function experiments were carried out to determine the oncogenic role of PRMT3 in HCC. Glucose consumption and lactate production assays, seahorse bioscience, mass spectrometry, co-immunoprecipitation, metabonomic analysis and site-specific mutation experiments were used to explore the underlying molecular mechanisms. Furthermore, a xenograft mouse model was established to investigate the effects of PRMT3 and its inhibitor, SGC707, treatment on tumour growth in vivo. RESULTS: The expression of PRMT3 was significantly upregulated in HCC, with high expression of which correlated with poor prognosis. PRMT3 knockdown led to the decrease in proliferation, glycolysis of HCC cells and tumour growth, whilst its overexpression showed opposite results. The catalytic activity of PRMT3 was important in mediating these biological processes. Mechanistically, our data showed that PRMT3 interacted with and mediated asymmetric dimethylarginine (ADMA) modification of lactate dehydrogenase A (LDHA) at arginine 112 (R112). Compared with LDHA-wild-type (LDHA-WT) cells, LDHA-R112K-mutant-expressing HCC cells exhibited a decrease in lactate dehydrogenase (LDH) activity, HCC cell glycolysis and proliferation. Furthermore, the administration of SGC707, a selective inhibitor of PRMT3, disrupted the PRMT3-mediated LDHA methylation and abolished PRMT3-induced HCC glycolysis and tumour growth. CONCLUSIONS: Our results suggested a novel oncogenic role of PRMT3 in HCC, and it could be a promising therapeutic target for HCC by linking post-translational modification and cancer metabolism.

Gut lumen formation defect can cause intestinal atresia: evidence from histological studies of human embryos and intestinal atresia septum.

Intestinal atresia (IA), a common cause of neonatal intestinal obstruction, is a developmental defect, which disrupts the luminal continuity of the intestine. Here, we investigated (i) the process of lumen formation in human embryos; and (ii) how a defective lumen formation led to IA. We performed histological and histochemical study on 6-10 gestation week human embryos and on IA septal regions. To investigate the topology of embryonic intestine development, we conducted 3D reconstruction. We showed that a 6-7th gestation week embryonic gut has no lumen, but filled with mesenchyme cells and vacuoles of a monolayer of epithelial cells. A narrow gut lumen was formed by gestation week-9, the gut was filled with numerous vacuoles of different sizes, some vacuoles were merging with the developing embryonic gut wall. At gestation week-10, a prominent lumen was developed, only few vacuoles were present and were merging with the intestine wall. At IA septal regions, vacuoles were located in the submucous layer, covered by a single layer of epithelium without glandular structure, and surrounded with fibrous tissue. The mucosal epithelium was developed with lamina propria and basement membrane, but the submucosa and the longitudinal smooth muscle layers were not properly developed. Hence, the vacuoles in IA septum could represent a remnant of vacuoles of embryonic gut. In conclusion, the fusion of vacuoles with the developing intestine wall associates with the disappearance of vacuoles and gut lumen formation in human embryos, and perturbation of these developmental events could lead to IA.

Development and prognostic relevance of a histologic grading and staging system for alcohol-related liver disease.

BACKGROUND & AIMS: The SALVE Histopathology Group (SHG) developed and validated a grading and staging system for the clinical and full histological spectrum of alcohol-related liver disease (ALD) and evaluated its prognostic utility in a multinational cohort of 445 patients. METHODS: SALVE grade was described by semiquantitative scores for steatosis, activity (hepatocellular injury and lobular neutrophils) and cholestasis. The histological diagnosis of steatohepatitis due to ALD (histological ASH, hASH) was based on the presence of hepatocellular ballooning and lobular neutrophils. Fibrosis staging was adapted from the Clinical Research Network staging system for non-alcoholic fatty liver disease and the Laennec staging system and reflects the pattern and extent of ALD fibrosis. There are 7 SALVE fibrosis stages (SFS) ranging from no fibrosis to severe cirrhosis. RESULTS: Interobserver κ-value for each grading and staging parameter was >0.6. In the whole study cohort, long-term outcome was associated with activity grade and cholestasis, as well as cirrhosis with very broad septa (severe cirrhosis) (p <0.001 for all parameters). In decompensated ALD, adverse short-term outcome was associated with activity grade, hASH and cholestasis (p = 0.038, 0.012 and 0.001, respectively), whereas in compensated ALD, hASH and severe fibrosis/cirrhosis were associated with decompensation-free survival (p = 0.011 and 0.001, respectively). On multivariable analysis, severe cirrhosis emerged as an independent histological predictor of long-term survival in the whole study cohort. Severe cirrhosis and hASH were identified as independent predictors of short-term survival in decompensated ALD, and also as independent predictors of decompensation-free survival in compensated ALD. CONCLUSION: The SALVE grading and staging system is a reproducible and prognostically relevant method for the histological assessment of disease activity and fibrosis in ALD. LAY SUMMARY: Patients with alcohol-related liver disease (ALD) may undergo liver biopsy to assess disease severity. We developed a system to classify ALD under the microscope by grading ALD activity and staging the extent of liver scarring. We validated the prognostic performance of this system in 445 patients from 4 European centers.

