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Diagnostic Pathology Dec 2011Application of virtual slides (VS), the digitalization of complete glass slides, is in its infancy to be implemented in routine diagnostic surgical pathology and to...
BACKGROUND
Application of virtual slides (VS), the digitalization of complete glass slides, is in its infancy to be implemented in routine diagnostic surgical pathology and to issues that are related to tissue-based diagnosis, such as education and scientific publication.
APPROACH
Electronic publication in Pathology offers new features of scientific communication in pathology that cannot be obtained by conventional paper based journals. Most of these features are based upon completely open or partly directed interaction between the reader and the system that distributes the article. One of these interactions can be applied to microscopic images allowing the reader to navigate and magnify the presented images. VS and interactive Virtual Microscopy (VM) are a tool to increase the scientific value of microscopic images.
TECHNOLOGY AND PERFORMANCE
The open access journal Diagnostic Pathology http://www.diagnosticpathology.org has existed for about five years. It is a peer reviewed journal that publishes all types of scientific contributions, including original scientific work, case reports and review articles. In addition to digitized still images the authors of appropriate articles are requested to submit the underlying glass slides to an institution (DiagnomX.eu, and Leica.com) for digitalization and documentation. The images are stored in a separate image data bank which is adequately linked to the article. The normal review process is not involved. Both processes (peer review and VS acquisition) are performed contemporaneously in order to minimize a potential publication delay. VS are not provided with a DOI index (digital object identifier). The first articles that include VS were published in March 2011.
RESULTS AND PERSPECTIVES
Several logistic constraints had to be overcome until the first articles including VS could be published. Step by step an automated acquisition and distribution system had to be implemented to the corresponding article. The acceptance of VS by the reader is high as well as by the authors. Of specific value are the increased confidence to and reputation of authors as well as the presented information to the reader. Additional associated functions such as access to author-owned related image collections, reader-controlled automated image measurements and image transformations are in preparation.
VIRTUAL SLIDES
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1232133347629819.
Topics: Access to Information; Humans; Image Processing, Computer-Assisted; Microscopy; Pathology, Clinical; Pathology, Surgical; Peer Review, Research; Periodicals as Topic; Telepathology; User-Computer Interface
PubMed: 22182763
DOI: 10.1186/1746-1596-6-124 -
SLAS Technology Aug 2017We present a mesodissection platform that retains the advantages of laser-based dissection instrumentation with the speed and ease of manual dissection. Tissue...
We present a mesodissection platform that retains the advantages of laser-based dissection instrumentation with the speed and ease of manual dissection. Tissue dissection in clinical laboratories is often performed by manually scraping a physician-selected region from standard glass slide mounts. In this manner, costs associated with dissection remain low, but spatial resolution is compromised. In contrast, laser microdissection methods maintain spatial resolution that matches the requirements for analysis of important tissue heterogeneity but remains costly and labor intensive. We demonstrate a microfluidic tool for rapid extraction of histological regions of interest from formalin-fixed paraffin-embedded tissue, which uses a simple and automated method that is compatible with most downstream enzymatic reactions, including protocols used for next-generation DNA sequencing.
Topics: Automation, Laboratory; Dissection; Humans; Microfluidics; Molecular Diagnostic Techniques; Neoplasms; Pathology, Molecular
PubMed: 27864340
DOI: 10.1177/2211068216680208 -
Modern Pathology : An Official Journal... Nov 2020Pathologists are responsible for rapidly providing a diagnosis on critical health issues. Challenging cases benefit from additional opinions of pathologist colleagues....
Pathologists are responsible for rapidly providing a diagnosis on critical health issues. Challenging cases benefit from additional opinions of pathologist colleagues. In addition to on-site colleagues, there is an active worldwide community of pathologists on social media for complementary opinions. Such access to pathologists worldwide has the capacity to improve diagnostic accuracy and generate broader consensus on next steps in patient care. From Twitter we curate 13,626 images from 6,351 tweets from 25 pathologists from 13 countries. We supplement the Twitter data with 113,161 images from 1,074,484 PubMed articles. We develop machine learning and deep learning models to (i) accurately identify histopathology stains, (ii) discriminate between tissues, and (iii) differentiate disease states. Area Under Receiver Operating Characteristic (AUROC) is 0.805-0.996 for these tasks. We repurpose the disease classifier to search for similar disease states given an image and clinical covariates. We report precision@k = 1 = 0.7618 ± 0.0018 (chance 0.397 ± 0.004, mean ±stdev ). The classifiers find that texture and tissue are important clinico-visual features of disease. Deep features trained only on natural images (e.g., cats and dogs) substantially improved search performance, while pathology-specific deep features and cell nuclei features further improved search to a lesser extent. We implement a social media bot (@pathobot on Twitter) to use the trained classifiers to aid pathologists in obtaining real-time feedback on challenging cases. If a social media post containing pathology text and images mentions the bot, the bot generates quantitative predictions of disease state (normal/artifact/infection/injury/nontumor, preneoplastic/benign/low-grade-malignant-potential, or malignant) and lists similar cases across social media and PubMed. Our project has become a globally distributed expert system that facilitates pathological diagnosis and brings expertise to underserved regions or hospitals with less expertise in a particular disease. This is the first pan-tissue pan-disease (i.e., from infection to malignancy) method for prediction and search on social media, and the first pathology study prospectively tested in public on social media. We will share data through http://pathobotology.org . We expect our project to cultivate a more connected world of physicians and improve patient care worldwide.
