Pre-exposure prophylaxis (PrEP) can be taken to prevent human immunodeficiency virus (HIV) infection. High levels of PrEP medication adherence (≥4 doses/week) decrease the chance of HIV infection to virtually zero. It is important for clinicians/fieldworkers and patients to be able to quantify PrEP adherence to help prevent treatment failure and HIV infection. Tenofovir diphosphate (TFV-DP) is the molecule that results after hydrolyzing and phosphorylating tenofovir disoproxil fumarate (TDF), a drug used in all approved oral PrEP regimens. Our lab recently developed the REverSe TRanscrIptase Chain Termination (RESTRICT) assay to accurately measure the concentration of TFV-DP based on the drug's activity as an inhibitor of DNA synthesis by HIV-1 Reverse Transcriptase (RT) enzyme. The RESTRICT assay currently relies on a microplate reader for fluorescence results. Moving the RESTRICT assay into a low cost reader will enable it to be used in point-of-care and low-resource settings. We did this by optimizing assay parameters such as DNA template concentration and nucleotide concentration to increase the analytical sensitivity of fluorescence readout in the low cost reader. Preliminary results show that we can measure RESTRICT fluorescence using a portable, battery-operable Axxin T-16 and can detect TFV-DP concentrations that overlap with the clinical range for PrEP adherence. Ongoing work is focused on measuring TFV-DP concentrations in diluted whole blood using the T-16 reader.

Evaluation of and diagnosis based on core needle biopsies at present requires trained pathologists on site for both sample manipulation and analysis of tissue structures. Microfluidic lab-on-chip architectures have been studied for automating cell-level pathology for decades, and the CoreView system developed in Eric Seibel’s lab applies similar technologies at the millimeter scale to tissue level analysis. Pulsatile flow has proven to be a reliable means by which to transport tissue samples without damage or adhesion to the flow channels, and high resolution microscope images can be taken in glass-covered channels for analysis by a remote pathologist or image processing system. I am developing a low cost and manufacturable on chip device to accurately cut and sort these tissue samples for further processing. To avoid unnecessary complexity and unreliability, compliant elastomeric actuators will be employed to actuate an on-chip knife which also acts as a valve controlling transport flow routing. This integrated compact device will achieve all of these goals in a system that can be mass-produced for low-cost and disposability if required for sterility. Such capabilities will enable tumor-rich regions to be sampled for genomic analyses that allow precision therapy, making cancer a treatable disease.

Complex phenomena in nature arise from surprisingly simple sets of rules, such as bee swarm motion, bird flight formations, ant movement and foraging, and traffic flow. Such complex macroscopic systems can all be accurately simulated using Markov models with simple governing rules and probabilities. Certain biomolecules on crystal substrates have been observed to display similar self-organizing capabilities, but understanding the mechanisms and rules that dictate their behavior has been elusive. Here we show that a set of simple computational rules in a Markov chain algorithm can model patterns in the spontaneous self-assembly of short peptides on two-dimensional surfaces with hexagonal lattices. The nature of this interface depends on the adopted molecular conformation of the peptide sequence upon binding. Additionally, the interface is coherent and can be tuned spatiotemporally by the peptide sequence and local environmental factors which affect folding and molecular interactions. We demonstrate, therefore, that self-organized peptides can act as molecular-scale programmable matter with controllable behavior. The ordered assembly of peptides causes instantaneous and discernible electronic responses in the substrate, paving the way for integrating biology with electronic devices. Possible real-world applications include biosensing, integrated prosthetics, brain-computer interfaces, or other biologically compatible electronic devices. The research was supported by the DMREF Program at National Science Foundation (NSF) through the MGI platform (Materials Genome Initiative) under grant numbers DMR# 1629071, 1848911, and 1922020.

