bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Use of TaqMan PCR Assay for Detection of Bordetella pertussis Infection From Clinical Specimens
Authors: Chan Edward L. , Antonishyn Nick , McDonald Ryan , Maksymiw Tara , Pieroni Peter , Nagle Evelyn , Horsman Greg B. 
Published: January 2021

Abstract
Objective.—The routine clinical laboratory detection of Bordetella pertussis is through culture, which can require 5 to 7 days for the bacteria to grow. Using a polymerase chain reaction (PCR) assay can shorten this detection time while increasing the sensitivity of detection with similar specificity. This study compared culture with TaqMan PCR for detection of B pertussis in clinical specimens and the turnaround time for each assay during the pertussis season.
Materials and Methods.—Nasopharyngeal swabs in Regan-Lowe transport media were collected from 1556 persons who had symptoms of whooping cough or who had had contact with infected persons; the swabs were submitted for B pertussis detection during the pertussis season. A single nasopharyngeal swab from each patient was submitted for both culture and TaqMan PCR detection. Upon receipt of the specimens, the swabs were inoculated onto Regan-Lowe agar for culture and incubated for up to 7 days. The same swab was processed for PCR detection using TaqMan PCR assay. A second nested PCR was used on positive specimens for resolution purposes. The TaqMan PCR assay was performed 3 to 5 days a week, whereas the culture was performed 6 days a week. All specimens were processed on the same day or earliest possible working day for TaqMan or culture, and specimens queued for resolution by nested PCR were batched.
Results.—There were a total of 275 PCR positives and 28 culture positives. After resolution with the second nested PCR, the sensitivity, specificity, positive predictive value, and negative predictive value were 100%, 97.4%, 87.6%, and 100% for TaqMan PCR and 11.6%, 100%, 100%, and 85.7% for culture. The average turnaround time for positive culture was 5.1 days, and the average turnaround time for PCR was 2.3 days.
Conclusion.—The TaqMan PCR assay has superior sensitivity and shorter turnaround time over culture because it can be finished within one working day. Furthermore, the same swab can be used for culture of the bacteria for antibiotic susceptibility testing. The early detection of pertussis using TaqMan PCR assay allows early intervention on the spread of the disease and the ability to culture the bacteria from the same swab, thereby eliminating the need for a second swab and allowing for detection of antibiotic resistance.
Utilizing Genomic DNA Purified From Clotted Blood Samples for Single Nucleotide Polymorphism Genotyping
Authors: Adkins Karissa K. , Strom Daniel A. , Jacobson Thomas E. , Seemann Cara R. , O'Brien Darin P. , Heath Ellen M. 
Published: January 2021

Abstract
Context.—Linking single nucleotide polymorphisms to disease etiology is expected to result in a substantial increase in the number of genetic tests available and performed at clinical laboratories. Whole blood serves as the most common DNA source for these tests. Because the number of blood samples rises with the number of genetic tests performed, alternative DNA sources will become important. One such alternative source is clotted blood, a by-product of serum extraction. Efficiently using an already procured blood sample would limit the overall number of samples processed by clinical laboratories.
Objective.—To determine if DNA purified from clotted blood can be effectively used for single nucleotide polymorphism genotyping.
Design.—DNA was purified from the clotted blood of 15 donors. Single nucleotide polymorphism genotyping for the methylenetetrahydrofolate reductase and factor V Leiden mutations was performed with each DNA sample by 2 independent methods.
Results.—High-quality DNA was obtained from each of the 15 individual clotted blood samples as demonstrated by UV spectrophotometric analysis, gel electrophoresis, and polymerase chain reaction amplification. The DNA was used successfully to obtain genotype data from both the methylenetetrahydrofolate reductase and factor V single nucleotide polymorphism assays for all samples tested.
Conclusions.—Clotted blood is a clinically abundant sample type that can be used as a source of high-quality DNA for single nucleotide polymorphism genotyping.
Molecular Testing in the Diagnosis and Management of Hepatitis C Virus Infection
Authors: Podzorski Raymond P. 
Published: January 2021