Topics: Algorithms; Deep Learning; Humans; Pathologists; Pathology; Social Media
PubMed: 32467650
DOI: 10.1038/s41379-020-0540-1 -
Archives of Pathology & Laboratory... Apr 2020Pathology-related advocacy is best when performed directly by pathologists. Practicing advocacy is included in the Milestones 2.0 and should be introduced during...
CONTEXT.—
Pathology-related advocacy is best when performed directly by pathologists. Practicing advocacy is included in the Milestones 2.0 and should be introduced during residency training.
OBJECTIVE.—
To understand advocacy education in residency training we surveyed pathologists to ask what training they had in residency, what resources were available, and what experiences were most impressionable.
DESIGN.—
Two types of inquiry were performed. First, a survey to program graduates asking about leadership and advocacy activities during training and about leadership and advocacy activities since graduation. Secondly, focused email and telephone inquiries were made to 12 pathologists-4 in practice for more than 20 years, 4 within the first 10 years of practice, and to 4 PGY4 (postgraduate year 4) residents-asking what training and experiences were available to them, and how they became motivated to become active in practice.
RESULTS.—
Our results showed that resources available outside of the home program have changed through the years and more national resident groups are available that were not available in the past. These groups may educate trainees in leadership and advocacy. Internally, opportunities to shadow faculty at interdepartmental leadership meetings, as well as selection of the chief resident, are enduring tools for honing these skills.
CONCLUSIONS.—
Teaching advocacy in training is important and part of the Accreditation Council for Graduate Medical Education core requirements as well as a level 5 Milestone. Education may require a balance of internal and external resources since different programs may offer different opportunities. Shadowing during real advocacy events was the most impressionable experience.
Topics: Education, Medical, Graduate; Humans; Internship and Residency; Leadership; Pathology; Surveys and Questionnaires
PubMed: 31313959
DOI: 10.5858/arpa.2019-0116-EP -
Fa Yi Xue Za Zhi Apr 2020Autopsy of patients who died of infectious diseases is of significance for public health management. Few forensic autopsies have been performed since the outbreak of the... (Review)
Review
Autopsy of patients who died of infectious diseases is of significance for public health management. Few forensic autopsies have been performed since the outbreak of the corona virus disease 2019 (COVID-19) due to some limitations, thus forensic pathological examination failed to contribute to the prevention and treatment of infectious diseases. Virtual autopsy has unique advantages in the forensic examination of patients who died of infectious diseases. Accumulated virtual autopsy image data are of great value to the study of the pathological mechanism and diagnosis of COVID-19. This article reviews the relationship between imaging changes and pathology of the COVID-19 as well as the application of virtual autopsy in autopsy of patients who died of infectious diseases, in order to provide reference for performing virtual autopsy in the outbreak of COVID-19.
Topics: Autopsy; Betacoronavirus; COVID-19; Coronavirus Infections; Forensic Pathology; Humans; Pandemics; Pneumonia, Viral; SARS-CoV-2
PubMed: 32212513
DOI: 10.12116/j.issn.1004-5619.2020.02.001 -
Discovery Medicine Aug 2018Historically, advanced lung cancer conferred a poor prognosis, and chemotherapy only improved outcomes in patients with good performance status. The identification of... (Review)
Review
Historically, advanced lung cancer conferred a poor prognosis, and chemotherapy only improved outcomes in patients with good performance status. The identification of certain molecular subtypes of non-small cell lung cancer changed the treatment paradigm by incorporating tumor genomic information into clinical decision-making. To meet the demands of this emerging approach, genomic technology rapidly expanded in an effort to detect specific driver mutations. While polymerase-chain reaction testing, immunohistochemistry, and fluorescent-in-situ hybridization have been standard-of-care, next-generation sequencing is increasingly replacing older technologies. Plasma-based testing is also gaining use given its convenience. Advances in molecular technology in this new era of precision medicine have led to the parallel development of companion diagnostics and novel tyrosine kinase inhibitors.