Children with cerebral palsy (CP) exhibit slower walking speeds and elevated energetic costs of walking compared to typically-developing children, limiting their ability to engage with peers. To increase walking speed and reduce the energetic demands of walking, children with CP are often prescribed ankle-foot orthoses (AFOs). However, changes in walking speed, step length, and the energy costs with AFOs compared to barefoot walking in children with CP are highly heterogeneous, limiting the potential efficacy of AFO prescription. The primary neurological impairment in CP: impaired motor control, is a potential contributor to heterogeneous response to AFOs. We are investigating how increased severity of impaired motor control impacts changes in speed, step length, and energy during walking in response to varying AFO flexion stiffness. We hypothesize that increasing motor impairment severity will correspond to increased sensitivity of walking energy, speed, and step length to AFO stiffness. We developed a musculoskeletal simulation framework used to simulate walking with AFOs of varying stiffness and for different levels of impairments severity. For each simulation, we will estimate the sensitivity of walking energy, step length, and walking speed to AFO stiffness. Preliminary results showed that walking energy with more severely-impaired control was more sensitive to AFO stiffness than unimpaired control. We have since expanded the framework’s capabilities to adopt different speeds and step lengths. We have shown that the framework is robust to uncertainty in initialization parameters: the coefficient of variation of simulated walking energy was 0.11, which is reasonable for human gait. Identifying the relationship between impairment severity and sensitivity to AFO stiffness may highlight the relative importance of precise AFO tuning to achieve positive gait outcomes in children with CP. This work provides an early step towards using motor control to inform clinical AFO prescription.

Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) that have been engineered into three-dimensional heart tissues (EHTs) are valuable research tools for investigating debilitating genetic diseases that afflict the heart, such as Duchenne muscular dystrophy (DMD). Ensuring iPSC-CMs can be sufficiently matured to model such diseases remains a hurdle in current research, and maturational analysis techniques for iPSC-CMs are either qualitative, manual, or primarily based in two dimensions, leaving much to be desired. In this project, we created a suite of MATLAB image-processing scripts that can quantify the effect of three-dimensional culture and disease-causing DMD mutations on cardiomyocyte structure and maturation state. The iPSC-CMs were differentiated from stem cells, cast into EHTs, stained using immunofluorescence, and imaged using a confocal microscope. Using the scripts to analyze these 3D images of iPSC-CM stains, key maturational features of the cells can be quantified such as nuclei count; cardiomyocyte area; and sarcomere length, orientation, and z-disk width. Analyzing cardiomyocyte area can give key information on cardiomyocyte hypertrophy while examining sarcomere length, orientation, and Z-disk width can provide information on myofibril structure and organization. The suite allows analysis of these maturational features in both 2D and 3D cultures and offers a method for quantitatively assessing maturation in an automated manner. Measuring iPSC-CM maturation will also allow better comparison of existing maturational methods, such as mechanical loading, electrical stimulation, and small molecule treatment. The suite can also create graphical outputs to elegantly display data. Overall, the suite will help improve maturational analysis of EHTs, and hopefully contribute to the discovery of new treatments for diseases that affect the heart.

The pupillary light reflex (PLR) curve is an important point-of-care biomarker for the diagnosis of traumatic brain injury (TBI). Using PLR, first responders can determine the severity of TBI in the field and direct patients to a trauma center where staff can continually assess PLR to monitor TBI severity. Manual pupillometry, the most commonly available method for first responders and most clinicians wishing to assess PLR, is qualitative and often inaccurate. The current gold-standard device for PLR measurement is digital infrared pupillometry, but such devices are fragile and expensive. Our research team has developed a smartphone-based pupillometer (PupilScreen) with the ability to assess PLR using a standard iPhone, assisted by a cloud-based neural network. To demonstrate the feasibility of using PupilScreen in a realistic clinical setting and compare the accuracy of the device to the current clinical gold-standard, we have built an annotated dataset of the PLR in n=120 patients with TBI who are hospitalized in a neurological intensive care unit. Pupillometry is performed using the mobile device and the gold-standard digital infrared pupillometer. Pupil videos are manually annotated and used in the further training of our machine learning algorithm that generates a PLR curve for each patient. We anticipate that our technology will demonstrate accuracy in assessing the PLR that exceeds that of manual pupillometry and is at least equivalent to the gold-standard digital pupillometer. This technology has the potential to alleviate the current undertreatment of many TBI patients in the United States and abroad that results from a lack of accurate and cost-effective pupillometry equipment.

