bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of the Y Chromosome: An Age-Related or Clonal Phenomenon in Acute Myelogenous Leukemia/Myelodysplastic Syndrome?
Authors: Wong Anna K. , Fang Belle , Zhang Ling , Guo Xiuqing , Lee Stephen , Schreck Rhona 
Published: February 2021

Abstract
Context.—The clinical association between loss of the Y chromosome and acute myelogenous leukemia and myelodysplastic syndrome (AML/MDS) has been debated because both phenomena are related to aging. A prior publication suggests that loss of the Y chromosome in more than 75% of cells may indicate a clonal phenomenon that could be a marker for hematologic disease.
Objective.—To evaluate the relationship between loss of the Y chromosome and AML/MDS.
Design.—A retrospective review of cytogenetic reports of 2896 male patients ascertained from 1996 to 2007 was performed. Results were stratified based on the percentage of cells missing the Y chromosome and were correlated with patients' ages and bone marrow biopsy reports through logistic regression analysis with adjustment for age.
Results.—Loss of the Y chromosome was found in 142 patients. Of these, 16 patients demonstrated myeloid disease, with 2 cases of AML and 14 cases of MDS. An increased incidence (P &lt; .05) of AML/MDS was seen only in the group composed of 8 patients with complete loss of the Y chromosome in all karyotyped cells (1 case of AML and 7 cases of MDS).
Conclusion.—Loss of the Y chromosome appears to be primarily an age-related phenomenon. However, in individuals in which all cells on cytogenetic analysis showed loss of the Y chromosome, there was a statistically significant increase in AML/MDS, suggesting that the absence of any normal-dividing cells in a bone marrow analysis may be indicative of AML/MDS.
Practical Detection of t(14;18)(IgH/BCL2) in Follicular Lymphoma
Authors: Gu Keni , Chan Wing C. , Hawley Robert C. 
Published: February 2021

Abstract
The t(14;18)(q32;q21) translocation is the genetic hallmark of follicular lymphoma. Detection of this translocation can facilitate the diagnosis of follicular lymphoma and can be used to monitor response to therapy and level of residual disease. We herein review and compare practical techniques for detecting t(14;18)(q32;q21), including conventional cytogenetics, fluorescence in situ hybridization, Southern blot analysis, and polymerase chain reaction–based assay. Emphasis is placed on fluorescence in situ hybridization and polymerase chain reaction–based assay, given the applicability of these techniques to fixed, paraffin-embedded tissue.
Specimen Labeling Errors: A Q-Probes Analysis of 147 Clinical Laboratories
Authors: Wagar Elizabeth A. , Stankovic Ana K. , Raab Stephen , Nakhleh Raouf E. , Walsh Molly K. 
Published: February 2021

Abstract
Context.—Accurate specimen identification is critical for quality patient care. Improperly identified specimens can result in delayed diagnosis, additional laboratory testing, treatment of the wrong patient for the wrong disease, and severe transfusion reactions. Specimen identification errors have been reported to occur at rates of 0.1% to 5%.
Objective.—To determine the frequency of labeling errors in a multi-institutional survey.
Design.—Labeling errors were categorized as: (1) mislabeled, (2) unlabeled, (3) partially labeled, (4) incompletely labeled, and (5) illegible label. Blood specimens for routine or stat chemistry, hematology, and coagulation testing were included. Labeling error rates were calculated for each participant and tested for associations with institutional demographic and practice variable information.
Results.—More than 3.3 million specimen labels were reviewed by 147 laboratories. Labeling errors were identified at a rate of 0.92 per 1000 labels. Two variables were statistically associated with lower labeling error rates: (1) laboratories with current, ongoing quality monitors for specimen identification (P = .008) and (2) institutions with 24/7 phlebotomy services for inpatients (P = .02). Most institutions had written policies for specimen labeling at the bedside or in outpatient phlebotomy areas (96% and 98%, respectively). Allowance of relabeling of blood specimens by primary collecting personnel was reported by 42% of institutions.
Conclusions.—Laboratories actively engaged in ongoing specimen labeling quality monitors had fewer specimen labeling errors. Also, 24/7 phlebotomy services were associated with lower specimen error rates. Establishing quality metrics for specimen labeling and deploying 24/7 phlebotomy operations may contribute to improving the accuracy of specimen labeling for the clinical laboratory.
ProEx C Immunocytochemistry and High-Risk Human Papillomavirus DNA Testing in Papanicolaou Tests With Atypical Squamous Cell (ASC-US) Cytology: Correlation Study With Histologic Biopsy
Authors: Siddiqui Momin T. , Hornaman Kelly , Cohen Cynthia , Nassar Aziza 
Published: February 2021

