
Joseph Abdelmalek, M.D.
· HS Clinical Professor, UC San DiegoVerifiedUniversity of California, San Diego · Nephrology
Active 2012–2025
Research topics
- Computer Science
- Physics
- Nanotechnology
- Materials science
- Optics
- Optoelectronics
- Computer hardware
- Internal medicine
- Cardiology
- Medicine
Selected publications
Paraneoplastic IgAN Associated with Sezary Syndrome
Journal of the American Society of Nephrology · 2025-10-01
articleSenior authorIntroduction: Prior case reports have described acute kidney injury associated with cutaneous T cell lymphoma due to renal infiltration and paraneoplastic glomerular diseases. Sezary syndrome is the rarer leukemic variant of cutaneous T cell lymphoma. We report a case of acute kidney injury due to paraneoplastic IgA nephropathy in a patient with newly diagnosed Sezary syndrome. Case Description: A 75-year-old man with 6 months of pruritic, widespread rash and lab abnormalities was admitted for expedited workup which showed Sezary syndrome. He also had a non-oliguric acute kidney injury. Despite appropriate treatment for obstruction, volume overload, and possible tumor lysis, his creatinine uptrended. Urinalysis showed 3+ blood, 3+ protein, and casts with a total protein to creatinine ratio of 10.74 g/g. ANA, ANCA, rheumatoid factor, hepatitis B, hepatitis C, and cryoglobulin were all negative. C3 and C4 were normal at 108 and 23 mg/dL respectively. A kidney biopsy on day 20 showed acute tubular injury and membranoproliferative glomerulonephritis most consistent with IgA nephropathy. High dose steroids were started on day 49 and creatinine peaked on day 51 at 5.94 mg/dL. Renal function gradually improved and the patient never required renal replacement therapy. Discussion: This case describes paraneoplastic IgA nephropathy related to Sezary syndrome and shows improvement in renal function after starting high dose steroids. More broadly, paraneoplastic glomerular diseases are a critical diagnosis in patients with malignancy and acute kidney injury.Creatinine trend, admission = day 1A. Light microscopy: membranoproliferative glomerulonephritis with neutrophilic exudates and IgA/C3 predominance. B. Electron microscopy: mesangial and subendothelial deposits.
Multifunction fluorescence open source in vivo/in vitro imaging system (openIVIS)
PLoS ONE · 2024 · 3 citations
- Computer Science
- Computer Science
- Materials science
The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study, we designed and built a multifunction fluorescent open source in vivo/in vitro imaging system (openIVIS) system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the potential applications of our system, we tested its performance against a diverse set of experiments including laboratory assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of ten days. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
Estimates of eskd risk and timely kidney replacement therapy education
BMC Nephrology · 2024-09-10
articleOpen accessAbstract Background Kidney replacement therapy (KRT) needs preparation and its timing is difficult to predict. Nephrologists’ predictions of kidney failure risk tend to be more pessimistic than the Kidney Failure Risk Equation (KFRE) predictions. We aimed to explore how physicians’ risk estimate related to referral to KRT education, vs. the objective calculated KFRE. Methods Prospective observational study of data collected in chronic kidney disease (CKD) clinics of the Veterans Affairs Medical Center San Diego and the University of California, San Diego. The study included 257 participants who were aged 18 years or older, English speaking, prevalent CKD clinic patients, with estimated glomerular filtration rate (eGFR) < 60 mL/min per 1.73 m 2 (MDRD equation). The exposure consisted of end stage kidney disease (ESKD) risk predictions. Nephrologists’ kidney failure risk estimations were assessed: “On a scale of 0–100%, without using any estimating equations, give your best estimate of the risk that this patient will need dialysis or a kidney transplant in 2 years.” KFRE was calculated using age, sex, eGFR, serum bicarbonate, albumin, calcium, phosphorus, urine