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Over the last twenty years, with the development of gene-driven therapies, numerous new drugs have entered clinical use. Very few of these new drugs are suitable for a large number of patients, and all require molecular genetic testing. In lung cancer, gene-targeted therapy has evolved rapidly and has placed demands on the development of diagnostics and tissue sample preparation and logistics. Rapid diagnosis and prevalence assessment are necessary to determine the prognosis of a lung cancer patient based on the latest research findings. Therefore, the molecular-genetic diagnostic pathway must also be accelerated and matured to do the necessary analyses on small samples. Because lung cancer rebiopsy can be difficult, liquid biopsy techniques should be developed to cover more of the treatable mutations. There are obstacles related to tissue sampling, new genomic techniques and access to gene-driven cancer drugs, including their affordability. With this review and case study, we go into the obstacles faced by our clinic and discuss how to tackle these obstacles in lung cancer. We use lung cancer as an example due to its complexity, though these same obstacles are found in different cancers on a minor scale.

Aims Molecular profiling of hepatocellular carcinoma (HCC) has helped identify actionable genomic alterations that could guide therapeutic decision-making and clinical trial enrollment. However, in clinical practice, next-generation sequencing (NGS) is not extensively used in routine clinical care to identify patients with HCC who are likely to benefit from genome-directed targeted therapies. Methods Here, we describe the case of a 66-year-old man with advanced HCC. After rapid progression on transarterial chemoembolization, the tissue sample obtained from biopsy was subjected to NGS to verify whether precision therapy was an option. Results Our analysis revealed high MET amplification. The patient received crizotinib (250 mg, bid) and showed a remarkable response. Conclusions Our case report suggests NGS could help identify patients with high MET amplification in HCC who were likely to benefit from MET inhibitors; moreover, this requires further investigation in clinical trials.

Acute infections of the hand can be a pathology with severe consequences. Alongside the surgical therapy, it is necessary to establish a systemic antiinfective therapy as well. The most frequent bacteria in acute hand infections are Staphylococcus aureus and, less frequently, different Streptococci. If the infection is the result of a bite wound, the most frequently found bacterium is Pasteurella multocida. Fortunately, the susceptibility to frequently used antibiotics in the (middle-)European area is quite good - according to the literature, resistances are rare. First line antibiotics are 1st and 2nd generation cephalosporins as well as aminopenicillins in combination with beta-lactamase inhibitors. Especially in multi-morbid patients or infections with unusual aetiology, a broader bacterial spectrum is to be expected. It is very effective to collect a tissue sample or swab for microbiological analysis before the establishment of the antiinfective therapy to gain valuable information about the prospective therapy. Ultimately, hand infections are a pathology to be treated with increased attention to avoid severe complications. A close cooperation with the involved specialties and physiotherapists should be sought to guarantee the best possible outcome.

Traditional management of newly diagnosed pediatric brain tumors (PBTs) consists of cranial imaging, typically magnetic resonance imaging (MRI), and is frequently followed by tissue diagnosis, through either surgical biopsy or tumor resection. Therapy regimes are typically dependent on histological diagnosis. To date, many treatment regimens are based on molecular biology. The scope of this article is to discuss the role of diagnosis and further treatment of PBTs based solely on MRI features, in light of the latest treatment protocols. Typical MRI findings and indications for surgical biopsy of these lesions are described.

The list of mammals of the Lake Glubokoe Nature Reserve (Ruza district, Moscow region, Russia) was supplemented with the flying squirrel (Pteromys volans). The contemporary border of the native range of the flying squirrel goes through the northeastern part of Moscow region (oblast). No individuals of this species had been recorded in the western parts of the region until the end of the 20th century. However, a flying squirrel population has recently appeared in the vicinity of the Zvenigorod Biological Station, Moscow State University. This population originates from several animals transported to the biological station for scientific purposes. As genetic studies have shown, individuals from this population belong to the endemic Far Eastern phylogenetic lineage. This lineage includes individuals recently recorded in other places in the western part of Moscow region. The sequence of the cytochrome b gene of mitochondrial DNA from a tissue sample of a flying squirrel individual found on the territory of the Lake Glubokoe Nature Reserve in July 2013 is identical to that known for animals from the Zvenigorod Biological Station, as well as to those from other places of the western part of Moscow region. The new record is the westernmost one among all other previous records, which confirms the enlarging of the Zvenigorod subrange of this species. Despite the Pteromys volans population in the vicinities of Glubokoe Lake appearing as a consequence of introduction, it is protected by the Red Data Book of Moscow region.