Abstract
Objectives.—To review hepatitis C virus (HCV), describe the types of molecular-based tests available for the diagnosis and management of HCV infection, and discuss the appropriate utilization of these tests.
Data Sources.—Current information is presented from the published literature, as well as new information where available.
Study Selection.—A major cause of posttransfusion and community-acquired non-A, non-B hepatitis worldwide is HCV. Approximately 4 million people in the United States are infected with HCV, resulting in 8000 to 10 000 deaths annually. Because HCV is not readily cultured, in vitro molecular-based tests have been developed for use in the diagnosis and treatment of HCV-infected patients. Molecular tests include qualitative and quantitative nucleic acid amplification tests, branched DNA tests, and HCV genotyping assays. Qualitative HCV nucleic acid amplification tests are used routinely in association with serologic tests to help make a diagnosis of infection with HCV. Quantitative HCV testing and genotyping methods have been found to be valuable tools in the treatment of infected patients. A patient's pretreatment HCV viral load and the rate of virus decline during therapy have been shown to correlate with the likelihood of long-term response to antiviral therapy. Information pertaining to the genotype of HCV infecting patients has been shown to be helpful in making recommendations regarding treatment. Certain genotypes of HCV are much more responsive to therapy, allowing a shorter course of treatment.
Conclusions.—Molecular tests are valuable tools for use in the diagnosis and treatment of patients infected with HCV.
Postmortem Diagnosis of “Occult” Klinefelter Syndrome in a Patient With Chronic Renal Disease and Liver Cirrhosis
Authors: Matsuoka Kentaro , Orikasa Hideki , Eyden Brian , Yamazaki Kazuto 
Published: January 2021

Abstract
This report describes a patient not suspected of having Klinefelter syndrome during life but diagnosed with it following postmortem examination using fluorescent in situ hybridization (FISH) for sex chromosomes and hormone serum analysis. A 49-year-old Japanese man had a history of nephrosis, heavy alcohol consumption, diabetes mellitus, and liver cirrhosis and had been undergoing dialysis for 10 years. He died of ruptured esophageal varices. Autopsy revealed hypogonadism, suggesting Klinefelter syndrome. This was confirmed by FISH, which showed a mosaic 46XY, 47XXY karyotype, and by serum analysis, which revealed high luteinizing hormone and follicle-stimulating hormone and low testosterone levels. Autopsy also revealed a nodular, bilateral, testicular Leydig cell hyperplasia. This report illustrates the value of postmortem laboratory investigations, particularly FISH for sex chromosomes and serum hormone analysis, for the demonstration of clinically uncertain or “occult” Klinefelter syndrome.
Altered Expression of G1 Regulatory Proteins in Human Soft Tissue Sarcomas
Authors: Yoo Jinyoung , Park Sonya Y. , Kang Seok Jin , Shim Sang In , Kim Byung Kee 
Published: January 2021

Abstract
Context.—Soft tissue sarcomas constitute a heterogeneous group of tumors for which tumorigenesis is not fully understood. Altered cell-cycle regulation may underlie the development and/or progression of human malignancies. However, data concerning the occurrence of cell-cycle aberrations in soft tissue sarcomas are very limited.
Objectives.—To detect the abnormal features of cell-cycle regulatory proteins in soft tissue sarcomas and to determine the potential role of these proteins in clinical behavior.
Design.—The p53 and Rb–cyclin D pathways were investigated by immunohistochemical studies of p53, mdm2, pRb, p16, cyclin D1, and cdk4 proteins, respectively.
Results.—Of the 67 sarcomas analyzed, nuclear accumulation of p53 was detected in 25 samples (37%), and overexpression of mdm2 was found in 16 samples (24%). Both p53 and mdm2 expression correlated with tumor grade. Abnormalities involving the Rb–cyclin D pathway were identified in all of the tumors by the altered expression of either pRb (72%) or p16 (94%). Fourteen (21%) and 64 (96%) cases demonstrated cyclin D1 or cdk4 expression, respectively. Overexpression of cyclin D1 showed an association with pRb and p53. There was no correlation between pRb, p16, cyclin D1, or cdk4 and tumor grade or relapse.
Conclusion.—Disturbance in the cell-cycle regulatory system involving the p53 pathway and the Rb–cyclin D pathway is relatively frequent in soft tissue sarcomas and may be a contributing factor in the tumorigenesis of these tumors. The alterations in the Rb–cyclin D pathway probably constitute an early event, whereas the abnormalities in the p53 pathway seem to be involved in tumor progression. It is noteworthy that cyclin D1 may play a key role in linking both pathways.
Detection of bcl-2/JH Translocation by Polymerase Chain Reaction
Authors: Hsi Eric D. , Tubbs Raymond R. , Lovell Mark A. , Braziel Rita M. , Gulley Margaret L. 
Published: January 2021

