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SLAS Technology

Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match SLAS Technology's content profile, based on 14 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Open-source robotic chip-to-plate interface for high-throughput microfluidic generation of materials libraries

Navarro, I. B.; Datto, G.; Beni, L.; Barragan, D.; Mossburg, K. J.; Shen, S.; Hanna, A. R.; Cormode, D. P.; Issadore, D.

2026-05-14 bioengineering 10.64898/2026.05.12.724546 medRxiv
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Data-driven materials development requires large, well-characterized libraries of precisely defined formulations. While microfluidic platforms excel at generating highly controlled materials, their throughput is often limited by the challenge of efficiently interfacing device outputs with standard well plates. This bottleneck frequently necessitates manual transfer or non-microfluidic workflows, constraining both throughput and reproducibility. Here, we present LMNOP-bot (Libraries of Micro- and Nano-materials, OPen-source bot), an open-source robotic platform for the automated generation and collection of micro- and nanomaterial libraries from serial microfluidic outputs. Using synchronized, pressure-driven flow, LMNOP-bot enables continuous formulation and direct deposition into standard well plates. The system is low-cost (<$700, excluding pressure regulators), constructed from readily available or easily fabricated components, and designed for broad accessibility. LMNOP-bot collects [&ge;]30 {micro}L per formulation at a rate of one sample every four seconds, representing an approximately 50x increase in throughput over existing serial microfluidic workflows, and operates robustly for over 10,000 runs without maintenance. We demonstrate compatibility with both PDMS/glass and commercial polycarbonate devices, with seamless interfacing to 96- and 384-well plates. Repeated sampling confirms high precision and reproducibility. By removing a key bottleneck in microfluidic library generation, LMNOP-bot enables rapid, scalable, and accessible exploration of material design spaces.

2
Shape, Shrink, Spheroid: A DIY High-throughput Spheroid Generation Device

Mogha, P.; Mukherjee, S.; Gangwar, T.; Roy, D.; Vichare, A.; Kulkarni, S.; Sharma, V.; Majumder, A.

2026-06-03 bioengineering 10.64898/2026.05.31.729042 medRxiv
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3D spheroids, which closely replicate three-dimensional cell-cell and cell-extracellular matrix interactions, offer superior predictive capabilities compared to conventional 2D monolayer cultures, positioning them as forward-looking platforms in drug testing, cancer biology, and regenerative medicine. However, high-throughput generation of uniform sized spheroids is still a technological challenge. In one hand, the use of conventional ultra-low attachment (ULA) multiwell plates for this purpose is labour intensive and complex. On the other hand, the use of microfabricated facilities demands cutting-edge infrastructure such as clean room, photolithography, and microfluidic setup which are often unavailable for the resource constrained laboratories. In this study, we addressed these problems by developing a low-cost Do-It-Yourself (DIY), polydimethylsiloxane (PDMS) and agarose-based spheroid generation device, capable of producing and maintaining hundreds of spheroids with minimal user intervention. We have demonstrated two variants based on their size, termed here as S1 and S2 devices which fit into 6-well and 12-well plates, and can generate 600 and 1200 uniform-sized spheroids respectively. We validated our device with various cell lines including primary and cancerous cell lines. We further demonstrated the drug testing capabilities of the device by estimating the IC50 value of the anticancer drug Temozolomide on U87-MG. The value was comparable with the same obtained from the spheroids generated using conventional ULA plates. Additional attachment of a perfusion system made the device suitable for long-term spheroid culture without much user intervention. Furthermore, the devices can also be used for the production of spheroids with gradually changing diameters in a controlled manner, resembling a size gradient. This feature is useful for checking the effect of drugs on different-sized spheroids and for co-culturing spheroids with varying cell densities, mimicking the disease architecture. We have co-cultured two types of the placental trophoblast cells, i.e., extravillous trophoblast (HTR-8) and syncytiotrophoblast (BeWo) with varying densities. In summary, this paper demonstrates a unique DIY method for a high-throughput uniform-sized spheroid generation at a fraction of cost which can be deployed to resource-constrained labs.

3
Calibration standards and sensitivity limits for fluorescence measurements with the Chi.Bio open-source bioreactor platform

Sambruna, A.; Tallarico, G.; Cosentino Lagomarsino, M.

