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Month wise articles
Figures next to the month indicate the number of articles in that month
2021
April
[
4
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March
[
7
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February
[
3
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January
[
6
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2020
December
[
2
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November
[
5
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October
[
3
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September
[
2
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August
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8
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July
[
4
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June
[
2
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May
[
1
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April
[
3
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March
[
3
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February
[
6
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January
[
1
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2019
December
[
6
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November
[
4
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September
[
4
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August
[
3
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July
[
6
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June
[
1
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May
[
2
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April
[
6
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March
[
3
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February
[
4
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January
[
2
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2018
December
[
10
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November
[
4
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October
[
3
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September
[
4
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August
[
1
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July
[
3
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June
[
5
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May
[
4
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April
[
10
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March
[
2
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February
[
4
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2017
December
[
5
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November
[
4
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October
[
3
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September
[
9
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July
[
5
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June
[
2
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May
[
4
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April
[
6
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March
[
6
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February
[
7
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2016
December
[
7
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November
[
5
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October
[
3
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September
[
7
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August
[
1
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July
[
7
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May
[
8
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April
[
7
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March
[
4
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February
[
2
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January
[
5
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2015
November
[
4
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October
[
5
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September
[
5
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August
[
4
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July
[
3
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June
[
19
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May
[
5
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April
[
1
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March
[
5
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February
[
9
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January
[
3
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2014
November
[
2
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October
[
5
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September
[
4
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August
[
6
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July
[
8
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June
[
1
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May
[
3
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March
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8
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February
[
3
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January
[
4
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2013
December
[
5
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November
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2
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October
[
4
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September
[
4
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August
[
3
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July
[
3
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June
[
5
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May
[
7
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March
[
18
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February
[
1
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January
[
1
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2012
December
[
6
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November
[
1
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October
[
4
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September
[
4
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August
[
7
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July
[
2
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June
[
1
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May
[
2
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April
[
7
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March
[
6
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February
[
7
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January
[
13
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2011
December
[
3
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November
[
1
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October
[
7
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August
[
9
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July
[
3
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June
[
7
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May
[
3
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March
[
6
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February
[
8
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January
[
6
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2010
December
[
4
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November
[
1
]
October
[
6
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September
[
1
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August
[
6
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July
[
6
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May
[
5
]
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Original Article:
Using image analysis as a tool for assessment of prognostic and predictive biomarkers for breast cancer: How reliable is it?
Mark C Lloyd, Pushpa Allam-Nandyala, Chetna N Purohit, Nancy Burke, Domenico Coppola, Marilyn M Bui
J Pathol Inform
2010, 1:29 (23 December 2010)
DOI
:10.4103/2153-3539.74186
PMID
:21221174
Background
: Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER2) are important and well-established prognostic and predictive biomarkers for breast cancers and routinely tested on patient's tumor samples by immunohistochemical (IHC) study. The accuracy of these test results has substantial impact on patient management. A critical factor that contributes to the result is the interpretation (scoring) of IHC. This study investigates how computerized image analysis can play a role in a reliable scoring, and identifies potential pitfalls with common methods.
Materials and Methods
: Whole slide images of 33 invasive ductal carcinoma (IDC) (10 ER and 23 HER2) were scored by pathologist under the light microscope and confirmed by another pathologist. The HER2 results were additionally confirmed by fluorescence
in situ
hybridization (FISH). The scoring criteria were adherent to the guidelines recommended by the American Society of Clinical Oncology/College of American Pathologists. Whole slide stains were then scored by commercially available image analysis algorithms from Definiens (Munich, Germany) and Aperio Technologies (Vista, CA, USA). Each algorithm was modified specifically for each marker and tissue. The results were compared with the semi-quantitative manual scoring, which was considered the gold standard in this study.
Results
: For HER2 positive group, each algorithm scored 23/23 cases within the range established by the pathologist. For ER, both algorithms scored 10/10 cases within range. The performance of each algorithm varies somewhat from the percentage of staining as compared to the pathologist's reading.
Conclusions
: Commercially available computerized image analysis can be useful in the evaluation of ER and HER2 IHC results. In order to achieve accurate results either manual pathologist region selection is necessary, or an automated region selection tool must be employed. Specificity can also be gained when strict quality assurance by a pathologist is invested. Quality assurance of image analysis by pathologists is always warranted. Automated image analysis should only be used as adjunct to pathologist's evaluation.
