Cortical processing of change detection: Dissociation between natural vowels and two-frequency complex tones

We compared magnetoencephalographic responses for natural vowels and for sounds consisting of two pure tones that represent the two lowest formant frequencies of these vowels. Our aim was to determine whether spectral changes in successive stimuli are detected differently for speech and nonspeech sounds. The stimuli were presented in four blocks applying an oddball paradigm (20% deviants, 80% standards): (i) /α/ tokens as deviants vs. /i/ tokens as standards; (ii) /e/ vs. /i/; (iii) complex tones representing /α/ formants vs. /i/ formants; and (iv) complex tones representing /e/ formants vs. /i/ formants. Mismatch fields (MMFs) were calculated by subtracting the source waveform produced by standards from that produced by deviants. As expected, MMF amplitudes for the complex tones reflected acoustic deviation: the amplitudes were stronger for the complex tones representing /α/ than /e/ formants, i.e., when the spectral difference between standards and deviants was larger. In contrast, MMF amplitudes for the vowels were similar despite their different spectral composition, whereas the MMF onset time was longer for /e/ than for /α/. Thus the degree of spectral difference between standards and deviants was reflected by the MMF amplitude for the nonspeech sounds and by the MMF latency for the vowels.

Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides

Incremental truncation for the creation of hybrid enzymes (ITCHY) is a novel tool for the generation of combinatorial libraries of hybrid proteins independent of DNA sequence homology. We herein report a fundamentally different methodology for creating incremental truncation libraries using nucleotide triphosphate analogs. Central to the method is the polymerase catalyzed, low frequency, random incorporation of α-phosphothioate dNTPs into the region of DNA targeted for truncation. The resulting phosphothioate internucleotide linkages are resistant to 3′→5′ exonuclease hydrolysis, rendering the target DNA resistant to degradation in a subsequent exonuclease III treatment. From an experimental perspective the protocol reported here to create incremental truncation libraries is simpler and less time consuming than previous approaches by combining the two gene fragments in a single vector and eliminating additional purification steps. As proof of principle, an incremental truncation library of fusions between the N-terminal fragment of Escherichia coli glycinamide ribonucleotide formyltransferase (PurN) and the C-terminal fragment of human glycinamide ribonucleotide formyltransferase (hGART) was prepared and successfully tested for functional hybrids in an auxotrophic E.coli host strain. Multiple active hybrid enzymes were identified, including ones fused in regions of low sequence homology.

Characterization of a high-voltage-activated IA current with a role in spike timing and locomotor pattern generation

Transient A-type K+ channels (IA) in neurons have been implicated in the delay of the spike onset and the decrease in the firing frequency. Here we have characterized biophysically and pharmacologically an IA current in lamprey locomotor network neurons that is activated by suprathreshold depolarization and is specifically blocked by catechol at 100 μM. The biophysical properties of this current are similar to the mammalian Kv3.4 channel. The role of the IA current both in single neuron firing and in locomotor pattern generation was analyzed. The IA current facilitates Na+ channel recovery from inactivation and thus sustains repetitive firing. The role of the IA current in motor pattern generation was examined by applying catechol during fictive locomotion induced by N-methyl-d-aspartate. Blockade of this current increased the locomotor burst frequency and decreased the firing of motoneurons. Although an alternating motor pattern could still be generated, the cycle duration was less regular, with ventral roots bursts failing on some cycles. Our results thus provide insights into the contribution of a high-voltage-activated IA current to the regulation of firing properties and motor coordination in the lamprey spinal cord.

P2Y1 purinergic receptors in sensory neurons: contribution to touch-induced impulse generation.

Somatic sensation requires the conversion of physical stimuli into the depolarization of distal nerve endings. A single cRNA derived from sensory neurons renders Xenopus laevis oocytes mechanosensitive and is found to encode a P2Y1 purinergic receptor. P2Y1 mRNA is concentrated in large-fiber dorsal root ganglion neurons. In contrast, P2X3 mRNA is localized to small-fiber sensory neurons and produces less mechanosensitivity in oocytes. The frequency of touch-induced action potentials from frog sensory nerve fibers is increased by the presence of P2 receptor agonists at the peripheral nerve ending and is decreased by the presence of P2 antagonists. P2X-selective agents do not have these effects. The release of ATP into the extracellular space and the activation of peripheral P2Y1 receptors appear to participate in the generation of sensory action potentials by light touch.

A rat genetic map constructed by representational difference analysis markers with suitability for large-scale typing.

Representational difference analysis (RDA) was applied to isolate chromosomal markers in the rat. Four series of RDA [restriction enzymes, BamHI and HindIII; subtraction of ACI/N (ACI) amplicon from BUF/Nac (BUF) amplicon and vice versa] yielded 131 polymorphic markers; 125 of these markers were mapped to all chromosomes except for chromosome X. This was done by using a mapping panel of 105 ACI x BUF F2 rats. To complement the relative paucity of chromosomal markers in the rat, genetically directed RDA, which allows isolation of polymorphic markers in the specific chromosomal region, was performed. By changing the F2 driver-DNA allele frequency around the region, four markers were isolated from the D1Ncc1 locus. Twenty-five of 27 RDA markers were informative regarding the dot blot analysis of amplicons, hybridizing only with tester amplicons. Dot blot analysis at a high density per unit of area made it possible to process a large number of samples. Quantitative trait loci can now be mapped in the rat genome by processing a large number of samples with RDA markers and then by isolating markers close to the loci of interest by genetically directed RDA.

