Biomedical Engineering - Research Publications
Now showing items 1-12 of 85
Hybrid diamond/ carbon fiber microelectrodes enable multimodal electrical/chemical neural interfacing
Implantable medical devices are now in regular use to treat or ameliorate medical conditions, including movement disorders, chronic pain, cardiac arrhythmias, and hearing or vision loss. Aside from offering alternatives to pharmaceuticals, one major advantage of device therapy is the potential to monitor treatment efficacy, disease progression, and perhaps begin to uncover elusive mechanisms of diseases pathology. In an ideal system, neural stimulation, neural recording, and electrochemical sensing would be conducted by the same electrode in the same anatomical region. Carbon fiber (CF) microelectrodes are the appropriate size to achieve this goal and have shown excellent performance, in vivo. Their electrochemical properties, however, are not suitable for neural stimulation and electrochemical sensing. Here, we present a method to deposit high surface area conducting diamond on CF microelectrodes. This unique hybrid microelectrode is capable of recording single-neuron action potentials, delivering effective electrical stimulation pulses, and exhibits excellent electrochemical dopamine detection. Such electrodes are needed for the next generation of miniaturized, closed-loop implants that can self-tune therapies by monitoring both electrophysiological and biochemical biomarkers.
A deep learning approach for designed diffraction-based acoustic patterning in microchannels.
(Nature Publishing Group, 2020-05-26)
Acoustic waves can be used to accurately position cells and particles and are appropriate for this activity owing to their biocompatibility and ability to generate microscale force gradients. Such fields, however, typically take the form of only periodic one or two-dimensional grids, limiting the scope of patterning activities that can be performed. Recent work has demonstrated that the interaction between microfluidic channel walls and travelling surface acoustic waves can generate spatially variable acoustic fields, opening the possibility that the channel geometry can be used to control the pressure field that develops. In this work we utilize this approach to create novel acoustic fields. Designing the channel that results in a desired acoustic field, however, is a non-trivial task. To rapidly generate designed acoustic fields from microchannel elements we utilize a deep learning approach based on a deep neural network (DNN) that is trained on images of pre-solved acoustic fields. We use then this trained DNN to create novel microchannel architectures for designed microparticle patterning.
Critical Review of Transcutaneous Vagus Nerve Stimulation: Challenges for Translation to Clinical Practice
(Frontiers Media, 2020-04-28)
Several studies have illustrated that transcutaneous vagus nerve stimulation (tVNS) can elicit therapeutic effects that are similar to those produced by its invasive counterpart, vagus nerve stimulation (VNS). VNS is an FDA-approved therapy for the treatment of both depression and epilepsy, but it is limited to the management of more severe, intervention-resistant cases as a second or third-line treatment option due to perioperative risks involved with device implantation. In contrast, tVNS is a non-invasive technique that involves the application of electrical currents through surface electrodes at select locations, most commonly targeting the auricular branch of the vagus nerve (ABVN) and the cervical branch of the vagus nerve in the neck. Although it has been shown that tVNS elicits hypo- and hyperactivation in various regions of the brain associated with anxiety and mood regulation, the mechanism of action and influence of stimulation parameters on clinical outcomes remains predominantly hypothetical. Suppositions are largely based on correlations between the neurobiology of the vagus nerve and its effects on neural activity. However, tVNS has also been investigated for several other disorders, including tinnitus, migraine and pain, by targeting the vagus nerve at sites in both the ear and the neck. As most of the described methods differ in the parameters and protocols applied, there is currently no firm evidence on the optimal location for tVNS or the stimulation parameters that provide the greatest therapeutic effects for a specific condition. This review presents the current status of tVNS with a focus on stimulation parameters, stimulation sites, and available devices. For tVNS to reach its full potential as a non-invasive and clinically relevant therapy, it is imperative that systematic studies be undertaken to reveal the mechanism of action and optimal stimulation modalities.
On-chip surface acoustic wave and micropipette aspiration techniques to assess cell elastic properties.
(A I P Publishing LLC, 2020-01)
The cytoskeletal mechanics and cell mechanical properties play an important role in cellular behaviors. In this study, in order to provide comprehensive insights into the relationship between different cytoskeletal components and cellular elastic moduli, we built a phase-modulated surface acoustic wave microfluidic device to measure cellular compressibility and a microfluidic micropipette-aspiration device to measure cellular Young's modulus. The microfluidic devices were validated based on experimental data and computational simulations. The contributions of structural cytoskeletal actin filament and microtubule to cellular compressibility and Young's modulus were examined in MCF-7 cells. The compressibility of MCF-7 cells was increased after microtubule disruption, whereas actin disruption had no effect. In contrast, Young's modulus of MCF-7 cells was reduced after actin disruption but unaffected by microtubule disruption. The actin filaments and microtubules were stained to confirm the structural alteration in cytoskeleton. Our findings suggest the dissimilarity in the structural roles of actin filaments and microtubules in terms of cellular compressibility and Young's modulus. Based on the differences in location and structure, actin filaments mainly contribute to tensile Young's modulus and microtubules mainly contribute to compressibility. In addition, different responses to cytoskeletal alterations between acoustophoresis and micropipette aspiration demonstrated that micropipette aspiration was better at detecting the change from actin cortex, while the response to acoustophoresis was governed by microtubule networks.
