http://idea.library.drexel.edu/handle/1860/829 Search the Channel search http://idea.library.drexel.edu/simple-search http://idea.library.drexel.edu/handle/1860/2741 Title: Atlas-based indexing of brain sections via 2-D to 3-D image registration <br/> <br/>Authors: Gefen, Smadar; Kiryati, Nahum; Nissanov, Jonathan <br/> <br/>Abstract: A 2-D to 3-D nonlinear intensity-based registration method is proposed in which the alignment of histological brain sections with a volumetric brain atlas is performed. First, sparsely cut brain sections were linearly matched with an oblique slice automatically extracted from the atlas. Second, a planar-to-curved surface alignment was employed in order to match each section with its corresponding image overlaid on a curved-surface within the atlas. For the latter, a PDE-based registration technique was developed that is driven by a local normalized-mutual-information similarity measure. We demonstrate the method and evaluate its performance with simulated and real data experiments. An atlasguided segmentation of mouse brains’ hippocampal complex, retrieved from the Mouse Brain Library (MBL) database, is demonstrated with the proposed algorithm. Sat, 29 Dec 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2716 Title: Flexural vibrations and resonance of piezoelectric cantilevers with a nonpiezoelectric extension <br/> <br/>Authors: Shen, Zuyan; Shih, Wan Y.; Shih, Wei-Heng <br/> <br/>Abstract: A piezoelectric cantilever (PEC) is a flexural transducer consisting of a piezoelectric layer [e.g., lead zirconate titanate (PZT)] bonded to a nonpiezoelectric layer (e.g., stainless steel). A PEC with a thin nonpiezoelectric extension has two distinctive sections, each with a different thickness, different axial density, and elastic-modulus profiles and has been increasingly used as an in-situ biosensor. It has the advantages of dipping only the nonpiezoelectric extension part in an aqueous solution without electrically insulating the piezoelectric section as well as serving as the bonding pad for receptor immobilization. In this study, we examined the effect of the thin nonpiezoelectric extension on the flexural resonance spectrum and resonance vibration waveforms of PEC; in particular, how the length ratio between the piezoelectric section and the nonpiezoelectric extension section affects the resonance frequencies and resonance peak intensities of PEC. Theoretical resonance frequencies and resonance vibration waveforms were obtained using an analytical transcendental equation we derived by solving the flexural wave equation. Both experimental and theoretical results showed that the two-section structure distorted the flexural vibration waveforms from those of PEC without an extension. As a result, the higher-mode resonance peaks of PEC with a nonpiezoelectric extension could be higher than the first resonance peak due to the two-section structure. With PEC that has a piezoelectric section of 0.25-mm thick PZT bonded to 0.07 mm thick stainless steel of various length l1 and a 0.07-mm thick nonpiezoelectric extension of length l2, we showed that the first-mode-to-second-mode resonance peak intensity ratio had a maximum of 5.6 at l1/l2 = 0.75 and the first-modeto- second-mode resonance frequency ratio a minimum of 2.2 at l1/l2 = 1.8. These findings will undoubtedly help optimize the design and performance of PEC. Fri, 28 Sep 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2697 Title: Interaction between rhythms in the human basal ganglia: application of bispectral analysis to local field potentials <br/> <br/>Authors: Marceglia, Sara; Bianchi, Anna Maria; Baselli, Giuseppe; Foffani, Guglielmo; Cogiamanian, Filippo; Modugno, Nicola; Mrakic-Sposta, Simona; Priori, Alberto; Cerutti, Sergio <br/> <br/>Abstract: The application of deep brain stimulation (DBS) for the treatment of Parkinson’s disease offered a direct “insight” into the human electrical activity in subcortical structures. The analysis of the oscillatory activity [local field potentials (LFPs)] disclosed the importance of rhythms and of interactions between rhythms in the human basal ganglia information processing. The aim of this study wasto investigate the existence of possible nonlinear interactions between LFP rhythms characterizing the output structure of the basal ganglia, the globus pallidus internus, by means of bispectral analysis. The results of this study disclosed that the rhythms expressed in the globus pallidus internus of the untreated parkinsonian patient are not independent and, in particular, the low-beta (13–20Hz)band generates harmonics that are included in the high-beta (20–35 Hz) band. Conversely, in the dystonic globus pallidus, as well as in the parkinsonian globus pallidus afterdopaminergic medication (i.e., in the more “normal” condition), the rhythms are substantially independent and characterized by a strong activity in the low-frequency band that generates a second harmonic (4–14 Hz), mostly included in the same band. The interactions between rhythms in the human globus pallidus are therefore different in different pathologies and in different patient’s states. The interpretation of these interactions