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Editorial:
The coming wave of change: ICD-10
Ji Yeon Kim, Bruce A Beckwith
J Pathol Inform
2010, 1:28 (23 December 2010)
DOI
:10.4103/2153-3539.74183
PMID
:21221173
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Book Review:
Lewis Paul D: R for Medicine and Biology
G William Moore
J Pathol Inform
2010, 1:27 (3 December 2010)
DOI
:10.4103/2153-3539.73505
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Original Article:
Informatics methods for laboratory evaluation of HPV ordering patterns with an example from a nationwide sample in the United States, 2003-2009
Brian H Shirts, Brian R Jackson
J Pathol Inform
2010, 1:26 (3 December 2010)
DOI
:10.4103/2153-3539.73504
PMID
:21189840
Background:
Laboratory data is a rich source of information that can be used to estimate adherence to physician guidelines and motivate improvement in clinical practice. Human papillomavirus (HPV) testing is an important component of cervical cancer screening programs with established screening guidelines. The purpose of this study was to develop methods to estimate concordance with published guidelines for HPV testing in order to provide clinicians and payors specific feedback about overscreening.
Methods:
This retrospective analysis of laboratory test ordering patterns evaluated 454,532 HPV tests ordered from September 2003 to October 2009 from 110 facilities and performed at ARUP laboratories. We used laboratory data including patient demographics, ordering frequency, timestamps and results to examine the proportion of HPV tests ordered on women under 21 years, ordered on women between 21 and 29 years apparently before cytological examination, repeated less than 1 year after a positive HPV result in women over 30 years, and repeated less than 3 years after a negative HPV result in women over 30 years.
Results:
The absolute number and proportion of HPV tests performed on women under 21 years declined from 20% in 2005 to 5% in October 2009. The proportion of HPV tests performed women between 21 and 29 years also declined during this period. Approximately one-third of HPV tests performed on women between 21 and 29 years arrived for HPV testing before cervical screening had presumably been completed. The most common follow-up intervals for HPV testing on women over 30 years were 6 months following a positive HPV result and 12 months following a negative HPV result. Only 6% of repeat HPV testing in women over 30 years followed a negative HPV result by 3 years or more. Approximately one-fourth of HPV tests ordered the year ending October 2009 were unnecessary based on the American Society for Colposcopy and Cervical Pathology guideline.
Conclusions:
We demonstrate simple methods to evaluate appropriate utilization of HPV testing using laboratory data. Our data illustrates that some aspects of HPV test ordering have become more consistent with guidelines over time. However, a large portion of HPV testing in the United States is unnecessary. This highlights opportunities for optimization of a rational cancer prevention strategy to reduce unnecessary screening, colposcopy and biopsies.
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Original Article:
Improving the visualization and detection of tissue folds in whole slide images through color enhancement
Pinky A Bautista, Yukako Yagi
J Pathol Inform
2010, 1:25 (27 November 2010)
DOI
:10.4103/2153-3539.73320
PMID
:21221170
Objective
: The objective of this paper is to improve the visualization and detection of tissue folds, which are prominent among tissue slides, from the pre-scan image of a whole slide image by introducing a color enhancement method that enables the differentiation between fold and non-fold image pixels.
Method:
The weighted difference between the color saturation and luminance of the image pixels is used as shifting factor to the original RGB color of the image.
Results:
Application of the enhancement method to hematoxylin and eosin (H&E) stained images improves the visualization of tissue folds regardless of the colorimetric variations in the images. Detection of tissue folds after application of the enhancement also improves but the presence of nuclei, which are also stained dark like the folds, was found to sometimes affect the detection accuracy.
Conclusion:
The presence of tissue artifacts could affect the quality of whole slide images, especially that whole slide scanners select the focus points from the pre-scan image wherein the artifacts are indistinguishable from real tissue area. We have a presented in this paper an enhancement scheme that improves the visualization and detection of tissue folds from pre-scan images. Since the method works on the simulated pre-scan images its integration to the actual whole slide imaging process should also be possible.
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Research Article:
Automated ancillary cancer history classification for mesothelioma patients from free-text clinical reports
Richard A Wilson, Wendy W Chapman, Shawn J DeFries, Michael J Becich, Brian E Chapman
J Pathol Inform
2010, 1:24 (11 October 2010)
DOI
:10.4103/2153-3539.71065
PMID
:21031012
Background:
Clinical records are often unstructured, free-text documents that create information extraction challenges and costs. Healthcare delivery and research organizations, such as the National Mesothelioma Virtual Bank, require the aggregation of both structured and unstructured data types. Natural language processing offers techniques for automatically extracting information from unstructured, free-text documents.
