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Results for “Bioengineering”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

An actuated neural probe architecture for reducing gliosis-induced recording degradation

Glial encapsulation of chronically implanted neural probes inhibits recording and stimulation, and this signal loss is a significant factor limiting the clinical viability of most neural implant topologies for decades-long implantation. We demonstrate a mechanical proof of concept for silicon shank-style neural probes intended to minimize gliosis near the recording sites. Compliant whiskers on the edges of the probe fold inward to minimize tissue damage during insertion. Once implanted to the target depth and retracted slightly, these whiskers splay outward. The splayed tips, on which recording sites could be patterned, extend beyond the typical 50-100 micron radius of a glial scar. The whiskers are micron-scale to minimize or avoid glial scarring. Electrically inactive devices with whiskers of varying widths and curvature were designed and monolithically fabricated from a five-micron silicon-on-insulator (SOI) wafer, and their mechanical functionality was demonstrated in a 0.6% agar brain phantom. Deflection was plotted versus deflection speed, and those that were most compliant actuated successfully. This probe requires no preparation for use beyond what is typical for a shank-style silicon probe.

bioengineering↗

bioRxiv2018

Motor module generalization across balance and walking is reduced after stroke

Here, we examined features of muscle coordination associated with reduced walking performance in chronic stroke survivors. Using motor module (a.k.a. muscle synergy) analysis, we identified differences in the modular control of overground walking and standing reactive balance in stroke survivors compared to age-similar neurotypical controls. In contrast to previous studies that demonstrated reduced motor module number post-stroke, our cohort of stroke survivors did not exhibit a reduction in motor module number compared to controls during either walking or reactive balance. Instead, the pool of motor modules common to walking and reactive balance was smaller, suggesting a reduction in generalizability of motor module function across behaviors. The motor modules common to walking and reactive balance tended to be less variable and more distinct, suggesting more reliable output compared to motor modules specific to one behavior. Indeed, higher levels of motor module generalization was associated with faster walking speeds in stroke survivors. Further, recruitment of a common independent plantarflexor module across both behaviors was associated with faster walking speeds. Our work is the first to show that motor module generalization across walking and balance may help to distinguish important and clinically-relevant differences in walking performance across stroke survivors that would have been overlooked by examining only a single behavior. Finally, as similar relationships between motor module generalization and walking performance have been demonstrated in healthy young adults and individuals with Parkinsons disease, our work suggests that motor module generalization across walking and balance may be important for well-coordinated walking.\n\nNew and NoteworthyOur study is the first to simultaneously examine neuromuscular control of walking and standing reactive balance in stroke survivors. We show that motor module generalization across these behaviors (i.e., recruiting common motor modules) is reduced compared to neurotypical controls, which is associated with slower walking speeds. This is true despite no difference in motor module number between groups within each behavior, suggesting that motor module generalization across walking and balance is important for well-coordinated walking.

bioengineering↗

bioRxiv2018

Characterizing Activity and Thermostability of GH5 Cellulase Chimeras from Mesophilic and Thermophilic Parents

Cellulases from glycoside hydrolase (GH) family 5 are key enzymes in the degradation of diverse polysaccharide substrates and are used in industrial enzyme cocktails to break down biomass. The GH5 family shares a canonical ({beta})8-barrel structure, where each ({beta}) module is essential for the enzyme stability and activity. Despite their shared topology, the thermostability of GH5 enzymes can vary significantly, and highly thermostable variants are often sought for industrial applications. Based on a previously characterized thermophilic GH5 cellulase from Talaromyces emersonii (TeEgl5A, with an optimal temperature of 90{degrees}C), we created ten hybrid enzymes with the mesophilic cellulase from Prosthecium opalus (PoCel5) to determine which elements are responsible for enhanced thermostability. Five of the expressed hybrid enzymes exhibit enzyme activity. Two of these hybrids exhibited pronounced increases in the temperature optima (10 and 20{degrees}C), T50 (15 and 19{degrees}C), Tm (16.5 and 22.9{degrees}C), and extended half life, t1/2 (~240- and 650-fold at 55{degrees}C) relative to the mesophilic parent enzyme, and demonstrated improved catalytic efficiency on selected substrates. The successful hybridization strategies were validated experimentally in another GH5 cellulase from Aspergillus nidulans (AnCel5), which demonstrated a similar increase in thermostability. Based on molecular dynamics simulations (MD) of both PoCel5 and TeEgl5A parent enzymes as well as their hybrids, we hypothesize that improved hydrophobic packing of the interface between 2 and 3 is the primary mechanism by which the hybrid enzymes increase their thermostability relative to the mesophilic parent PoCel5.\n\nIMPORTANCEThermal stability is an essential property of enzymes in many industrial biotechnological applications, as high temperatures improve bioreactor throughput. Many protein engineering approaches, such as rational design and directed evolution, have been employed to improve the thermal properties of mesophilic enzymes. Structure-based recombination has also been used to fuse TIM-barrel fragments and even fragments from unrelated folds, to generate new structures. However, there are not many research on GH5 cellulases. In this study, two GH5 cellulases, which showed TIM-barrel structure, PoCel5 and TeEgl5A with different thermal properties were hybridized to study the roles of different ({beta}) motifs. This work illustrates the role that structure guided recombination can play in helping to identify sequence function relationships within GH5 enzymes by supplementing natural diversity with synthetic diversity.

