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  1. Article ; Online: Analysis of Sampling Bias in Large Health Care Claims Databases.

    Dahlen, Alex / Charu, Vivek

    JAMA network open

    2023  Volume 6, Issue 1, Page(s) e2249804

    MeSH term(s) Humans ; Selection Bias ; Delivery of Health Care ; Data Management ; Health Facilities
    Language English
    Publishing date 2023-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2574-3805
    ISSN (online) 2574-3805
    DOI 10.1001/jamanetworkopen.2022.49804
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Expert Discussion on Challenges in C3G Diagnosis: A Podcast Article on Best Practices in Kidney Biopsies.

    Lafayette, Richard A / Charu, Vivek

    Advances in therapy

    2023  Volume 40, Issue 12, Page(s) 5557–5566

    Abstract: Complement 3 glomerulopathy (C3G) is an ultra-rare, progressive kidney disease resulting from dysregulation of the alternative complement pathway. Clinical presentation of C3G is heterogeneous and definitive diagnosis relies on kidney biopsy and ... ...

    Abstract Complement 3 glomerulopathy (C3G) is an ultra-rare, progressive kidney disease resulting from dysregulation of the alternative complement pathway. Clinical presentation of C3G is heterogeneous and definitive diagnosis relies on kidney biopsy and immunofluorescence staining. The term C3G encompasses two subgroups, dense deposit disease and C3 glomerulonephritis, distinguished via electron microscopy. In this podcast article, the authors discuss the challenges associated with C3G diagnosis and the central role of kidney biopsy. Using an illustrative case study, key histological observations are described, and best practices are discussed from the perspectives of a nephrologist and a nephropathologist. Podcast Audio (MP4 141866 KB).
    MeSH term(s) Humans ; Complement C3/metabolism ; Glomerulonephritis, Membranoproliferative/diagnosis ; Glomerulonephritis, Membranoproliferative/pathology ; Complement Pathway, Alternative ; Kidney ; Biopsy
    Chemical Substances Complement C3
    Language English
    Publishing date 2023-09-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 632651-1
    ISSN 1865-8652 ; 0741-238X
    ISSN (online) 1865-8652
    ISSN 0741-238X
    DOI 10.1007/s12325-023-02654-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Challenges in IgA Nephropathy Management: An Era of Complement Inhibition.

    Tesař, Vladimir / Radhakrishnan, Jai / Charu, Vivek / Barratt, Jonathan

    Kidney international reports

    2023  Volume 8, Issue 9, Page(s) 1730–1740

    Abstract: IgA nephropathy (IgAN) is the most common glomerular disease worldwide, with an estimated annual incidence of 25 per million adults. Despite optimized supportive care, some patients fail to achieve disease control and suffer progressive deterioration of ... ...

    Abstract IgA nephropathy (IgAN) is the most common glomerular disease worldwide, with an estimated annual incidence of 25 per million adults. Despite optimized supportive care, some patients fail to achieve disease control and suffer progressive deterioration of kidney function. In this subpopulation of patients, the Kidney Disease: Improving Global Outcomes 2021 guidelines recommend consideration of corticosteroids; however, their use is associated with significant side effects. Ongoing clinical trials are expected to identify corticosteroid-sparing therapies to help improve treatment and prognosis for patients with IgAN. It has been well-documented that the complement system plays a significant role in IgAN pathogenesis, and several complement inhibitors are now entering late-stage clinical development. This review evaluates what we know about the role of complement in the pathophysiology of IgAN and considers how the availability of targeted complement inhibitors may impact future clinical practice. Key knowledge gaps are evaluated, and research opportunities are recommended to help guide clinical decision-making and optimize patient outcomes. Such gaps include evaluating the relative contribution of the alternative and lectin pathways to disease pathogenesis, and the importance of determining the dominant pathway driving IgAN progression. Continued research into the staining of complement proteins in kidney biopsies and identifying targeted biomarkers to assess disease progression and treatment responses will also be needed to support the implementation of newer therapies in clinical practice. Considering the future horizons for enhancing the care of patients with IgAN, tackling the outstanding challenges now will help prepare for the best possible future outcomes.
    Language English
    Publishing date 2023-06-21
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2468-0249
    ISSN (online) 2468-0249
    DOI 10.1016/j.ekir.2023.06.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Liver Pathology After Hematopoietic Stem Cell Transplantation.

    Phansalkar, Ragini / Kambham, Neeraja / Charu, Vivek

    Surgical pathology clinics

    2023  Volume 16, Issue 3, Page(s) 519–532

    Abstract: Hematopoietic stem cell transplantation is used to treat a variety of hematologic malignancies and autoimmune conditions. The immunosuppressive medications as well as other therapies used both before and after transplantation leave patients susceptible ... ...