Methods:
Five hundred and eight history and physical reports from mesothelioma patients were split into development (208) and test sets (300). A reference standard was developed and each report was annotated by experts with regard to the patient's personal history of ancillary cancer and family history of any cancer. The Hx application was developed to process reports, extract relevant features, perform reference resolution and classify them with regard to cancer history. Two methods, Dynamic-Window and ConText, for extracting information were evaluated. Hx's classification responses using each of the two methods were measured against the reference standard. The average Cohen's weighted kappa served as the human benchmark in evaluating the system.
Results:
Hx had a high overall accuracy, with each method, scoring 96.2%. F-measures using the Dynamic-Window and ConText methods were 91.8% and 91.6%, which were comparable to the human benchmark of 92.8%. For the personal history classification, Dynamic-Window scored highest with 89.2% and for the family history classification, ConText scored highest with 97.6%, in which both methods were comparable to the human benchmark of 88.3% and 97.2%, respectively.
Conclusion:
We evaluated an automated application's performance in classifying a mesothelioma patient's personal and family history of cancer from clinical reports. To do so, the Hx application must process reports, identify cancer concepts, distinguish the known mesothelioma from ancillary cancers, recognize negation, perform reference resolution and determine the experiencer. Results indicated that both information extraction methods tested were dependant on the domain-specific lexicon and negation extraction. We showed that the more general method, ConText, performed as well as our task-specific method. Although Dynamic-Window could be modified to retrieve other concepts, ConText is more robust and performs better on inconclusive concepts. Hx could greatly improve and expedite the process of extracting data from free-text, clinical records for a variety of research or healthcare delivery organizations.
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Technical note:
The use of multispectral imaging to distinguish reactive urothelium from neoplastic urothelium
Christopher Michael Gilbert, Anil Parwani
J Pathol Inform
2010, 1:23 (11 October 2010)
DOI
:10.4103/2153-3539.71064
PMID
:21031011
Context:
The interpretation of urothelial atypia in a setting of chronic inflammation and reactive changes can prove difficult with small biopsies. Limited recuts lessen the efficacy of ancillary studies such as CK20, P53 and CD44 in these instances.
Objective:
To evaluate a triple-immunostain with the assistance of multispectral microscopy.
Design:
Fifty-three bladder biopsies with previous diagnosis of benign/reactive, dysplastic, carcinoma in situ or carcinoma were prepared using a triple-immunostain cocktail consisting of CK20, P53 and CD44. Three control stains were used for the purpose of creating a spectral library for the Nuance CRI Flex microscopy system. All specimens were interpreted by light microscopy, processed with the Nuance 2.71 software, and CK20 and P53 were scored blinded to the case diagnoses. CD44 was not scored as it proved difficult to interpret in many cases.
Results:
The results demonstrated that it was possible to separate CK20, P53 and the counterstain that were co-localized in the biopsies. Separation of the stains demonstrated a correlation of p53 and CK20 dual expression in biopsies diagnosed as carcinoma. Low or undetectable levels of expression were seen in biopsies later diagnosed as reactive or benign.
Conclusion:
The combination of multispectral microscopy and multiple immunostain cocktails form a powerful and useful tool for the interpretation of small biopsies with faint or difficult to interpret staining and for cases with limited material such as small-bladder biopsies.
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Research Article:
Design and utilization of the colorectal and pancreatic neoplasm virtual biorepository: An early detection research network initiative
Waqas Amin, Harpreet Singh, Lynda Ann Dzubinski, Robert E Schoen, Anil V Parwani
J Pathol Inform
2010, 1:22 (1 October 2010)
DOI
:10.4103/2153-3539.70831
PMID
:21031013
Background:
The Early Detection Research Network (EDRN) colorectal and pancreatic neoplasm virtual biorepository is a bioinformatics-driven system that provides high-quality clinicopathology-rich information for clinical biospecimens. This NCI-sponsored EDRN resource supports translational cancer research. The information model of this biorepository is based on three components: (a) development of common data elements (CDE), (b) a robust data entry tool and (c) comprehensive data query tools.
Methods:
The aim of the EDRN initiative is to develop and sustain a virtual biorepository for support of translational research. High-quality biospecimens were accrued and annotated with pertinent clinical, epidemiologic, molecular and genomic information. A user-friendly annotation tool and query tool was developed for this purpose. The various components of this annotation tool include: CDEs are developed from the College of American Pathologists (CAP) Cancer Checklists and North American Association of Central Cancer Registries (NAACR) standards. The CDEs provides semantic and syntactic interoperability of the data sets by describing them in the form of metadata or data descriptor. The data entry tool is a portable and flexible Oracle-based data entry application, which is an easily mastered, web-based tool. The data query tool facilitates investigators to search deidentified information within the warehouse through a "point and click" interface thus enabling only the selected data elements to be essentially copied into a data mart using a dimensional-modeled structure from the warehouse's relational structure.
