Abstract:
CONTEXT:In the normal course of activity, pathologists create and archive immense data sets of scientifically valuable information. Researchers need pathology-based data sets, annotated with clinical information and linked to archived tissues, to discover and validate new diagnostic tests and therapies. Pathology records can be used for research purposes (without obtaining informed patient consent for each use of each record), provided the data are rendered harmless. Large data sets can be made harmless through 3 computational steps: (1) deidentification, the removal or modification of data fields that can be used to identify a patient (name, social security number, etc); (2) rendering the data ambiguous, ensuring that every data record in a public data set has a nonunique set of characterizing data; and (3) data scrubbing, the removal or transformation of words in free text that can be used to identify persons or that contain information that is incriminating or otherwise private. This article addresses the problem of data scrubbing. OBJECTIVE:To design and implement a general algorithm that scrubs pathology free text, removing all identifying or private information. METHODS:The Concept-Match algorithm steps through confidential text. When a medical term matching a standard nomenclature term is encountered, the term is replaced by a nomenclature code and a synonym for the original term. When a high-frequency "stop" word, such as a, an, the, or for, is encountered, it is left in place. When any other word is encountered, it is blocked and replaced by asterisks. This produces a scrubbed text. An open-source implementation of the algorithm is freely available. RESULTS:The Concept-Match scrub method transformed pathology free text into scrubbed output that preserved the sense of the original sentences, while it blocked terms that did not match terms found in the Unified Medical Language System (UMLS). The scrubbed product is safe, in the restricted sense that the output retains only standard medical terms. The software implementation scrubbed more than half a million surgical pathology report phrases in less than an hour. CONCLUSIONS:Computerized scrubbing can render the textual portion of a pathology report harmless for research purposes. Scrubbing and deidentification methods allow pathologists to create and use large pathology databases to conduct medical research.
journal_name
Arch Pathol Lab Medjournal_title
Archives of pathology & laboratory medicineauthors
Berman JJdoi
10.1043/1543-2165(2003)127<680:CMDS>2.0.CO;2subject
Has Abstractpub_date
2003-06-01 00:00:00pages
680-6issue
6eissn
0003-9985issn
1543-2165journal_volume
127pub_type
杂志文章abstract:CONTEXT.—:Resection of breast carcinoma with adequate margins reduces the risk of local recurrence and reoperation. Tozuleristide (BLZ-100) is an investigational peptide-fluorophore agent that may aid in intraoperative tumor detection and margin assessment. In this study, fluorescence imaging was conducted ex vivo on g...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.5858/arpa.2018-0197-OA
更新日期:2019-09-01 00:00:00
abstract::A case of acquired von Willebrand's syndrome associated with an extranodal pulmonary lymphoma is reported in a 58-year-old man. His initial factor VIII-von Willebrand factor (vWF) complex parameters included a factor VIII activity of 29 U/dL, a vWF protein of 17 U/dL, and a ristocetin cofactor of less than 10 U/dL. A ...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1988-01-01 00:00:00
abstract:OBJECTIVE:To investigate ras gene alteration in human gastric adenocarcinomas and its potential relationship to ras signal transduction mediators. DESIGN:Genomic DNA from 104 gastric tumors were analyzed by sequencing of polymerase chain reaction-amplified products for the presence of ras mutations. All the samples we...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/0003-9985(2002)126<1096:RGMAEO>2.0.CO;2
更新日期:2002-09-01 00:00:00
abstract:CONTEXT:Diagnostic use of immunohistochemistry has been extensively studied in prostate needle biopsy, but its use in routine practice and the quality assurance and associated cost have not been previously addressed. OBJECTIVE:To examine the routine use of immunohistochemistry in prostate biopsies in a tertiary academ...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.5858/arpa.2012-0145-OA
更新日期:2013-04-01 00:00:00
abstract::A certain proportion of soft-tissue sarcomas are difficult to classify accurately. In this case report, initial light microscope observations of a soft-tissue tumor suggested a diagnosis of a monophasic synovial sarcoma. However, critical evaluation of the histologic features, results of studies with special stains, a...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1981-04-01 00:00:00
abstract::A 43-year-old man with a history and symptomatology of hereditary spherocytosis underwent splenectomy and cholecystectomy for treatment of his underlying disease and of cholelithiasis. The removed gallbladder showed a serosal encapsulated nodule, supported by a short mesentery, measuring 11 x 6 x 4 mm, that histologic...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:
更新日期:1989-08-01 00:00:00
abstract::We report findings from an autopsy of a 45-year-old woman with the rare lysosomal storage disease mucolipidosis type III α/β. Her disease manifested most notably as multiple bone and cartilage problems with tracheal and bronchial malacia. Principal autopsy findings included gross abnormalities in bone and cartilage wi...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/2010-0236-CR.1
更新日期:2011-04-01 00:00:00
abstract::Previous immunohistochemical studies of cardiac myxomas are few in number, limited in scope and, in part, discrepant. We studied the immunoreactivity of five cardiac myxomas for factor VIII-related antigen, Ulex europaeus agglutinin I, smooth-muscle myosin, alpha 1-antitrypsin, and alpha 1-antichymotrypsin. Positive s...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1986-02-01 00:00:00
abstract::We report a case of primary cerebral lymphoma metastasizing to the kidney with exclusive involvement of the glomeruli. We discuss the possible explanations of this unusual phenomenon, and present some of the unusual clinical features of the case. Nephropathologists interpreting glomerular hypercellularity should alway...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1985-06-01 00:00:00
abstract::A case of tracheal neurilemoma that was removed by segmental tracheal resection was studied. Only seven other cases of benign neurogenic tracheal tumor (three neurofibromas and four neurilemomas) were found in the literature. Failure to consider this rare tracheal tumor as a cause of respiratory distress has frequentl...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1981-04-01 00:00:00
abstract::Assays for Chlamydia trachomatis antigen are being increasingly used in lieu of traditional cell culture methods for detection of the organism in patient specimens. While results from these assays are available considerably earlier than are those from culture, the assays have been less sensitive and specific than cult...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:
更新日期:1989-05-01 00:00:00
abstract:CONTEXT:Implementation of proficiency testing for gynecologic cytology was delayed 20 years because of challenges addressing the subjective nature of cytologic interpretation and replicating normal working conditions. Concern remains regarding test scoring, slide validation, test environment, and other issues. How thes...
journal_title:Archives of pathology & laboratory medicine
pub_type: 共识发展会议,杂志文章
doi:10.5858/arpa.2012-0094-OA
更新日期:2013-02-01 00:00:00
abstract::In cases of obscure gastrointestinal bleeding, when a source for blood loss is not apparent from examination of the colon and upper gastrointestinal tract, the small bowel usually becomes the focus of investigation. A tumor with interesting pathologic features was found in a patient who presented with recurrent episod...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/1543-2165(2004)128<214:JGSTAC>2.0.CO;2
更新日期:2004-02-01 00:00:00
abstract::A 3680-g term male neonate developed bilateral bronchopneumonia at 9 days of age. The labor, delivery, and immediate postnatal period had been unremarkable. Despite standard antibiotic therapy, the patient progressed to respiratory failure and died 4 days later. Adenovirus particles were found in oropharyngeal secreti...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:
更新日期:1992-01-01 00:00:00
abstract:CONTEXT:The pyrimidine nucleoside analog, cytosine arabinoside (Ara-C), is an effective therapeutic agent for acute leukemia. The phosphorylated triphosphate, cytosine arabinoside triphosphate, competes with deoxycytosine triphosphate as a substrate for incorporation into DNA. Once incorporated into DNA, it inhibits DN...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/1543-2165(2004)128<1364:CASDTF>2.0.CO;2
更新日期:2004-12-01 00:00:00
abstract::Carcinoembryonic antigen (CEA) is recommended as a serologic marker to monitor colorectal carcinoma recurrence. Elevations of CEA due to causes other than carcinoma exist and may lead to a misdiagnosis of recurrent carcinoma. We report a case of bowel sequestration with mucocele formation at the site of previous colo-...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/1543-2165(2003)127<1376:CAEDTB>2.0.CO;2
更新日期:2003-10-01 00:00:00
abstract::The dramatic rise and equally dramatic fall in the mortality from coronary heart disease in the 20th century is only partly explained. This article reviews the development of our ideas concerning possible pathways other than lipids that might play a role in the development of human atherosclerosis alone or in combinat...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:
更新日期:1988-10-01 00:00:00
abstract:CONTEXT:In immunohistochemistry, nonstandardized antigen retrieval protocols and fluids, poor-quality antibodies, and the presence of endogenous biotin frequently lead to incorrect results. Recently, advanced reagents including bifunctional SkipDewax pretreatment solution (BSPS), rabbit monoclonal (RM) antibodies, and ...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/1543-2165(2007)131[1047:TCOBSP]2.0.CO;2