albumin/creatinine ratio. The outcomes were the pattern of referral to KRT education (within 90 days of initial visit) and kidney failure evaluated by chart review. The population was divided into groups either by nephrologists’ predictions or by KFRE. Referral to KRT education was examined by group and sensitivity and specificity were calculated based on whether participants reached kidney failure at 2 years. Results A fifth were referred for education by 90 days of enrollment. Low risk patients by both estimates had low referral rates. In those with nephrologists’ predictions ≥ 15% ( n = 137), sensitivity was 71% and specificity 76%. In those with KFRE ≥ 15% ( n = 55), sensitivity was 85% and specificity 41%. Conclusions Although nephrologists tend to overestimate patients’ kidney failure risk, they do not appear to act on this overestimation, as the rates of KRT education referrals are lower than expected when a nephrologist identifies a patient as high risk. Clinical Trial Number Not applicable
Multifunction Fluorescence Open-Source <i>In Vivo/In Vitro</i> Imaging System (openIVIS)
bioRxiv (Cold Spring Harbor Laboratory) · 2023
- Computer Science
- Computer Science
- Nanotechnology
Abstract The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study we designed and built a multifunction fluorescent open-source in-vivo/in-vitro imaging system (openIVIS) fluorescent imaging system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the various potential applications of our system, we tested its performance against a diverse set of experiments including laboratory type assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of a couple of weeks. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
The American Journal of Cardiology · 2020 · 7 citations
- Medicine
- Internal medicine
- Cardiology
Clinical Journal of the American Society of Nephrology · 2019-01-10 · 50 citations
articleOpen accessBackground and objectives The rate of progression to ESKD is variable, and prognostic information helps patients and physicians plan for future ESKD. We assessed the estimations of ESKD risk of patients with CKD and physicians and compared them with risk calculators and outcomes at 2 years. Design, setting, participants, & measurements This prospective observational study assessed 257 adult patients with CKD stages 3–5 and their nephrologists at University of California, San Diego and Veterans Affairs San Diego CKD clinics. Patients’ and nephrologists’ estimations of 2-year ESKD risk were evaluated, and objective estimation of 2-year risk was determined using kidney failure risk equations; actual incidence rates of ESKD and death were ascertained by chart review. Participants’ baseline characteristics were compared across kidney failure risk equation risk levels and according to whether patients’ estimations were more optimistic or pessimistic than physicians’ estimations. We examined correlations between estimations and compared estimations with outcomes using c statistics and calibration plots. Results Average age was 65 (±13) years old, and eGFR was 34 (±13) ml/min per 1.73 m 2 . Overall, 13% reached ESKD, and 9% died. About one quarter of patients gave estimates that were >20% more optimistic than physicians, and more than one in ten gave estimates that were >20% more pessimistic. Physicians’ and kidney failure risk equation estimations had the strongest correlation ( r =0.72; P <0.001) compared with 0.50 ( P <0.001) between physicians and patients and 0.47 ( P <0.001) between patients and kidney failure risk equation. Although all three estimations provided reasonable risk rankings ( c statistics >0.8), physicians and patients overestimated risk compared with actual outcomes; no patient whose physician estimated a risk of ESKD <15% reached ESKD at 2 years. The kidney failure risk equation was best calibrated to actual ESKD risk. Conclusions Compared with actual ESKD incidence, the kidney failure risk equation outperformed patients’ and physicians’ estimations of ESKD incidence. Patients and physicians overestimated risk compared with the kidney failure risk equation.