Results:
The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository database contains multimodal datasets that are available to investigators via a web-based query tool. At present, the database holds 2,405 cases and 2,068 tumor accessions. The data disclosure is strictly regulated by user's authorization. The high-quality and well-characterized biospecimens have been used in different translational science research projects as well as to further various epidemiologic and genomics studies.
Conclusions:
The EDRN Colorectal and Pancreatic Neoplasm Virtual Biorepository with a tangible translational biomedical informatics infrastructure facilitates translational research. The data query tool acts as a central source and provides a mechanism for researchers to efficiently query clinically annotated datasets and biospecimens that are pertinent to their research areas. The tool ensures patient health information protection by disclosing only deidentified data with Institutional Review Board and Health Insurance Portability and Accountability Act protocols.
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Research Article:
Tolerance testing of passive radio frequency identification tags for solvent, temperature, and pressure conditions encountered in an anatomic pathology or biorepository setting
Alina A Leung, Jerry J Lou, Sergey Mareninov, Steven S Silver, Mark J Routbort, Michael Riben, Gary Andrechak, William H Yong
J Pathol Inform
2010, 1:21 (1 October 2010)
DOI
:10.4103/2153-3539.70710
PMID
:21031010
Background:
Radio frequency identification (RFID) tags have potential for use in identifying and tracking biospecimens in anatomic pathology and biorepository laboratories. However, there is little to no data on the tolerance of tags to solutions, solvents, temperatures, and pressures likely to be encountered in the laboratory. The functioning of the Hitachi Mu-chip RFID tag, a candidate for pathology use, was evaluated under such conditions.
Methods:
The RFID tags were affixed to cryovials containing tissue or media, glass slides, and tissue cassettes. The tags were interrogated for readability before and after each testing condition or cycle. Individual tags were subjected to only one testing condition but for multiple cycles. Testing conditions were: 1) Ten wet autoclave cycles (121˚C, 15 psi); 2) Ten dry autoclave cycles (121˚C, 26 psi); 3) Ten tissue processor cycles; 4) Ten hematoxylin and eosin (H&E) staining cycles; 5) Ten antigen retrieval pressure cooker cycles (125˚C, 15 psi); 6) 75
o
C for seven days; 7) 75-59
o
C day/night cycles for 7 days; 8) -80
o
C, -150
o
C, or -196
o
C for 12 months; 9) Fifty freeze-thaw cycles (-196
o
C to 22
o
C).
Results:
One hundred percent of tags exposed to cold temperatures from -80 to -196
o
C (80 tags, 1120 successful reads), high temperatures from 52 to 75
o
C (40 tags, 420 reads), H & E staining (20 tags, 200 reads), pressure cooker antigen retrieval (20 tags, 200 reads), and wet autoclaving (20 tags, 200 reads) functioned well throughout and after testing. Of note, all 20 tested tags tolerated 50 freeze-thaw cycles and all 60 tags subjected to sustained freezing temperatures were readable after 1 year. One dry autoclaved tag survived nine cycles but failed after the tenth. The remaining 19 tags were readable after all 10 dry autoclave cycles. One tag failed after the first tissue processing cycle while the remaining 19 tags survived all 10 tissue processing cycles.
Conclusions:
In this preliminary study, these RFID tags show a high-degree of tolerance to tested solutions, solvents, temperature, and pressure conditions. However, a measurable failure rate is detectable under some circumstances and redundant identification systems such as barcodes may be required with the deployment of RFID systems. We have delineated testing protocols that may be used as a framework for preliminary assessments of candidate RFID tag tolerance to laboratory conditions.
