Cric searchable image database as a public platform for conventional pap smear cytology data.
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ABSTRACT:
SUBMITTER: Rezende MT
PROVIDER: S-EPMC8192784 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The fourth most prevalent cancer in women is cervical cancer, and early detection is crucial for effective treatment and prognostic prediction. Conventional cervical cancer screening and classifying methods are less reliable and accurate as they heavily rely on the expertise of a pathologist. As such, colposcopy is an essential part of preventing cervical cancer. Computer-assisted diagnosis is essential for expanding cervical cancer screening because visual screening results in misdiagnosis and low diagnostic effectiveness due to doctors' increased workloads. Classifying a single cervical cell will overwhelm the physicians, in addition to the existence of overlap between cervical cells, which needs efficient algorithms to separate each cell individually. Focusing on the whole image is the best way and an easy task for the diagnosis. Therefore, looking for new methods to diagnose the whole image is necessary and more accurate. However, existing recognition algorithms do not work well for whole-slide image (WSI) analysis, failing to generalize for different stains and imaging, and displaying subpar clinical-level verification. This paper describes the design of a full ensemble deep learning model for the automatic diagnosis of the WSI. The proposed network discriminates between four classes with high accuracy, reaching up to 99.6%. This work is distinct from existing research in terms of simplicity, accuracy, and speed. It focuses on the whole staining slice image, not on a single cell. The designed deep learning structure considers the slice image with overlapping and non-overlapping cervical cells.
| S-EPMC9689383 | biostudies-literature
Project description:BACKGROUND: SPIEDw is a web tool designed to facilitate fast and simple quantitative querying of publically available gene expression data. The resource is motivated by the observation that transcriptional profiles can serve as effective means of comparing biological states across a wide set of experiments. RESULTS: Gene expression data for over 200,000 experiments across multiple species and platforms have been collected into a searchable database. The new resource is a development of the previously published SPIED, which was designed to be downloaded and queried locally with SPIED software. SPIEDw features three significant improvements over the original version. Firstly, the number of experiments covered has been doubled and now includes Agilent and Illumina technologies. Secondly, SPIEDw has an enhanced search algorithm for speedy web-based querying and lastly an abridged dataset comprising the most regulated genes has been included for a speedier search and searching for enrichment of gene sets. CONCLUSIONS: SPIEDw is simple to use, not requiring any expertise in microarray analysis, and the output straightforward to interpret. It is hoped that this will open up gene expression data mining to the wider research community.
| S-EPMC4046673 | biostudies-literature
Project description:BACKGROUND: In recent decades, the incidence of cervical cancer and cervical cancer mortality in Austria has declined by varying degrees. The Pap smear is to be considered a causal factor for this decline. METHODS: This longitudinal analysis is based on a data set of Pap smear assessments collected by the Committee for Quality Assurance of the Austrian Society of Cytology. Data from 15 laboratories participating in a voluntary self-monitoring program was analyzed for the time span 2004-2008. The data was analyzed in terms of smear quality and assessment quality.A rank-correlation-test for a monotonic trend analysis in the proportion of the three parameters Pap 0, "satisfactory, but limited/SBL", and Pap IIID/IV for the timespan 2004 to 2008 was carried out. RESULTS: For this study, we analyzed an average number of 730,000 smears per year over a five-year period. Specimens from all but two laboratories, i.e. < 2% of all smears, met the quality criterion for Pap 0 (Bethesda 2001 equivalent: Specimen processed and examined, but unsatisfactory for evaluation of epithelial abnormality), whilst only four laboratories, i.e. < 10% of all smears, reached the national requirement for smears classified as "satisfactory, but limited/SBL".When using the Pap IIID/IV ratio (LSIL: HSIL/AIS ratio) of 3:1 to 8:1 as a surrogate quality marker for the interpretation of smears, only five laboratories met this criterion during the survey period.The trend analysis indicated only that an increasing number of samples per year is correlated with an increased proportion of Pap 0 and "satisfactory, but limited/SBL" smears. CONCLUSIONS: Although participants get regular feedback about their results, no general improvements in smear taking or assessment were observed over the years, so mandatory quality management, including the possibility of sanctions, is suggested in order to reduce adverse health effects for women.