Metallic foams have long been sought after for their conductive and structural properties, but have not become widespread due to the extraordinarily difficult processes typically used to produce such materials. Utilizing conventional Fused Filament Fabrication (FFF), also known as Fused Deposition Modeling (FDM), 3D printing equipment and the viscous properties exhibited by the molten filament extruded during printing, we have established that these properties can produce fully customizable metallic foams. The material properties of these foams are configurable to produce varying degrees of density, scale, and geometry via the manipulation of standard printing variables such as print height, print speed, and extrusion speed. Preliminary results with polymeric FFF filaments have successfully produced foams demonstrating significant compressive strength in every direction despite being an open celled geometry with an extremely high surface area to volume ratio. Conversely, polymer foams printed with flexible materials allow us to tailor material properties for energy absorption over structural integrity. This work will establish the minimum and maximum limits of the fabrication process as well as the material properties of metallic foams. To date, our experiments have demonstrated this technique of manufacturing metallic foams is reliable, controllable and scalable with great potential to change the availability and usage of metallic foams, and could significantly impact fields such as structural engineering, automotive, and aerospace where these types of metallic foams are highly sought after.

Medical tape is used to hold essential devices to the skin for long periods of time. Unfortunately, without means for safe removal, these strong adhesives are painfully removed from the skin, often resulting in medical adhesive-related skin injuries (MARSI). Initial stakeholder interviews have indicated that medical tape removal is painful for the patient, and causes significant anxiety for nurses and caregivers. A 2015 study showed 98.6% of nurses considered skin tears common, occurring in 15% of senior patients and 17% of neonatal patients. A medical tape that offers high adhesion with means for safe removal is needed to eliminate MARSI and increase quality of care. UnTape addresses this need by providing a medical tape that has high adhesion during use but allows for easy and injury-free removal, by simply heating the tape for a few seconds with a heat pack prior to removal. The result is a rapid reduction of the force needed to remove the tape from the patient’s skin without risking MARSI. The tape is formulated with pressure-sensitive adhesive (PSA) that contains an embedded temperature-responsive additive (TRA). The additive will migrate to the surface of the tape upon heating, and melt in the range of 38-43°C, forming puddles that disrupt the adhesive and skin interface. The TRA is selected with a melting temperature that is high enough to avoid accidental peel strength reduction during fever, but below the pain threshold (45-47°C) for skin. Different additives have exhibited over a 50% reduction in peel force. This work focuses on optimization of product definition to yield consistent in vitro testing results, paving the way to clinical studies. The unique properties of UnTape allow for stronger skin adhesion for critical medical devices while eliminating the risk of MARSI upon removal, reducing nurse and patient stress, and providing higher quality medical care.

Antiretroviral therapy (ART) and pre-exposure prophylaxis (PrEP) can treat and prevent Human Immunodeficiency Virus (HIV), respectively. However, good medication adherence (≥4 doses/week) is crucial for these treatments to work effectively. Our research group recently developed the REverse TranscrIptase Chain Termination (RESTRICT) assay, a rapid enzymatic assay that measures the amount of tenofovir diphosphate (TFV-DP) present in blood, a drug that is a good indicator of long-term (1-3 month) ART/PrEP adherence. The goal of this project is to modify RESTRICT to additionally measure the amount of emtricitabine triphosphate (FTC-TP) in blood, which serves as a good indicator of short-term (1 week) adherence. RESTRICT provides the HIV reverse transcriptase (HIV RT) enzyme all the required reagents for synthesizing double-stranded DNA (dsDNA) and measures the concentration of TFV-DP and FTC-TP based on their inhibition of HIV RT activity. We designed custom DNA templates that bind preferentially to either TFV-DP or FTC-TP based on the nucleotides that they mimic. We also designed molecular beacon probes with different fluorescence dyes that bind to each DNA template and can provide fluorescence output corresponding to the amount of complementary DNA (cDNA) synthesized by HIV RT. High drug levels will lead to less cDNA synthesis and lower fluorescence intensities, indicating good adherence to treatment. Preliminary results indicate that molecular beacon probes can distinguish between the cDNA associated with each drug, which would allow for the simultaneous detection of TFV-DP and FTC-TP in a single reaction tube through the fluorescence measurements of the two types of dyes. Ongoing work is focused on optimizing RESTRICT reactions to measure clinically relevant concentrations of TFV-DP and FTC-TP. Gaining information about long- and short-term adherence to treatment through the detection of TFV-DP and FTC-TP respectively, would allow for more informed interventions by healthcare professionals to help patients improve adherence, leading to better health outcomes.