Abstract
Context.—Papanicolaou tests with atypical squamous cells of undetermined significance (ASC-US) cytology and adjunct testing for high-risk human papillomaviruses (hr-HPV) are helpful in detecting high-grade disease. Detection of disease may be further improved with molecular markers known to be overexpressed in cervical carcinoma. ProEx C detects 2 such molecular markers, minichromosome maintenance protein 2 and topoisomerase II, which are associated with abnormal cell cycle regulation.
Objective.—To determine the utility of ProEx C as a marker for high-grade cervical intraepithelial neoplasia 2+ disease when compared with hr-HPV status in Papanicolaou tests with ASC-US cytology.
Design.—A SurePath slide was prepared on all ASC-US cases from the residual SurePath vial pellet and stained using the ProEx C reagent prediluted with water-bath antigen retrieval, using a Dako autostainer. Nuclear staining of cytologically atypical squamous cells was considered a positive result. Adjunct testing for hr-HPV used Digene Hybrid Capture 2. Follow-up biopsy results were available for review following the Papanicolaou test.
Results.—Two hundred patients with ASC-US diagnoses were part of this study. The sensitivities of ProEx C and hr-HPV testing in detecting high-grade cervical intraepithelial neoplasia 2+ disease were 98.04% and 82.35%, respectively, whereas the specificity for detecting high-grade disease was 74.50% and 73.15%, respectively.
Conclusions.—ProEx C staining is a more sensitive and specific biomarker for detecting cervical disease than adjunct testing for hr-HPV status in Papanicolaou tests with ASC-US.
Primary Malignant Melanoma of the Esophagus With Separate Foci of Melanoma In Situ and Atypical Melanocytic Hyperplasia in a Patient Positive for Human Immunodeficiency Virus: A Case Report and Review of the Literature
Authors: Fredricks Jennifer Rose Chapman , Bejarano Pablo A. 
Published: February 2021

Abstract
Primary malignant melanoma of the esophagus (PMME) is a rare neoplasm. The primary nature of esophageal melanoma has been questioned in the past because most reported cases have not been able to demonstrate local tumorigenesis or evolution of the malignancy from a preceding benign lesion or cell. In addition, the occurrence of metastatic melanoma to the esophagus is much more common than PMME. We report a case of PMME with separate foci of melanoma in situ and atypical melanocytic hyperplasia in a patient with human immunodeficiency virus infection. To our knowledge, this is the first reported case of PMME in a patient with a previous diagnosis of human immunodeficiency virus infection. In addition to adding data to the limited literature on this subject, we also provide histologic evidence that demonstrates the primary nature of some esophageal melanomas. This case also documents the occurrence of PMME in a patient positive for human immunodeficiency virus. We also provide a review of the relevant literature.
Hypersensitivity Pneumonitis: Clinical Perspectives
Authors: Madison J. Mark 
Published: February 2021

Abstract
Context.—The clinical course of hypersensitivity pneumonitis (HSP) is highly variable and its diagnosis clinically challenging.
Objective.—To provide a concise review of major clinical, radiographic, and laboratory findings that permits diagnosis of HSP from the standpoint of a clinician/pulmonologist.
Data Sources.—Review of major contemporary and historical literature in combination with the author's experience and viewpoints.
Conclusions.—The approach to the diagnosis of HSP is multidisciplinary. For patients being evaluated for unexplained dyspnea and cough and an unknown interstitial disease process, the initial evaluation should include detailed environmental and occupational histories with ancillary testing such as serology, chest imaging, inhalation challenges, and bronchoalveolar lavage, as indicated. In uncertain cases, lung biopsy is recommended.
Hypersensitivity Pneumonitis: Histopathology
Authors: Barrios Roberto J. 
Published: February 2021