Diagnostic and therapeutic ERß, HER2, BRCA biomakers in the histological subtypes of lung adenocarcinoma according to the IASLC/ATS/ERS classification.

Several studies revealed that non-small cell lung cancers (NSCLCs) frequently express ER, PR, HER2 and carry BRCA mutation. However, these markers in histological subtypes of lung adenocarcinoma have not been thoroughly investigated. We retrospectively evaluated a total of 640 lung adenocarcinoma samples for ERα, ERß, PR and HER2 expression by immunohistochemistry and western-blotting, for EGFR and BRCA mutation by real-time PCR and sequencing. Furthermore, HER2 amplification and mutation were explored in samples harboring immunopositivity HER2 using fluorescence in situ hybridization and real-time PCR, respectively. The micropapillary and invasive mucinous predominant adenocarcinoma were frequently detected the higher level of cytoplasmic ERß (64.9% and 56.6%), HER2 (68.1% and 60.1%) protein expression. But, amplification of HER2 was detected in only three cases (3/110, 2.7%) and 26 HER2 mutations in 110 cases were identified (23.6%) in the HER2 immunopositivity patients. Logistic regression analysis showed that cytoplasmic ERß (P = 0.032) and HER2 (P = 0.015) expression were independently associated with EGFR mutation. 8 patients (8/640, 1.25%) harbored pathogenic BRCA mutations, 6 with germline BRCA mutations and 2 with somatic BRCA1 mutations were detected with lacking ERß, PR and HER2 expression. Acinar predominant adenocarcinoma had the higher percentage of BRCA mutations than other subtypes. A systematic examination of ERß, HER2 and BRCA biomarkers could potentially be useful to diagnosis and identify patients with the histological subtypes of lung adenocarcinoma, who might benefit from the further individualized treatment of anti-hormone, anti-HER2 and/or PARP inhibitors therapeutics.

PINK1/PRKN-dependent mitophagy in the burn injury model.

Burn injury leads to mitochondrial dysfunction and autophagy, also known as mitophagy. The alleviation of mitochondrial damage may be a potential method for the treatment of burn injury and complications. In this animal study, we analyzed the expression of mitochondrial damage- and mitophagy-related factors, specifically PINK1 and PRKN. The results showed mitochondria damage in the skin; compared with the normal control group, genes involved in the mitochondrial damage, such as Nrf-1, UQCRC2, CYC1, and NDUFA9, as well as in the mitophagy, including PINK1, PRKN, MFN1, and USP30, were differentially expressed. Furthermore, PINK1 interacted with PRKN and participated in mitophagy in the skin. In conclusion, our data reveal more about the mechanism underlying mitophagy in burns, providing a potential clinical treatment.

Medical Devices; Hematology and Pathology Devices; Classification of a Cervical Intraepithelial Neoplasia Test System. Final order.

The Food and Drug Administration (FDA or we) is classifying the cervical intraepithelial neoplasia (CIN) test system into class II (special controls). The special controls that apply to the device type are identified in this order and will be part of the codified language for the CIN test system's classification. We are taking this action because we have determined that classifying the device into class II (special controls) will provide a reasonable assurance of safety and effectiveness of the device. We believe this action will also enhance patients' access to beneficial innovative devices, in part by reducing regulatory burdens.