Abstract
Context.—The t(14;18)(q32;;t6q21) translocation, found in about 85% of follicular lymphomas, brings the bcl-2 gene on 18q21 under control of the immunoglobulin heavy-chain gene transcriptional regulatory elements on 14q32. Detection of this translocation in a clinical sample suspected of containing lymphoma can assist the pathologist in diagnosis and classification of lymphoma. Polymerase chain reaction is a technology that is frequently used to detect the t(14;18)(q32;q21) translocation (bcl-2/JH). This article reviews the utility of polymerase chain reaction testing for bcl-2/JH detection and summarizes the experience of participants in the Molecular Oncology Proficiency Survey of the College of American Pathologists from 1997 through 2000.
Objective.—To describe current practice and encourage improvement of bcl-2/JH testing in clinical laboratories.
Design.—Retrospective analysis of Molecular Oncology Proficiency Survey data.
Participants.—Laboratory participants in the College of American Pathology Molecular Oncology Proficiency Survey.
Results.—Twenty-four well-characterized specimens were sent to participants, of which 6 contained bcl-2/JH major breakpoint region translocations. Eight hundred nineteen major breakpoint region and 323 minor cluster region determinations were performed, with an overall correct response rate of 91% and 94%, respectively. No significant difference in correct response could be found for frozen versus paraffin-embedded tissues. Many laboratories did not know their assay sensitivity.
Conclusions.—Overall performance was good; however, there was great variability in the methods reported and lack of knowledge of the limits of detection was common. Continued participation in external quality control programs, such as the Molecular Oncology Survey; dissemination of information that impacts on test performance; and technical recommendations from the molecular diagnostics community are critical for improved testing for bcl-2/JH.
Blinded Review as a Method for Quality Improvement in Surgical Pathology
Authors: Renshaw Andrew A. , Pinnar Nat E. , Jiroutek Michael R. , Young Mary L. 
Published: January 2021

Abstract
Context.—Several studies have shown that blinded review, because it is less biased and may improve vigilance, is an excellent method for detecting errors and improving performance in gynecologic cytology. The value of blinded review in surgical pathology is not known.
Objective.—To determine the value of blinded review in surgical pathology.
Methods.—Five hundred ninety-two biopsy cases were reviewed without knowledge of the original diagnosis or history, and the results were compared with those of the original diagnosis.
Results.—Complete agreement was obtained in 567 (96%) of 592 cases. The technique of blinded review of biopsy material had a sensitivity of 98%, failing to identify a lesion in 7 cases; no cases of malignancy were missed. The specificity was 100%. Differences in diagnostic threshold were the most common source of disagreement. False-negative cases were identified by the technique and were clinically significant. Power studies show that the number of cases requiring review to identify significant errors are large, but potentially achievable by blinded review.
Conclusion.—Blinded review is a sensitive and effective method for identifying areas of disagreement, including false-negative cases, and for decreasing errors in surgical pathology biopsy material.
A Malignant Gastrointestinal Stromal Tumor With Osteoclast-like Giant Cells
Authors: Leung Kai Man , Wong Shun , Chow Tat Chong , Lee Kam Cheong 
Published: January 2021

