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  1. Article ; Online: Hydrophilic polymer embolus in the bone marrow.

    Rangan, Aruna / Norgan, Andrew P

    Blood

    2023  Volume 142, Issue 10, Page(s) 939

    MeSH term(s) Bone Marrow/pathology ; Humans ; Polymers
    Chemical Substances Polymers
    Language English
    Publishing date 2023-09-05
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood.2023021763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The Brief Case:

    Wilcock, Jonathan / Pritt, Bobbi S / Norgan, Andrew P

    Journal of clinical microbiology

    2024  Volume 62, Issue 2, Page(s) e0030823

    MeSH term(s) Humans ; Animals ; Dirofilaria ; Florida ; Zoonoses ; Dirofilariasis/diagnosis
    Language English
    Publishing date 2024-02-14
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00308-23
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  3. Article ; Online: Spatial proteomics reveals phenotypic and functional differences in T cell and macrophage subsets during villitis of unknown etiology.

    Lothert, Petra K / Fedyshyn, Bohdana / Girard, Sylvie / Chakraborty, Rana / Norgan, Andrew P / Enninga, Elizabeth Ann L

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 914

    Abstract: Villitis of unknown etiology (VUE) is a prevalent inflammatory pathology of the placenta characterized by infiltration of maternal T cells and accumulation of fetal macrophages into chorionic villi. VUE is associated with a variety of adverse clinical ... ...

    Abstract Villitis of unknown etiology (VUE) is a prevalent inflammatory pathology of the placenta characterized by infiltration of maternal T cells and accumulation of fetal macrophages into chorionic villi. VUE is associated with a variety of adverse clinical outcomes, including fetal growth restriction and fetal demise. Evaluation of the phenotypic and functional differences between two immune cell types associated with this pathology, namely T cells and macrophages, was completed to gain a deeper understanding of the immuno-pathogenesis of VUE. GeoMx Digital Spatial Profiling was performed on placental tissue from 4 high grade VUE cases and 4 controls with no underlying pathology. Placental tissues were fluorescently labeled with CD3 and CD68 antibodies and oligo-conjugated antibodies against 48 protein targets. Overall, T cells in VUE exhibited upregulated markers of activation, memory, and antigen experience compared to controls and were altered based on placental location (villi vs. decidua). Additionally, villous macrophages in VUE upregulated costimulatory and major histocompatibility complex class I and II molecules compared to controls and macrophage subtypes in the decidua. Data herein provides new mechanistic insights into T cell and macrophage biology in VUE which contribute to this abnormal immune response to pregnancy.
    MeSH term(s) Pregnancy ; Female ; Humans ; Placenta ; Proteomics ; T-Lymphocytes ; Chorioamnionitis ; Macrophages
    Language English
    Publishing date 2024-01-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-51545-2
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  4. Article ; Online: Schistosomiasis of the Urinary Bladder.

    Gupta, Sounak / Norgan, Andrew P / Erickson, Lori A

    Mayo Clinic proceedings

    2021  Volume 98, Issue 7, Page(s) 1100–1101

    MeSH term(s) Humans ; Urinary Bladder ; Schistosomiasis/diagnosis ; Urinary Bladder Neoplasms
    Language English
    Publishing date 2021-10-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 124027-4
    ISSN 1942-5546 ; 0025-6196
    ISSN (online) 1942-5546
    ISSN 0025-6196
    DOI 10.1016/j.mayocp.2023.05.018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Seeing the random forest through the decision trees. Supporting learning health systems from histopathology with machine learning models: Challenges and opportunities.

    Gonzalez, Ricardo / Saha, Ashirbani / Campbell, Clinton J V / Nejat, Peyman / Lokker, Cynthia / Norgan, Andrew P

    Journal of pathology informatics

    2023  Volume 15, Page(s) 100347

    Abstract: This paper discusses some overlooked challenges faced when working with machine learning models for histopathology and presents a novel opportunity to support "Learning Health Systems" with them. Initially, the authors elaborate on these challenges after ...