Flow cytometry is an effective and widely used tool for determination of ploidy in fish, but it is not always possible to access the fresh samples for analysis. We investigated the potential for extended storage of fish tissue with sterlet and tench as representative species of Chondrostei and Teleostei, using blood and fin of subadult/adult specimens and tail of larvae. Thirteen procedures for extending storage, selected for rapidity and simplicity in both field and laboratory conditions, were tested for each tissue sample. Flow cytometry was applied to fresh tissue immediately after sampling and to tissue subjected to experimental protocols, always along with species‐specific standard, after 1, 5, and 10 days storage at 0–4°C or freezing at −80°C. The fluorochrome 4′,6‐diamidine‐2′‐phenylindole dihydrochloride was used with excitation/emission maximum 358/461 nm. Based on the measurability of stored samples, evaluation of directly measured coefficients of variation of their DNA peaks and the changes in fluorescence intensity compared to fresh tissue, optimal procedures for extended storage of the selected tissue types of the model species are suggested. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.

The objective was to study the possibilities of using the C-arm based universal angiographic complex as a navigation system in transthoracic biopsies of pulmonary nodules.Methods and materials. The study is based on the data of 60 patients with lesion size from 10 to 103 mm (mean 51 mm) have been underwent the transthoracic biopsy using C-arm based universal angiographic complex navigation. A total of 69 biopsies were performed (60 primary, 9 repeated). The procedure was made with local anesthesia in an interventional operating room. The postoperative observation time was 1 day.Results. A tissue sample was got in all cases. As a result of a biopsy, a malignant tumor was confirmed in 70 % of patients (42 people). At the primary biopsy, data for the malignant process were not obtained in 30 % (18 people), however, in half of the cases (9 people), the diagnosis of a malignant tumor was confirmed after repeated biopsy. The radiation dose received by the patient was 2.05-60.50 mSv (mean 13.94mSv), which is comparable to the radiation dose in traditional CT navigation and less than the average dose of radiation obtained using CT fluoroscopy. Sensitivity, specificity, accuracy were 82.35, 100 и 35 % respectively. Complications occurred in 18 cases (26.09 %). There was no need to perform interventions under general anesthesia. Transfer of patients to the intensive care unit was not required. No fatal complications occurred.Conclusion. This navigation system is safe and effective and can be used routinely.

This article belongs to the Special Issue 10th Trends in Medical Mycology. The diagnosis and initiation of appropriate treatment against invasive fungal infections depend upon accurate identification of pathogens by pathologists and clinical microbiologists. Histopathology is often critical in providing diagnostic insight in patients with suspected fungal in fections, and such findings are incorporated into the definitions of proven or probable disease caused by certain pathogens. Such examinations can offer provisional identifications of fungal organisms, which can help guide initial therapy while laboratory results are pending. Common etiologic agents of invasive mycoses may be recognized based on morphologic characteristics observed in tissue and biologic fluids, such as those obtained from bronchoalveolar lavage and bronchial washings. However, care should be taken in the interpretation of these findings, as there may be a false sense of the ability to correctly categorize fungal organisms to the genus or species level by morphologic features alone. Studies have demonstrated discordant results between histopathology and laboratory results due to overlapping morphologic features, morphologic mimics, and sampling errors. Thus, histopathology plays an integral role in providing a differential of potential fungal pathogens but must be combined with results from laboratory studies, including cultures, antigen tests, serology, and molecular assays, in order to improve accuracy in the identification of etiologic agents of fungal infections. Inaccurate identification of the infecting organism can lead to inappropriate antifungal therapy and possibly poor clinical outcomes. info:eu-repo/semantics/publishedVersion