2026-07-09 systems biology 10.64898/2026.06.29.735387 medRxiv
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Automated platforms such as Chi.Bio enable simultaneous monitoring of optical density and fluorescent reporter expression in 20 ml reactor cultures with controllable pump systems. As such, they provide an appealing option for contemporary gene expression quantification, quantitative physiology, and laboratory evolution and ecology experiments. While optical density calibration for this device is well established, no equivalent calibration framework exists for fluorescence, making quantitative comparison with reference instruments unreliable. Here, we characterize Chi.Bio fluorescence capabilities using fluorescent calibration microspheres and fixed GFP-expressing S. cerevisiae and E. coli cells, compared with orthogonal plate-reader measurements. We show that microsphere fluorescence is detectable and scales linearly with concentration, whereas the GFP signal from both species falls below the device detection limit. Comparison of background-correction strategies indicates that direct subtraction of a non-fluorescent control measured within the same device yields more reliable fluorescence estimates than the commonly used on-line normalization method. Knowledge of these sensitivity boundaries of the device provides practical guidelines for experimental design of future studies.

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Servo-Actuated 3D-Printed Disposable Microvalves for Automated, Scalable Organoid Culture in Standard Incubators

Zeraatkar, M.; Ehrlich, D.; Hernandez Cifuentes, J. S.; Schweiger, H.; Pessoa de Melo, M.; Wachtel, E.; Ozcakir, D.; Seiler, S.; Voitiuk, K.; Rosen, Y.; Josephson, C.; Mostajo-Radji, M.; Haussler, D.; R. Salama, S.; Teodorescu, M.

2026-06-17 bioengineering 10.64898/2026.06.16.732526 medRxiv
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Automation of organoid and cell culture processes is essential for achieving scalable and standardized experimentation in regenerative medicine and stem cell research. However, existing microfluidic platforms often rely on complex setups, limiting their integration within standard incubator environments. To address these challenges, we developed a compact, scalable multi-well platform featuring 3D-printed, servo-actuated disposable microvalves for fully automated media and drug exchange. This design eliminates the need for external pressure sources and control channels, providing a simplified and cost-effective solution for organoid culture. The platform integrates an internet-connected microscopy module with a motorized XYZ stage, allowing continuous, real-time imaging of individual wells directly within the incubator. It supports precise and reliable fluid handling under physiological conditions, improving throughput, reproducibility, and accessibility. We validate the platform through bench-top testing and in both mouse and human organoid models. Morphological analysis, immunohistochemistry (IHC), and qPCR demonstrate comparable viability, growth, and gene expression profiles between automated and manual culture conditions. These results establish a robust and scalable framework for fully automated organoid culture, offering a simplified and accessible alternative to conventional microfluidic systems with broad applications in regenerative medicine, drug discovery, and scalable biological screening. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/732526v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@5efd07org.highwire.dtl.DTLVardef@3600d0org.highwire.dtl.DTLVardef@16f85f5org.highwire.dtl.DTLVardef@c39fbd_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Quantifying the Environmental Impact of Cell Culture

Taylor-Hearn, I. S.; Llewellyn, J.; Mellor, C. E. L.; Farley, M.

2026-05-25 cell biology 10.64898/2026.05.21.720586 medRxiv
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Laboratory research generates substantial plastic waste and associated greenhouse gas emissions, yet researchers often lack practical tools for quantifying the environmental impact of routine protocols or identifying realistic opportunities for reduction. Here, we present an open-source calculator for estimating plastic use and carbon dioxide equivalent emissions from laboratory protocols, using item weight, plastic composition, and estimated cradle-to-grave carbon footprint factors. We apply the tool to a standard cell culture workflow to demonstrate how evidence-based protocol adjustments can reduce plastic consumption and emissions without affecting experimental design or efficiency. The calculator is designed to be transparent, adaptable, and extendable, allowing researchers to add new consumables and tailor analyses to their own laboratory practices. This work provides a quantitative framework for translating sustainability principles into measurable, protocol-level changes and supports more environmentally responsible decision-making in biomedical research.

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Design and development of online pressure sensing for microbial batch cultivation

Borch, M. M.; Kehr, P.; Torres, R. A.; Gorter de Vries, P. J.; Larsen, N. J.; Padfield, N.; Nielsen, A. T.