Abstract
Context.—The classic histopathology of hypersensitivity pneumonitis (HSP) is well known but variations do occur and at times the diagnosis can be difficult. This is particularly true in the chronic stage of the disease.
Objective.—To review the wide variety of histopathologic changes that can be seen in HSP and to offer a practical approach to diagnosis, including the diagnosis of recently described variants of HSP such as the so-called hot tub lung.
Data Sources.—This review draws from the author's own experience and a concurrent search of national and international literature.
Conclusions.—The diagnosis of HSP can be made with confidence only in light of clinical, serologic, and radiographic data. A particular challenge for pathologists is the recognition of the disease in its chronic stage. In this stage, the identification of poorly formed granulomas in association with (1) a pattern of homogeneous linear fibrosis and (2) irregular fibrosis in a partially peribronchiolar distribution would facilitate the diagnosis.
Hypersensitivity Pneumonitis: An Immunopathology Review
Authors: Woda Bruce A. 
Published: February 2021

AbstractContext.—Hypersensitivity pneumonitis (HSP) is an immunologically mediated alveolar and interstitial lung disease caused by repeated inhalation of organic dusts and some occupational agents.Objective.—The pathogenesis of HSP is uncertain. A number of unexplained features of HSP remain, namely (1) why do so few exposed individuals develop clinical HSP, (2) what triggers an acute episode after prolonged periods of previous sensitization, and (3) what leads to disease progression. This article considers these issues and aims to discuss and clarify current concepts in pathogenesis.Data Sources.—Pertinent literature review in conjunction with the author's personal interpretive opinion.Conclusions.—Current data suggest that individuals with a TH1 dominant response are likely to develop clinical disease. There is also some evidence that genetic factors such as polymorphisms in the major histocompatibility complex, tumor necrosis factor α, and tissue inhibitor of metalloproteinase 3 are associated with the development of or resistance to the disease.
Application of Immunohistochemistry to Thyroid Neoplasms
Authors: Fischer Sandra , Asa Sylvia L. 
Published: February 2021

AbstractContext.—Thyroid lesions with nodular architecture and follicular pattern of growth often pose difficulties in accurate diagnosis during the assessment of cytologic and histologic specimens. The diagnosis of follicular neoplasm on cytology or of follicular tumor of uncertain malignant potential on histology is likely to cause confusion among clinicians and delay effective management of these lesions. Occasionally, thyroid tumors represent unusual or metastatic lesions and their accurate diagnosis requires immunohistochemical confirmation.Objective.—To review the literature on the applications of immunohistochemistry in the differential diagnosis of thyroid tumors.Data Sources.—Relevant articles indexed in PubMed (National Library of Medicine) between 1976 and 2006.Conclusions.—Our review supports the use of ancillary techniques involving a panel of antibodies suitable for immunohistochemistry and molecular analysis in the assessment of thyroid nodules. These tools can improve diagnostic accuracy when combined with standard morphologic criteria.
Application of Immunohistochemistry in the Diagnosis of Non-Hodgkin and Hodgkin Lymphoma
Authors: Higgins Russell A. , Blankenship Jennifer E. , Kinney Marsha C. 
Published: February 2021

AbstractContext.—Beginning with the immunologic classifications of Lukes and Collins and Kiel and culminating in the Revised European-American Lymphoma and World Health Organization classifications, the diagnosis of lymphoid tumors relies heavily on the determination of cell lineage, maturation, and function, based on antigen expression in addition to morphology and clinical features. Technologic advances in immunology, antibody production, genetic analysis, cloning, and the identification of new genes and proteins by microarray and proteomics have provided pathologists with many antibodies to use in routine diagnosis.Objective.—To provide guidance to the practicing pathologist in the appropriate selection of an antibody panel for the diagnosis of lymphoma based on morphology and relevant clinical data and to avoid pitfalls in the interpretation of immunohistochemical data. Attention is given to some of the newer antibodies, particularly against transcription factors, that are diagnostically and prognostically useful.Data Sources.—The information presented in this article is based on review of the literature using the OVID database (Ovid MEDLINE 1950 to present with daily update) and 20 years of experience in diagnostic hematopathology.Conclusions.—Immunophenotyping is required for the diagnosis and classification of lymphoid malignancies. Many paraffin-reactive antibodies are available to the pathologist but most are not specific. To avoid diagnostic pitfalls, interpretation of marker studies must be based on a panel and knowledge of a particular antigen's expression in normal, reactive, and neoplastic conditions.
The Impact of the Distribution of Human Papillomavirus Types and Associated High-Risk Lesions in a Colposcopy Population for Monitoring Vaccine Efficacy
Authors: Antonishyn Nick A. , Horsman Greg B. , Kelln Rod A. , Saggar Jasdeep , Severini Alberto 
Published: February 2021