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Editorial:
Ten important lessons we have learned as pathology bloggers
Keith J Kaplan, Bruce A Friedman, Mark D Pool
J Pathol Inform
2010, 1:20 (1 October 2010)
DOI
:10.4103/2153-3539.70709
PMID
:21031009
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Editorial:
Optimizing the pathology workstation "cockpit": Challenges and solutions
Elizabeth A Krupinski
J Pathol Inform
2010, 1:19 (1 October 2010)
DOI
:10.4103/2153-3539.70708
PMID
:21031008
The 21
st
century has brought numerous changes to the clinical reading (i.e., image or virtual pathology slide interpretation) environment of pathologists and it will continue to change even more dramatically as information and communication technologies (ICTs) become more widespread in the integrated healthcare enterprise. The extent to which these changes impact the practicing pathologist differ as a function of the technology under consideration, but digital "virtual slides" and the viewing of images on computer monitors instead of glass slides through a microscope clearly represents a significant change in the way that pathologists extract information from these images and render diagnostic decisions. One of the major challenges facing pathologists in this new era is how to best optimize the pathology workstation, the reading environment and the new and varied types of information available in order to ensure efficient and accurate processing of this information. Although workstations can be stand-alone units with images imported via external storage devices, this scenario is becoming less common as pathology departments connect to information highways within their hospitals and to external sites. Picture Archiving and Communications systems are no longer confined to radiology departments but are serving the entire integrated healthcare enterprise, including pathology. In radiology, the workstation is often referred to as the "cockpit" with a "digital dashboard" and the reading room as the "control room." Although pathology has yet to "go digital" to the extent that radiology has, lessons derived from radiology reading "cockpits" can be quite valuable in setting up the digital pathology reading room. In this article, we describe the concept of the digital dashboard and provide some recent examples of informatics-based applications that have been shown to improve the workflow and quality in digital reading environments.
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Abstract:
Abstracts: Pathology Informatics 2010 Meeting
J Pathol Inform
2010, 1:18 (18 September 2010)
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Symposium - New Frontiers in Digital Pathology:
Digital pathology in clinical consultation practice
Subodh M Lele
J Pathol Inform
2010, 1:17 (10 August 2010)
DOI
:10.4103/2153-3539.68334
PMID
:20922028
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Symposium - New Frontiers in Digital Pathology:
Application of virtual microscopy in consultation practice of gastrointestinal and liver pathology
Shriram Jakate
J Pathol Inform
2010, 1:16 (10 August 2010)
DOI
:10.4103/2153-3539.68333
PMID
:20922027
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Symposium - New Frontiers in Digital Pathology:
Digital images and the future of digital pathology
Liron Pantanowitz
J Pathol Inform
2010, 1:15 (10 August 2010)
DOI
:10.4103/2153-3539.68332
PMID
:20922032
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Symposium - New Frontiers in Digital Pathology:
Medical education in the digital age: Digital whole slide imaging as an e-learning tool
Kirk Foster
J Pathol Inform
2010, 1:14 (10 August 2010)
DOI
:10.4103/2153-3539.68331
PMID
:20922031
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Brief Report:
The state of telepathology in Japan
Takashi Sawai, Miwa Uzuki, Akihisa Kamataki, Ikuo Tofukuji
J Pathol Inform
2010, 1:13 (10 August 2010)
DOI
:10.4103/2153-3539.68327
PMID
:20922030
Telepathology began in Japan in the early 1990s in response to advances in computing and telecommunications equipment development and a dearth of pathologists. Telepathology in Japan is most often used for rapid intraoperative pathological diagnosis using frozen section, followed by second opinions and consultation. Intraoperatively, telepathology is used to determine malignancy, metastasis of malignant tumors, and the extent of excision. Infrastructure and equipment has evolved from analog lines to digital lines like integrated services digital network (ISDN) and asymmetric digital subscriber line (ADSL), and recently to fiber optics. The use of communications satellites is also being considered. Image quality is being improved to Hi-Vision (HDTV), and from still images to real-time video. Digital microscopy has been introduced, and is used in education and consultation.
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Review Article:
A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research
Waqas Amin, Harpreet Singh, Andre K Pople, Sharon Winters, Rajiv Dhir, Anil V Parwani, Michael J Becich
J Pathol Inform
2010, 1:12 (10 August 2010)
DOI
:10.4103/2153-3539.68314
PMID
:20922029
Context:
Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models.
Design:
Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 9.2.0.1 server tools and software applications and the model-driven architecture is implemented in a J2EE framework.
Result:
The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource (
http://www.cpctr.info/
), Pennsylvania Cancer Alliance Bioinformatics Consortium (
http://pcabc.upmc.edu/main.cfm
), EDRN Colorectal and Pancreatic Neoplasm Database (
http://edrn.nci.nih.gov/
) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database (
http://spores.nci.nih.gov/current/hn/index.htm
). The model-based architecture is represented by the National Mesothelioma Virtual Bank (
http://mesotissue.org/
). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet.
Conclusion:
These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems.