| S-EPMC4015555 | biostudies-other
Project description:While a publicly available benchmark dataset provides a base for the development of new algorithms and comparison of results, hospital-based data collected from the real-world clinical setup is also very important in AI-based medical research for automated disease diagnosis, prediction or classifications as per standard protocol. Primary data must be constantly updated so that the developed algorithms achieve as much accuracy as possible in the regional context. This dataset would support research work related to image segmentation and final classification for a complete decision support system (https://doi.org/10.1016/j.tice.2020.101347) [1]. Liquid-based cytology (LBC) is one of the cervical screening tests. The repository consists of a total of 963 LBC images sub-divided into four sets representing the four classes: NILM, LSIL, HSIL, and SCC. It comprises pre-cancerous and cancerous lesions related to cervical cancer as per standards under The Bethesda System (TBS). The images were captured in 40x magnification using Leica ICC50 HD microscope collected with due consent from 460 patients visiting the O&G department of the public hospital with various gynaecological problems. The images were then viewed and categorized by experts of the pathology department.
| S-EPMC7186519 | biostudies-literature
Project description:Three sets of polymerase chain reaction (PCR) primers were designed for heminested PCR amplification of the target DNA fragments in the human genome which include the site of BRCA1 c.68_69del, BRCA1 c.5266dup and BRCA2 c.5946del respectively, to prepare the templates for direct Sanger sequencing screen of these three founder mutations. With a robust PCR mixture, crude proteinase K digestate of the fixed cervicovaginal cells in the liquid-based Papanicolaou (Pap) cytology specimens can be used as the sample for target DNA amplification without pre-PCR DNA extraction, purification and quantitation. The post-PCR products can be used directly as the sequencing templates without further purification or quantitation. By simplifying the frontend procedures for template preparation, the cost for screening these three founder mutations can be reduced to about US $200 per test when performed in conjunction with human papillomavirus (HPV) assays now routinely ordered for cervical cancer prevention. With this projected price structure, selective patients in a high-risk population can be tested and each provided with a set of DNA sequencing electropherograms to document the absence or presence of these founder mutations in her genome to help assess inherited susceptibility to breast and ovarian cancer in this era of precision molecular personalized medicine.
| S-EPMC4783961 | biostudies-literature
Project description:BACKGROUND: Transcriptional data covering multiple platforms and species is collected and processed into a searchable platform independent expression database (SPIED). SPIED consists of over 100,000 expression fold profiles defined independently of control/treatment assignment and mapped to non-redundant gene lists. The database is thus searchable with query profiles defined over genes alone. The motivation behind SPIED is that transcriptional profiles can be quantitatively compared and ranked and thus serve as effective surrogates for comparing the underlying biological states across multiple experiments. RESULTS: Drug perturbation, cancer and neurodegenerative disease derived transcriptional profiles are shown to be effective descriptors of the underlying biology as they return related drugs and pathologies from SPIED. In the case of Alzheimer's disease there is high transcriptional overlap with other neurodegenerative conditions and rodent models of neurodegeneration and nerve injury. Combining the query signature with correlating profiles allows for the definition of a tight neurodegeneration signature that successfully highlights many neuroprotective drugs in the Broad connectivity map. CONCLUSIONS: Quantitative querying of expression data from across the totality of deposited experiments is an effective way of discovering connections between different biological systems and in particular that between drug action and biological disease state. Examples in cancer and neurodegenerative conditions validate the utility of SPIED.