2026-06-11 bioengineering 10.64898/2026.06.08.729494 medRxiv
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Gas production and consumption is a direct consequence of microbial activity in environmental and industrial settings. In closed batch cultivations, headspace pressure changes therefore give valuable insights into the microbial metabolism. For laboratory scale anaerobic batch cultivations, manual manometer measurements are routinely applied, as a simple and robust method, but it is labour intensive, causes disturbances in the headspace gas and temperature, leading to suboptimal growth, inhibition and noisy data. We built and tested an automated online pressure sensor for closed batch cultivations. It is designed for microbial cultivation and integrates with sterile and anaerobic cultivation workflows. The system uses an absolute pressure sensor (0-30 bar) mounted on a custom designed PCB, with a gas-tight needle mount. An ESP32 microcontroller logs pressure and temperature locally and generates a Wi-Fi access point for real-time visualization and direct CSV download through a local homepage. We detail hardware and software design decisions, assembly, and validation including long-term stability. Case studies demonstrate the applicability for: a multiphasic biogas kinetics during anaerobic digestion, capturing gas uptake dynamics and metabolic shifts during syngas fermentations and co-feeding experiments, and long-term robustness in a multi-year monitoring of a compressed-air system. More than 130 individual sensors have been deployed over 3 years in laboratories, at various academic and industrial settings. The platform provides reproducible, high-resolution pressure measurements that enable calculation of gas formation/consumption rates and improve experimental throughput without disturbing cultures. Design files, firmware, and example analysis scripts are openly available to support adoption and further development.

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Functional Assessment of Cardiac Beat Dynamics Under Dynamic Flow: Insights from the Mera Microphysiological System

Almeida, N.; Coffey, V. S.; Costello, P.; Madden, C.; Devitt, S.; Mukkunda, S. R.; Keshava, B. B.; Sunil, S.; Riley, L. G.; Deely, S.; de Benedictis, C. A.; Lyons, M.; Cliffe, F.

2026-05-22 bioengineering 10.64898/2026.05.20.726520 medRxiv
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Cardiac rhythm is a critical clinical indicator for cardiac arrhythmias and adverse events during drug toxicity studies. In vivo, cardiomyocyte responses to pharmacological agents occur within minutes and are strongly influenced by dynamic drug delivery through blood flow. However, conventional 2D and 3D static culture systems fail to replicate these fluid flow kinetics, limiting their physiological relevance for assessing beat rate responses. Here, we present Mera, an advanced microphysiological system (MPS) developed by Hooke Bio, designed for high-throughput, long-term culture and functional analysis of 3D cardiac spheroids composed of human induced pluripotent stem cell-derived cardiomyocytes and cardiac fibroblasts. Mera enables dynamic perfusion, allowing investigation of cardiomyocyte beat rates under physiologically relevant flow conditions. The platform supports up to 640 spheroids per run and integrates automated imaging, fluid handling, and user-friendly software, operating under controlled physiological conditions (37{degrees}C, 5% CO2). Flow rates are tunable between 0 and 12.5 mL/min to mimic in vivo environments. Pharmacological testing with verapamil, isoproterenol, calcium chloride, and propranolol demonstrated real-time, reversible modulation of beat rate under flow, including recovery following drug-induced suppression. System variability was comparable to a temperature-controlled reference platform, supporting robust statistical analysis. Dose-response studies yielded IC values consistent with literature, confirming physiological relevance. Collectively, these results demonstrate that Mera provides a reproducible, scalable, and human-relevant platform for cardiac drug testing. By enabling dynamic drug exposure and automated analysis, Mera represents a powerful new approach methodology (NAM) for improving the predictive assessment of cardiac safety and beat-rate modulation drug responses.

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Online characterization of surrogate metrics for metabolic phenotype in human induced pluripotent stem cell bioprocessing

Colter, J.; Kallos, M.; Murari, K.

2026-05-12 bioengineering 10.64898/2026.05.08.723750 medRxiv
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Human induced pluripotent stem cells (hiPSCs) are the most accessible source material for derivation of stem-cell-based therapies at scale. However, a disconnect exists between quality characteristics of phenotype in the pluripotent state, and downstream metrics for efficacy and safety. Bridging this gap is a major challenge. Given hiPSC plasticity, environmental conditioning plays a crucial role in guiding phenotype. This work presents a parallelizable scale-down approach, acquiring real-time data to inform hiPSC phenotype throughout biomanufacturing. We developed an optoelectronic instrumentation suite capable of measuring pH, dissolved oxygen, and cell density as important surrogates for phenotype in a scale-down expansion bioprocess. We were successful in obtaining continuous, integrated parametric data throughout cultivation and estimating metabolic characteristics of hiPSC phenotype. This system functions as a proof-of-concept tool for development of predictive models and monitoring strategies around the elucidation of phenotypic dynamics within hiPSC biomanufacturing. We have demonstrated a feasible open-source multivariate continuous monitoring approach at research scale that combines common process parameters with a scattering measurement against aggregate density. The combination of these parameters enables surrogate measurement of a metric for metabolic phenotype. This contribution emphasizes monitoring how the bioprocess influences variables important in the context of cell state, in broader pursuit of better understanding the link to downstream functionality and global optima in hiPSC biomanufacturing for regenerative medicine.