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Editorial:
Computerized provider order entry systems - Research imperatives and organizational challenges facing pathology services
Andrew Georgiou, Johanna Westbrook, Jeffrey Braithwaite
J Pathol Inform
2010, 1:11 (13 July 2010)
DOI
:10.4103/2153-3539.65431
PMID
:20805962
Information and communication technologies (ICT) are contributing to major changes taking place in pathology and within health services more generally. In this article, we draw on our research experience for over 7 years investigating the implementation and diffusion of computerized provider order entry (CPOE) systems to articulate some of the key informatics challenges confronting pathology laboratories. The implementation of these systems, with their improved information management and decision support structures, provides the potential for enhancing the role that pathology services play in patient care pathways. Beyond eliminating legibility problems, CPOE systems can also contribute to the efficiency and safety of healthcare, reducing the duplication of test orders and diminishing the risk of misidentification of patient samples and orders. However, despite the enthusiasm for CPOE systems, their diffusion across healthcare settings remains variable and is often beset by implementation problems. Information systems like CPOE may have the ability to integrate work, departments and organizations, but unfortunately, health professionals, departments and organizations do not always want to be integrated in ways that information systems allow. A persistent theme that emerges from the research evidence is that one size does not fit all, and system success or otherwise is reliant on the conditions and circumstances in which they are located. These conditions and circumstances are part of what is negotiated in the complex, messy and challenging area of ICT implementation. The solution is not likely to be simple and easy, but current evidence suggests that a combination of concerted efforts, better research designs, more sophisticated theories and hypotheses as well as more skilled, multidisciplinary research teams, tackling this area of study will bring substantial benefits, improving the effectiveness of pathology services, and, as a direct corollary, the quality of patient care.
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Original Article:
The pathology informatics curriculum wiki: Harnessing the power of user-generated content
Ji Yeon Kim, Thomas M Gudewicz, Anand S Dighe, John R Gilbertson
J Pathol Inform
2010, 1:10 (13 July 2010)
DOI
:10.4103/2153-3539.65428
PMID
:20805963
Background:
The need for informatics training as part of pathology training has never been so critical, but pathology informatics is a wide and complex field and very few programs currently have the resources to provide comprehensive educational pathology informatics experiences to their residents. In this article, we present the "pathology informatics curriculum wiki", an open, on-line wiki that indexes the pathology informatics content in a larger public wiki, Wikipedia, (and other online content) and organizes it into educational modules based on the 2003 standard curriculum approved by the Association for Pathology Informatics (API).
Methods and Results:
In addition to implementing the curriculum wiki at http://pathinformatics.wikispaces.com, we have evaluated pathology informatics content in Wikipedia. Of the 199 non-duplicate terms in the API curriculum, 90% have at least one associated Wikipedia article. Furthermore, evaluation of articles on a five-point Likert scale showed high scores for comprehensiveness (4.05), quality (4.08), currency (4.18), and utility for the beginner (3.85) and advanced (3.93) learners. These results are compelling and support the thesis that Wikipedia articles can be used as the foundation for a basic curriculum in pathology informatics.
Conclusions:
The pathology informatics community now has the infrastructure needed to collaboratively and openly create, maintain and distribute the pathology informatics content worldwide (Wikipedia) and also the environment (the curriculum wiki) to draw upon its own resources to index and organize this content as a sustainable basic pathology informatics educational resource. The remaining challenges are numerous, but largest by far will be to convince the pathologists to take the time and effort required to build pathology informatics content in Wikipedia and to index and organize this content for education in the curriculum wiki.
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Original Article:
The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data
Hyunseok P Kang, Charles D Borromeo, Jules J Berman, Michael J Becich
J Pathol Inform
2010, 1:9 (13 July 2010)
DOI
:10.4103/2153-3539.65347
PMID
:20805954
Background:
Tissue microarrays (TMAs) are enormously useful tools for translational research, but incompatibilities in database systems between various researchers and institutions prevent the efficient sharing of data that could help realize their full potential. Resource Description Framework (RDF) provides a flexible method to represent knowledge in triples, which take the form Subject- Predicate-Object. All data resources are described using Uniform Resource Identifiers (URIs), which are global in scope. We present an OWL (Web Ontology Language) schema that expands upon the TMA data exchange specification to address this issue and assist in data sharing and integration.
Methods:
A minimal OWL schema was designed containing only concepts specific to TMA experiments. More general data elements were incorporated from predefined ontologies such as the NCI thesaurus. URIs were assigned using the Linked Data format.
Results:
We present examples of files utilizing the schema and conversion of XML data (similar to the TMA DES) to OWL.