bioengineering↗

bioRxiv2018

Skin Lesion Segmentation with Improved C-UNet Networks

--This paper proposes an innovative method for Part1, skin lesion segmentation of the ISIC 2018 Challenge. Our network C-UNet is based on UNet network, we combined several methods on this basic network which made some improvements on Jaccard Index ultimately, our method yield an average Jaccard Index of 0.77 on the On-line validation dataset.

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bioRxiv2018

Nanoscale investigation in 3D scaffolds of cell-material interactions for tissue-engineering

Cell fate is largely determined by interactions that occur at the interface between cells and their surrounding microenvironment. For this reason, especially in the field of cell- and tissue-engineering, there is a growing interest in developing characterization techniques that allow a deep evaluation of cell-material interaction at the nanoscale, particularly focusing on cell adhesion processes. While for 2D culturing systems a consolidated series of tools already satisfy this need, in 3D environments, more closely recapitulating complex in vivo structures, there is still a lack of procedure furthering the comprehension of cell-material interactions. Here, we report for the first time the use of a SEM/FIB system for the characterization of cellular adhesion in 3D scaffolds fabricated by means of different techniques. Our results clearly show the capability of the developed approach to finely resolve both scaffold-cells interface and nanometer scale features of cell bodies involved in the upregulation of cellular behavior. These results are relevant for studying cellular guidance strategies and for the consequent design of more efficient cell-instructive platforms for tissue-engineering applications as well as for in vitro 3D models.

bioengineering↗

bioRxiv2018

Mesenchymal Stem Cell Chondroinduction on Cellulose-Silk Composites is Driven by Substrate Elasticity

Biomaterials that can physically control the fate of stem cells are critical for the application of in situ tissue engineering. However, the mechanisms underlying this phenomenon remain unclear. In this study, cellulose and silk composite substrates, known to induce physically the chondrogenic differentiation of human mesenchymal stem cells (MSCs), were regenerated to fabricate two-dimensional film surfaces. MSCs were grown on these surfaces in the presence of chemicals that interfere with the biochemical and mechanical signalling pathwys of MSCs. The data shows that preventing substrate surface elasticity transmission results in significant downregulation of chondrogenic gene expression. Interference with the classical, chondrogenic Smad2/3 Phosphorylation pathway does not impact the chondrogenic capacity of the substrates. The results highlight the importance of the substrate mechanical elasticity on chondrogenic MSCs and its independence of known chondrogenic biochemical pathways.

bioengineering↗

bioRxiv2018

A pilot investigation of chemonucleolysis-induced intervertebral disc degeneration in the ovine lumbar spine