Background: In patients with advanced high-grade serous ovarian cancer (HGSOC) and prostate adenocarcinoma, the identification of somatic/germline BRCA1/2 mutations allows new therapeutic opportunities. To estimate the prevalence of somatic and germline BRCA1/2 mutations in non-mucinous high grade ovarian/fallopian tube/peritoneal extraovarian cancer (NMHGOC) and prostate adenocarcinoma. Methods: Prevalence was established by analyzing patients with NMHGOC or prostate adenocarcinoma, with a BRCA1/2 study in the tumor between 2017 and 2018. Whether a germline study had been carried out was subsequently reviewed. Results: 10 patients out of 43 (23.3%) with NMHGOC had a BRCA1/2 mutation in the tumor. 9 patients (20.9%) presented a BRCA1/2 mutation in the germline setting (2 without tumor result due to limited tissue sample). 3 patients (6.9%) had only somatic mutations. 30% of the mutations in the tumor were, therefore, somatic mutations. Of the 9 patients with prostate adenocarcinoma, 2 (22.2%) had a BRCA2 mutation in the tumor. While 1 (11.1%) had the mutation in the germline setting, 1 patient (11.1%) had only somatic mutations. Conclusion: In our series, the prevalence of somatic and germline BRCA1/2 mutations in NMHGOC is similar to that reported in the literature. Whereas somatic mutations are only present at the neoplastic tissue, the rate of mutations in the tumor is higher than in the germline setting. A more effective diagnostic and predictive strategy could be achieved with tumor BRCA analysis as the first attempt. Initial results in prostate adenocarcinoma point to the same conclusion for this tumor.

Background & Aims Microvascular invasion (MVI) is a critical prognostic factor for operable hepatocellular carcinoma (HCC). This study aimed to explore the performance of circulating tumour DNA (ctDNA) in evaluating MVI status preoperatively. Methods Seventy‐three HCC patients were enrolled and randomly divided into a training cohort and a validation cohort in a 2:1 ratio, and preoperative blood and surgical tissue samples were obtained. Genomic alterations were analysed using targeted deep sequencing with a 1021‐gene panel. Results In training cohort, 260 somatic mutations were identified in 40 blood samples (81.6%). CtDNA mutation was verified in paired tissue sample in 39 patients (97.5%). In univariate analysis, ctDNA allele frequency (AF) and largest tumour diameter were associated with the presence of MVI, but ctDNA AF was the only independent risk factor in multivariate analysis. With the cut‐off value of 0.83%, ctDNA AF determined the presence of MVI with the sensitivity of 89.7% and specificity of 80.0% in the training cohort, and the sensitivity of 78.6% and the specificity of 81.8% in the validation cohort. In preoperative evaluation, ctDNA AF, AFP level and BCLC staging were associated with recurrence‐free survival in both univariate and multivariate analysis. Conclusions CtDNA can serve as an independent risk factor of MVI for operable HCC and help determining precise treatment strategies. The integration of ctDNA in the management of operable HCC may achieve better clinical outcomes.

Intraosseous lipomas are rare primary benign bone tumors which present with highly nonspecific radiographic features that may lead to equivocal diagnoses. Advanced imaging studies such as MRI with and without contrast and, in some selected cases, tissue sample analyses are required in the diagnostic pathway. Here we describe the second case in the literature of an intraosseous lipoma of the clavicle and the first with extraosseous extension. Subsequent to histologic confirmation the lesion was monitored with clinical and radiologic evaluation.

Modern consumers attach increasing importance to tactile sensations and the general perception of the surface of fabrics, therefore, the study of the structure and properties of woven textures is an urgent task of textile production. In textile technologies, organoleptic research methods are used mainly, which give a subjective visual and tactile assessment of the surface of the tissues. Therefore, there was a need to develop an instrumental method for determining the texture of fabrics, which was implemented on the basis of the existing method for studying the texture of hard surfaces. It is based on the idea of creating a constant mode of illumination of the object of observation, which is a tissue sample. The proposed method is based on the use of a special optical device for determining the qualitative and quantitative characteristics of textures and is a viewing chamber containing a mechanism for changing the lighting mode and a mechanism for capturing tissue images. For an objective assessment of the state of the surface of the tissues, the invoice indicator is calculated − the invoice coefficient. The implementation of the developed method allows to increase the efficiency of the processes of design-design of fabrics, to predict the appearance of fabrics and to ensure compliance with the texture of the fabric of the model of the garment.