Utility of Spot Urine Specimens to Assess Tubular Secretion
American Journal of Kidney Diseases · 2017-03-08 · 11 citations
letterOpen accessBlood Pressure Monitoring · 2015-12-18 · 1 citations
articleOpen accessOBJECTIVES: The objective of this study was to determine the relationship between chronic kidney disease [CKD; measured using cystatin C-based estimated glomerular filtration rate (eGFR)] and abnormal ambulatory blood pressure (including nocturnal dipping) in healthy older adults. Further, this study aimed to assess the agreement between clinic and ambulatory blood pressure monitoring. METHODS: Serum cystatin C levels were measured to calculate eGFR. Participants underwent clinic and 24-h ambulatory blood pressure measurements. Multiple linear regression was performed to examine the association between reduced cystatin C-based eGFR (CKDcys) and blood pressure parameters. Bland-Altman analysis was carried out to evaluate the agreement between clinic and ambulatory measurements. RESULTS: The average age was 72 years. There were 60 individuals with CKDcys (eGFR<60 ml/min/1.73 m). Compared with those without CKDcys, individuals with CKDcys were older, more likely to have hypertension, and less likely to have normal dipping patterns. On multivariate analysis, the presence of CKDcys was found to be significantly associated with a lower mean ambulatory diastolic blood pressure (-2 mmHg, P=0.048), but not with nocturnal dipping or other blood pressure parameters. Clinic systolic blood pressure (SBP) significantly overestimated the mean wake-time ambulatory SBP; the mean difference was 11 mmHg for those without CKDcys (95% limits of agreement -14 to 35 mmHg) and 14 mmHg for those with CKDcys (95% limits of agreement -13 to 41 mmHg); there was no statistically significant effect modification by CKD status. CONCLUSION: In older, seemingly healthy adults, mild CKD was associated with lower ambulatory diastolic blood pressure. The presence of CKD did not affect interpretation of clinic versus ambulatory blood pressure monitoring, although the accuracy of clinic SBP was poor.
2014-01-01
article1st authorCorrespondingBackground: Albumin-creatinine ratio (ACR) in spot urine samples is recommended for albuminuria screening instead of measured albumin excretion rate (mAER) in 24-hour urine collections. In patients with extremes of muscle mass, differences in spot urine creatinine values may lead to under- or overestimation of mAER by ACR. We hypothesized that calculating estimated AER (eAER) using spot ACR and estimated creatinine excretion rate (eCER) may improve albuminuria assessment. Study Design: Diagnostic test study. Setting & Participants: 2,711 community-living individuals from the general population of the Netherlands participating in the PREVEND (Prevention of Renal and Vascular Endstage Disease) Study. Index Test: eAER was computed as the product of ACR and eCER. eCER was computed using 3 previously validated methods (Ix, Ellam, and Walser). Reference Test: mAER, based on two 24-hour urine collections. Accuracy of the eAER and ACR were defined as the percentage of participants falling within 30% (P30) of mAER. Results: Mean age was 49 years, 46% were men, mean estimated glomerular filtration rate was 84 6 15 mL/min/1.73 m 2 , and median mAER was 7.2 (IQR, 5.4-11.0) mg/d. Mean measured CER was 1,381 mg/d, and median ACR was 4.9 mg/g. Using the Ix equation, median eAER was 6.4 mg/d. In the full cohort, eAER was more accurate and less biased compared to ACR (P30, 48.9% vs 33.6%; bias, 234.2% vs 214.1%, respectively). In subgroup analysis, improvement was most notable in the middle and highest weight tertiles and in men. Using the other methods for eCER produced similar results. Limitations: Little ethnic heterogeneity and a generally healthy cohort make extension of findings to other races and the chronically ill uncertain. Conclusions: In a large community-dwelling cohort, eAER was more accurate than ACR in assessing albuminuria.
American Journal of Kidney Diseases · 2013-12-21 · 46 citations
article1st authorCorresponding
Frequent coauthors
- 27 shared
Dena E. Rifkin
University of California, San Diego
- 11 shared
Tyler B. Woodell
University of California, San Diego
- 9 shared
Tiffany V. Tran
Cornell University
- 9 shared
Jan M. Hughes‐Austin
University of California, San Diego
- 9 shared
Atul Malhotra
University of California, San Diego
- 8 shared
Joachim H. Ix
University of California, San Diego
- 6 shared
Onur Potok
A. Alikhanyan National Laboratory
- 5 shared
Hiddo J.L. Heerspink
University of Groningen
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