更新日期:2007-07-01 00:00:00
abstract::A 9-year-old boy with metachromatic leukodystrophy (MLD) was found to have diffuse papillomatosis of the gallbladder that was virtually obliterating the lumen of the gallbladder. To our knowledge, two other examples of this lesion have been reported previously in MLD. ...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1985-01-01 00:00:00
abstract::Mucosa-associated lymphoid tissue (MALT) lymphomas are low-grade B-cell lymphomas that occur in a variety of extranodal sites but rarely as a primary hepatic lymphoma. We describe the histological findings, immunophenotype, and immunohistochemistry of one such lymphoma found incidentally in a 69-year-old woman. The ly...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/0003-9985(1999)123<0716:PHBCLO>2.0.CO;2
更新日期:1999-08-01 00:00:00
abstract:OBJECTIVE:To evaluate the reasons (indications) for and immediate intraoperative surgical results (outcomes) associated with pathology intraoperative consultation. DESIGN:In 1992 and 1993, surgeons collaborated with pathologists in 472 voluntarily participating institutions from the United States (462), Canada (7), Au...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,多中心研究
doi:
更新日期:1996-01-01 00:00:00
abstract::The utility of a laboratory test for differential diagnosis depends on the degree that test results for different disease states overlap. I developed a new overlap index that ranges from zero, for an ideal test with no overlap, to one if the median test result is the same for the two disease states. The index does not...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1984-01-01 00:00:00
abstract:CONTEXT:Epidermal growth factor receptor (EGFR) mutations have been identified as predictors of response to EGFR tyrosine kinase inhibitors in non-small cell lung cancer. OBJECTIVE:To investigate the relationship of EGFR mutation status to the histologic subtype of adenocarcinoma according to the new International Ass...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.5858/arpa.2013-0376-OA
更新日期:2014-10-01 00:00:00
abstract:CONTEXT:Recently we have observed distinctive acidophilic intranuclear inclusions in cases of usual intraductal hyperplasia of the breast. Similar inclusions were described almost 20 years ago in cases of mammary hyperplasia. These correlated ultrastructurally with so-called helioid inclusions. However, there since has...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/2010-0377-OA.1
更新日期:2011-06-01 00:00:00
abstract:CONTEXT:The College of American Pathologists periodically surveys laboratories to determine changes in cytopathology practices. We report the results of a 2011 gynecologic cytology survey. OBJECTIVE:To provide a cross-sectional survey of gynecologic cytology practices in 2010. DESIGN:In 2011, a survey was sent to 160...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.5858/arpa.2015-0004-CP
更新日期:2016-01-01 00:00:00
abstract:OBJECTIVE:To study the expression of thyroid transcription factor 1 (TTF-1) and cytokeratin 20 (CK20) in pulmonary small cell carcinomas, extrapulmonary small cell carcinomas, and Merkel cell carcinomas, and thereby determine whether these markers are helpful in distinguishing these 3 groups of small cell neuroendocrin...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:10.1043/0003-9985(2001)125<0228:IFTTFA>2.0.CO;2
更新日期:2001-02-01 00:00:00
abstract:CONTEXT:Digital viewing of histologic images is moving from presentations and publications to incorporation into the daily work of practicing pathologists. Many technologic limitations have been overcome recently, which should make widespread adoption more practical. The task now is for pathologists to become actively ...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:10.1043/2009-0579-RAR1.1
更新日期:2010-11-01 00:00:00
abstract:CONTEXT:- Fine-needle aspiration of thyroid nodules is a reliable diagnostic method to determine the nature of thyroid nodules. Nonetheless, indeterminate cytology diagnoses remain a diagnostic challenge. The development of multiplex molecular techniques and the identification of genetic alterations associated with dif...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章,评审
doi:10.5858/arpa.2016-0100-RA
更新日期:2016-12-01 00:00:00
abstract::We identified 100 patients (51 males and 49 females) as having the lupus anticoagulant. The following diagnoses were found in the patient population: human immunodeficiency virus positivity, 20%; systemic lupus erythematosus, 10%; prolonged preoperative activated partial thromboplastin time (APTT), 10%; procainamide h...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1993-06-01 00:00:00
abstract::Two autopsy cases of sympodial monsters, sympus dipus, were studied. They are of interest not only because they show the characteristic malformations of the limbs and the viscera below the diaphragm, but because one case also shows Potter's face and an atrial septal defect of the heart. In addition, histologic determi...
journal_title:Archives of pathology & laboratory medicine
pub_type: 杂志文章
doi:
更新日期:1981-10-01 00:00:00