9
Experimental Methods for CRISPR Enzyme Assays with Fluorescence Readout

Jiang, Q.; Avaro, A. S.; Bae, H.; Sorensen, A.; Santiago, J. G.

2026-06-03 biochemistry 10.64898/2026.06.03.729647 medRxiv
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Fluorescence-based CRISPR diagnostic assays have become a popular platform for nucleic acid detection due to their programmability, configurability, specificity, and compatibility with standard laboratory equipment. However, reported enzymatic kinetic rates and limits of detection for CRISPR trans-cleavage assays vary by several orders of magnitude across the literature. This variation in performance parameters is coupled with and exacerbated by inconsistent calibration, incomplete correction of measurement biases, and nonstandardized or incomplete data-analysis procedures. We present an experimental protocol and quantitative analysis framework for fluorescence-based enzyme assays using routine laboratory instrumentation, including thermocyclers and fluorescence microplate readers. Building on previous studies of CRISPR enzyme kinetics and fluorescence calibration, we describe procedures for flat-field and background correction; comprehensive fluorescence calibration including correction for inner-filter-effect; quantification and implications of reporter degradation; extraction of Michaelis-Menten kinetic parameters; and determination of assay limits of detection. We provide step-by-step experimental guidelines and open-source Python implementations for each stage of the workflow. Using representative Cas12 trans-cleavage datasets, we demonstrate that explicit fluorescence calibration and correction procedures substantially reduce systematic bias in measured kinetic rates and improve consistency between experiments. Our framework aims to establish standardized practices for quantitative fluorescence-based CRISPR assays and provides researchers with practical tools for reproducible kinetic characterization and rational assay design.

10
Semi-quantitative Classification of HIV-1 Nucleic Acids Using ResNet Image Analysis of Discretized Isothermal Amplification Reactions in a Microfluidic Chip

Martin, C.; Benson, N.; Gummalla, N.; Shimazu, K.; Bender, A.; Beck, D.; Posner, J.

2026-06-24 bioengineering 10.64898/2026.06.24.734232 medRxiv
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Isothermal nucleic acid amplification tests enable rapid and decentralized molecular diagnostics but often lack robust quantitative readouts compared to quantitative PCR. Here, we present a semi-quantitative nucleic acid measurement approach using machine learning to extract spatiotemporal features from real-time fluorescence imaging of rapid isothermal amplification reactions in microfluidic chips. A convolutional neural network was trained on multiple images sampled throughout a chip-based recombinase polymerase amplification reaction to classify samples into clinically relevant or logarithmically spaced concentration ranges spanning five orders of magnitude. The clinical classification model achieved 94.6% accuracy, and the logarithmic model achieved 92.7% accuracy, with most errors occurring between adjacent concentration categories. By learning spatiotemporal patterns of fluorescence development rather than relying on explicit feature extraction, the model remained accurate at both high and low nucleic acid concentration regimes where other quantitative isothermal molecular tests struggle. This approach enables automated interpretation of amplification reactions and extends the usable dynamic range of the assay. These results demonstrate that integrating machine learning with image-based amplification methods can support rapid semi-quantitative molecular testing and may facilitate broader deployment of nucleic acid diagnostics outside centralized laboratory settings. Author summaryMany rapid nucleic acid testing methods for infectious diseases are simple to run but struggle to measure how much genetic material is present, which limits their usefulness in clinical decision-making. In our work, we study a technique that produces visible fluorescent patterns during nucleic acid amplification reactions. Traditionally, the amount of nucleic acids present are measured by counting individual bright spots, but this becomes difficult when the target nucleic acid concentration is high and the spots merge together. We developed a machine learning approach that models how the fluorescence pattern changes over time. By analyzing a sequence of images from each reaction, our model can assign samples to concentration ranges across a wide span. This allows us to extract meaningful information even when traditional analysis methods break down. Because this approach works with simple imaging systems and does not require complex equipment, it could help support more informative and accessible diagnostic testing in point-of-care and low-resource settings.

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CascadeMAP: Autonomous Closed-loop Optimization of Enzyme Cascades via Microfluidics, Machine Learning and Agentic AI

Vasina, M.; Kovar, D.; Kizovsky, M.; Lacko, D.; Vanacek, P.; Herich, M.; Volf, E.; Drdla, L.; Cabalova, S.; Sikorova, P.; Jirasek, M.; Solansky, P.; Jezek, J.; Samek, O.; Dousek, F.; Walner, H.; Zemanek, P.; deMello, A.; Pilat, Z.; Damborsky, J.; Stavrakis, S.; Mazurenko, S.; Prokop, Z.