A hardware approach for histological and histopathological digital image stain normalization.

Advances in technology made the migration of pathological diagnosis to digital slides possible. As the need for objectivity and automation emerged, new computer software algorithms were proposed. Computer algorithms demand accurate color and intensity values in order to provide reliable results. The tissue samples undergo several processing steps from histological preparation to digitalization, which cannot be completely standardized. Thus, non-standardized input data generates unreliable output data. In this article, we discuss a new computational normalization algorithm for histopathological stained slides that uses a hardware color marker. The marker is added to the glass slide together with the tissue section, exposed to all the processing steps and altered in the same manner as the biological material of interest, thus becoming a solid color marker for image normalization. The results of the proposed method are numerically and perceptually tested in order to prove the advantages of the method. We conclude that our combined hardware-software technique for staining normalization of digital slides is superior to the existing methods based on only software normalization, and that its implementation will tackle not only the acquisition errors but also the technical errors that may occur during the staining process.

Histomorfometria testicular do morcego Phyllostomus discolor (Chiroptera: Phyllostomidae) em áreas de Mata Atlântica de Pernambuco / Histomorphometry Testis the bat Phyllostomus discolor (Chiroptera: Phyllostomidae) in areas of Atlantic Forest of Pernambuco

Este estudo analisou a condição reprodutiva, por meio da histomorfometria, de P. discolor coletados em fragmentos de Mata Atlântica do litoral sul de Pernambuco, durante as estações seca e chuvosa. Os animais são de coleção e foram classificados de acordo com a posição testicular (descendentes e não descendentes). Para as análises histomorfométricas, foram selecionados aleatoriamente 18 espécimes durante as estações seca e chuvosa, dos quais (n = 11) com testículos descendentes e (n = 7) com testículos não descendentes. Os resultados demonstraram que as maiores médias da área de ocupação dos túbulos seminíferos foram na estação chuvosa, independente dos espécimes apresentarem os testículos descendentes ou não. Isso pode estar relacionado a um maior investimento em produção espermática, já que na estação chuvosa, existe uma maior disponibilidade de alimentos devido às precipitações pluviométricas.

This study analyzed the reproductive condition, by histomorphometry, of P. discolor collected in forest fragments of the South Coast of Pernambuco during the dry and rainy seasons. The animals are Collection and were classified according to the position testicular (descendants and not descendants). For histomorphometric analysis, 18 were randomly selected specimens during the rainy and dry seasons, being (n = 11) with descendant testicles and (n = 7) with testicles no descendant. The results showed that the highest area average occupancy of the seminiferous tubules were in the rainy season, regardless of the present specimens the testes descendant or not. This may be related to a greater investment in sperm production, since the rainy season, there is a greater availability of food due to rainfall.

Deep UV autofluorescence microscopy for cell biology and tissue histology.

BACKGROUND INFORMATION: Autofluorescence spectroscopy is a powerful tool for molecular histology and for following metabolic processes in biological samples as it does not require labelling. However, at the microscopic scale, it is mostly limited to visible and near infrared excitation of the samples. Several interesting and naturally occurring fluorophores can be excited in the UV and deep UV (DUV), but cannot be monitored in cellulo nor in vivo due to a lack of available microscopic instruments working in this wavelength range. To fulfil this need, we have developed a synchrotron-coupled DUV microspectrofluorimeter which is operational since 2010. An extended selection of endogenous autofluorescent probes that can be excited in DUV, including their spectral characteristics, is presented. The distribution of the probes in various biological samples, including cultured cells, soft tissues, bone sections and maize stems, is shown to illustrate the possibilities offered by this system. In this work we demonstrate that DUV autofluorescence is a powerful tool for tissue histology and cell biology. RESULTS: To fulfil this need, we have developed a synchrotron-coupled DUV microspectrofluorimeter which is operational since 2010. An extended selection of endogenous autofluorescent probes that can be excited in DUV, including their spectral characteristics, is presented. The distribution of the probes in various biological samples, including cultured cells, soft tissues, bone sections and maize stems, is shown to illustrate the possibilities offered by this system. In this work we demonstrate that DUV autofluorescence is a powerful tool for tissue histology and cell biology. CONCLUSIONS: In this work we demonstrate that DUV autofluorescence is a powerful tool for tissue histology and cell biology.

