Biology subjects

Durr, N. J.

Publications and source records attributed to Durr, N. J..

4 recordsLinked to original sources

bioRxiv2025

Chromatix: a differentiable, GPU-accelerated wave-optics library

Modern microscopy methods incorporate computational modeling as an integral part of the imaging process, either to solve inverse problems or optimize the optical system design itself. These methods often depend on differentiable optics simulations, yet no standardized framework exists--forcing computational optics researchers to repeatedly and independently implement simulations with limited reusability and performance. These common problems limit the potential impact of computational optics as a field. Here we present Chromatix: an open-source, GPU-accelerated, differentiable wave optics simulation library. Chromatix builds on JAX to democratize fast, parallelized simulation of diverse optical systems and expand the design space in computational optics. Chromatix standardizes a growing collection of optical elements and propagation methods allowing a broad range of applications, which we demonstrate here for snapshot microscopy, holography, and phase retrieval. We demonstrate speed improvements of 2-6x on a single GPU and up to 22x on 8 GPUs.

bioinformatics↗

bioRxiv2024

Thermal Characterization and Preclinical Validation of an Accessible, Carbon Dioxide-Based Cryotherapy System

To investigate the potential of an affordable cryotherapy device for accessible treatment of breast cancer, the performance of a novel carbon dioxide-based device was evaluated through both benchtop and in vivo canine models. This novel device was quantitatively compared to a commercial device that utilizes argon gas as the cryogen. The thermal behavior of each device was characterized through calorimetry and by measuring the temperature profiles of iceballs generated in tissue phantoms. A 45-minute treatment from the carbon dioxide device in a tissue phantom produced a 1.67 {+/-} 0.06 cm diameter lethal isotherm that was equivalent to a 7-minute treatment from the commercial argon-based device which produced a 1.53 {+/-} 0.15 cm diameter lethal isotherm. In vivo validation was performed with the carbon dioxide-based device in one spontaneously occurring canine mammary mass with two standard 10-minutes freezes. Following cryotherapy, this mass was surgically resected and analyzed for necrosis margins via histopathology. The histopathology margin of necrosis from the in vivo treatment with the carbon dioxide device at 14 days post cryoablation was 1.57 cm. While carbon dioxide gas has historically been considered an impractical cryogen due to its low working pressure and high boiling point, this study shows that carbon dioxide-based cryotherapy may be equivalent to conventional argon-based cryotherapy in the size of the ablation zone in a standard treatment time. The validation of the carbon dioxide device performed in this study is an important step towards bringing accessible breast cancer treatment to women in low-resource settings.

bioengineering↗

bioRxiv2018

Validation of a low-cost, carbon dioxide-based cryoablation system for percutaneous tumor ablation

Breast cancer rates are rising in low- and middle-income countries (LMICs), yet there is a lack of accessible and cost-effective treatment. As a result, the cancer burden and death rates are highest in LMICs. In an effort to meet this need, our work presents the design and feasibility of a low-cost cryoablation system using widely-available carbon dioxide as the only consumable. This system uses an 8-gauge outer-diameter needle and Joule-Thomson expansion to percutaneously necrose tissue with cryoablation. Bench top experiments characterized temperature dynamics in ultrasound gel demonstrated that isotherms greater than 2 cm were formed. Further, this system was applied to mammary tumors in an in vivo rat model and necrosis was verified by histopathology. Finally, freezing capacity under a large heat load was assessed with an in vivo porcine study, where volumes of necrosis greater than 1.5 cm in diameter confirmed by histopathology were induced in a highly perfused liver after two 7-minute freeze cycles. These results demonstrate the feasibility of a carbon-dioxide based cryoablation system for improving solid tumor treatment options in resource-constrained environments.

bioengineering↗

bioRxiv2018

Quality of eyeglass prescriptions from a low-cost wavefront autorefractor evaluated in rural India: results of a 708-participant field study

ABSTACTO_ST_ABSAimC_ST_ABSTo assess the quality of eyeglass prescriptions provided by an affordable wavefront autorefractor operated by a minimally-trained technician in a low-resource setting.\n\nMethods708 participants were recruited from consecutive patients registered for routine eye examinations at Aravind Eye Hospital in Madurai, India, or an affiliated rural satellite vision centre. Visual acuity (VA) and patient preference were compared for eyeglasses prescribed from a novel wavefront autorefractor versus eyeglasses prescribed from subjective refraction by an experienced refractionist.\n\nResultsMean {+/-} standard deviation VA was 0.30 {+/-} 0.37, -0.02 {+/-} 0.14, and -0.04 {+/-} 0.11 LogMAR units before correction, with autorefractor correction, and with subjective refraction correction, respectively (all differences P < 0.01). Overall, 25% of participants had no preference, 33% preferred eyeglasses from autorefractor prescriptions, and 42% preferred eyeglasses from subjective refraction prescriptions (P < 0.01). Of the 438 patients 40 years old and younger, 96 had no preference and the remainder had no statistically-significant difference in preference for subjective refraction prescriptions (51%) versus autorefractor prescriptions (49%) (P = 0.52).\n\nConclusionsAverage VAs from autorefractor-prescribed eyeglasses were one letter worse than those from subjective refraction. More than half of all participants either had no preference or preferred eyeglasses prescribed by the autorefractor. This marginal difference in quality may warrant autorefractor-based prescriptions, given the portable form-factor, short measurement time, low-cost, and minimal training required to use the autorefractor evaluated here.\n\nSYNOPSISEyeglass prescriptions can be accurately measured by a minimally-trained technician using a low-cost wavefront autorefractor in rural India. Objective refraction may be a feasible approach to increasing eyeglass accessibility in low-resource settings.

bioengineering↗