2026-06-07 biochemistry 10.64898/2026.06.04.730034 medRxiv
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Enzyme cascades enable complex biochemical transformations, but their optimization is resource-intensive, requiring navigation through high-dimensional parameter spaces encompassing reaction conditions, enzyme ratios, and buffer composition. Here we introduce CascadeMAP, an autonomous microfluidic platform for closed-loop optimization of enzyme cascades, integrating high-throughput microfluidics with Bayesian optimization and multi-agent AI system. We demonstrate the platform across two cascades: (i) a glycerol detection pathway monitored by fluorescence and (ii) a 1,2,3-trichloropropane degradation pathway monitored by label-free Raman spectroscopy providing orthogonal detection modalities. Bayesian optimization identified optimal conditions three times faster than Design of Experiments. Multi-agent AI system automated hypothesis generation, processing 11 GB of experimental data, pattern recognition, and insight synthesis. Operating without human intervention for 7 days, CascadeMAP processed [~]220,000 reactions across [~]7,400 different conditions. This capability establishes a generalizable framework for the autonomous optimization of enzyme cascades and metabolic pathways and accelerates the development of biocatalytic and synthetic biological systems.

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A Passive-Oxygenation Silicone Platform for Biomass Production: Maximizing Labor Productivity and Process Efficiency in Cellular Agriculture Development

Hatano, H.; Takagaki, Y.; Sawada, M.; Kokido, I.; Okabe, H.; Inoue, S.; Miyaoku, K.; Helena, G. A.; Shiotsuka, K.; Tatsumi, S.; Kawashima, I.

2026-06-07 bioengineering 10.64898/2026.06.02.729703 medRxiv
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The commercial production of cell-based food is currently hindered by existing bioreactor technologies, which require substantial capital investment, specialized operating skills, and complex processing setups. To democratize cell-based food production, we developed the "oxy-thru cultivator"--a simple, autoclavable, closed-bag bioreactor fabricated from polydimethylsiloxane (PDMS). By leveraging the high oxygen-permeability of PDMS, this platform enables passive oxygenation across the entire vessel wall, eliminating the need for external aeration or mechanical sparging. During testing, the cultivator maintained a stable culture environment over 23 days, showing no cytotoxic leachables and retaining both structural integrity and sterility across 10 autoclave cycles. This robustness supported the continuous cultivation of DF-1 cells for 74 days. Using a standardized subculture scheme, we successfully harvested an estimated 2.60 g of cell-based biomass per cultivator over five passages. Notably, the platform achieved a 127% monthly labor productivity compared to conventional bioreactors and was easily operated by researchers without specialized training. Additionally, the system successfully supported the expansion of both mammalian and primary avian cell lines. With a minimal equipment footprint that reduces CapEx, and a reusable silicone vessel that lowers OpEx, the oxy-thru cultivator offers a highly practical, accessible pathway toward scaling up cellular agriculture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/729703v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@bf2abforg.highwire.dtl.DTLVardef@8f9231org.highwire.dtl.DTLVardef@1c6fc63org.highwire.dtl.DTLVardef@e3e537_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Development of Shelf-Stable Reagents and Assay Kits for Bioluminescence Applications using the Capillary-Assisted Vitrification Platform Stabilization Technology

Shank-Retzlaff, M.; Radford, S.; Peris-Taverner, Y.; Dibble, M.; Corn, K.; Zhu, T.; Martello, S.; Mayeau, M.; Ladd, A.; Renu, S.; Chunduri, T.; Jadhav, A.; Dart, M.; Rafat, M.; Bronsart, L.

2026-07-13 biochemistry 10.64898/2026.07.11.737891 medRxiv
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Luminescence is a powerful method for detecting trace analytes and monitoring biological processes. However, most bioluminescence reagents, including luciferase and its substrates, are sensitive to temperature, limiting their useable shelf lives, and resulting in inconsistent performance. Enhancing the stability of these reagents could improve data quality, simplify workflows, and address cold chain storage issues. In this study, we demonstrate the application of the platform stabilization technology, capillary-assisted vitrification (CAV), as a tool to stabilize different luciferases and their substrates, and the application of the stabilized reagents in both in vitro and in vivo bioluminescent assays. We demonstrate that CAV-stabilized reagents can be stored and shipped ambiently, maintain consistent performance over time, and are suitable for use in cell viability quantification, tumor monitoring, in vivo imaging, microbial detection, and immunoassays. Additionally, different reagents can be co-formulated to make ready-to-use assay kits that can also be shipped and stored ambiently. Our results demonstrate that CAV stabilization is a viable alternative to traditional storage methods, with broad potential to improve bioluminescence workflows.