    Abstract This paper discusses some overlooked challenges faced when working with machine learning models for histopathology and presents a novel opportunity to support "Learning Health Systems" with them. Initially, the authors elaborate on these challenges after separating them according to their mitigation strategies: those that need innovative approaches, time, or future technological capabilities and those that require a conceptual reappraisal from a critical perspective. Then, a novel opportunity to support "Learning Health Systems" by integrating hidden information extracted by ML models from digitalized histopathology slides with other healthcare big data is presented.
    Language English
    Publishing date 2023-11-04
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2579241-6
    ISSN 2153-3539 ; 2229-5089
    ISSN (online) 2153-3539
    ISSN 2229-5089
    DOI 10.1016/j.jpi.2023.100347
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  6. Article: Performance of externally validated machine learning models based on histopathology images for the diagnosis, classification, prognosis, or treatment outcome prediction in female breast cancer: A systematic review.

    Gonzalez, Ricardo / Nejat, Peyman / Saha, Ashirbani / Campbell, Clinton J V / Norgan, Andrew P / Lokker, Cynthia

    Journal of pathology informatics

    2023  Volume 15, Page(s) 100348

    Abstract: Numerous machine learning (ML) models have been developed for breast cancer using various types of data. Successful external validation (EV) of ML models is important evidence of their generalizability. The aim of this systematic review was to assess the ...

    Abstract Numerous machine learning (ML) models have been developed for breast cancer using various types of data. Successful external validation (EV) of ML models is important evidence of their generalizability. The aim of this systematic review was to assess the performance of externally validated ML models based on histopathology images for diagnosis, classification, prognosis, or treatment outcome prediction in female breast cancer. A systematic search of MEDLINE, EMBASE, CINAHL, IEEE, MICCAI, and SPIE conferences was performed for studies published between January 2010 and February 2022. The Prediction Model Risk of Bias Assessment Tool (PROBAST) was employed, and the results were narratively described. Of the 2011 non-duplicated citations, 8 journal articles and 2 conference proceedings met inclusion criteria. Three studies externally validated ML models for diagnosis, 4 for classification, 2 for prognosis, and 1 for both classification and prognosis. Most studies used Convolutional Neural Networks and one used logistic regression algorithms. For diagnostic/classification models, the most common performance metrics reported in the EV were accuracy and area under the curve, which were greater than 87% and 90%, respectively, using pathologists' annotations/diagnoses as ground truth. The hazard ratios in the EV of prognostic ML models were between 1.7 (95% CI, 1.2-2.6) and 1.8 (95% CI, 1.3-2.7) to predict distant disease-free survival; 1.91 (95% CI, 1.11-3.29) for recurrence, and between 0.09 (95% CI, 0.01-0.70) and 0.65 (95% CI, 0.43-0.98) for overall survival, using clinical data as ground truth. Despite EV being an important step before the clinical application of a ML model, it hasn't been performed routinely. The large variability in the training/validation datasets, methods, performance metrics, and reported information limited the comparison of the models and the analysis of their results. Increasing the availability of validation datasets and implementing standardized methods and reporting protocols may facilitate future analyses.
    Language English
    Publishing date 2023-11-05
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2579241-6
    ISSN 2153-3539 ; 2229-5089
    ISSN (online) 2153-3539
    ISSN 2229-5089
    DOI 10.1016/j.jpi.2023.100348
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Parasitic Infections of the Skin and Subcutaneous Tissues.

    Norgan, Andrew P / Pritt, Bobbi S

    Advances in anatomic pathology

    2018  Volume 25, Issue 2, Page(s) 106–123

    Abstract: A variety of arthropods, protozoa, and helminths infect the skin and subcutaneous tissues and may be identified by anatomic pathologists in standard cytology and histology preparations. The specific organisms seen vary greatly with the patient's exposure ...