Intro: The 2018 ASCO/CAP HER2 guidelines eliminated the equivocal category for in situ hybridization (ISH). Additional workup is recommended for definitive classification of tumors that are sorted into ISH groups 2, 3 or 4. Evaluation of HER2 IHC using sections from the same tissue sample used for ISH is recommended to guide the selection of areas to score by ISH. Here we seek to evaluate the utility of selecting the area for ISH testing in IHC equivocal (2+) cases based on the staining intensity of the IHC staining. Methods: A total of 66 cases with equivocal HER2 IHC (2+) and reflexed to FISH were prospectively collected from 8/22/18 to 6/26/2019. The areas of most and least intense HER2 IHC staining were separately identified and scored by FISH. The mean HER2:CEP17 ratio and mean HER2 signals/tumor cell were calculated for both populations and statistical significance was evaluated using the Wilcoxon Ranked Sum test. Results: The distribution of the high intensity area was 58 ISH group 5, 4 ISH group 4, and 8 ISH group 1. The distribution of the low intensity area was 51 ISH group 5, 9 ISH group 4, 2 ISH group 2, and 5 ISH group 5. In the high and low intensity areas, 59 of 66 (95.5%) cases sorted into the same ISH group and 7 (10.6%) sorted into different ISH groups. Of these 7, 3 (4.5%) had different final FISH categorizations. All 3 cases were ISH Group 1 (amplified) in the high intensity area and ISH group 2, 4 or 5 (not amplified in the absence of 3+ IHC) in the low intensity area. The other 4 cases with different ISH groups did not have different final HER2 categorizations. The mean HER2/CEP17 ratios for the high and low intensity areas were 1.50 and 1.39 (p = 0.075). There was no statistically significant difference in mean HER2 copy number for the high and low intensity areas (p = 0.92). Discussion: When areas with high and low HER2 IHC intensity were compared, there was a small difference in the mean HER2:CEP17 ratio with a trend toward statistical significance. However, the absolute difference in the means was small (0.11) and only a minority of cases (4.5%) showed discordant final HER2 categorization between the two groups. All of the cases with discordant HER2 categorization were amplified (ISH Group 1) in the IHC high intensity area and not amplified (ISH Groups 2, 4 and 5) in the low intensity area. The data suggests that using HER2 IHC to guide selection of areas for ISH testing may identify amplified tumors (or clones) in a minority of cases (4.5%). Additional analysis of a larger number of cases is required to validate these findings. Citation Format: Johann D Hertel, Kathleen A Kaiser-Rogers, Siobhan O'Connor, Benjamin Calhoun. Utility of HER2 IHC intensity in selecting areas for FISH testing in equivocal (2+) cases [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-21.

Background To explore the differential expression of apolipoproteinA1 (APOA1) in urologic neoplasm patient compared with controls, as well as investigates whether APOA1 correlated with infiltration of urologic neoplasm. Methods A total of 59 tissue sections of surgically-resected urologic neoplasm and 6 cases of normal tissue sections were collected. Fourteen cases of urine samples from transitional cell carcinoma patients and 6 cases urine samples from controls were also applied in this experiment. We also selected 6 cases of fresh bladder transitional cell carcinoma tissues. The urologic neoplasm tissue sections were classified into infiltration and non-infiltration urologic neoplasm groups. The expressions of APOA1 between urologic neoplasm and normal control were detected by Western blot, Immunohistochemistry and qRT-PCR. The method of Immunohistochemistry was applied to examine the differences of APOA1 expression between infiltration and non-infiltration urologic neoplasm tissue section groups. Results Compared with none expression in normal controls, APOA1 was exhibited higher level in urologic neoplasm patient’s urine and fresh bladder transitional cell carcinoma tissues (P