    Abstract Hematopoietic stem cell transplantation is used to treat a variety of hematologic malignancies and autoimmune conditions. The immunosuppressive medications as well as other therapies used both before and after transplantation leave patients susceptible to a wide spectrum of complications, including liver injury. Causes for liver damage associated with stem cell transplantation include sinusoidal obstruction syndrome, graft-versus-host disease, iron overload, and opportunistic infection. Here, the authors review the clinical and pathological findings of these etiologies of liver injury and provide a framework for diagnosis.
    MeSH term(s) Humans ; Hematopoietic Stem Cell Transplantation/adverse effects ; Liver Diseases/etiology ; Hepatic Veno-Occlusive Disease/diagnosis ; Hepatic Veno-Occlusive Disease/etiology ; Hepatic Veno-Occlusive Disease/drug therapy ; Iron Overload/complications
    Language English
    Publishing date 2023-06-01
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1875-9157
    ISSN (online) 1875-9157
    DOI 10.1016/j.path.2023.04.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Antineutrophil Cytoplasmic Antibody-Associated Vasculitis with Active Kidney Involvement in the United States: 2016-2020.

    Tao, Jianling / Liu, Sai / Montez-Rath, Maria / Charu, Vivek / Chertow, Glenn M

    Glomerular diseases

    2024  Volume 4, Issue 1, Page(s) 33–42

    Abstract: Introduction: Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and its subtypes, granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic GPA (EGPA), frequently present with acute kidney injury and ... ...

    Abstract Introduction: Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and its subtypes, granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic GPA (EGPA), frequently present with acute kidney injury and can often lead to kidney failure, even with successful induction therapy. Few contemporary, nationally representative studies have described hospital complications of AAV.
    Methods: Using data from the 2016-2020 National Inpatient Sample, a nationally representative database, we identified hospitalizations from adults with a new diagnosis of AAV (subtype or unspecified) and an inpatient kidney biopsy during the index hospitalization. We described baseline characteristics, associated inpatient procedures and complications, and compared lengths of stay and costs by geographic region, hospital characteristics, and AAV subtype.
    Results: We identified an average of 1,329 cases of hospitalized AAV with a concurrent kidney biopsy per year over the 5-year period. More than 50% were not designated as having a specific subtype, likely owing to delays in documentation of histopathology. Kidney involvement was severe as the majority of patients developed acute kidney injury, and the proportion of patients who required inpatient dialysis was approximately 24%. Approximately 20% of patients developed hypoxia. Inpatient plasmapheresis was delivered to 20.4% and 20.6% of patients with GPA and MPA, respectively. There were no clinically meaningful or statistically significant differences in adjusted length of stay or inpatient costs among AAV subtypes. Admission in the Midwest region was associated with shorter hospital stays and lower costs than that in the Northeast, South, or West regions of the USA (adjusted
    Conclusion: AAV with acute kidney involvement remains a challenging, high-risk condition. Maintaining a high index of suspicion and a low threshold for kidney biopsy should help ameliorate short- and long-term complications.
    Language English
    Publishing date 2024-01-10
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2673-3633
    ISSN (online) 2673-3633
    DOI 10.1159/000536168
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Benchmarking clinical risk prediction algorithms with ensemble machine learning for the non-invasive diagnosis of liver fibrosis in NAFLD.

    Charu, Vivek / Liang, Jane W / Mannalithara, Ajitha / Kwong, Allison / Tian, Lu / Kim, W Ray

    Hepatology (Baltimore, Md.)

    2024  

    Abstract: Ensemble machine learning methods, like the superlearner, combine multiple models into a single one to enhance predictive accuracy. Here we explore the potential of the superlearner as a benchmarking tool for clinical risk prediction, illustrating the ... ...

    Abstract Ensemble machine learning methods, like the superlearner, combine multiple models into a single one to enhance predictive accuracy. Here we explore the potential of the superlearner as a benchmarking tool for clinical risk prediction, illustrating the approach in identifying significant liver fibrosis among patients with non-alcoholic fatty liver disease (NAFLD). We used 23 demographic/clinical variables to train superlearner(s) on data from the NASH-CRN observational study (n=648) and validated models with data from the FLINT trial (n=270) and NHANES participants with NAFLD (n=1244). Comparing the superlearner's performance to existing models (FIB-4, NFS, Forns, APRI, BARD, and SAFE), it exhibited strong discriminative ability in the FLINT and NHANES validation sets, with AUCs of 0.79 (95% CI: 0.73-0.84) and 0.74 (95% CI: 0.68-0.79) respectively. Notably, the SAFE score performed similarly to the superlearner, both of which outperformed FIB-4, APRI, Forns, and BARD scores in the validation datasets. Surprisingly, the superlearner derived from 12 base models matched the performance of one with 90 base models. Overall, the superlearner, being the "best-in-class" ML predictor, excelled in detecting fibrotic NASH, and this approach can be used to benchmark the performance of conventional clinical risk prediction models.
    Language English
    Publishing date 2024-04-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 604603-4
    ISSN 1527-3350 ; 0270-9139
    ISSN (online) 1527-3350
    ISSN 0270-9139
    DOI 10.1097/HEP.0000000000000908
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: The Utilization of Packed Red Blood Cell Transfusion and Angiography in Pediatric Inpatients after Kidney Biopsy in the United States.

