scholarly journals The Dynamics of Pathology Dataset Creation Using Urine Cytology as an Example

2021 ◽  
pp. 1-9
Author(s):  
Ewen David McAlpine ◽  
Pamela M. Michelow ◽  
Turgay Celik
Keyword(s):  
Quality Assurance ◽  
Morphological Diversity ◽  
Urine Cytology ◽  
Urothelial Cell ◽  
Quality Data ◽  
Training Algorithms ◽  
Urothelial Cells ◽  
Perfect Agreement ◽  
Labelling Process ◽  
Label Time

<b><i>Introduction:</i></b> Dataset creation is one of the first tasks required for training AI algorithms but is underestimated in pathology. High-quality data are essential for training algorithms and data should be labelled accurately and include sufficient morphological diversity. The dynamics and challenges of labelling a urine cytology dataset using The Paris System (TPS) criteria are presented. <b><i>Methods:</i></b> 2,454 images were labelled by pathologist consensus via video conferencing over a 14-day period. During the labelling sessions, the dynamics of the labelling process were recorded. Quality assurance images were randomly selected from images labelled in previous sessions within this study and randomly distributed throughout new labelling sessions. To assess the effect of time on the labelling process, the labelled set of images was split into 2 groups according to the median relative label time and the time taken to label images and intersession agreement were assessed. <b><i>Results:</i></b> Labelling sessions ranged from 24 m 11 s to 41 m 06 s in length, with a median of 33 m 47 s. The majority of the 2,454 images were labelled as benign urothelial cells, with atypical and malignant urothelial cells more sparsely represented. The time taken to label individual images ranged from 1 s to 42 s with a median of 2.9 s. Labelling times differed significantly among categories, with the median label time for the atypical urothelial category being 7.2 s, followed by the malignant urothelial category at 3.8 s and the benign urothelial category at 2.9 s. The overall intersession agreement for quality assurance images was substantial. The level of agreement differed among classes of urothelial cells – benign and malignant urothelial cell classes showed almost perfect agreement and the atypical urothelial cell class showed moderate agreement. Image labelling times seemed to speed up, and there was no evidence of worsening of intersession agreement with session time. <b><i>Discussion/Conclusion:</i></b> Important aspects of pathology dataset creation are presented, illustrating the significant resources required for labelling a large dataset. We present evidence that the time taken to categorise urine cytology images varies by diagnosis/class. The known challenges relating to the reproducibility of the AUC (atypical) category in TPS when compared to the NHGUC (benign) or HGUC (malignant) categories is also confirmed.

scholarly journals Reactivation of BK Polyomavirus in Urine Cytology Is Not Associated with Urothelial Cell Carcinoma

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1412
Author(s):  
Faisal Klufah ◽  
Ghalib Mobaraki ◽  
Axel zur Hausen ◽  
Iryna V. Samarska
Keyword(s):  
Cell Carcinoma ◽  
Urine Cytology ◽  
Urothelial Cell ◽  
The Other ◽  
Urothelial Cell Carcinoma ◽  
Tissue Samples ◽  
Bk Polyomavirus ◽  
Ffpe Tissues ◽  
Immunosuppressed Patients ◽  
History Of

BK polyomavirus (BKPyV) has been associated with some high-grade and special urothelial cell carcinoma (UCC) subtypes in immunosuppressed patients. Here, we evaluated the relationship of BKPyV-positive urine cytology specimens (UCS) with UCC. A large single-institution database was retrospectively searched for UCS positive for decoy cells, suggesting BKPyV infection. These were tested for the presence of BKPyV by PCR and immunohistochemistry (IHC) in urine sediments and formalin-fixed paraffin-embedded (FFPE) tissue samples of UCC. Decoy cells were reported in 30 patients out of the database with 22.867 UCS. Of these 30 patients, 16 (53.3%) had no history of UCC. Six patients out of these 16 had a history of transplantation, 4 had a history of severe chronic medical conditions, and 6 had no chronic disease. The other fourteen patients were diagnosed with either in situ or invasive UCC of the urinary bladder (14/30; 46.6%) prior to the detection of decoy cells in the urine. Nine of these UCC patients received intravesical treatment (BCG or mitomycin) after the first presentation with UCC. However, the clinical data on the treatment of the other five UCC patients was lacking. IHC identified BKPyV-positivity in the urine samples of non-UCC and UCC patients, while no BKPyV positivity was found in FFPE tissues of primary UCCs and metastases. In addition, BKPyV-PCR results revealed the presence of BKPyV DNA in the urine of the UCC cases, yet none in the UCC tissues itself. These data strongly indicate that BKPyV reactivation is not restricted to immunosuppression. It can be found in UCS of the immunocompetent patients and may be related to the intravesical BCG or mitomycin treatment of the UCC patients.