Background: Black dust deposited in the lungs is called anthracosis. By damaging bronchial mucosa, anthracosis can affect the mucociliary cleaning function. Initial reports indicate that there is a relationship between anthracosis and pulmonary tuberculosis. Due to obstructive effects of anthracosis on distal airways and disruption in a proper sampling of bronchoalveolar lavage (BAL), other diagnostic methods are necessary for estimating the tuberculosis prevalence in these patients. The aims of this study was to evaluate tissue samples adjacent to an anthracotic plaque for acid-fast bacilli smear and culture. Methods: his is a cross-sectional analysis study on 100 patients referred to Shahid Sadoughi Hospital who required bronchoscopy and anthracotic plaque based on bronchoscopy results. Bronchial fluid lavage, two biopsy samples for culture, and a smear of Mycobacterium tuberculosis from the surrounding of these plaques were prepared. Data analyses were carried out using SPSS (version 18). Results: One-hundred patients og the age range 46-91years were studied. The patients with tuberculosis diagnosis based on the smear of BAL and bronchial tissue samples and culture of BAL and bronchial tissue samples were 7%, 13%, 6% and 8% respectively. The presence of granuloma in histopathology was seen in 15 patients infected with tuberculosis. (κ > 0.04, p-value Conclusions: Diagnostic value of BAL method and tissue biopsy in anthracosis patients with tuberculosis did not show a statistically significant difference. As compared with other methods, BAL culture was more positive. Therefore, tissue biopsy is not a good alternative to BAL.

Crucial to establishing the etiology of an undiagnosed pleural exudate after basic investigations is the acquisition of an adequate tissue sample. Pleural biopsy is effected via thoracoscopy or the transthoracic route. Initial studies which utilized “blind” transthoracic pleural biopsy techniques earned the procedure a reputation for high complication rates and low diagnostic yields. Subsequently, the addition of image-guidance has markedly improved both these limitations. In the hands of experienced practitioners, closed plural biopsy under image guidance is an effective and safe tool, with a diagnostic yield approaching that of thoracoscopy. The type of needle and imaging modality chosen should be appropriate to the likely underlying diagnosis, the morphology of the pleural abnormality, and local expertise.

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This "liquid biopsy" approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.

Objective We have described the integrated use of a neuronavigation-guided system for frameless stereotaxy (VarioGuide [Brainlab AG, Munich, Germany]) with intraoperative magnetic resonance imaging (iMRI) and 5-aminolevulinic acid (5-ALA) and report the advantages and disadvantages that the use of these tools together can have in the treatment of various types of intracerebral lesions. Methods After the skin incision, creation of a burr hole at the entry point, and dura opening, the VarioGuide procedure was started. Initially, the wizard software will require positioning of the stereotactic arm over the burr hole and provides feedback regarding the correct position. The procedure is performed in an iMRI theater furnished with a surgical microscope (Kinevo [Carl Zeiss AG, Oberkochen, Germany]) supplied with a violet-blue excitation light for 5-ALA fluorescence. At the end of the surgery, iMRI was performed. We present 2 exemplary cases to describe the application and workflow of these tools. Results When used for traditional biopsy, the possibility of performing a new iMRI scan could be of paramount importance because the brain shift can be compensated for and an alternative trajectory can be calculated from the new images and fiber tracking reconstruction. The fluorescence of the tissue sample examined under the microscope filter can provide immediate information about the nature of the lesion, allowing for the possibility of converting the procedure to open craniotomy and tumor removal. Conclusion The use of combination frameless stereotaxy with iMRI and 5-ALA has shown benefits in terms of safety and precision. Moreover, the use of these tools can simplify tumor removal after simple biopsy, widening the spectrum of indications.

Fish species substitution and fraud has become a worldwide economic issue in the seafood industry. In this study, an ultraviolet-visible (UV-Vis) spectroscopy-based method was developed for the identification of fish samples. Sixty fish samples from twelve commonly consumed fish species in China were analyzed as models to testify the protocol. The obtained results show that UV-Vis spectroscopy combined with chemometric analysis, such as principal component analysis (PCA), can accurately distinguish two fish species by boiling fish tissue sample in trifluoroacetic acid (TFA) solution for 2 min and analyzing the resultant samples using a UV-Vis spectrometer. The developed strategy was successfully applied to the classification and identification of fish samples on the market. It is a promising strategy that can be applied to the classification and authenticity testing of closely related fish species in order to detect and recognize fish substitution.