Abstract
Context.—Impact studies of the new human papillomavirus (HPV) vaccines will be biased unless local baseline distribution studies are conducted. Vaccine cross protection for other important oncogenic HPV types and the emergence of potential genotype replacements require the knowledge of the prevaccine epidemiology of HPV.
Objective.—To determine the prevaccine distribution of HPV types in Saskatchewan, using a subpopulation of women referred to a colposcopy clinic.
Design.—One thousand three hundred fifty-five specimens obtained during colposcopic examination were typed for HPV using L1 or E1 gene polymerase chain reaction and direct sequencing. HPV-16 and HPV-31 infections were confirmed with real-time E6 polymerase chain reaction. Indeterminate samples were analyzed using Luminex technology. Correlations of the HPV type and histology were examined for statistical significance.
Results.—The most commonly identified genotype in patients with cervical intraepithelial neoplasia grade 2 or worse was HPV-16 (46.7%) followed by HPV-31 (14.7%) and then HPV-18 (3.9%). Fifteen of 330 specimens that were positive for HPV-16 or HPV-31 were further resolved to be mixed HPV-16/HPV-31 infections by real-time polymerase chain reaction. The risk of cervical intraepithelial neoplasia associated with HPV-18 infection (0.4–1.7) is substantially lower than with either HPV-16 (3.6–11.0) or HPV-31 (1.8–12.6).
Conclusions.—HPV-31 is contributing significantly to the proportion of women with cervical intraepithelial neoplasia in our population and shows a higher prevalence than HPV-18 in high-grade lesions. The clinical significance of HPV-31 may be underestimated and its continued significance will depend on the level of cross protection offered by the new vaccines.
Pseudosarcomas of Soft Tissue
Authors: Rosenberg Andrew E. 
Published: February 2021

Abstract
One of the most common and important pitfalls in soft tissue pathology are the so-called pseudosarcomas. These lesions are nonneoplastic; however, their rapid growth, hypercellularity, cytologic atypia, and mitotic activity makes them prone to be misinterpreted as sarcoma. The most common of these lesions are fibroblastic/myofibroblastic and matrix-forming proliferations, including nodular fasciitis, proliferative fasciitis and myositis, ischemic fasciitis, massive localized edema, myositis ossificans, and bizarre parosteal osteochondromatous proliferation and related entities. Most of these lesions rarely recur following simple excision; therefore, their accurate recognition helps prevent excessive therapy.
Placental Pathology, a Survival Guide
Authors: Roberts Drucilla J. 
Published: February 2021

Abstract
Placental pathology continues to be an underutilized, undertaught, and inadequately handled surgical subspecialty. The requests for placental pathology are soaring, due partly to demands from obstetricians and to the litigious environment in which they practice, and to improved obstetrical care leading to pregnancies in medically challenging situations. Evaluation of the placenta requires a good understanding of the questions and issues concerning both the fetus/infant and the mother. Information from placental pathology can be critical in early neonatal care and in reproductive planning for the family, and it can provide risk assessment for neurologic outcome of the infant. A comfortable interaction among the obstetric staff, mothers, and pathologists often obviates need for legal intervention in unexpected pregnancy outcomes. Some critical pathologic features that involve maternal and fetal management are illustrated herein. A template for gross examination and a few critical histopathologic diagnostic features with clincopathologic correlation are included.
Proteomic Comparison of Nasopharyngeal Cancer Cell Lines C666-1 and NP69 Identifies Down-Regulation of Annexin II and β2-Tubulin for Nasopharyngeal Carcinoma
Authors: Chan Charles M. L. , Wong S. C. Cesar , Lam Money Y. Y. , Hui Edwin P. , Chan John K. C. , Lo Elena S. F. , Cheuk W. , Wong Manson C. K. , Tsao S. W. , Chan Anthony T. C. 
Published: February 2021

