A dual-channel imaging system with single fluorophore sensitivity was assembled in this lab. Inclusion of an integrated laser combiner was introduced to facilitate simultaneous dual-channel imaging. The imaging system has been applied to study the structure, stoichiometry, distance and function of the phi29 DNA packaging motor. Approaches including single molecule photobleaching, single molecule FRET and binomial distribution quantification were carried out to clarify the stoichiometry and distance of pRNA on the biologically active packaging motor. The results were statistically analyzed to access the copy number of pRNA, and the distance constraint was used to verify the 3D structure of the computer model of phi29 DNA packaging motor.
A cortical neuron with carbon nanotube circuit elements that performs nonlinear dendritic computations with excitatory and inhibitory post-synaptic potentials is presented. An inhibitory synapse with controllable parameters that implement plasticity is described. The circuit design was simulated using carbon nanotube spice models, showing that the neuron fires as long as the inhibitory post-synaptic potential is weak or absent. Strong inhibitory potentials prevent the neuron from firing.
Plasmon-resonant gold nanorods have been examined as multifunctional agents for imaging and photoactivated therapies. Au nanorods can be imaged with single-particle sensitivity by two-photon luminescence (TPL) when excited by pulsed NIR laser irradiation, and have been detected in vivo while passing through blood vessels at subpicomolar concentrations. TPL imaging can also be used to characterize the targeted delivery of ligand-functionalized nanorods to tumor cells. Nanorods were coated with oligoethyleneglycol (OEG) units using in situ dithiocarbamate formation, a novel and robust method of surface functionalization. Nanorods coated with OEG were shielded from nonspecific cell uptake, whereas those functionalized with folate-terminated OEG chains accumulated on the surface of tumor cells expressing their cognate receptor. Cells labeled with folate-conjugated nanorods can mediate photothermal effects when irradiated at NIR wavelengths, often resulting in a dramatic blebbing of the cell membrane, which was determined to be caused indirectly by the influx of extracellular Ca 2+ following perforation of the cell membrane. With respect to preclinical testing, a protocol has been developed for the exhaustive removal of CTAB, a cytotoxic surfactant used in nanorod synthesis. Treatment with polystyrenesulfonate can yield “CTAB-free” nanorods with negligible toxicity.
Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive interactive methods. The goal of segmentation is to identify the regions inside the density map that correspond to individual components. We present a multi-scale segmentation method for accomplishing this task that requires very little user interaction. The method uses the concept of scale space, which is created by convolution of the input density map with a Gaussian filter. The latter process smoothes the density map. The standard deviation of the Gaussian filter is varied, with smaller values corresponding to finer scales and larger values to coarser scales. Each of the maps at different scales is segmented using the watershed method, which is very efficient, completely automatic, and does not require the specification of seed points. Some detail is lost in the smoothing process. A sharpening process reintroduces detail into the segmentation at the coarsest scale by using the segmentations at the finer scales. We apply the method to simulated density maps, where the exact segmentation (or ground truth) is known, and rigorously evaluate the accuracy of the resulting segmentations.
Advancements in low power wireless communication and system on chip design have opened up the possibility of developing miniaturized sensor nodes. These sensors can either be deployed on the human body (non-invasive) or implanted inside it (invasive) to collect vital physiological information and wirelessly transmit it to the system database. At the system backend this data is stored, processed, analyzed, and taken action if required. In this paper we propose the hardware architecture of a low-power, low-cost, small footprint, plug & play sensor node that is suitable for monitoring the vital signs. An event driven operating system is built for the sensor node to efficiently run the house keeping tasks and communicate with the gateway. As a proof of concept, an Electrocardiogram (ECG) monitoring application for body area networks using this sensor node has been developed.
Nanotopographic structures occur naturally within the extracellular matrix of many tissues, influencing a wide range of properties through mechanotransductive interactions. Synthetic cell-nanotopography interactions have been explored as a way of controlling cell behaviors including orientation, adhesion, migration, proliferation and cytoskeletal organization. Until recently these processes have been explored using traditional cell culture substrates for laboratory investigations, including titanium, glass, ceramics, silicon, polystyrene and PolyDiMethylSiloxane (PDMS), as well as on numerous disordered nanostructured materials such as collagen. Nanopatterned PDMS exhibits unique utility for in vitro studies including fundamental studies on cell-nanotopography interactions as well as structures that can serve as template for tissue organization. Emerging research is exploring nanoscale mechanotransduction on biodegradable substrates suitable for implantation, thereby paving the way for the development of engineered tissues with tunable mechanical and functional properties. Here recent developments in nanoscale modification of substrates for tissue engineering and regenerative medicine are described, with an emphasis on how these studies might ultimately lead to advanced approaches for patient care.