Elemental and molecular imaging play a crucial role in understanding disease pathogenesis. To accurately correlate elemental and molecular markers, it is desirable to perform sequential elemental and molecular imaging on a single-tissue section. However, very little is known about the impact of performing these measurements in sequence. In this work, we highlight some of the challenges and successes associated with performing elemental mapping in sequence with mass spectrometry imaging. Specifically, the feasibility of molecular mapping using the mass spectrometry imaging (MSI) techniques matrix-assisted laser desorption ionization (MALDI) and desorption electrospray ionization (DESI) in sequence with the elemental mapping technique particle-induced X-ray emission (PIXE) is explored. Challenges for integration include substrate compatibility, as well as delocalization and spectral changes. We demonstrate that while sequential imaging comes with some compromises, sequential DESI-PIXE imaging is sufficient to correlate sulfur, iron, and lipid markers in a single tissue section at the 50 μm scale.

The collection of blood and tissue provides an opportunity for an objective comparison of autopsy results. Occasionally, a viable tissue sample is not available during autopsy. Expanding upon collected tissues to include a tissue that is accessible, is a possible drug depot, and is amendable to various analytical techniques may complement information obtained from other specimens. Given its absorption of ions, nutrients, and likely drugs via its rich blood supply, we evaluated the use of submandibular salivary gland tissue as an alternative postmortem specimen. The submandibular salivary glands of 52 decedents were excised. The tissue was homogenized, extracted, and analyzed via liquid chromatography tandem mass spectrometry for 43 opioids and 5 nonopioids. Liquid chromatography tandem mass spectrometry salivary tissue results were compared with the decedent's blood results. Results revealed that opioids were detected in salivary gland tissue at a sensitivity and specificity of 94.4% and 94.1%, respectively. Nonopioid drugs were detected at a sensitivity and specificity of 88.2% and 100.0%, respectively. This study suggests a comparable correlation exists between salivary gland tissue and blood results for certain drugs. Further evaluation is warranted. To our knowledge, this is the first report of salivary gland tissue being used for postmortem toxicology testing in humans.

In the chemical analyses of tissues for trace elements, quality control of the tissue sample for its anatomic composition is a critically important step that is frequently overlooked. This is because the analyst often assumes a degree of homogeneity that does not exist. The means of attaining a representative sample vary greatly depending on the organ or tissue involved, and also on the level of resolution chosen, i.e., the size of the sample.

Food adulteration is a serious concern faced by the importers of various food products across the globe. In this study, a simple, sensitive and robust method for detecting pork in processed/complex food samples using next-generation DNA sequencing (NGS) technology is described. The experimentation involves a generalized library preparation kit for performing shotgun sequencing of the genomic DNA irrespective of its intactness. The method was applied on different complex food samples containing pork along with other species (up to twelve) as well as without pork to test the specificity of the method. The DNA sequences were mapped with the online NCBI nucleotide database for their identification followed by a calculation of the relative abundance of the reads. The adulteration of pork was correctly identified in the analyzed samples. Although the relative abundance of pork DNA reads could not make a precise quantitative relevance with the contributed amount of the tissue sample, yet this method has the potential to determine extremely low as well as high contents of adulterating/contaminating species in complex food products.

Background Visualizing and quantifying cellular heterogeneity is of central importance to study tissue complexity, development, and physiology and has a vital role in understanding pathologies. Mass spectrometry-based methods including imaging mass cytometry (IMC) have in recent years emerged as powerful approaches for assessing cellular heterogeneity in tissues. IMC is an innovative multiplex imaging method that combines imaging using up to 40 metal conjugated antibodies and provides distributions of protein markers in tissues with a resolution of 1 μm2 area. However, resolving the output signals of individual cells within the tissue sample, i.e., single cell segmentation, remains challenging. To address this problem, we developed MATISSE (iMaging mAss cyTometry mIcroscopy Single cell SegmEntation), a method that combines high-resolution fluorescence microscopy with the multiplex capability of IMC into a single workflow to achieve improved segmentation over the current state-of-the-art. Results MATISSE results in improved quality and quantity of segmented cells when compared to IMC-only segmentation in sections of heterogeneous tissues. Additionally, MATISSE enables more complete and accurate identification of epithelial cells, fibroblasts, and infiltrating immune cells in densely packed cellular areas in tissue sections. MATISSE has been designed based on commonly used open-access tools and regular fluorescence microscopy, allowing easy implementation by labs using multiplex IMC into their analysis methods. Conclusion MATISSE allows segmentation of densely packed cellular areas and provides a qualitative and quantitative improvement when compared to IMC-based segmentation. We expect that implementing MATISSE into tissue section analysis pipelines will yield improved cell segmentation and enable more accurate analysis of the tissue microenvironment in epithelial tissue pathologies, such as autoimmunity and cancer.