    Afolabi, Halimat / O'Shaughnessy, Michelle M / Charu, Vivek

    Kidney360

    2022  Volume 3, Issue 8, Page(s) 1423–1426

    Abstract: This article contains the largest analysis of pRBC transfusion and renal angiogram in inpatient pediatric patients.We provide accurate estimates of rates of pRBC transfusion and renal angiography after kidney biopsy in inpatient pediatric patients. ...

    Abstract This article contains the largest analysis of pRBC transfusion and renal angiogram in inpatient pediatric patients.We provide accurate estimates of rates of pRBC transfusion and renal angiography after kidney biopsy in inpatient pediatric patients.
    MeSH term(s) Angiography ; Biopsy/adverse effects ; Child ; Erythrocyte Transfusion ; Health Services Research ; Humans ; Inpatients ; Kidney/diagnostic imaging ; Kidney/pathology ; United States
    Language English
    Publishing date 2022-05-18
    Publishing country United States
    Document type Journal Article
    ISSN 2641-7650
    ISSN (online) 2641-7650
    DOI 10.34067/KID.0000022022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: NELL1-Positive HIV-Associated Lupus-Like Membranous Nephropathy with Spontaneous Remission.

    Dinesh, Kumar P / Charu, Vivek / Troxell, Megan L / Andeen, Nicole K

    Glomerular diseases

    2022  Volume 2, Issue 4, Page(s) 184–188

    Abstract: Introduction: Kidney biopsy findings in patients with human immunodeficiency virus (HIV) are diverse, and optimal therapy for the various immune complex diseases in the setting of HIV is unknown.: Case presentation: A man with well-controlled HIV ... ...

    Abstract Introduction: Kidney biopsy findings in patients with human immunodeficiency virus (HIV) are diverse, and optimal therapy for the various immune complex diseases in the setting of HIV is unknown.
    Case presentation: A man with well-controlled HIV developed nephrotic range proteinuria, and kidney biopsy revealed lupus-like glomerulonephritis with a predominantly membranous pattern of injury. He opted for conservative therapy and experienced spontaneous and sustained remission. Subsequent testing revealed neural epidermal growth factor-like 1 (NELL1)-positive glomerular immune deposits. NELL1-positive glomerular immune deposits were identified in a total of 2 of 5 tested HIV-associated membranous nephropathy (MN), which were morphologically dissimilar and one of which weakly co-expressed phospholipase A2 receptor (PLA2R).
    Discussion: This case suggests potentially different outcomes in patients with immune complex diseases in the setting of HIV based on disease etiology and histopathology. HIV-associated MN is occasionally NELL1-positive.
    Language English
    Publishing date 2022-06-29
    Publishing country Switzerland
    Document type Case Reports
    ISSN 2673-3633
    ISSN (online) 2673-3633
    DOI 10.1159/000525541
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: EXT1 and NCAM1-associated membranous lupus nephritis in a cohort of patients undergoing repeat kidney biopsies.

    Miller, Paul P / Caza, Tiffany / Larsen, Christopher P / Charu, Vivek

    Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association

    2022  Volume 38, Issue 2, Page(s) 396–404

    Abstract: Background: Exostosin 1/2 (EXT1/2) and neural cell adhesion molecule 1 (NCAM1) associated membranous lupus nephritis (MLN) may represent distinct disease phenotypes with prognostic significance.: Methods: We searched our archives for patients with ... ...