Pattern recognition techniques can potentially be used to quantitatively analyze a wide variety of biomedical images. A challenge in applying this methodology is that biomedical imaging uses many imaging modalities and subjects. Pattern recognition relies on numerical image descriptors (features) to describe image content. Thus, the application of pattern recognition to biomedical imaging requires the development of a wide variety of image features. In this study we compared the efficacy of different techniques for constructing large feature spaces. A two-stage method was employed where several types of derived images were used as inputs for a bank of feature extraction algorithms. Image pyramids, subband filters, and image transforms were used in the first-stage. The feature bank consisted of polynomial coefficients, textures, histograms and statistics as previously described [1]. The basis for comparing the performance of these feature sets was the biological imaging benchmark described in [2]. Our results show that a set of image transforms (Fourier, Wavelet, Chebyshev) performed significantly better than a set of image filters (image pyramids, sub-band filters, and spectral decompositions). The transform technique was used to analyze images of H&E-stained tissue biopsies from two cancers: lymphoma (three types of malignancies) and melanoma (benign, primary, and five secondary tumor sites). The overall classification accuracy for these cancer data sets was 97%.
Bacteriophage phi29 DNA packaging motor is geared by a six-pRNA ring. pRNA is able to form a multimeric complex and patterned superstructures via the interaction of two reengineered interlocking loops. This unique feature makes it an ideal polyvalent vehicle for nanomachine fabrication, pathogen detection, and the delivery of therapeutics. This report describes novel approaches for the fabrication of polyvalent therapeutic pRNA nanoparticles, especially tetramers for specific siRNA delivery to cancer cells and for the silencing of targeted genes. RNA 3-D design, circular permutation, folding energy alteration, and nucleotide modification were applied to generate stable RNA nanoparticles with low toxicity. Animal trials demonstrated the high efficiency of the polyvalent RNA nanoparticles in the prevention and treatment of cancer. Using such protein-free nanoparticles as therapeutic reagents would allow for long-term administration to avoid the induction of antibody due to repeated treatment for chronic diseases.
Bio-medical implantable devices have appeared for more than fifty years. With more understandings of neuroscience, some diseases caused by neural abnormal discharge or disable may be cured or improved by neural stimulation techniques. Most of the wireless implantable devices transmit power and data into the no-battery implantable device by magnetic coupling. This paper presents an efficient power and data transmission, including LDO power regulator and ASK demodulator for biomedical implantable devices. The modulation index and rate are relative to power transmission efficiency. Results show that with a 2MHz carrier, the proposed ASK demodulator structure has a maximum modulation index up to 2.86% and a 50 % maximum modulation rate. The modulation index is also tunable for different applications. The power regulator provides a stable 1.8V for the ASK demodulation. This design uses TSMC 0.18um 1P6M CMOS technology.
We report multifactorial analysis of candidate mechanisms of Alzheimer's disease utilizing high content analysis, gene expression microarray, and linear regression model to integrate neuronal imaging data with hippocampal gene expression data. Our analysis led to the identification of several genes that may contribute to different image traits or phenotypes in the amyloid-beta (Aβ) injured neurons. Gene network and biological pathways analysis for those genes were further analyzed and led to several novel pathways that may contribute to amyloid plaque triggered neurite loss.
An overview of the latest efforts in integrated polarization imaging sensors are presented. We describe two approaches for creating focal plane polarization imaging sensors. The first approach combines polymer polarization filters with CMOS active pixel sensor and computes polarization information at the focal plane. The second approach outlines our initial work on polarization filters using aluminum nano wires. Measurements from the first polarization image sensor prototype are discussed in detail and applications for material detection using polarization techniques are described.
Currently, there are no widely used methods of optically recording rapid electrical events over a wide cortical area in freely moving animals. This paper presents an image sensor for recording electrical activity of large regions (4-9 mm2) of the nervous tissue at high speeds (> 500 Hz) using voltage sensitive dye imaging (VSDI) in freely moving animals. Each 75 mum x 75 mum pixel consists of a photodiode of 74 mum x 34 mum and a storage capacitor of 788 fF. The image sensor has a signal-to-noise ratio of 76 dB.