Intervertebral disc (IVD) degeneration (IVDD) initiates in the nucleus pulposus (NP) and is marked by elevated levels of pro-inflammatory cytokines and matrix-degrading proteases, leading to structural and functional disruption. IVDD therapeutics are currently being investigated; however, such approaches require validation using large animal models that recapitulate clinical, biochemical, and biomechanical hallmarks of the human pathology. Others have previously utilized intradiscal administration of chondroitinase-ABC (C-ABC) to initiate IVDD in the NP of sheep lumbar IVDs. While these studies examined changes in IVD height, hydration, and tissue micro-architecture, changes in biochemical content and mechanical properties were not assessed. Thus, the objective herein was to comprehensively characterize this ovine model IVDD for salient features reported in human degenerate IVDs by evaluating biochemical, biomechanical, and histological changes. Briefly, C-ABC (1U) was administered via intradiscal injection into the L1/2, L2/3, and L3/4 IVDs, and degeneration was assessed at 6- and 10-weeks via longitudinal magnetic resonance (MR) imaging. After 6 weeks, degenerative samples showed significant reductions in IVD heights (p=0.048) and MR imaging index (p=0.048), which worsened at 10 weeks. Post-mortem degenerate and controls IVDs were evaluated for differences in interleukin-1{beta} concentration, axial and torsional functional spinal unit kinematics, and histological microarchitecture. Degenerate IVDs demonstrated significantly elevated concentrations of interleukin-1{beta} (p=0.002). Additionally, degenerative samples showed increased creep displacement (p=0.022) and compressive stiffnesss (p=0.007) concurrent with decreased long-term elastic (p=0.007) and viscous dampening coefficients (p=0.002). Histological analysis of degenerative IVDs showed changes in microarchitecture, including derangement of the nucleus pulposus and annulus fibrosus tissue as well as cartilaginous end-plate irregularities. This pilot study demonstrated that intradiscal injection of 1U C-ABC induces significant and progressive degeneration of sheep lumbar IVDs over the time course investigated. The changes observed in this pilots study small sample size resemble the hallmarks of moderate to severe IVD degeneration observed in humans. Further study is warranted on a larger sample size to further validate these findings.

bioengineering↗

bioRxiv2018

MEMS-Actuated Carbon Fiber Microelectrode for Neural Recording

Microwire and microelectrode arrays used for cortical neural recording typically consist of tens to hundreds of recording sites, but often only a fraction of these sites are in close enough proximity to firing neurons to record single-unit activity. Recent work has demonstrated precise, depth-controllable mechanisms for the insertion of single neural recording electrodes, but these methods are mostly only capable of inserting electrodes which elicit adverse biological response. We present an electrostatic-based actuator capable of inserting individual carbon fiber microelectrodes which elicit minimal to no adverse biological response. The device is shown to insert a carbon fiber recording electrode into an agar brain phantom and can record an artificial neural signal in saline. This technique provides a platform generalizable to many microwire-style recording electrodes.

bioengineering↗

bioRxiv2018

Proprioceptive Sonomyographic Control: A novel method of intuitive proportional control of multiple degrees of freedom for upper-extremity amputees

Technological advances in multi-articulated prosthetic hands have outpaced the methods available to amputees to intuitively control these devices. Amputees often cite difficulty of use as a key contributing factor for abandoning their prosthesis, creating a pressing need for improved control technology. A major challenge of traditional myoelectric control strategies using surface electromyography electrodes has been the difficulty in achieving intuitive and robust proportional control of multiple degrees of freedom. In this paper, we describe a new control method, proprioceptive sonomyographic control that overcomes several limitations of myoelectric control. In sonomyography, muscle mechanical deformation is sensed using ultrasound, as compared to electrical activation, and therefore the resulting control signals can directly control the position of the end effector. Compared to myoelectric control which controls the velocity of the end-effector device, sonomyographic control is more congruent with residual proprioception in the residual limb. We tested our approach with 5 upper-extremity amputees and able-bodied subjects using a virtual target achievement and holding task. Amputees and able-bodied participants demonstrated the ability to achieve positional control for 5 degrees of freedom with an hour of training. Our results demonstrate the potential of proprioceptive sonomyographic control for intuitive dexterous control of multiarticulated prostheses.

bioengineering↗

bioRxiv2018

Proton Conductivity of Glycosaminoglycans

Proton (H+) conductivity is important in many natural phenomena including oxidative phosphorylation in mitochondria and archea, uncoupling membrane potentials by the antibiotic Gramicidin, and proton actuated bioluminescence in dinoflagellate. In all of these phenomena, the conduction of H+ occurs along chains of hydrogen bonds between water and hydrophilic residues. These chains of hydrogen bonds are also present in many hydrated biopolymers and macromolecule including collagen, keratin, chitosan, and various proteins such as reflectin. All of these materials are also proton conductors. Recently, our group has discovered that the jelly found in the Ampullae of Lorenzini-sharks electrosensing organs- is the highest naturally occurring proton conducting substance. The jelly has a complex composition, but we attributed the conductivity to the glycosaminoglycan keratan sulfate (KS). Here, we have measured the proton conductivity of hydrated keratan sulfate using PdHx contacts to be 0.50 {+/-} 0.11 mS cm -1- consistent to that of Ampullae of Lorenzini jelly, 2 {+/-} 1 mS cm -1. Proton conductivity, albeit with lower values, is also shared by other glycosaminoglycans with similar chemical structures including dermatan sulfate, chondroitin sulfate A, heparan sulfate, and hyaluronic acid. This observation confirms the structure property relationship between proton conductivity and the chemical structure of biopolymers.