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Characterization of pre-analytical blood collection and stabilization parameters to maintain endogenous protein levels for remote blood sampling technology

Cook, S. R.; Alizai, M. Y.; Tu, W.-c.; Robertson, I.; Wei, X.; Adams, K.; Su, X.; Thongpang, S.; Berthier, E.; Theberge, A. B.

2026-05-29 biochemistry 10.64898/2026.05.27.728347 medRxiv
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Blood biomarkers are central to monitoring disease progression and evaluating treatment responses, yet traditional venipuncture captures a single physiological snapshot in time and becomes burdensome with repeated sampling. Remote blood self-sampling offers a path toward longitudinal, decentralized monitoring, but maintaining protein integrity from draw to analysis remains a critical challenge. Here, we optimized pre-analytical blood collection and stabilization parameters to maintain protein levels at the time of collection for use with remote sampling technology. First, we optimized blood collection time with Tasso remote self-sampling devices to minimize interference from clotting, finding that a 2.5 min collection time best reduces clot formation while collecting enough blood. Next, we found that Protein Plus, a commercial protein stabilizer, limited hemolysis (a metric for stabilizer efficacy) in venous blood for up to 5 days at 25{degrees}C-35{degrees}C and for 1 day at 40{degrees}C. In addition, we optimized the stabilizer volume and acceptable blood volume range for self-sampling as the stabilizer efficacy is impacted by the stabilizer to blood ratio and collection volume can vary with remote self-sampling devices. Finally, we incubated stabilized blood samples collected via Tasso device at 25{degrees}C-35{degrees}C for 72 h, mimicking a 2-day shipping period. Using a panel of 21 inflammatory proteins, we found that Protein Plus limited intracellular protein release for various proteins (e.g., VEGF-A, CCL11, and IL-8), inhibited protein degradation for CCL2, and enabled minimal hemolysis. These results support Protein Plus as a viable stabilization strategy for remote blood collection technology targeting longitudinal inflammatory protein monitoring.

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Organoid-in-Bead (OrB): vortex-based compartmentalization enables scalable, high-density intestinal organoid culture

Hattori, K.; Kirisako, H.; Matsuo, M.; Ota, S.

2026-06-23 bioengineering 10.64898/2026.06.21.733630 medRxiv
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Intestinal organoids are powerful in vitro models, but their use in large-scale analyses remains constrained by the low throughput, labor-intensive handling, and high reagent consumption of conventional Matrigel dome culture. Here, we present Organoid-in-Bead (OrB), a vortex-based compartmentalization workflow that partitions organoid fragments into thousands of discrete Matrigel microbeads, enabling scalable, high-density culture from a single batch preparation. OrB maintains dome-comparable organoid growth and epithelial polarity, supports passaging-based culture expansion, yields more than 5,000 organoids in the final 10 cm dish format, and reduces Matrigel and medium consumption by approximately 70% on a per-organoid basis. OrB therefore provides a practical and scalable upstream workflow for generating screening-scale intestinal organoids. HighlightsO_LIOrB generates Matrigel microcompartments by vortexing without microfluidics C_LIO_LIOrB enables scalable, high-density intestinal organoid culture in one batch C_LIO_LIOrB maintains dome-comparable growth and epithelial polarity and supports passaging C_LIO_LIOrB yields >5,000 organoids per batch with [~]70% less Matrigel/medium per organoid C_LI

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Microfluidic bioprinting of a physiologically relevant thyroid three-dimensional in vitro model

Sana, M.; Giselbrecht, S.; Romitti, M.; Kip, A. M.; Costagliola, S.; Mota, C.; Moroni, L.