scholarly journals Substance P Increases Cell-Surface Expression of CD74 (Receptor for Macrophage Migration Inhibitory Factor): In Vivo Biotinylation of Urothelial Cell-Surface Proteins

2009 ◽  
Vol 2009 ◽  
pp. 1-8 ◽  
Author(s):  
Katherine L. Meyer-Siegler ◽  
Shen-Ling Xia ◽  
Pedro L. Vera
Keyword(s):  
Substance P ◽  
Cell Surface ◽  
Migration Inhibitory Factor ◽  
Macrophage Migration Inhibitory Factor ◽  
Urothelial Cell ◽  
Inhibitory Factor ◽  
Cell Surface Expression ◽  
Macrophage Migration ◽  
Urothelial Cells

Macrophage migration inhibitory factor (MIF), an inflammatory cytokine, and its receptor CD74 are upregulated by bladder inflammation. MIF-mediated signal transduction involves binding to cell-surface CD74, this study documents, in vivo, MIF-CD74interactions at the urothelial cell surface. N-hydroxysulfosuccinimide biotin ester-labeled surface urothelial proteins in rats treated either with saline or substance P (SP, 40 μg/kg). The bladder was examined by histology and confocal microscopy. Biotinylated proteins were purified by avidin agarose, immunoprecipitated with anti-MIF or anti-CD74 antibodies, and detected with strepavidin-HRP. Only superficial urothelial cells were biotinylated. These cells contained a biotinylated MIF/CD74 cell-surface complex that was increased in SP-treated animals. SP treatment increased MIF and CD74 mRNA in urothelial cells. Our data indicate that intraluminal MIF, released from urothelial cells as a consequence of SP treatment, interacts with urothelial cell-surface CD74. These results document that our previously described MIF-CD74 interaction occurs at the urothelial cell surface.

scholarly journals Detecting Malignant Urothelial Cells by Morphometric Analysis of ThinPrep® Liquid-based Urine Cytology Specimens

2008 ◽  
Vol 19 (2) ◽  
pp. 136 ◽  
Author(s):  
Bong Kyung Shin ◽  
Young Suk Lee ◽  
Hoiseon Jeong ◽  
Sang Ho Lee ◽  
Hyunchul Kim ◽  
...  
Keyword(s):  
Morphometric Analysis ◽  
Urine Cytology ◽  
Urothelial Cells

scholarly journals Distance from Africa, not climate, explains within-population phenotypic diversity in humans

2008 ◽  
Vol 276 (1658) ◽  
pp. 809-814 ◽  
Author(s):  
Lia Betti ◽  
François Balloux ◽  
William Amos ◽  
Tsunehiko Hanihara ◽  
Andrea Manica
Keyword(s):  
Climatic Factors ◽  
Phenotypic Diversity ◽  
Morphological Diversity ◽  
Sub Saharan Africa ◽  
Relative Role ◽  
Morphometric Traits ◽  
Perfect Agreement ◽  
Skull Measurements ◽  
Sub Saharan

The relative importance of ancient demography and climate in determining worldwide patterns of human within-population phenotypic diversity is still open to debate. Several morphometric traits have been argued to be under selection by climatic factors, but it is unclear whether climate affects the global decline in morphological diversity with increasing geographical distance from sub-Saharan Africa. Using a large database of male and female skull measurements, we apply an explicit framework to quantify the relative role of climate and distance from Africa. We show that distance from sub-Saharan Africa is the sole determinant of human within-population phenotypic diversity, while climate plays no role. By selecting the most informative set of traits, it was possible to explain over half of the worldwide variation in phenotypic diversity. These results mirror those previously obtained for genetic markers and show that ‘bones and molecules’ are in perfect agreement for humans.

scholarly journals Building a high quality data linkage spine using a targeted approach to clerical review

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Nadine Wiggins ◽  
Brian Stokes
Keyword(s):  
Quality Assurance ◽  
Data Linkage ◽  
Quality Data ◽  
High Confidence ◽  
Software Module ◽  
High Quality ◽  
Confidence Levels ◽  
Lower Confidence ◽  
Linkage Quality