bioengineering↗

bioRxiv2018

Real time monitoring of transtibial elevated vacuum prostheses: a case series on socket air pressure

Elevated vacuum is a prosthetic suspension method used to reduce slippage between the prosthetic socket and the residual limb. Evaluation of the effectiveness of these systems is limited due to a lack of correlation to actual socket air pressure, particularly during unconstrained movements. This may explain some of the variability in functional outcomes reported in the literature. We developed a light-weight portable socket measurement system to quantify internal socket air pressure, temperature, and acceleration. We implemented the system onto the sockets of three transtibial prosthesis users with mechanical elevated vacuum pumps. Participants completed five functional tasks with and without the vacuum pumps actively connected, including the 2-Minute Walk test, 5-Times Sit-to-Stand test, 4-Square Step test, L-Test, and Figure-8 test. Results demonstrated that the use of elevated vacuum pumps produced different gait profiles and pressure ranges for each user, with significant differences between pump conditions. Two of the participants demonstrated substantially lower air pressure (higher vacuum) over time while the pump was active compared to inactive. The minimum air pressure measured at the completion of the 2-Minute Walk test was -34.6 {+/-} 7.7 kPa, which is not as low as pressures reported in literature during benchtop experiments. One participant did not show substantial changes in pressure over time for either pump condition. Functional task performance was not significantly different between pump conditions. Correlation with accelerometer readings allowed air pressure data to be aligned with the gait cycle; peak positive pressures occurred just following initial contact of the foot in early stance, and the most negative pressures (vacuum) were observed throughout swing. This study has demonstrated the use of a portable data logging tool that may serve the clinical and research communities to quantify the operation of elevated vacuum systems, and better understand the variability of mechanical pump operation and overall system performance.

bioengineering↗

bioRxiv2018

Experimental study of Young modulus of Attacus atlas, Vespa crabro, and Libellula depressa wings

This paper describes a scientific research aimed at obtaining data for determining Young modulus of the wings of selected insects species. A small testing machine intended for three-point bending and equipped with instruments registering low forces was constructed for the needs of the experiment. The machine was used to perform numerous bending tests of wings of three species of insects (obtained from a breeding farm): Attacus atlas, Vespa crabro, Libellula depressa in various air-humidity conditions. Values of the force and displacement obtained in the course of the tests were used to calculate Young modulus. In order to do so, it was also necessary to obtain the moment of inertia of the wing cross-section. These values were measured on the basis of the images obtained with a SEM microscope. Obtained results were averaged and presented with a breakdown by air-humidity conditions. It was observed that Young modulus decreased with an increase of humidity; hence the calculations of the percentage decrease of this mechanical parameter were performed. Obtained results were compared with the observed structure which was also presented under light microscope. It transpired that the construction of a wing does not only influence the mechanical values but also it influences their susceptibility to the changes occurring in the environment. Thereby, differences between Lepidoptera and Hymenoptera insects were indicated also within the aspect discussed in this paper.

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↗

bioRxiv2018

Surface Plasmon Resonance Imaging of Excitable Cells

Surface plasmons are highly sensitive to refractive index variations adjacent to the surface. This sensitivity has been exploited successfully for chemical and biological assays. In these systems, a surface plasmon resonance (SPR)-based sensor detects temporal variations in the refractive index at a point. SPR has also been used in imaging systems where the spatial variations of refractive index in the sample provide the contrast mechanism. A high numerical aperture objective lens has been used to design SPR microscopy systems with the ability to image adherent live cells. Addressing research questions in cell physiology and pharmacology often requires the development of a multimodal microscope where complementary information can be obtained.\n\nIn this paper, we present the development of a multimodal microscope that combines surface plasmon resonance imaging with a number of additional imaging modalities including bright-field, epi-fluorescence, total internal reflection microscopy (TIRM) and SPR fluorescence microscopy. We used a high numerical aperture objective lens to achieve SPR and TIR microscopy with the ability to image adherent live cells non-invasively. The platform has been used to image live cell cultures demonstrating both fluorescent and label-free techniques. The SPR and TIR imaging systems feature a wide field of view (300 {micro}m) that allows measurements from multiple cells while the resolution is sufficient to image fine cellular processes. The ability of the platform to perform label-free functional imaging of living cell was demonstrated by imaging the spatial variations in contraction of stem cell-derived cardiomyocytes. This technique has a promise for non-invasive imaging of the development of cultured cells over very long periods of time.