is likely critical for fully understanding the role of LFP rhythms in the pathophysiology of human basal ganglia. Wed, 28 Nov 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2665 Title: Silicon as a millimeter-wave monolithically integrated substrate - A new look <br/> <br/>Authors: Rosen, Arye; Caulton, Martin; Stabile, Paul <br/> <br/>Abstract: An important goal of microwave research has now been attained with the development of the technologies needed to fabricate monolithic microwave (mm-wave) integrated circuits. Questions regarding the use of monolithic versus hybrid circuits are investigated. Attention is given to the pros and cons of materials considered for use as monolithic substrates at mm-wave frequencies, the properties of the microstrip, and the effects of shorter wavelengths as the wavelengths become comparable with the microstrip cross section. A novel technology is considered for the fabrication of mm-wave devices utilizing ion-implantation, laser annealing, and unique secondary-ion mass spectrometry diagnostics. Thu, 14 Feb 2008 21:33:40 GMT http://idea.library.drexel.edu/handle/1860/2633 Title: Respiratory rhythm entrainment by somatic afferent stimulation <br/> <br/>Authors: Potts, Jeffrey T.; Rybak, Ilya A.; Paton, Julian F. R. <br/> <br/>Abstract: Respiratory and locomotor patterns are coupled during locomotion. The objectives of this study were to (1) demonstrate that respiratory rhythms are entrained by sensory input from somatic afferents, (2) establish whether the parabrachial nucleus mediates entrainment, (3) examine responses of single respiratory neurons in the ventral respiratory group (VRG) to somatic afferent stimulation, and (4) use a computational model of the pontomedullary respiratory network (Rybak et al., 2004a,b) to suggest neuronal mechanisms for entrainment. We used an in situ preparation in young rats that retained pontomedullary respiratory circuits and spinal pathways transmitting somatosensory input. We demonstrate that rhythmic stimulation of somatic afferents entrains respiratory rhythm on a 1:1 basis (1:1), increasing breathing frequency up to 1.4 –2.2 times greater than spontaneous frequency. Stable entrainment occurred only when stimuli were delivered during expiration. Reversible blockade of the lateral parabrachial nucleus eliminated entrainment. Somatic afferent stimulation produced significant increases in the firing rate of augmenting expiratory (E2) neurons but shortened the firing duration of postinspiratory (post-I) neurons.Acomputational model reproduced 1:1 entrainment and other experimental findings based on the assumption that the somatic afferents initiate early onset of inspiration via activation of medullary E2 neurons. The model also predicted that afferent stimulation evoked transient hyperpolarization of ramp-inspiratory (ramp-I) neurons. This was confirmed experimentally by intracellular recording from ramp-I neurons. Our experimental and modeling results demonstrate that an entrainment pathway from somatic afferents to the VRG via the lateral parabrachial nucleus causes resetting of respiratory rhythm through excitation of E2 and consequent inhibition of post-I neurons. Tue, 22 Feb 2005 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2611 Title: Detecting cognitive activity related hemodynamic signal for brain computer interface using functional near infrared spectroscopy <br/> <br/>Authors: Ayaz, Hasan; Izzetoglu, Meltem; Bunce, Scott; Heiman-Patterson, Terry; Onaral, Banu <br/> <br/>Abstract: The ideal non-invasive brain computer interface (BCI) transforms signals originating from human brain into commands that can control devices and applications. Hence, BCI provides a way for brain output that does not involve neuromuscular system. This represents an advantage for those individuals suffering from neuromuscular impairments such as Amyotrophic Lateral Sclerosis (ALS) or various types of paralysis. In this study we propose to design a new noninvasive BCI that is based on optical means to measure brain activity by monitoring hemodynamic response. The proposed system uses functional near infrared (fNIR) spectroscopy to detect cognitive activity from prefrontal cortex elicited voluntarily by performing a mental task namely N-back test. Our findings indicate that fNIR signal correlates with cognitive tasks associated with working memory. These experimental outcomes compare favorably with previous functional magnetic resonance imaging (fMRI) and complement electroencephalogram (EEG) findings. Since fNIR can be implemented in the form of a wearable and minimally intrusive device, it also has the capacity to monitor brain activity under real life conditions in everyday environments leading the way to potential applications of fNIR in BCI development for communication and entertainment purposes. Tue, 01 May 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2603 Title: Signaling perturbations induced by invading H. pylori proteins in the host epithelial cells: a mathematical modeling approach <br/> <br/>Authors: Dampier, William; Tozeren, Aydin <br/> <br/>Abstract: Helicobacter pylori (H. pylori), a gram-negative bacterium, infects the stomach