ABSTRACTObjectivesThe Tasmanian Data Linkage Unit (TDLU) was established through the University of Tasmania in 2011 with the first dataset imported to its Master Linkage Map (MLM) during 2014. Tasmania an island state of Australia, has a population of approximately 516,000. From the TDLU’s earliest inception, it was deemed important to build a high quality linkage spine comprising key administrative data representative of significant state health and related datasets to support quality population level research.ApproachThe TDLU has embraced a model of continual quality and process enhancement as a determined strategy to support ongoing business improvement. Initial linkage approaches utilised ‘traditional’ methods of reviewing record pairs within an upper and lower confidence range. This approach resulted in false record pairs with high confidence levels being linked (false positives) and true record pairs at lower confidence levels not linked (false negatives). To improve linkage quality, the TDLU has continually refined and modified its clerical review methodology with a specialist software module developed to identify specific record attributes within groups that require the group to be manually reviewed and resolved. A range of SQL queries have also been developed to identify incorrect links and further enhance the linkage quality of the MLM.ResultsThe linkage quality tools implemented have led to improved clerical review and quality assurance processes which in turn have increased the overall quality of the linkage spine. The ‘targeted’ method of clerical review provides easy identification of false positive records, particularly those with high confidence scores such as twins and husband/wife combinations. The review of groups at lower confidence levels has minimised the rate of false negative pairs however further refinement of tools is required to minimise the time spent on reviewing these groups. The clerical review software module has equipped staff with the necessary information to make informed and timely decisions when reviewing groups of records. Detailed documentation is maintained for each linkage project providing continual feedback for system and process improvements as the linkage spine increases in size.ConclusionThe process of clerical review and quality assurance requires a commitment to continual refinement of tools and techniques resulting in a higher quality linkage spine and a reduction in the total time and resource required to link datasets.

scholarly journals MP027: Automated cardiopulmonary resuscitation quality data abstraction for complete episodes of out-of-hospital cardiac arrest resuscitation

CJEM ◽  
2016 ◽  
Vol 18 (S1) ◽  
pp. S75-S75
Author(s):  
A.K. Taher ◽  
S. Lin ◽  
A. Turgulov ◽  
J.E. Buick ◽  
A. Byers ◽  
...  
Keyword(s):  
Quality Assurance ◽  
Cardiac Arrest ◽  
Cardiopulmonary Resuscitation ◽  
Error Rates ◽  
Quality Data ◽  
Data Abstraction ◽  
Internal Validation ◽  
Software Program ◽  
Cpr Quality ◽  
The Impact

Introduction: Cardiopulmonary resuscitation (CPR) quality assurance and research has traditionally been limited to the first five minutes of resuscitation due to significant costs in time, resources and personnel from manual data abstraction. Moreover, CPR quality can be affected during prolonged resuscitations, which represents significant knowledge gaps. The objective of this study was to develop a software program to help automate the abstraction of CPR quality data from electronic defibrillators. Methods: We developed a software program to facilitate and help automate data abstraction from electronic defibrillator files for entire resuscitation episodes. Internal validation of the software program was performed on 50 randomly selected cardiac arrest cases with resuscitation durations of up to 60 minutes. CPR quality data variables such as number of ventilations, number of compressions, minute compression rate, minute compression depth, minute compression fraction, minute end-tidal CO2, were manually abstracted independently by two trained data abstractors and by the automated software program. Error rates and the time needed for data abstraction were measured. Results: A total of 9826 data points were abstracted. Manual data abstraction resulted in a total of six errors (0.06%) compared to zero errors by the software program. The mean time ± SD needed for manual data abstraction was 20.3 ± 2.7 minutes compared to 5.3 ± 1.4 minutes using the software program (p=0.003). Conclusion: Our CPR quality data abstraction software was 100% accurate in abstracting CPR quality data for complete resuscitation episodes and showed a significant reduction in data abstraction duration. This software will enable quality assurance programs and future cardiac arrest studies to evaluate the impact of CPR quality during prolonged resuscitations.

Prevalence of atypical urine cytology in patients treated with gemcitabine-cisplatin (GC) for urothelial carcinoma (UC).