Topics: High-Throughput Nucleotide Sequencing; History, 21st Century; Humans; Lung Neoplasms; Medical Oncology; Pathology, Molecular; Protein Kinase Inhibitors
PubMed: 30265852
DOI: No ID Found -
Clinical & Translational Oncology :... Nov 2018Cancer of unknown primary (CUP) is defined as a heterogeneous group of tumours that present with metastasis, and in which attempts to identify the original site have... (Review)
Review
Cancer of unknown primary (CUP) is defined as a heterogeneous group of tumours that present with metastasis, and in which attempts to identify the original site have failed. They differ from other primary tumours in their biological features and how they spread, which means that they can be considered a separate entity. There are several hypotheses regarding their origin, but the most plausible explanation for their aggressiveness and chemoresistance seems to involve chromosomal instability. Depending on the type of study done, CUP can account for 2-9% of all cancer patients, mostly 60-75 years old. This article reviews the main clinical, pathological, and molecular studies conducted to analyse and determine the origin of CUP. The main strategies for patient management and treatment, by both clinicians and pathologists, are also addressed.
Topics: Aged; Consensus; Humans; Medical Oncology; Middle Aged; Neoplasms, Unknown Primary; Pathology, Clinical; Societies, Medical; Spain
PubMed: 29808414
DOI: 10.1007/s12094-018-1899-z -
Archives of Pathology & Laboratory... Mar 2018- Fine-needle aspiration cytology has been increasingly used as the first tool in the evaluation of several diseases. Although cytology has a relevant role in the... (Review)
Review
CONTEXT
- Fine-needle aspiration cytology has been increasingly used as the first tool in the evaluation of several diseases. Although cytology has a relevant role in the discrimination between benign and malignant lesions, conventional slides cannot lead to 100% conclusive results. It was hoped that the introduction of liquid-based cytology (LBC) would improve the efficacy of cytology through standardization, quality improvement, and the possibility of carrying out ancillary techniques on the residual stored material. In recent decades, the application of genomic alterations has been studied on cytologic samples with feasible and reliable results. The molecular analysis offers a powerful aid to define the best clinical or surgical approaches and follow-up for patients. In recent years, the application of different ancillary techniques has been carried out on conventional slides even though LBC represents a useful additional and alternative method for molecular testing.
OBJECTIVE
- To demonstrate the relevance of LBC as a valid aid to overcoming the difficulties encountered in the application of ancillary techniques on conventional slides.
DATA SOURCES
- We examined and reviewed our experience with the application of ancillary techniques on LBC performed on different body sites.
CONCLUSIONS
- We emphasize that LBC achieves significant and accurate results. It represents a valid method for cytologic evaluation and it provides highly reproducible and informative molecular yields.
Topics: Humans; Liquid Biopsy; Pathology, Molecular
PubMed: 29494225
DOI: 10.5858/arpa.2017-0148-RA -
Biotechnology Journal Aug 2012In the past 15 years, new "omics" technologies have made it possible to obtain high-resolution molecular snapshots of organisms, tissues, and even individual cells at... (Review)
Review
In the past 15 years, new "omics" technologies have made it possible to obtain high-resolution molecular snapshots of organisms, tissues, and even individual cells at various disease states and experimental conditions. It is hoped that these developments will usher in a new era of personalized medicine in which an individual's molecular measurements are used to diagnose disease, guide therapy, and perform other tasks more accurately and effectively than is possible using standard approaches. There now exists a vast literature of reported "molecular signatures". However, despite some notable exceptions, many of these signatures have suffered from limited reproducibility in independent datasets, insufficient sensitivity or specificity to meet clinical needs, or other challenges. In this paper, we discuss the process of molecular signature discovery on the basis of omics data. In particular, we highlight potential pitfalls in the discovery process, as well as strategies that can be used to increase the odds of successful discovery. Despite the difficulties that have plagued the field of molecular signature discovery, we remain optimistic about the potential to harness the vast amounts of available omics data in order to substantially impact clinical practice.
Topics: Animals; Biomarkers; Biomedical Research; Computational Biology; Databases, Factual; Gene Expression Profiling; Humans; Pathology, Molecular
PubMed: 22528809
DOI: 10.1002/biot.201100305 -
Magnetic Resonance in Medical Sciences... 2010In Japan, the medical examiner system is not widespread, the rate of autopsy is low, and many medical institutions therefore perform postmortem imaging using clinical... (Review)
Review
In Japan, the medical examiner system is not widespread, the rate of autopsy is low, and many medical institutions therefore perform postmortem imaging using clinical equipment. Postmortem imaging is performed to clarify cause of death, select candidates for autopsy, make a guide map for autopsy, or provide additional information for autopsy. Findings are classified into 3 categories: cause of death and associated changes, changes induced by cardiopulmonary resuscitation, and postmortem changes. Postmortem magnetic resonance imaging shows characteristic changes in signal intensity related to low body temperature after death; they are low temperature images.
Topics: Body Temperature; Brain; Brain Neoplasms; Cadaver; Cause of Death; Cerebrospinal Fluid; Forensic Pathology; Freezing; Humans; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Postmortem Changes
PubMed: 20885082
DOI: 10.2463/mrms.9.101