IEEE Transactions on Biomedical Engineering, 66 (10), ISSN:0018-9294, ISSN:1558-2531

Introduction: Lung cancer is the most common cause of cancer-related death among males and females. The diagnosis of lung cancer is of great importance for clinical considerations and follow-up treatment. This study aimed to examine the expression of CEA, LUNX, and CK19 biomarkers in the cancerous and healthy tissues of patients suffering from NSCLC. Methods: In this study, 30 patients with NSCLCs referring to Masih Daneshvari Hospital in Tehran were voluntarily selected prior to taking any treatment. A tissue sample from the center and a sample of healthy tissues close to the cancerous masses were prepared by a specialist in the bronchoscopy sector and tested using real-time RT-PCR. Results: Positive CEA mRNA was observed in cancerous tissues in the center of tumors of 25 out of 30 cases. In the healthy tissue group, the same was found in 10 out of 30 cases (P

The unearthing of two Iron Age bog bodies in the Irish midlands within a few months of each other in 2003 prompted the development of new strategies for recording, investigating, preserving and dis...

Summary Background Allograft contamination during extraction represents a major limiting factor for tissue bank availability. Contamination rates remain persistently high independent of the hospital, country or year considered. Aim To analyse the factors associated with contamination of bone and tendon samples extracted from Spanish donors. Methods Data for 1162 bone and tendon samples extracted from 102 donors between 2014 and 2017 were collected retrospectively from the hospital database. Descriptive statistics, potentially associated factors and correlation of contamination between samples extracted from different anatomical locations of the same donor were analysed. Findings In total, 227 (19.54%) of the extracted samples [131 (18.49%) bone samples and 96 (20.92%) tendon samples] rendered positive cultures and were discarded. Male sex [odds ratio (OR) 2.023; P=0.019], extraction of >10 samples per donor (OR 1.997; P 240 min (OR 1.755; P=0.001) were factors independently associated with a higher contamination rate. Meanwhile, the tissue sample type ‘bone-patellar tendon-bone’ was associated with a significantly lower contamination rate (OR 0.446; P=0.001). Significant correlation between certain localization of contaminated samples and the concordance of bacterial species was also observed. Conclusion Factors related to the extraction procedure, such as total extraction time, extraction sequence, number of samples extracted and anatomical location of extracted samples, play a major role in allograft contamination. Further optimization of procedures, guided by the contamination patterns analysed in this study, should help to increase tissue bank availability.

Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data. Texomer results in substantially improved accuracy in sample categorization and functional variant prioritization.

Filter papers have been used for many years in different applications of molecular biology and have been proven to be a stable way to store DNA waiting to be analyzed. Sampling of DNA on FTA (Flinders Technology Associates) cards is convenient and cost effective compared to alternative approaches involving DNA extractions and storage of DNA extracts. FTA cards are analyzed at many forensic laboratories, and the way to perform direct genetic profiling on buccal swab cards has developed into an almost industrial process. The possibility to include postmortem (PM) samples into an FTA-based workflow would facilitate and speed up the genetic identification process compared to conventional methods, both on a regular basis and in a mass casualty event. In this study, we investigated if FTA cards may be used to carry tissue DNA from deceased and present a high-quality DNA profile from the individual in order to be useful for the identification process. The study also aimed to investigate if a specific body tissue would be preferable, and if decomposed tissue is suitable at all to put on an FTA card in order to obtain a DNA profile. We have compared the quality of the DNA profiles acquired from postmortem tissue on FTA cards, with the results acquired with conventional methods from reference bone/muscle samples from the same individual. Several types of tissues have been tested from different identification cases and scenarios. We concluded that tissue cells from inner organs are suitable to put on FTA cards, and that the obtained DNA profiles have the potential to serve as PM data for identification purposes. In cases including compromised samples, however, it is recommended to keep the tissue sample as a backup if further DNA has to be extracted.