2015 ◽  
Vol 33 (7_suppl) ◽  
pp. 363-363
Author(s):  
Kimberly R. Kruczek ◽  
Lu Wang ◽  
Guliz Barkan ◽  
Elizabeth Henry
Keyword(s):  
General Population ◽  
Median Number ◽  
Urine Cytology ◽  
Intravesical Therapy ◽  
Urothelial Cells ◽  
Single Institution ◽  
Previously Treated ◽  
Number Of Cycles ◽  
The Impact ◽  
Post Therapy

363 Background: The prevalence of atypical urothelial cells (AUC) in the general population is estimated to range between 2-23% with known variability between individual pathologists’ use of this diagnosis. At our institution, the AUC rate for all urinary tract cytology (UTC) is 6.1%. Increased rates of urothelial atypia have been described in pts receiving certain systemic and intravesical therapies for UC. This may confound the use of UTC for post-therapy surveillance. Our objective is to describe the prevalence of urothelial atypia in pts treated with GC, as it is currently unknown. Methods: Patients who received at least one cycle of GC for UC at a single institution from 1/1/2007-9/30/2014 were identified. Demographics, clinical characteristics, treatment setting, number of cycles, and specimen type were recorded. Urine cytology reports were reviewed and tabulated. Results: Seventy-four pts treated with GC were identified. Median age at treatment was 65 (range 42-80); 58 (78%) were male. Median number of cycles was 4 (range 1-9). Treatment settings were: 15 (20%) neoadjuvant, 38 (51%) adjuvant, and 21 (28%) metastatic. Ten (14%) pts were previously treated with intravesical therapy (9 BCG, 1 mitomycin). Thirty-six (49%) pts had urine cytology available. Twenty-seven (75%) pts had at least 1 urine cytology within 12 months post-chemotherapy, with 44 total specimens. Nine (25%) pts had cytology performed >1-year post treatment. Cytology specimens within 12 months post-chemotherapy were reviewed. Two out of 44 specimens had AUC (5%), with all other cases negative. The pts with AUC were male, received adjuvant therapy, had prior radical cystectomy with orthotopic neobladder reconstruction, and had no intravesical therapy. Conclusions: The prevalence of AUC in pts treated with GC was similar to the general population. Chemotherapy with GC does not appear to morphologically affect urothelial cells. If atypical UTC is seen in this population, the cause should be investigated, as GC does not appear to influence urothelial changes. Additional study is needed to characterize the impact of systemic therapy on urothelial atypia and to guide the use of urine cytology for post-therapy surveillance.

scholarly journals IPSE, an Abundant Egg-Secreted Protein of the Carcinogenic Helminth Schistosoma haematobium, Promotes Proliferation of Bladder Cancer Cells and Angiogenesis

2020 ◽  
Author(s):  
Evaristus C. Mbanefo ◽  
Chinwike Terry Agbo ◽  
Yuanlong Zhao ◽  
Olivia K. Lamanna ◽  
Kimberly H. Thai ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Schistosoma Haematobium ◽  
Causal Link ◽  
Urothelial Cell ◽  
Cell Uptake ◽  
Interleukin 4 ◽  
Nuclear Localization Sequence ◽  
Urothelial Cells ◽  
Cell Nuclei ◽  
Urogenital Schistosomiasis

Abstract Background: Schistosoma haematobium, the helminth causing urogenital schistosomiasis, is a known bladder carcinogen. Despite the causal link between S. haematobium and bladder cancer, the underlying mechanisms are poorly understood. S. haematobium oviposition in the bladder is associated with angiogenesis and urothelial hyperplasia. These changes may be pre-carcinogenic events in the bladder. We hypothesized that the Interleukin-4-inducing principle of Schistosoma mansoni eggs (IPSE), an S. haematobium egg-secreted “infiltrin” protein that enters host cell nuclei to alter cellular activity, is sufficient to induce angiogenesis and urothelial hyperplasia. Methods: Mouse bladders injected with S. haematobium eggs were analyzed via microscopy for angiogenesis and urothelial hyperplasia. Endothelial and urothelial cell lines were incubated with recombinant IPSE protein or an IPSE mutant protein that lacks the native nuclear localization sequence (NLS-) and proliferation measured using CFSE staining and real-time monitoring of cell growth. IPSE’s effects on urothelial cell cycle status was assayed through propidium iodide staining. Endothelial and urothelial cell uptake of fluorophore-labeled IPSE was measured. Findings: Injection of S. haematobium eggs into the bladder triggers angiogenesis, enhances leakiness of bladder blood vessels, and drives urothelial hyperplasia. Wild type IPSE, but not NLS-, increases proliferation of endothelial and urothelial cells and skews urothelial cells towards S phase. Finally, IPSE is internalized by both endothelial and urothelial cells. Interpretation: IPSE drives endothelial and urothelial proliferation, which may depend on internalization of the molecule. The urothelial effects of IPSE depend upon its NLS. Thus, IPSE is a candidate pro-carcinogenic molecule of S. haematobium.

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