AbstractContext.—Nasopharyngeal carcinoma (NPC), common in southern China and North Africa, has a complex etiology involving interplay between viral, environmental, and hereditary factors and is almost constantly associated with the Epstein-Barr virus. Since the prognosis of locally advanced and metastatic diseases is poor, increased understanding of the pathogenesis of NPC would be important for discovering novel markers for patients' management.Objectives.—To compare the proteomic expression profile between an Epstein-Barr virus–associated NPC cell line (C666-1) and a normal NP cell line (NP69). The proteins with differential expression were analyzed in 40 undifferentiated NPC paraffin-embedded specimens.Design.—Differentially expressed proteins discovered between the two cell lines were identified by mass spectrometry. After confirmation by immunocytochemical staining, their expression in patient samples was measured using 40 pairs of undifferentiated NPCs together with their adjacent normal epithelia.Results.—Proteomic findings indicated that adenosine triphosphate synthase α chain was up-regulated, whereas annexin II, annexin V, β2-tubulin, and profilin 1 were down-regulated. After confirming the results in agar-processed cell lines, annexin II and β2-tubulin expression were found to be lower in tumor cells than in adjacent normal epithelial cells in 100% and 90% of the patients' specimens, respectively. Finally, annexin II down-regulation was positively associated with lymph node metastasis, suggesting that it may be a prognostic factor in NPC.Conclusions.—The results suggest that annexin II and β2-tubulin down-regulation is important in NPC formation and may represent potential targets for further investigations.
Urine Culture Contamination: A College of American Pathologists Q-Probes Study of 127 Laboratories
Authors: Bekeris Leonas G. , Jones Bruce Allen , Walsh Molly K. , Wagar Elizabeth A. 
Published: February 2021

Abstract
Context.—While urine culture contamination may not be completely avoidable, some laboratories have lower contamination rates than others. A College of American Pathologists (CAP) 1998 Q-Probes study showed that many interventions commonly assumed to reduce contamination were not demonstrably effective. This article revisits the issue.
Objective.—To examine the frequency of urine culture contamination, review current laboratory practices in the collection of urine culture specimens, and determine practice characteristics that may be associated with the contamination rate.
Design.—Laboratories participating in a CAP Q-Probes study were required to prospectively collect data on 120 consecutive urine culture specimens and provide information on the patient's demographics (age and sex), the location where the specimen was collected, how the specimen was handled, the number of isolates in quantities greater than or equal to 10 000 colony-forming units (CFU)/mL, and whether the laboratory considered the specimen to be contaminated. Specific inclusion and exclusion criteria were provided to the participants. Each laboratory completed a supplemental questionnaire that probed for specific laboratory urine culture collection practices.
Results.—One hundred twenty-seven laboratories participated in the study. Results from a total of 14 739 urine specimens were received. For the purpose of this study, a urine specimen was determined to be contaminated if the culture yielded more than 2 isolates in quantities greater than or equal to 10 000 CFU/mL. Using these criteria the median institution had a contamination rate of 15.0%. Laboratories in the 10th percentile (low performance) had an average contamination rate of 41.7%, while laboratories in the 90th percentile had an average rate of 0.8%. The collection site had no influence on the contamination rate, but postcollection processing, especially refrigeration of the specimen, had a substantial effect. Providing instruction to patients produced a statistically significant lowering of contamination rates for specimens from male patients (P = .006) but not for female patients, except when written instructions were provided in the emergency room, in which case specimen contamination rates for both male and female patients dropped (P = .01).
Conclusions.—The median contamination rates remain at a level comparable to the results seen in a previous Q-Probes study, and some laboratories have very high contamination rates. Specimen refrigeration is associated with lower overall urine culture specimen contamination rate. Providing patient instruction is also associated with lower contamination rates under specific circumstances.