    Abstract A variety of arthropods, protozoa, and helminths infect the skin and subcutaneous tissues and may be identified by anatomic pathologists in standard cytology and histology preparations. The specific organisms seen vary greatly with the patient's exposure history, including travel to or residence in endemic countries. Arthropods are the most commonly encountered parasites in the skin and subcutaneous tissues and include Sarcoptes scabei, Demodex species, Tunga penetrans, and myiasis-causing fly larvae. Protozoal parasites such as Leishmania may also be common in some settings. Helminths are less often seen, and include round worms (eg, Dirofilaria spp.), tapeworms (eg, Taenia solium, Spirometra spp.), and flukes (eg, Schistosoma spp.). This review covers the epidemiologic and histopathologic features of common parasitic infections of the skin and subcutaneous tissues.
    MeSH term(s) Animals ; Humans ; Skin Diseases, Parasitic/parasitology ; Skin Diseases, Parasitic/pathology ; Subcutaneous Tissue/parasitology ; Subcutaneous Tissue/pathology
    Language English
    Publishing date 2018-01-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1212493-x
    ISSN 1533-4031 ; 1072-4109
    ISSN (online) 1533-4031
    ISSN 1072-4109
    DOI 10.1097/PAP.0000000000000183
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  8. Article ; Online: Panviral metagenomic sequencing provides further evidence for human papillomavirus 42 association with digital papillary adenocarcinoma.

    Tekin, Burak / Enninga, Elizabeth Ann L / Norgan, Andrew P / Erickson, Lori A / Vanderbilt, Chad / Gupta, Sounak / Guo, Ruifeng

    Human pathology

    2023  Volume 143, Page(s) 77–80

    MeSH term(s) Humans ; Adenocarcinoma, Clear Cell ; Adenocarcinoma, Papillary/genetics ; DNA, Viral/genetics ; Human Papillomavirus Viruses ; Papillomaviridae/genetics ; Papillomavirus Infections ; Metagenomics
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2023-11-14
    Publishing country United States
    Document type Letter
    ZDB-ID 207657-3
    ISSN 1532-8392 ; 0046-8177
    ISSN (online) 1532-8392
    ISSN 0046-8177
    DOI 10.1016/j.humpath.2023.10.004
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  9. Article ; Online: Toto, we're not in Kansas anymore: First reported case of

    Dumais, Mitchell G / Wengenack, Nancy L / Norgan, Andrew P / Amin, Shreyasee / Sia, Irene G / Rhee, Peter C / Connelly, Brian J / Arment, Courtney A

    Journal of clinical tuberculosis and other mycobacterial diseases

    2023  Volume 31, Page(s) 100352

    Abstract: In this report, we describe a case of septic arthritis caused by the newly ... ...

    Abstract In this report, we describe a case of septic arthritis caused by the newly described
    Language English
    Publishing date 2023-03-03
    Publishing country England
    Document type Case Reports
    ISSN 2405-5794
    ISSN (online) 2405-5794
    DOI 10.1016/j.jctube.2023.100352
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  10. Article ; Online: 16S rRNA Gene PCR/Sequencing of Heart Valves for Diagnosis of Infective Endocarditis in Routine Clinical Practice.

    Hong, Hyo-Lim / Flurin, Laure / Greenwood-Quaintance, Kerryl E / Wolf, Matthew J / Pritt, Bobbi S / Norgan, Andrew P / Patel, Robin

    Journal of clinical microbiology

    2023  Volume 61, Issue 8, Page(s) e0034123

    Abstract: Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. Subjects whose heart ... ...

    Abstract Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. Subjects whose heart valves were sent to the clinical microbiology laboratory for 16S rRNA gene PCR/sequencing from August 2020 through February 2022 were studied. A PCR assay targeting V1 to V3 regions of the 16S rRNA gene was performed, followed by Sanger and/or next-generation sequencing (NGS) (using an Illumina MiSeq), or reported as negative, depending on an algorithm that included the PCR cycle threshold value. Fifty-four subjects, including 40 with IE, three with cured IE, and 11 with noninfective valvular disease, were studied. Thirty-one positive results, 11 from NGS and 20 from Sanger sequencing, were generated from analysis of 16S rRNA gene sequence(s). Positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 55% and 75%, respectively (
    MeSH term(s) Humans ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; DNA, Bacterial/analysis ; Endocarditis, Bacterial/diagnosis ; Endocarditis, Bacterial/microbiology ; Heart Valves/microbiology ; Endocarditis/diagnosis ; Endocarditis/microbiology ; Polymerase Chain Reaction/methods
    Chemical Substances RNA, Ribosomal, 16S ; DNA, Bacterial
    Language English
    Publishing date 2023-07-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00341-23
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