Histologia e histoquímica do intestino anterior de tilápia do Nilo (Oreochromis niloticus) alimentadas com dietas contendo silagem de peixe / Histology and histochemical the medium intestine in Nile tilapia (Oreochromis niloticus) fed diets with fish silage

O objetivo deste trabalho foi avaliar a histologia e a histoquímica do intestino anterior de tilápia do Nilo alimentadas com dietas contendo farinha de peixe ou silagem de peixe como fonte de proteína de origem animal. A espessura da vilosidade intestinal dos peixes alimentados com silagem fermentada de resíduo de tilápia foi influenciada pelos teores proteicos, independente das proporções de proteína de origem animal das dietas. Observou-se que a variação da intensidade de secreção de glicoproteínas pelas células caliciformes está diretamente ligada com o tipo de dieta fornecida aos animais. O intestino médio de Oreochromis niloticus apresentou diferenças no padrão de secreção de muco glicoproteico neutro, glicoproteínas ácidas e glicoconjugados, dependendo da origem da proteína e da porcentagem utilizada na dieta, demonstrando que esta espécie pode adaptar seu sistema de secreção para a proteção do aparelho digestório durante a absorção de diferentes fontes proteicas.

This work was carried out to evaluate the action of the fermented fish silage and fish meal in the histochemical of the middle intestine of O. niloticus. A great epithelium intestinal was present in fishes fed with fish silage, independent of the animal origin protein proportions in diets. It was observed that the variation of the goblet cells secretion glicoproteic intensity is linked directly to the diet supplied to animals. The middle intestine of Oreochromis niloticus showed differences in the neutral mucus glicoproteic, acid glicoproteic and glicoconjugated secretion pattern, depending on the protein origin and the percentage used in the diet, demonstrating that this species can adapt its secretion system for the protection of the digesting apparatus during the absorption of different protein sources.

Real-time histology with the endocytoscope.

Endoscopic Imaging has progressed tremendously over the last few decades. Novel imaging technologies such as high-resolution and high-magnification white light endoscopy, narrow band imaging, optimal band imaging, autoflourescence imaging and optical coherence tomography not only aid the endoscopist in detecting malignant or pre-malignant lesions but also assist in predicting histology. Recently, the introduction of Endocytoscopy (EC) and Confocal Endomicroscopy has taken us into a new realm of diagnostic endoscopy. With the ability to magnify up to 1000 ×, cellular structures can be visualized in real-time. This advance in technology could potentially lead to a paradigm shift negating the need to obtain biopsies. EC is, however, still in the early stages of development and further research needs to be carried out before it can be accepted as standard practice. This review will focus on the diagnostic utility of the Endocytoscope.

Papulosis linfomatoide en la infancia: presentación de 9 casos y revisión de la literatura / Lymphomatoid Papulosis in Children: Report of 9 Cases and Review of the Literature

Introducción: La papulosis linfomatoide es un proceso linfoproliferativo de células T CD30+ poco frecuente y de pronóstico excelente que generalmente afecta a adultos y, en menor medida a niños, por lo que tanto el espectro clínicopatológico como el riesgo de progresión a otro tipo de linfoma en el grupo pediátrico no está bien establecido. Objetivo: Analizar las características de la papulosis linfomatoide infantil a partir de la descripción de nuevos casos y de la revisión de la literatura. Material y método: Se realizó un estudio retrospectivo de 9 pacientes menores de 18 años diagnosticados de papulosislinfomatoide atendidos en nuestro servicio entre 1995 y 2009. Resultados: Se incluyeron 7 niños y 2 niñas de edades entre 2 y 17 años. Las lesiones de papulosis linfomatoide se vieron precedidas en 2 casos y seguidas en 1 de otras compatibles con pitiriasis liquenoide aguda. La resolución de las lesiones fue espontánea, dejando hiperpigmentación (77%) o hipopigmentación postinflamatoria (23%) y cicatrices en el 77% de los casos. Histológicamente todos los casos presentaron el patrón tipo A de papulosis linfomatoide. El estudio molecular mostró monoclonalidad en los 3 casos en los que fue realizado. Conclusiones: La papulosis linfomatoide infantil es una entidad rara que se manifiesta clínicamente como la forma adulta. Esta enfermedad linfoproliferativa, que ocasionalmente se asocia a pitiriasis liquenoide aguda, muestra hallazgos histológicos compatibles con el patrón histiocitoide o tipo A. El desarrollo de otros procesos linfoproliferativos malignos en el seguimiento posterior es menos frecuente en la papulosis linfomatoide infantil comparado con la variante adulta. La frecuente asociación de pitiriasis liquenoide y de papulosis linfomatoide encontrada en nuestro análisis, así como la dificultad que supone en algunos casos el diferenciar entre ambos procesos, permite sugerir que ambas patologías podrían formar parte de un espectro clínico-patológico común (AU)