| S-EPMC3305579 | biostudies-literature
Project description:Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status
| PRJEB25778 | ENA
Project description:ObjectiveExploiting their ability to differentiate into mesenchymal lineages like cartilage, bone, fat, and muscle, and to elicit paracrine effects, mesenchymal stem cells (MSCs) are widely used in clinical settings to treat tissue injuries and autoimmune disorders. One of accessible sources of MSC is the samples used for Papanicolaou (Pap) test, which is a cervical screening method for detecting potentially pre-cancerous and cancerous alterations in the cervical cells and to diagnose genetic abnormalities in fetuses. This study aimed to identify and isolate the stem cells from Pap smear samples collected from pregnant women, and to trace the origin of these cells to maternal or fetal tissue, and characterize their stem cell properties.MethodsTo investigate the possibility and efficiency of establishing MSC lines from the Pap smear samples, we were able to establish 6 cell lines from Pap smear samples from 60 pregnant women at different stages of gestation.ResultsThe 3 cell lines randomly selected among the 6 established in this study, displayed high proliferation rates, several characteristics of MSCs, and the capacity to differentiate into adipocytes, osteocytes, and chondrocytes. Our study identified that the stem cell lines obtainable from Pap smear sampling were uterine cervical stromal cells (UCSCs) and had 10% efficiency of establishment.ConclusionDespite their low efficiency of establishment, human UCSCs from Pap smear samples can become a simple, safe, low-cost, and donor-specific source of MSCs for stem cell therapy and regenerative medicine.
| S-EPMC7494764 | biostudies-literature
Project description:Background and study aims Endoscopic ultrasound (EUS)-guided fine-needle aspiration (EUS-FNA) has limitations of inadequate sampling and false-negative results for malignancy. It has been performed using conventional smear (CS) cytology with rapid on-site evaluation (ROSE) with reasonable diagnostic accuracy. An alternative to ROSE is liquid-based cytology (LBC). Commonly used LBC techniques include precipitation-based (SurePath™) and filtration-based (ThinPrep ® , CellPrep ® ). Data regarding the diagnostic efficacy of LBC compared with CS are limited. Methods Multiple databases were searched through March 2020 to identify studies reporting diagnostic yield of EUS-guided CS and LBC in pancreatic lesions. Pooled diagnostic odds and rates of performance for the cytologic diagnoses of benign, suspicious, and malignant lesions were calculated. Diagnostic efficacy was evaluated by pooled rates of accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV). Results Nine studies with a total of 1308 patients were included in our final analysis. Pooled diagnostic odds of CS cytology were 1.69 (CI 1.02-2.79) and 0.39 (CI 0.19-0.8) for malignant lesions when compared to filtration-based and precipitation-based LBC techniques, respectively. For CS, precipitation-based and filtration-based LBC, pooled diagnostic accuracy was 79.7 %, 85.2 %, 77.3 %, sensitivity was 79.2 %, 83.6 %, 68.3 %, and specificity was 99.4 %, 99.5 %, 99.5 %, respectively. Conclusions The precipitation-based LBC technique (SurePath™) had superior diagnostic odds for malignant pancreatic lesions compared with CS cytology in the absence of ROSE. It showed superior accuracy and sensitivity, but comparable specificity and PPV. Diagnostic odds of CS cytology in the absence of ROSE were superior to the filtration-based LBC technique (ThinPrep ® , Cellprep ® ) for diagnosing malignant pancreatic lesions.
| S-EPMC7581473 | biostudies-literature
Project description:As digital imaging is becoming a fundamental part of medical and biomedical research, the demand for computer-based evaluation using advanced image analysis is becoming an integral part of many research projects. A common problem when developing new image analysis algorithms is the need of large datasets with ground truth on which the algorithms can be tested and optimized. Generating such datasets is often tedious and introduces subjectivity and interindividual and intraindividual variations. An alternative to manually created ground-truth data is to generate synthetic images where the ground truth is known. The challenge then is to make the images sufficiently similar to the real ones to be useful in algorithm development. One of the first and most widely studied medical image analysis tasks is to automate screening for cervical cancer through Pap-smear analysis. As part of an effort to develop a new generation cervical cancer screening system, we have developed a framework for the creation of realistic synthetic bright-field microscopy images that can be used for algorithm development and benchmarking. The resulting framework has been assessed through a visual evaluation by experts with extensive experience of Pap-smear images. The results show that images produced using our described methods are realistic enough to be mistaken for real microscopy images. The developed simulation framework is very flexible and can be modified to mimic many other types of bright-field microscopy images.
| S-EPMC4374707 | biostudies-literature