Abstract
Gastrointestinal stromal tumors (GISTs) are a heterogeneous group of mesenchymal tumors with a wide spectrum of histologic features and consistent expression of c-Kit. We describe an 85-year-old woman who presented with left lower quadrant abdominal pain and was subsequently diagnosed as having a malignant GIST. The tumor was composed of short fascicles of spindle cells. In addition to the presence of tumor giant cells, the tumor also demonstrated many osteoclast-like giant cells, a feature that has not been previously described in the literature. These giant cells expressed histiocytic markers CD68 and α1-antitrypsin but not c-Kit, a marker for GISTs. Electron microscopy showed no features of smooth muscle differentiation in the giant cells. The possible origin of the osteoclast-like giant cells is discussed in the context of immunohistochemical and ultrastructural characteristics.
Hibernoma
Authors: Lele Subodh M. , Chundru Satish , Chaljub Gregory , Adegboyega Patrick , Haque Abida K. 
Published: January 2021

Abstract
Hibernomas are rare neoplasms composed of brown adipose tissue. The behavior of these neoplasms has been described as uniformly benign in humans. The only recurrence cited in the English literature involved a sarcoma with hibernoma-like features, which was reported in abstract form. We present 2 cases of hibernoma, one that continued to grow following partial excision and another at an unusual site (anterior abdominal wall). Both of these tumors overexpressed p53 protein by immunohistochemistry, which was a novel finding. A review of the literature highlights recent advances that may help confirm the diagnosis and explain the biology of these rare tumors.
The Role of the Autopsy in Medical Malpractice Cases, II
Authors: Bove Kevin E. , Iery Clare 
Published: January 2021

Abstract
Context.—We studied 99 appellate court records in cases of alleged medical malpractice and found no relationship between discrepant clinical and autopsy findings and outcome of litigation. Standard-of-care issues and not diagnostic accuracy were at the heart of every case.
Objective.—To characterize and discuss issues related to the autopsy and/or pathologist behavior that were raised in court records of medical malpractice litigation.
Design.—In 18 appellate court records, issues were raised about quality of autopsy performance and reporting or about death certification. The details of these controversies are succinctly reported here in a manner intended to be instructive to pathologists who perform autopsies in a hospital setting or on a private fee-for-service basis.
Conclusion.—Autopsy reports are intended to provide objective medical information in a coherent format to the patient's medical record, to the attending physician and other concerned staff physicians, to other health care professionals, and to the families of the deceased. Inevitably, occasions arise that require legal counsel to be added to this list of parties with a legitimate interest. Our findings emphasize that incomplete, incoherent, obfuscated, or delayed reporting of autopsy findings do not meet professional standards, are unethical if intentional, and may be counterproductive.
Immunohistochemical Confirmation of Pulmonary Papillary Adenocarcinoma Metastatic to Ovaries
Authors: Householder Jean Marie , Han Aaron , Edelson Mitchell I. , Eager J. Michael , Rosenblum Norman G. 
Published: January 2021

Abstract
Metastatic papillary adenocarcinomas of the ovary are rare compared to primary ovarian papillary serous carcinomas. We report a case of pulmonary papillary adenocarcinoma metastatic to the ovary and show how this tumor can be differentiated immunohistochemically from an ovarian primary. Paraffin blocks of the ovarian tumor were analyzed for carcinoembryonic antigen, CA 125, surfactant, E-cadherin, N-cadherin, and vimentin. These markers are useful in differentiating epithelial tumors of lung versus ovarian origin. The papillary tumor showed expression of carcinoembryonic antigen, surfactant, and E-cadherin, but was negative for CA 125, N-cadherin, and vimentin. These findings support a lung carcinoma metastatic to the ovary.
Malignant Melanoma of the Oral Mucosa in a 17-Year-Old Adolescent Girl
Authors: D'Silva Nisha J. , Kurago Zoya , Polverini Peter J. , Hanks Carl T. , Paulino Augusto F. 
Published: January 2021

Abstract
Mucosal melanomas of the oral cavity are rarely seen in the United States. The hard palate is the most common intraoral site. This unusual case occurred in the oral cavity of a 17-year-old Asian girl, who presented to her dentist with complaints of pain and swelling in the upper jaw. The lesion was distal and palatal to the maxillary left second molar, which was vital. Interestingly, the clinical presentation was a hyperplastic, tender lesion that bled when probed. Histopathologically, the biopsy demonstrated a sheet of spindle-shaped cells arranged in nests and fascicles. The nuclei were vesicular, oval to spindle-shaped, and some contained nucleoli that were distinguishable but not prominent. No melanin pigment was observed in the lesion. Tumor cells strongly expressed S100 protein, gp100 (HMB-45), and microphthalmia transcription factor, and variably expressed MART1, but not cytokeratins, CD34, or muscle-specific actin. The histopathologic features and immunohistochemical findings are consistent with a diagnosis of malignant melanoma.
Carcinosarcoma of the Pancreas
Authors: Darvishian Farbod , Sullivan James , Teichberg Saul , Basham Kevin 
Published: January 2021