2026-04-27 bioengineering 10.64898/2026.04.23.720314 medRxiv
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Endocrine disruptors (EDs) are an exogenous group of compounds associated with thyroid malfunctioning in the human body. Nonetheless, there are currently no adequate in vivo or in vitro models for the preclinical testing of these compounds since both animal and two-dimensional (2D) cell-based models are not able to mimic thyroid physiological conditions from both functional and three-dimensional (3D) organization perspective. Recently, bioprinting technologies emerged as an innovative tool in the field of regenerative medicine and advanced 3D in vitro models that allow the creation of 3D well-organized structures able to mirror physiologically relevant tissue and organ architectures. In this study, we evaluated microfluidic bioprinting as a biofabrication technology to develop a 3D in vitro model of the thyroid gland. We studied the fundamental parameters to obtain a fine control over the bioprinted fibres for different biomaterials. Then, we assessed the possibility to bioprint single thyroid cells, thyroid spheroids and finally mouse embryonic stem cell-derived thyroid follicles. The different cell types maintained high viability and metabolic activity. The bioprinted thyroid model showed high expression of different early and late functional markers and to be responsive to ED exposure. These bioprinted thyroid constructs could provide a new set of advanced 3D in vitro models to test potential EDs and possible adverse outcomes that may be associated with their administration or exposure.

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Overcoming oxygen impermeability in PDMS-free organ-on-a-chip microfluidics with nanoporous thermoplastic

Buck, F.; Bugter, J.; Kruckenbaum, G.; Staecker, I.; Harzi, M.; Lavrentieva, A.; Winkler, T. E.

2026-05-26 bioengineering 10.64898/2026.05.22.727128 medRxiv
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Oxygen availability is a critical yet all-too-often overlooked variable in organ-on-a-chip (OoC) systems. PDMS-based microfluidics remain the most common approach to facilitating oxygen equilibration with the incubator environment, but the materials tendency to ad- and absorb small hydrophobic molecules can pose significant concerns for pharmacological and toxicological studies. Yet there remains a lack of alternative gas-exchange materials feasible for OoC integration, even as the use of thermoplastic microfluidics in particular has otherwise proliferated. Here, we present commercially available track-etched nanoporous polycarbonate (50 nm pores, 1.18% porosity, [~]0.1 {euro}/cm2) as a practical alternative to polydimethylsiloxane (PDMS) for gas exchange in OoC. We show that nanoporous polycarbonate provides a thermoplastic material with an oxygen permeability of 3290 {+/-} 240 fs mol / kg, over an order of magnitude higher than PDMS. We demonstrate integration into existing lamination-based thermoplastic microfluidic fabrication workflows with sustained leak-free operation well above physiologically relevant pressures. We find that nanoporous polycarbonate does not compromise cell viability, but that high water vapor permeance necessitates a high-humidity environment around the device - though thickness-normalized water vapor permeability is notably similar to PDMS. We validate the OoC application with Caco-2 intestinal epithelial cells by monitoring oxygen levels during the critical cell attachment phase, with nanoporous polycarbonate allowing for maintenance of stable oxygen tension, in stark contrast to severe hypoxia in nonporous controls within 30 minutes. We further show that this uncontrolled hypoxia correlates with a time-delayed increase in cellular hypoxia inducible factor-1 reporter expression. Overall, our findings position nanoporous polycarbonate as a low-cost, mechanically robust, and fabrication-friendly alternative that can bring controlled oxygen availability to PDMS-free microfluidics and OoC.

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Biocompatible designated Resin-3D-printed polymers exhibit reproductive toxicity prevented by Parylene-C

Campo, H.; Tran, U.; Zhu, Y.; Lee, H. C.; Duncan, F.

2026-06-10 bioengineering 10.64898/2026.06.05.730268 medRxiv
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Resin three-dimensional (3D) printing is an increasingly popular manufacturing and prototyping method used to create microphysiological systems (MPS), but resin cytotoxicity significantly hinders its adoption, especially when sensitive cell models are incorporated. The mammalian oocyte and early preimplantation embryo consist of cells that are highly sensitive to toxicants and thus represent stringent cell-based models for biocompatibility testing. We developed a Multi-Endpoint Oocyte Safety Assay (MEIOSA) to evaluate the biocompatibility of four ISO 10993 biocompatible BioMed resins (Clear, Durable, Elastic 50A, and Flex 80A). MEIOSA assesses the viability, morphology, meiotic stage, and meiotic spindle morphology of the oocyte after in vitro maturation (IVM). Oocytes were in vitro matured in plate inserts 3D printed with the four BioMed resins. Oocytes cultured in rigid resins (Clear and Durable) or elastomeric resins (Elastic 50A, and Flex 80A) exhibited impaired meiotic progression and complete oocyte degeneration, respectively, relative to controls cultured in polystyrene which matured normally. To determine whether such cytotoxicity could be prevented, we coated the resin inserts with a 5 {micro}m impermeable Parylene-C (PC) barrier. PC coating completely rescued the degeneration and meiotic maturation defect phenotypes for all resins. Remarkably, when the most cytotoxic material (Flex 80A) was coated with PC, the resulting eggs were fertilization-competent and produced embryos capable of normal preimplantation development via in vitro fertilization. Our findings demonstrate that standardized viability-based biocompatibility tests do not identify cytotoxic effects for all cell types and establish MEIOSA as a high sensitivity test model to robustly evaluate biomaterial biocompatibility. Furthermore, PC coating prevents the toxic effects of all resin-3D-printed materials tested, opening up a new toolbox to create MPS compatible with reproductive, and by extension, other sensitive cell cultures. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/730268v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@18fab44org.highwire.dtl.DTLVardef@1352e5forg.highwire.dtl.DTLVardef@77889forg.highwire.dtl.DTLVardef@1aabd89_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Precursor of chemically expanded hepatocytes (pre-cHep) with 1-million-fold expansion potential and liver repopulation capacity