The recent years have been marked by a surge of interdisciplinary collaborations among scientists, engineers, researchers, and medical practitioners focused on solving complex problems in medicine and related fields. These activities have resulted in the development of bio-inspired silicon, neural prosthetics, image processing systems, sensors and intravenous drug delivery devices that support diagnosis, treatment, and prevention of disease in patients. The IEEE Circuits and Systems (CAS) community has a track record of excellence and has played an active role in the research and design of these and other novel systems. This paper presents an overview of the life sciences and biomedical research under investigation within the Biomedical CAS (BioCAS) technical committee.
The post genomic era introduced the need to define single gene functions within biological pathways. A systems biology approach can be realized by automating image acquisition and phenotype classification. While machinery for automated data acquisition have been developing rapidly in the past years, the main bottleneck remains the effectiveness of the computer vision algorithms. Here we describe a fully automated process for finding phenotype similarities within a dataset acquired from an RNAi screen. The source code for the algorithms is available for free download.
Continuous-wave He-Ne laser exposures (Intensity=35 mW/cm2, lambda=632.8nm, Fluence range: 1J/cm2 to 50 J/cm2) on non-confluent and actively dividing human malignant glioblastoma cells was found to increase the cellular production levels of H2O2. Modulations in the cellular metabolic activity were detected (through the MTS assay) three days after laser irradiation. The metabolic activity was found to be dependent on the laser dose of exposure (i.e., fluence). In addition, three days after the laser exposure, the potential laser induced ldquobystanderrdquo effect was tested through the transfer of growth media from laser irradiated cells onto non-irradiated cells. After two additional days of incubation (5 days post exposure), the non-laser irradiated cells were found to have a significant increase in their metabolic activities. Modulations in the metabolic activities in the non-irradiated cells were found to be fluence dependent from the initial laser exposed cells treatment conditions. The results herein support the hypothesis of an important functional role for light enhanced cellular H2O2 generation to yield bio-modulatory effects locally and at a distance. The classical ldquobi-phasicrdquo modulation response of cells to light irradiation is hypothesized to depend upon the quantity of light-enhanced H2O2 molecules generated from the mitochondria and the number of cells which interact with the H2O2 molecules.
The advancements of wireless body area networks (WBAN) and wireless personal area networks (WPAN) has led to a recent increase of viable applications in wireless medical and healthcare devices. Developing biomedical sensors such as electroencephalograph (EEG) and electrocardiogram (ECG) sensors often require numerous connecting wires which may introduce noise and increase patient discomfort. In this paper we propose a system design and realization of a wireless EEG and ECG sensor network focusing on issues such as time synchronization, bandwidth, and power constraints constituent of WBANs. Our WSN comprises three transmitting nodes for a total of four EEG channels and an ECG channel. We solve problems such as data throughput requirements for EEG and ECG signal processing as well as time synchronization of received data at the base station. This paper keeps in consideration the possible implementation of our proposed system onto a system-on-chip (SOC) by putting focus on the chip size and low power consumption of the analog-front-end system.
We present fundamental principals and features of novel approaches in biophotonics and nanobiophotonics field for biomedical applications with spatial resolution beyond the diffraction barrier in the subwavelength (below 100 nm) nanoscale range.
This paper investigates wireless electricity (witricity) and its application to medical sensors and implantable devices. Several coupling scenarios of resonators are analyzed theoretically. In vitro experiments are conducted in open air and through an agar phantom of the human head. An in vivo animal experiment is also carried out. Our studies indicate that witricity is a suitable tool for providing wireless power to a variety of medical sensors and implanted devices.
We report a novel active pixel sensor with adaptive in-pixel thresholding for optical spike detection. The adaptive threshold is set by ultra-low-power current-mode CMOS circuits which continuously compute the mean and standard deviation of the photocurrents generated by eight representative pixels in real-time. Sensor pixels discriminate between light and dark by integrating onto the photodiode junction capacitance the difference between the photocurrent and an opposing bias current whose magnitude is set by the mean and standard deviation circuits. We have characterized the active pixel sensor with and without an integrated fluorescence filter for biosensing applications and measured results agree with theory and simulations.
