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10.2196/23436 ◽  
2021 ◽  
Vol 23 (2) ◽  
pp. e23436
Author(s):  
Max Schmitt ◽  
Roman Christoph Maron ◽  
Achim Hekler ◽  
Albrecht Stenzinger ◽  
Axel Hauschild ◽  
...  

Background An increasing number of studies within digital pathology show the potential of artificial intelligence (AI) to diagnose cancer using histological whole slide images, which requires large and diverse data sets. While diversification may result in more generalizable AI-based systems, it can also introduce hidden variables. If neural networks are able to distinguish/learn hidden variables, these variables can introduce batch effects that compromise the accuracy of classification systems. Objective The objective of the study was to analyze the learnability of an exemplary selection of hidden variables (patient age, slide preparation date, slide origin, and scanner type) that are commonly found in whole slide image data sets in digital pathology and could create batch effects. Methods We trained four separate convolutional neural networks (CNNs) to learn four variables using a data set of digitized whole slide melanoma images from five different institutes. For robustness, each CNN training and evaluation run was repeated multiple times, and a variable was only considered learnable if the lower bound of the 95% confidence interval of its mean balanced accuracy was above 50.0%. Results A mean balanced accuracy above 50.0% was achieved for all four tasks, even when considering the lower bound of the 95% confidence interval. Performance between tasks showed wide variation, ranging from 56.1% (slide preparation date) to 100% (slide origin). Conclusions Because all of the analyzed hidden variables are learnable, they have the potential to create batch effects in dermatopathology data sets, which negatively affect AI-based classification systems. Practitioners should be aware of these and similar pitfalls when developing and evaluating such systems and address these and potentially other batch effect variables in their data sets through sufficient data set stratification.


2021 ◽  
Vol 15 (1) ◽  
pp. e0009032
Author(s):  
Felix Bosch ◽  
Marta S. Palmeirim ◽  
Said M. Ali ◽  
Shaali M. Ame ◽  
Jan Hattendorf ◽  
...  

Background Soil-transmitted helminths infect about one fifth of the world’s population and have a negative impact on health. The Kato-Katz technique is the recommended method to detect soil-transmitted helminth eggs in stool samples, particularly in programmatic settings. However, some questions in its procedure remain. Our study aimed to investigate the effect of storage time, storage temperature and stirring of stool samples on fecal egg counts (FECs). Methodology/Principal findings In the framework of a clinical trial on Pemba Island, United Republic of Tanzania, 488 stool samples were collected from schoolchildren. These samples were evaluated in three experiments. In the first experiment (n = 92), two Kato-Katz slides were prepared from the same stool sample, one was stored at room temperature, the other in a refrigerator for 50 hours, and each slide was analyzed at nine time points (20, 50, 80, 110, 140 minutes, 18, 26, 42 and 50 hours). In the second experiment (n = 340), whole stool samples were split into two, one part was stored at room temperature, and the other part was put in a refrigerator for 48 hours. From each part one Kato-Katz slide was prepared and analyzed at three time points over two days (0, 24 and 48 hours). In the third experiment (n = 56), whole stool samples where stirred for 15 seconds six times and at each time point a Kato-Katz slide was prepared and analyzed. Mean hookworm FECs of Kato-Katz slides stored at room temperature steadily decreased following slide preparation. After two hours, mean hookworm FECs decreased from 22 to 16, whereas no reduction was observed if Kato-Katz slides were stored in the refrigerator (19 vs 21). The time x storage interaction effect was statistically significant (coefficient 0.26, 95% CI: 0.17 to 0.35, p < 0.0001). After 24 hours mean hookworm FECs dropped close to zero, irrespective of the storage condition. Whole stool samples stored at room temperature for one day resulted in a mean hookworm FEC decrease of 23% (p < 0.0001), compared to a 13% reduction (p < 0.0001) if samples were stored in the refrigerator. Fecal egg counts of A. lumbricoides and T. trichiura remained stable over time regardless of storage temperature of whole stool samples. Finally, we found a significant reduction of the variation of hookworm and T. trichiura eggs with increasing rounds of stirring the sample, but not for A. lumbricoides. For hookworm we observed a simultaneous decrease in mean FECs, making it difficult to draw recommendations on stirring samples. Conclusions/Significance Our findings suggest that stool samples (i) should be analyzed on the day of collection and (ii) should be analyzed between 20–30 minutes after slide preparation; if that is not possible, Kato-Katz slides can be stored in a refrigerator for a maximum of 110 minutes.


Author(s):  
Zaibo Li ◽  
Rhona J. Souers ◽  
Sana O. Tabbara ◽  
Kristen E. Natale ◽  
Lananh N. Nguyen ◽  
...  