Conclusion:
By utilizing predefined ontologies and global unique identifiers, this OWL schema provides a solution to the limitations of XML, which represents concepts defined in a localized setting. This will help increase the utilization of tissue resources, facilitating collaborative translational research efforts.
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Original Article:
Development of electronic medical record charting for hospital-based transfusion and apheresis medicine services: Early adoption perspectives
Rebecca Levy, Liron Pantanowitz, Darlene Cloutier, Jean Provencher, Joan McGirr, Jennifer Stebbins, Suzanne Cronin, Josh Wherry, Joseph Fenton, Eileen Donelan, Vandita Johari, Chester Andrzejewski
J Pathol Inform
2010, 1:8 (13 July 2010)
DOI
:10.4103/2153-3539.65345
PMID
:20805955
Background:
Electronic medical records (EMRs) provide universal access to health care information across multidisciplinary lines. In pathology departments, transfusion and apheresis medicine services (TAMS) involved in direct patient care activities produce data and documentation that typically do not enter the EMR. Taking advantage of our institution's initiative for implementation of a paperless medical record, our TAMS division set out to develop an electronic charting (e-charting) strategy within the EMR.
Methods:
A focus group of our hospital's transfusion committee consisting of transfusion medicine specialists, pathologists, residents, nurses, hemapheresis specialists, and information technologists was constituted and charged with the project. The group met periodically to implement e-charting TAMS workflow and produced electronic documents within the EMR (Cerner Millenium) for various service line functions.
Results:
The interdisciplinary working group developed and implemented electronic versions of various paper-based clinical documentation used by these services. All electronic notes collectively gather and reside within a unique
Transfusion Medicine Folder
tab in the EMR, available to staff with access to patient charts. E-charting eliminated illegible handwritten notes, resulted in more consistent clinical documentation among staff, and provided greater real-time review/access of hemotherapy practices. No major impediments to workflow or inefficiencies have been encountered. However, minor updates and corrections to documents as well as select work re-designs were required for optimal use of e-charting by these services.
Conclusion:
Documentation of pathology subspecialty activities such as TAMS can be successfully incorporated into the EMR. E-charting by staff enhances communication and helps promote standardized documentation of patient care within and across service lines. Well-constructed electronic documents in the EMR may also enhance data mining, quality improvement, and biovigilance monitoring activities.
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Commentary:
Whole slide imaging for teleconsultation and clinical use
Bryan Dangott, Anil Parwani
J Pathol Inform
2010, 1:7 (13 July 2010)
DOI
:10.4103/2153-3539.65342
PMID
:20805956
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Editorial:
HIMSS10 - Perspectives from a newcomer pathologist and a seasoned attendee pathologist: Pathologists should attend!
Alexis B Carter, Raymond Aller
J Pathol Inform
2010, 1:6 (13 July 2010)
DOI
:10.4103/2153-3539.65340
PMID
:20805957
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Technical Note:
Stepwise approach to establishing multiple outreach laboratory information system-electronic medical record interfaces
Liron Pantanowitz, Wayne LaBranche, William Lareau
J Pathol Inform
2010, 1:5 (26 May 2010)
DOI
:10.4103/2153-3539.63829
PMID
:20805958
Clinical laboratory outreach business is changing as more physician practices adopt an electronic medical record (EMR). Physician connectivity with the laboratory information system (LIS) is consequently becoming more important. However, there are no reports available to assist the informatician with establishing and maintaining outreach LIS-EMR connectivity. A four-stage scheme is presented that was successfully employed to establish unidirectional and bidirectional interfaces with multiple physician
EMRs. This approach involves planning (step 1), followed by interface building (step 2) with subsequent testing (step 3), and finally ongoing maintenance (step 4). The role of organized project management, software as a service (SAAS), and alternate solutions for outreach connectivity are discussed.
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Original Article:
Cytologic evaluation of image-guided fine needle aspiration biopsies via robotic microscopy: A validation study
Guoping Cai, Lisa A Teot, Walid E Khalbuss, Jing Yu, Sara E Monaco, Drazen M Jukic, Anil V Parwani
J Pathol Inform
2010, 1:4 (26 May 2010)
DOI
:10.4103/2153-3539.63826
PMID
:20805959
Background:
This study carried out was to assess the feasibility of using robotic microscopy (RM) for cytologic evaluation of direct smears from fine needle aspiration biopsy (FNAB).