bioengineering↗

bioRxiv2018

Fast, versatile, and quantitative annotation of complex images

We report a generic smartphone app for quantitative annotation of complex images. The app is simple enough to be used by children, and annotation tasks are distributed across app users, contributing to efficient annotation. We demonstrate its flexibility and speed by annotating >30,000 images, including features of rice root growth and structure, stem cell aggregate morphology, and complex worm (C. elegans) postures, for which we show that the speed of annotation is >130-fold faster than state-of-the-art techniques with similar accuracy.

bioengineering↗

bioRxiv2018

The saturation gap: a simple transformation of oxygen saturation using virtual shunt

ObjectivePeripheral oxygen saturation (SpO2) obtained from pulse oximetry is a widely used physiological measurement. Clinical interpretation is limited by the nonlinear relationship between SpO2, degree of impairment in gas exchange, and effect of altitude. SpO2 is frequently dichotomized to overcome these limitations during prediction modelling. Using the known physiological relationship between virtual shunt and SpO2, we propose the saturation gap as a transformation of SpO2.\n\nApproachWe computed the theoretical virtual shunt corresponding to various SpO2 values and derived an accurate approximation formula between virtual shunt and SpO2. The approximation was based on previously described empiric observations and known physiological relationships. We evaluated the utility of the saturation gap in a clinical study predicting the need for facility admission in children in a rural health-care setting.\n\nMain ResultsThe transformation was saturation gap = 49.314*log10(103.711 - SpO2) -37.315. The ability to predict hospital admission based on a continuous variable SpO2 or saturation gap produced an identical area under the curve of 0.71 (95% CI: 0.69-0.73), compared to only 0.57 (CI: 0.56-0.58) based on diagnosis of hypoxemia (defined as SpO2<90%). However, SpO2 demonstrated a lack of fit compared to saturation gap (goodness-of-fit test p-value <0.0001 versus 0.098). The observed admission rates varied linearly with saturation gap but varied nonlinearly with SpO2.\n\nSignificanceThe saturation gap estimates a continuous linearly interpretable disease severity from SpO2 and improves clinical prediction models. The saturation gap will also allow for straightforward incorporation of altitude in interpretation of measurements of SpO2.

bioengineering↗

bioRxiv2018

Stable biphasic interfaces for open microfluidic platforms

We present an open microfluidic platform that enables stable flow of an organic solvent over an aqueous solution. The device features apertures connecting a lower aqueous channel to an upper solvent compartment that is open to air, enabling easy removal of the solvent for analysis. We have previously shown that related open biphasic systems enable steroid hormone extraction from human cells in microscale culture and secondary metabolite extraction from microbial culture; here we build on our prior work by determining conditions under which the system can be used with extraction solvents of ranging polarities, a critical feature for applying this extraction platform to diverse classes of metabolites. We develop an analytical model that predicts the limits of stable aqueous-organic interfaces based on analysis of Laplace pressure. With this analytical model and experimental testing, we developed generalized design rules for creating stable open microfluidic biphasic systems with solvents of varying densities, aqueous-organic interfacial tensions, and polarities. The stable biphasic interfaces afforded by this device will enable on-chip extraction of diverse metabolite structures and novel applications in microscale biphasic chemical reactions.

bioengineering↗

bioRxiv2018

Generation of Highly Diverse Peptide Library by Linear-double-stranded DNA Based AND Logic Computation in Mammalian Cells

DNA-encoded peptide libraries are ideal functional peptide discovery platforms for their extremely large capacity. However, its still difficult to build high content peptide library in intact mammalian cells, which offer advantages associated with appropriate protein modification, proper protein folding, and natural status of membrane protein. Our previous work established linear-double-stranded DNAs (ldsDNAs) as innovative biological parts to implement AND gate genetic circuits in mammalian cell line. In the current study, we employ ldsDNA with terminal NNK degenerate codons as AND gate input to build highly diverse peptide library in mammalian cells. This ldsDNA-based AND gate (LBAG) peptide strategy is easy to conduct, only PCR reaction and cell transfection experiments are needed. High-throughput sequencing (HTS) results reveal that our new LBAG strategy could generate peptide library with both amino acid sequence and peptide length diversities. Moreover, by a mammalian cell two-hybrid system, we pan an MDM2 protein interacting peptide through the LBAG peptide library. Our work establishes ldsDNA as biological parts for building highly diverse peptide library in mammalian cells.

bioengineering↗