Abstract
We report the case of a 74-year-old white man with a mass in the head of the pancreas, which was found incidentally on computerized tomographic scan during a workup for deep vein thrombosis. Endoscopy with pancreatic duct brushings yielded a diagnosis of adenocarcinoma. A pancreaticoduodenectomy followed, with complete resection of the tumor. Pathologic examination showed 2 distinct components. One component was a conventional infiltrating pancreatic ductal adenocarcinoma, and the other component was high-grade sarcoma with features of malignant fibrous histiocytoma. To our knowledge, this carcinosarcoma is the seventh reported case of a primary pancreatic neoplasm with mixed carcinomatous and sarcomatous elements.
College of American Pathologists Consensus Conference XXXVI: Diagnostic Issues in Thrombophilia
Authors: Olson John D. 
Published: January 2021

AbstractObjectives.—To review the state of the art relating to laboratory testing for thrombophilia, as reflected by the medical literature and the consensus opinion of recognized experts in the field, and to make recommendations regarding laboratory testing (whom to test, when to test, what tests to perform, rationale for testing, and other issues) in the assessment of thrombotic risk in individual patients and their family members.Data Sources.—Review of the medical literature (primarily from the last 10 years) and the experience and opinions of experts in the field were used as data sources.Data Extraction and Synthesis.—Participating authors evaluated the medical literature and prepared manuscripts with specific proposed recommendations. Drafts of all of the manuscripts were prepared and circulated to every participant in the College of American Pathologists Conference XXXVI: Diagnostic Issues in Thrombophilia prior to the conference. Each of the conclusions and associated recommendations was then presented for discussion. Recommendations were accepted if a consensus of 70% or more of the 27 experts attending the conference was reached. The results of the discussion were then used to revise the manuscripts and recommendations into final form.Conclusions.—Consensus was reached on 179 recommendations, all of which are presented in articles in this issue of the Archives. Detailed discussion of the rationale for each of these recommendations is found in the text of the respective articles, along with citations to justify the level of evidence for the recommendations. This is an evolving area of research, and it is certain that further clinical studies will change many of the recommendations, cause some to be deleted, and add others in the future.
Dysfibrinogenemia and Thrombosis
Authors: Hayes Timothy 
Published: January 2021

AbstractObjectives.—To review the state of the art relating to congenital dysfibrinogenemia as a potential risk factor for thrombosis, as reflected by the medical literature and the consensus opinion of recognized experts in the field, and to make recommendations for the use of laboratory assays for assessing this thrombotic risk in individual patients.Data Sources.—Review of the medical literature, primarily from the last 10 years.Data Extraction and Synthesis.—After an initial assessment of the literature, key points were identified. Experts were assigned to do an in-depth review of the literature and to prepare a summary of their findings and recommendations. A draft manuscript was prepared and circulated to every participant in the College of American Pathologists Conference on Diagnostic Issues in Thrombophilia. Each of the key points and associated recommendations were then presented for discussion at the conference. Recommendations were accepted if a consensus of experts attending the conference was reached. The results of the discussion were used to revise the manuscript into its final form.Conclusions.—Consensus was reached on 5 conclusions and 2 recommendations concerning the use of testing for dysfibrinogens in the assessment of thrombotic risk in individual patients. Detailed discussion of the rationale for each of these recommendations is found in the text of this article. Compared with the other, more common hereditary thrombophilias, dysfibrinogenemia encompasses a diverse group of defects with varied clinical expressions. Congenital dysfibrinogenemia is a relatively rare cause of thrombophilia. Therefore, routine testing for this disorder is not recommended as part of the laboratory evaluation of a thrombophilic patient. This is an evolving area of research, and further clinical studies may change these recommendations in the future.