of approximately 50% of the world population. H. pylori infection is a risk factor for developing chronic gastric ulcers and gastric cancer. The bacteria produce two main cytotoxic proteins: Vacuolating cytotoxin A (VacA) and Cytotoxin-Associated gene A (CagA). When these proteins enter the host cell they interfere with the host MAP Kinase and Apoptosis signaling pathways leading to aberrant cell growth and premature apoptosis. The present study expanded existing quantitative models of the MAP Kinase and Apoptosis signaling pathways to take into account the protein interactions across species using the CellDesigner tool. The resulting network contained hundreds of differential equations in which the coefficients for the biochemical rate constants were estimated from previously published studies. The effect of VacA and CagA on the function of this network were simulated by increasing levels of bacterial load. Simulations showed that increasing bacterial load affected the MAP Kinase signaling in a dose dependant manner. The introduction of CagA decreased the activation time of mapK signaling and extended activation indefinitely despite normal cellular activity to deactivate the protein. Introduction of VacA produced a similar response in the apoptosis pathway. Bacterial load activated both pathways even in the absence of external stimulation. Time course of emergence of transcription factors associated with cell division and cell death predicted by our simulation showed close agreement with that determined from a publicly accesible microarray dataset of H. pylori infected stomach epithelium. The quantitative model presented in this study lays the foundation for investigating the affects of single nucleotide polymorphisms (SNPs) on the efficiency of drug treatment. Tue, 16 Jan 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2595 Title: Accelerated search for biomolecular network models to interpret high-throughput experimental data <br/> <br/>Authors: Datta, Suman; Sokhansanj, Bahrad A. <br/> <br/>Abstract: Background: The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from highthroughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables. Results: Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics. Conclusion: Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular data sets. This approach yields multiple alternative models that are consistent with the data, yielding a constrained set of hypotheses that can be used to optimally design subsequent experiments. Tue, 17 Jul 2007 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2568 Title: Modeling a piezoelectric TSM sensor to study kinetics of multi-layer biosensing structure <br/> <br/>Authors: Shah, Piyushkumar; Lec, Ryszard M.; Kwoun, Sun Jong <br/> <br/>Abstract: Most of the biological processes are surface mediated; but limited techniques are available to study interfacial biological processes. These techniques exhibit significant limitation due to their low sensitivity and selectivity, and poor temporal resolution. We are studying a novel measurement technique which utilizes piezoelectric thickness shear mode (TSM) sensor for the study of interfacial biological processes in real time. A typical real-life biological system is a multi-layer system comprising of several biological surfaces or interfaces. This multi-layer sensing structure loaded on piezoelectric TSM sensor has been simulated based on Mason's model, which represents each layer as T-network of acoustic and electrical impedances. Each layer is described by its mechanical properties (stiffness, viscosity, density) and geometrical properties (thickness). These properties can be varied for a variety of material parameters which represent broad range of biologically relevant operation conditions. Our model predicts the changes in the total impedance of the sensor system, which is related to the resonance frequency and amplitude of the sensor. In turn, these changes can be related to the ongoing biological processes. The study shows three different processes simulating interfacial phenomena and gelation (solidification) of materials. Wed, 29 Oct 2003 22:58:59 GMT http://idea.library.drexel.edu/handle/1860/2555 Title: Domain switching in lead magnesium niobate-lead titanate polycrystalline sheets at single grain level <br/> <br/>Authors: Su, Wei-Sheng; Chen, Yang-Fang; Shih, Wan Y.; Luo, Hongyu; Shih, Wei-Heng <br/> <br/>Abstract: The authors provide direct evidence of non-180 degrees domain switching in the piezoelectric response of substrate-free 40 mu m thick polycrystalline [Pb(Mg1/3Nb2/3)O-3](0.63)(PbTiO3)(0.37) (PMN-37PT) sheets under dc electric fields through piezoresponse force microscopy (PFM) at the single grain level. The sheet's polarization preferred pointing in the planar direction which was switched to the normal direction at electric field ranging between 1.3 and 1.9 kV/cm. An independent d(31) measurement of PMN-37PT sheets deduced from the axial tip displacement measurements of a 4 mm long PMN-PT/copper cantilever showed enhanced d(31) values that peaked at -2700 pm/V in the same range of electric field, consistent with the PFM observation. Mon, 10 Sep 2007 22:58:59 GMT