Background: Lymphomatoid papulosis is a rare lymphoproliferative T cell CD30+ disease with excellent prognosis which affects almost exclusively adult patients, being rarely in the childhood; thus the clinic and pathologic spectrum and the risk of evolution to another type of lymphoma are not well defined in the pediatric group. Objective: The aim of this article is to analyze the characteristics of infantile lymphomatoid papulosis and review the literature. Material and method: A retrospective study analyzing the characteristics of 9 patients aged up to 18 diagnosed of lymphomatoid papulosis attended in our department from 1995 to 2009 was performed. Results: The study included 7 boys and 2 girls aged between 2 and 17. Pityriasis lichenoides acuta's lesions appeared associated before and after lymphomatoid papulosisŒ development in 2 and 1 cases respectively.The lesions resolved spontaneously, leaving a postinflammatory hyperpigmentation (77%) or hypopigmentation (23%). The development of varioliform scars occurred in over 77% of cases. Histologically, all cases showed features compatible with type A of lymphomatoid papulosis. Molecular studies showed monoclonality in the 3 cases in which this technique was done. Conclusions: Infantile lymphomatoid papulosis is a rare entity clinically manifested as the adult form. This lymphoproliferative disease, which is occasionally associated with pityriasis lichenoides acuta, shows features compatible with the type A or histiocytoid pattern in the histological analysis. The development of other lymphoproliferative disorders is less frequent in the infantile form than in the adulthood. The prevalent association among pityriasis lichenoides and lymphomatoid papulosis observed in our analysis, as well as the difficulties which supposed to differentiate between these two pathologies in various cases, suggest that those entities could be part of a common clinical and pathological spectrum (AU)

[Tibor Péterfi, the founder of micromanipulation]. / Péterfi Tibor, a mikrurgia megalapítója.

Tibor Péterfi (1883-1953) was an eminent and internationally renowned biologist. He made great advances in the field of experimental physiology focusing his cytological research on microscopic examination of living cells. For this task, he created a tool named micromanipulator basing the development of microsurgery and that of cell surgery as well. His histological and cytological researches took their beginning first in Kolozsvár/Cluj (then Hungary, now Romania), where he worked as an assistant of professor István Apáthy then in Budapest where he spent fruitful years under the tutorship of professor Mihály Lenhossék. His scientific career however was broken by the political persecution which followed the fall of the communist revolution in 1919. He emigrated and spent the following decades in Prague, in Jena, in Berlin and in Cambridge. The apogee however of his scientific career proved to be the period he spent in Istanbul as a guest professor of the local university. He returned home only after the war already mortally ill. His illness did not allow him to continue his activity any more. Present article evaluates Tibor Péterfi's scientific achievements based mostly on recent archival researches.

Extraction of color features in the spectral domain to recognize centroblasts in histopathology.

In this paper, we are proposing a novel automated method to recognize centroblast (CB) cells from non-centroblast (non-CB) cells for computer-assisted evaluation of follicular lymphoma tissue samples. The method is based on training and testing of a quadratic discriminant analysis (QDA) classifier. The novel aspects of this method are the identification of the CB object with prior information, and the introduction of the principal component analysis (PCA) in the spectral domain to extract color texture features. Both geometric and texture features are used to achieve the classification. Experimental results on real follicular lymphoma images demonstrate that the combined feature space improved the performance of the system significantly. The implemented method can identify centroblast cells (CB) from non-centroblast cells (non-CB) with a classification accuracy of 82.56%.