Context.— The College of American Pathologists surveys provide national benchmarks of pathology practice for laboratories. Objective.— To investigate breast fine-needle aspiration (FNA) biopsy practice in domestic and international laboratories in 2019. Design.— We analyzed data from the College of American Pathologists Breast FNA Practice Supplemental Questionnaire that was distributed to laboratories participating in the 2019 College of American Pathologists Non-Gynecologic Cytopathology Education Program. Results.— Sixty-one percent (499 of 816) of respondent laboratories routinely evaluated breast FNAs. Cystic lesions were the most common indication, and radiologists primarily performed FNAs in most settings. Forty-five percent (220 of 491) of laboratories performed ancillary studies on breast FNA samples, but 33.8% (70 of 207) did not report fixation time for breast biomarker studies. Only 54.5% (271 of 497) of laboratories had a standardized reporting system and only 16.8% (82 of 488) were aware of the International Academy of Cytology Yokohama Breast FNA Biopsy Cytology Reporting System. There were significant differences among different types of institutions in several aspects of breast FNA practice, including frequency of concurrent FNA and core needle biopsy for the same lesion, primary personnel who performed the FNA, etc. Significant differences existed between domestic and international laboratories in slide preparation, ancillary studies, fixation time reporting, standardized/descriptive diagnosis, and International Academy of Cytology Yokohama Reporting System awareness. Conclusions.— This is the first survey from the College of American Pathologists Cytopathology Committee to investigate breast FNA practices. The data reveal significant differences in breast FNA practice among different types of institutions and between domestic and international laboratories, and provide a baseline for future breast FNA studies in a variety of practice settings.


2020 ◽  
Vol 19 (2) ◽  
Author(s):  
Fajarudin Ahmad ◽  
Yuyu Suryasari Poerba

Chromosome counting is the basis in describing the chromosomes number of organism that might useful for genetic study and classification. In banana studies, the root tip with a combination of non-fluorescent staining methods such as carmine or orcein and squash is the most common material for chromosome counting. In this study, we presented the usefulness of young anther of banana male bud with enzymatic maceration method for cell spreading and 4,6-diamino-2-phenyl-indole (DAPI) for staining agent to get a satisfying chromosomes image at metaphase for mitotic study of diploid and tetraploid bananas. The principle of this study is fixation using ethanol:acetic acid (3:1), enzymatic digestion, maceration and staining using DAPI. Our result showed that this method can provide well spread cells with intensely contrast of chromosomes images that satisfying for chromosome counting. 


2020 ◽  
Author(s):  
Max Schmitt ◽  
Roman Christoph Maron ◽  
Achim Hekler ◽  
Albrecht Stenzinger ◽  
Axel Hauschild ◽  
...  

BACKGROUND An increasing number of studies within digital pathology show the potential of artificial intelligence (AI) to diagnose cancer using histological whole slide images, which requires large and diverse data sets. While diversification may result in more generalizable AI-based systems, it can also introduce hidden variables. If neural networks are able to distinguish/learn hidden variables, these variables can introduce batch effects that compromise the accuracy of classification systems. OBJECTIVE The objective of the study was to analyze the learnability of an exemplary selection of hidden variables (patient age, slide preparation date, slide origin, and scanner type) that are commonly found in whole slide image data sets in digital pathology and could create batch effects. METHODS We trained four separate convolutional neural networks (CNNs) to learn four variables using a data set of digitized whole slide melanoma images from five different institutes. For robustness, each CNN training and evaluation run was repeated multiple times, and a variable was only considered learnable if the lower bound of the 95% confidence interval of its mean balanced accuracy was above 50.0%. RESULTS A mean balanced accuracy above 50.0% was achieved for all four tasks, even when considering the lower bound of the 95% confidence interval. Performance between tasks showed wide variation, ranging from 56.1% (slide preparation date) to 100% (slide origin). CONCLUSIONS Because all of the analyzed hidden variables are learnable, they have the potential to create batch effects in dermatopathology data sets, which negatively affect AI-based classification systems. Practitioners should be aware of these and similar pitfalls when developing and evaluating such systems and address these and potentially other batch effect variables in their data sets through sufficient data set stratification.


Author(s):  
Mahmoud RAHDAR ◽  
Sharif MARAGHI

Norwegian scabies (hyperkeratosis scabies) is an acute form of skin disease seen in immune-compromised patients. This study aimed to describe two cases of Norwegian scabies from Ahvaz, southwest of Iran in 2015. Two patients included a 55 year old man with renal transplant history and a 49 yr old man with diabetic mellitus and autoimmune disease, complained of dermatitis lesions and itching with sever hyperkeratosis, several macula and papules on neck and armpits for one-month duration were referred to a Iran Zamin Medical Diagnostic Laboratory in Ahvaz, Southwestern Iran in 2015. Patients were referred for fungal examination. Scraping from the crusted lesions of skin and slide preparation with 20% KOH was done. Microscopic examination presented that huge infestation of Sarcoptes scabiei in all forms of parasite included adult female, nymph stage and eggs. One of the patients spouse was also infested by Sarcoptes and appeared mild clinical symptoms. The disease was diagnosed with Norwegian scabies and the patients were successfully treated with topical 5% permethrin ointment for two weeks continuously. Overall, Norwegian scabies should be considered in immune- compromised patients with contaminated areas.


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