Methods:
Three board-certified cytopathologists reviewed representative direct smears from 40 image-guided FNABs using RM and subsequently re-reviewed the same smears using conventional microscopy. Adequacy of the smears and cytologic diagnosis, as determined using the two approaches, were compared for each individual cytopathologist (intraobserver) and between the three cytopathologists (interobserver). The intraobserver and interobserver discrepancies were analyzed and discussed in a follow-up consensus conference.
Results:
For assessment of adequacy, there were high concordance rates (intraobserver: 92.5-97.5%; interobserver: 90-92.5%), with a few discrepancies involving distinctions between suboptimal and satisfactory smears. Analysis of diagnostic interpretations showed correct classification of 92.5-95% (intraobserver) or 90-92.5% (interobserver) of benign and malignant cases combined, with the discrepancies being between benign and atypical cells in the benign group, and between suspicious and malignant in the malignant group. Within the malignant group, 94% of cases were accurately subclassified via RM. The quality of images viewed by using RM was rated adequate (fair or good) for 95% of the slides.
Conclusions:
The results demonstrate that cytologic evaluation of direct smears from FNABs using RM is feasible. Problems encountered included the longer times needed to evaluate cases with thick, bloody smears and/or low numbers of diagnostic cells, and difficulties in recognizing neuroendocrine differentiation and mimics of hepatocellular carcinoma.
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Original Article:
Overview of laboratory data tools available in a single electronic medical record
Neil R Kudler, Liron Pantanowitz
J Pathol Inform
2010, 1:3 (26 May 2010)
DOI
:10.4103/2153-3539.63824
PMID
:20805960
Background:
Laboratory data account for the bulk of data stored in any given electronic medical record (EMR). To best serve the user, electronic laboratory data needs to be flexible and customizable. Our aim was to determine the various ways in which laboratory data get utilized by clinicians in our health system's EMR.
Method:
All electronic menus, tabs, flowsheets, notes and subsections within the EMR (Millennium v2007.13, Cerner Corporation, Kansas City, MO, US) were explored to determine how clinicians utilize discrete laboratory data.
Results:
Laboratory data in the EMR were utilized by clinicians in five distinct ways: within flowsheets, their personal inbox (EMR messaging), with decision support tools, in the health maintenance tool, and when incorporating laboratory data into their clinical notes and letters.
Conclusions
: Flexible electronic laboratory data in the EMR hava many advantages. Users can view, sort, pool, and appropriately route laboratory information to better support trend analyses, clinical decision making, and clinical charting. Laboratory data in the EMR can also be utilized to develop clinical decision support tools. Pathologists need to participate in the creation of these EMR tools in order to better support the appropriate utilization of laboratory information in the EMR.
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Original Article:
Development and use of a genitourinary pathology digital teaching set for trainee education
Li Li, Bryan J Dangott, Anil V Parwani
J Pathol Inform
2010, 1:2 (26 May 2010)
DOI
:10.4103/2153-3539.63822
PMID
:20805961
Background
: Automated, high-speed, high-resolution whole slide imaging (WSI) robots are becoming increasingly robust and capable. This technology has started to have a significant impact on pathology practice in various aspects including resident education. To be sufficient and adequate, training in pathology requires gaining broad exposure to various diagnostic patterns through teaching sets, which are traditionally composed of glass slides.
Methods:
A teaching set of over 295 glass slides has been used for resident training at the Division of Genitourinary Pathology, Department of Pathology, University of Pittsburgh Medical Center. Whole slide images were prepared from these slides using an Aperio ScanScope CS scanner. These images and case-related information were uploaded on a web-based digital teaching model.
Results:
The web site is available at:
https://www.secure.opi.upmc.edu/genitourinary/index.cfm
. Once logged in, users can view the list of cases, or search cases with or without diagnoses shown. Each case can be accessed through an option button, where the clinical history, gross findings are initially shown. Whole slide images can be accessed through the links on the page, which allows users to make diagnoses on their own. More information including final diagnosis will display when the diagnosis-button is clicked.
Conclusion:
The web-based digital study set provides additional educational benefits to using glass slides. Residents or other users can remotely access whole slide images and related information at their convenience. Searching and sorting functions and self-testing mode allow a more targeted study. It would also prepare residents with competence to work with whole slide images. Further, the model can be expanded to include pre-rotation and post-rotation exams, and/or a virtual rotation system, which may potentially make standardization of pathology resident training possible in the future.
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Editorial:
Introducing the Journal of Pathology Informatics
Liron Pantanowitz, Anil V Parwani
J Pathol Inform
2010, 1:1 (26 May 2010)
DOI
:10.4103/2153-3539.63821
PMID
:20805964
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March, 2010