    Abstract Background: Exostosin 1/2 (EXT1/2) and neural cell adhesion molecule 1 (NCAM1) associated membranous lupus nephritis (MLN) may represent distinct disease phenotypes with prognostic significance.
    Methods: We searched our archives for patients with systemic lupus erythematous (SLE) and at least two kidney biopsies demonstrating MLN. Each biopsy was stained for EXT1 and NCAM1 and scored as positive or negative. Histopathologic and clinical data were reviewed.
    Results: We identified 31 patients with a clinical diagnosis of SLE and at least two kidney biopsies with MLN. A total of 28 patients (90%) showed concordant staining for EXT1 and NCAM1 in both biopsies; 8 patients (26%) were EXT1 positive and NCAM1 negative, 18 patients (58%) were EXT1 negative and NCAM1 negative and 2 patients (7%) were EXT1 negative and NCAM1 positive. A total of three patients (10%) had discordant EXT1 staining between their first and last biopsies; two patients (7%) were EXT1 positive in their first biopsy and EXT1 negative in the last biopsy and one patient (3%) was EXT1 negative in his first biopsy and EXT1 positive in the last biopsy. Compared with the EXT1-negative cohort at the time of the first biopsy, the EXT1-positive cohort had a higher average estimated glomerular filtration rate (eGFR; 141 versus 108 mL/min/1.73 m2; P = 0.04), lower average percent global glomerulosclerosis (0.5 versus 12%; P = 0.05), lower average interstitial fibrosis and tubular atrophy (2.5 versus 11.7%; P = 0.06) and lower average total National Institutes of Health (NH) chronicity scores (0.75 versus 2.33; P = 0.05). On long-term follow-up, the rate of change in eGFR did not significantly differ between the two groups (P = 0.24). One EXT1-positive patient (12.5%) developed stage 4 chronic kidney disease (CKD) or end-stage kidney disease (ESKD) compared with four patients (20%) in the EXT-negative group and two of the three EXT1-discordant patients (P = 0.38).
    Conclusions: We performed the largest retrospective repeat-biopsy study to evaluate EXT1 and NCAM1 autoantigens in MLN. Our data demonstrate that EXT1 positivity is associated with better kidney function at the time of diagnosis and raises the possibility that EXT1 status may change throughout the disease course of MLN.
    MeSH term(s) Humans ; Lupus Nephritis/pathology ; Retrospective Studies ; Glomerulonephritis, Membranous/pathology ; Lupus Erythematosus, Systemic/pathology ; Biopsy ; Kidney/pathology ; Neural Cell Adhesion Molecules ; CD56 Antigen
    Chemical Substances Neural Cell Adhesion Molecules ; NCAM1 protein, human ; CD56 Antigen
    Language English
    Publishing date 2022-01-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 90594-x
    ISSN 1460-2385 ; 0931-0509
    ISSN (online) 1460-2385
    ISSN 0931-0509
    DOI 10.1093/ndt/gfac058
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Benchmarking clinical risk prediction algorithms with ensemble machine learning: An illustration of the superlearner algorithm for the non-invasive diagnosis of liver fibrosis in non-alcoholic fatty liver disease.

    Charu, Vivek / Liang, Jane W / Mannalithara, Ajitha / Kwong, Allison / Tian, Lu / Kim, W Ray

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Background and aims: Ensemble machine learning (ML) methods can combine many individual models into a single 'super' model using an optimal weighted combination. Here we demonstrate how an underutilized ensemble model, the superlearner, can be used as a ...

    Abstract Background and aims: Ensemble machine learning (ML) methods can combine many individual models into a single 'super' model using an optimal weighted combination. Here we demonstrate how an underutilized ensemble model, the superlearner, can be used as a benchmark for model performance in clinical risk prediction. We illustrate this by implementing a superlearner to predict liver fibrosis in patients with non-alcoholic fatty liver disease (NAFLD).
    Methods: We trained a superlearner based on 23 demographic and clinical variables, with the goal of predicting stage 2 or higher liver fibrosis. The superlearner was trained on data from the Non-alcoholic steatohepatitis - clinical research network observational study (NASH-CRN, n=648), and validated using data from participants in a randomized trial for NASH ('FLINT' trial, n=270) and data from examinees with NAFLD who participated in the National Health and Nutrition Examination Survey (NHANES, n=1244). We compared the performance of the superlearner with existing models, including FIB-4, NFS, Forns, APRI, BARD and SAFE.
    Results: In the FLINT and NHANES validation sets, the superlearner (derived from 12 base models) discriminates patients with significant fibrosis from those without well, with AUCs of 0.79 (95% CI: 0.73-0.84) and 0.74 (95% CI: 0.68-0.79). Among the existing scores considered, the SAFE score performed similarly to the superlearner, and the superlearner and SAFE scores outperformed FIB-4, APRI, Forns, and BARD scores in the validation datasets. A superlearner model derived from 12 base models performed as well as one derived from 90 base models.
    Conclusions: The superlearner, thought of as the "best-in-class" ML prediction, performed better than most existing models commonly used in practice in detecting fibrotic NASH. The superlearner can be used to benchmark the performance of conventional clinical risk prediction models.
    Language English
    Publishing date 2023-08-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.02.23293569
    Database MEDical Literature Analysis and Retrieval System OnLINE

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