Huynh, L. M.; Higuchi, Y.; Law, C. T.-Y.; Jeriha, J.; Battle, I.; Granskog, R.; Uehara, S.; Kawamura, F.; Gadd, V. L.; Man, T. Y.; Forbes, S. J.; Yusa, K.; Tsui, S. K.-W.; Suemizu, H.; Kaji, K.

2026-05-19 bioengineering 10.64898/2026.05.15.725446 medRxiv
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Primary human hepatocytes (PHHs) are the gold standard for toxicology and drug metabolism studies in industry. However, their limited availability, substantial batch-to-batch variability, and high cost restrict their use. Here, we report a novel culture condition that reprograms PHHs into a proliferative state. These proliferating cells, termed precursors of chemically expanded hepatocytes (pre-cHep), expand over 106-fold within 30 days while retaining liver repopulation capacity comparable to PHHs. pre-cHep can further differentiate into chemically expanded hepatocytes (cHep) as three-dimensional (3D) spheroids within 7 days in vitro, exhibiting global gene expression profiles, albumin production, and cytochrome P450 (CYP) activities similar to 3D-cultured PHH spheroids (3D PHH). Efficient genetic manipulation of pre-cHep using CRISPR/Cas9 is also achievable. Together, pre-cHep and cHep represent a promising alternative to high-quality PHHs, providing a more affordable, reproducible, and scalable source of human hepatocytes for toxicology, drug metabolism studies, disease modelling, towards precision drug development.

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A Universal Free-Degree Orientation Extrusion Head Enables Conformal and Non-Planar Bio-Additive Manufacturing toward Adaptive and Future-Ready Bioprinting

Janarthanan, G.; Chand, R.; Vijayavenkataraman, S.

2026-06-24 bioengineering 10.64898/2026.06.23.734010 medRxiv
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Conventional extrusion-based 3D bioprinting encounters limitations in fabricating intricate tissue architectures due to fixed nozzle diameters and fixed deposition orientations. These constraints restrict conformal printing on curved or non-planar surfaces and often necessitate support-intensive fabrication strategies. This work introduces a mechanically simplified extrusion platform inspired by the swivel jet nozzle, featuring a free-degree-of-orientation extrusion head termed the universal extrusion head (Univ-Ex head), coupled with a modular nozzle architecture. The Univ-Ex head employs a swivel-like mechanical design that enables orientation freedom without external actuation in its current implementation, thereby minimizing mechanical complexity while supporting deposition on physiologically relevant, non-planar geometries. Multiple nozzle concepts were developed through comparative CAD iterations, with two representative geometries--a flat nozzle and a conical nozzle--selected for experimental validation. The platform is evaluated through parametric CAD design, stereolithography-printed prototypes, proof-of-concept extrusion experiments, and fluid dynamics simulations performed using FLOW-3D software. Numerical and experimental results demonstrate stable filament formation and clear diameter-dependent extrusion behavior, while simulations further confirm the feasibility of angled and non-planar deposition. A variable-diameter nozzle concept is proposed as a forward design direction to enable real-time adjustment of bioink flow rate and deposition resolution in principle; however, the present study intentionally validates the system using fixed-diameter nozzle variants to maintain stable numerical and experimental boundary conditions. A gear-integrated Univ-Ex head is also presented as a forward upgrade and demonstrated as a single-piece prototype. Collectively, this work establishes a scalable, hardware-focused pathway toward conformal bio-additive manufacturing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/734010v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@8833caorg.highwire.dtl.DTLVardef@33dforg.highwire.dtl.DTLVardef@14d8d11org.highwire.dtl.DTLVardef@685ef0_HPS_FORMAT_FIGEXP M_FIG C_FIG