Assessing Species Diversity Using Metavirome Data: Methods and Challenges
(ELSEVIER SCIENCE BV, 2017-01-01)
Assessing biodiversity is an important step in the study of microbial ecology associated with a given environment. Multiple indices have been used to quantify species diversity, which is a key biodiversity measure. Measuring species diversity of viruses in different environments remains a challenge relative to measuring the diversity of other microbial communities. Metagenomics has played an important role in elucidating viral diversity by conducting metavirome studies; however, metavirome data are of high complexity requiring robust data preprocessing and analysis methods. In this review, existing bioinformatics methods for measuring species diversity using metavirome data are categorised broadly as either sequence similarity-dependent methods or sequence similarity-independent methods. The former includes a comparison of DNA fragments or assemblies generated in the experiment against reference databases for quantifying species diversity, whereas estimates from the latter are independent of the knowledge of existing sequence data. Current methods and tools are discussed in detail, including their applications and limitations. Drawbacks of the state-of-the-art method are demonstrated through results from a simulation. In addition, alternative approaches are proposed to overcome the challenges in estimating species diversity measures using metavirome data.
CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision
BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge. In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. CoMet utilizes coverage values and the compositional features of metagenomic contigs. The binning strategy in CoMet includes the initial grouping of contigs in guanine-cytosine (GC) content-coverage space and refinement of bins in tetranucleotide frequencies space in a purely unsupervised manner. With CoMet, the clustering algorithm DBSCAN is employed for binning contigs. The performances of CoMet were compared against four existing approaches for binning a single metagenomic sample, including MaxBin, Metawatt, MyCC (default) and MyCC (coverage) using multiple datasets including a sample comprised of multiple strains. RESULTS: Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. CoMet yielded higher or comparable precision in comparison to the existing binning methods on benchmark datasets of varying complexities. MyCC (coverage) had the highest ranking score in F1-score. However, the performances of CoMet were higher than MyCC (coverage) on the dataset containing multiple strains. Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. CoMet resulted in higher precision than MyCC (default) and MyCC (coverage) on a real metagenome. CONCLUSIONS: The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. The F1-scores obtained from different binning strategies vary with different datasets; however, CoMet yields the highest F1-score with a sample comprised of multiple strains.
Methods for the Detection of Seizure Bursts in Epilepsy
(FRONTIERS MEDIA SA, 2019-02-27)
Background: Seizure clusters and “bursts” are of clinical importance. Clusters are reported to be a marker of antiepileptic drug resistance. Additionally, seizure clustering has been found to be associated with increased morbidity and mortality. However, there are no statistical methods described in the literature to delineate bursting phenomenon in epileptic seizures. Methods: We present three automatic burst detection methods referred to as precision constrained grouping (PCG), burst duration constrained grouping (BCG), and interseizure interval constrained grouping (ICG). Concordance correlation coefficients were used to confirm the pairwise agreement between common bursts isolated using these three automatic burst detection procedures. Additionally, three graphical methods were employed to demonstrate seizure bursts: modified scatter plots, staircase plots, and dropline plots. Burst detection procedures are demonstrated on data from continuous intracranial ambulatory EEG monitoring in a patient diagnosed with drug-refractory focal epilepsy. Results: We analyzed 1,569 seizures, from our assigned index patient, captured on ambulatory intracranial EEG monitoring. A total of 31, 32, and 32 seizure bursts were detected by the three quantitative methods (BCG, ICG, and PCG), respectively. The concordance correlation coefficient was ≥0.99 signifying considerably stronger than chance burst detector agreements with one another. Conclusions: Bursting is a quantifiable temporal phenomenon in epilepsy and seizure bursts can be reliably detected using our methodology.
Is seizure frequency variance a predictable quantity?
Background: There is currently no formal method for predicting the range expected in an individual's seizure counts. Having access to such a prediction would be of benefit for developing more efficient clinical trials, but also for improving clinical care in the outpatient setting. Methods: Using three independently collected patient diary datasets, we explored the predictability of seizure frequency. Three independent seizure diary databases were explored: SeizureTracker (n = 3016), Human Epilepsy Project (n = 93), and NeuroVista (n = 15). First, the relationship between mean and standard deviation in seizure frequency was assessed. Using that relationship, a prediction for the range of possible seizure frequencies was compared with a traditional prediction scheme commonly used in clinical trials. A validation dataset was obtained from a separate data export of SeizureTracker to further verify the predictions. Results: A consistent mathematical relationship was observed across datasets. The logarithm of the average seizure count was linearly related to the logarithm of the standard deviation with a high correlation (R2 > 0.83). The three datasets showed high predictive accuracy for this log-log relationship of 94%, compared with a predictive accuracy of 77% for a traditional prediction scheme. The independent validation set showed that the log-log predicted 94% of the correct ranges while the RR50 predicted 77%. Conclusion: Reliably predicting seizure frequency variability is straightforward based on knowledge of mean seizure frequency, across several datasets. With further study, this may help to increase the power of RCTs, and guide clinical practice.
Simulating Clinical Trials With and Without Intracranial EEG Data.
OBJECTIVE: It is currently unknown if knowledge of clinically silent (electrographic) seizures improves the statistical efficiency of clinical trials. METHODS: Using data obtained from 10 patients with chronically implanted subdural electrodes over an average of 1 year, a Monte Carlo bootstrapping simulation study was performed to estimate the statistical power of running a clinical trial based on A) patient reported seizures with intracranial EEG (icEEG) confirmation, B) all patient reported events, or C) all icEEG confirmed seizures. A "drug" was modeled as having 10%, 20%, 30%, 40% and 50% efficacy in 1000 simulated trials each. Outcomes were represented as percentage of trials that achieved p<0.05 using Fisher Exact test for 50%-responder rates (RR50), and Wilcoxon Rank Sum test for median percentage change (MPC). RESULTS: At each simulated drug strength, the MPC method showed higher power than RR50. As drug strength increased, statistical power increased. For all cases except RR50 with drug of 10% efficacy, using patient reported events (with or without icEEG confirmation) was not as statistically powerful as using all available intracranially confirmed seizures (p<0.001). SIGNIFICANCE: This study demonstrated using simulation that additional accuracy in seizure detection using chronically implanted icEEG improves statistical power of clinical trials. Newer invasive and noninvasive seizure detection devices may have the potential to provide greater statistical efficiency, accelerate drug discovery and lower trial costs.
Critical slowing down as a biomarker for seizure susceptibility.
(Nature Research (part of Springer Nature), 2020-05-01)
The human brain has the capacity to rapidly change state, and in epilepsy these state changes can be catastrophic, resulting in loss of consciousness, injury and even death. Theoretical interpretations considering the brain as a dynamical system suggest that prior to a seizure, recorded brain signals may exhibit critical slowing down, a warning signal preceding many critical transitions in dynamical systems. Using long-term intracranial electroencephalography (iEEG) recordings from fourteen patients with focal epilepsy, we monitored key signatures of critical slowing down prior to seizures. The metrics used to detect critical slowing down fluctuated over temporally long scales (hours to days), longer than would be detectable in standard clinical evaluation settings. Seizure risk was associated with a combination of these signals together with epileptiform discharges. These results provide strong validation of theoretical models and demonstrate that critical slowing down is a reliable indicator that could be used in seizure forecasting algorithms.
Stimulation Strategies for Improving the Resolution of Retinal Prostheses.
(Frontiers Media, 2020-03-26)
Electrical stimulation using implantable devices with arrays of stimulating electrodes is an emerging therapy for neurological diseases. The performance of these devices depends greatly on their ability to activate populations of neurons with high spatiotemporal resolution. To study electrical stimulation of populations of neurons, retina serves as a useful model because the neural network is arranged in a planar array that is easy to access. Moreover, retinal prostheses are under development to restore vision by replacing the function of damaged light sensitive photoreceptors, which makes retinal research directly relevant for curing blindness. Here we provide a progress review on stimulation strategies developed in recent years to improve the resolution of electrical stimulation in retinal prostheses. We focus on studies performed with explanted retinas, in which electrophysiological techniques are the most advanced. We summarize achievements in improving the spatial and temporal resolution of electrical stimulation of the retina and methods to selectively stimulate neurons with different visual functions. Future directions for retinal prostheses development are also discussed, which could provide insights for other types of neuromodulatory devices in which high-resolution electrical stimulation is required.
Spider-silk inspired polymeric networks by harnessing the mechanical potential of β-sheets through network guided assembly.
(Springer Nature, 2020-04-02)
The high toughness of natural spider-silk is attributed to their unique β-sheet secondary structures. However, the preparation of mechanically strong β-sheet rich materials remains a significant challenge due to challenges involved in processing the polymers/proteins, and managing the assembly of the hydrophobic residues. Inspired by spider-silk, our approach effectively utilizes the superior mechanical toughness and stability afforded by localised β-sheet domains within an amorphous network. Using a grafting-from polymerisation approach within an amorphous hydrophilic network allows for spatially controlled growth of poly(valine) and poly(valine-r-glycine) as β-sheet forming polypeptides via N-carboxyanhydride ring opening polymerisation. The resulting continuous β-sheet nanocrystal network exhibits improved compressive strength and stiffness over the initial network lacking β-sheets of up to 30 MPa (300 times greater than the initial network) and 6 MPa (100 times greater than the initial network) respectively. The network demonstrates improved resistance to strong acid, base and protein denaturants over 28 days.