Isolation and characterization of a pseudoautosomal region-specific genetic marker in C57BL/6 mice using genomic representational difference analysis.

Representational difference analysis was used to identify strain-specific differences in the pseudoautosomal region (PAR) of mouse X and Y chromosomes. One second generation (C57BL/6 x Mus spretus) x Mus spretus interspecific backcross male carrying the C57BL/6 (B6) PAR was used for tester DNA. DNA from five backcross males from the same generation that were M. spretus-type for the PAR was pooled for the driver. A cloned probe designated B6-38 was recovered that is B6-specific in Southern analysis. Analysis of genomic DNA from several inbred strains of laboratory mice and diverse Mus species and subspecies identified a characteristic Pst I pattern of fragment sizes that is present only in the C57BL family of strains. Hybridization was observed with sequences in DBA/2J and to a limited extent with Mus musculus (PWK strain) and Mus castaneus DNA. No hybridization was observed in DNA of different Mus species, M. spretus, M. hortulanus, and M. caroli. Genetic analyses of B6-38 was conducted using C57BL congenic males that carry M. spretus alleles for distal X chromosome loci and the PAR and outcrosses of heterozygous congenic females with M. spretus. These analyses demonstrated that the B6-38 sequences were inherited with both the X and Y chromosome. B6-38 sequences were genetically mapped as a locus within the PAR using two interspecific backcrosses. The locus defined by B6-38 is designated DXYRp1. Preliminary analyses of recombination between the distal X chromosome gene amelogenin (Amg) and the PAR loci for either TelXY or sex chromosome association (Sxa) suggest that the locus DXYRp1 maps to the distal portion of the PAR.

Electroencephalogram based Causality Graph Analysis in Behavior Tasks of Parkinson’s Disease Patients

Electroencephalographic (EEG) signals of the human brains represent electrical activities for a number of channels recorded over a the scalp. The main purpose of this thesis is to investigate the interactions and causality of different parts of a brain using EEG signals recorded during a performance subjects of verbal fluency tasks. Subjects who have Parkinson's Disease (PD) have difficulties with mental tasks, such as switching between one behavior task and another. The behavior tasks include phonemic fluency, semantic fluency, category semantic fluency and reading fluency. This method uses verbal generation skills, activating different Broca's areas of the Brodmann's areas (BA44 and BA45). Advanced signal processing techniques are used in order to determine the activated frequency bands in the granger causality for verbal fluency tasks. The graph learning technique for channel strength is used to characterize the complex graph of Granger causality. Also, the support vector machine (SVM) method is used for training a classifier between two subjects with PD and two healthy controls. Neural data from the study was recorded at the Colorado Neurological Institute (CNI). The study reveals significant difference between PD subjects and healthy controls in terms of brain connectivities in the Broca's Area BA44 and BA45 corresponding to EEG electrodes. The results in this thesis also demonstrate the possibility to classify based on the flow of information and causality in the brain of verbal fluency tasks. These methods have the potential to be applied in the future to identify pathological information flow and causality of neurological diseases.

Holocene flood frequency across the Central Alps

The frequency of large-scale heavy precipitation events in the European Alps is expected to undergo substantial changes with current climate change. Hence, knowledge about the past natural variability of floods caused by heavy precipitation constitutes important input for climate projections. We present a comprehensive Holocene (10,000 years) reconstruction of the flood frequency in the Central European Alps combining 15 lacustrine sediment records. These records provide an extensive catalog of flood deposits, which were generated by flood-induced underflows delivering terrestrial material to the lake floors. The multi-archive approach allows suppressing local weather patterns, such as thunderstorms, from the obtained climate signal. We reconstructed mainly late spring to fall events since ice cover and precipitation in form of snow in winter at high-altitude study sites do inhibit the generation of flood layers. We found that flood frequency was higher during cool periods, coinciding with lows in solar activity. In addition, flood occurrence shows periodicities that are also observed in reconstructions of solar activity from 14C and 10Be records (2500-3000, 900-1200, as well as of about 710, 500, 350, 208 (Suess cycle), 150, 104 and 87 (Gleissberg cycle) years). As atmospheric mechanism, we propose an expansion/shrinking of the Hadley cell with increasing/decreasing air temperature, causing dry/wet conditions in Central Europe during phases of high/low solar activity. Furthermore, differences between the flood patterns from the Northern Alps and the Southern Alps indicate changes in North Atlantic circulation. Enhanced flood occurrence in the South compared to the North suggests a pronounced southward position of the Westerlies and/or blocking over the northern North Atlantic, hence resembling a negative NAO state (most distinct from 4.2 to 2.4 kyr BP and during the Little Ice Age). South-Alpine flood activity therefore provides a qualitative record of variations in a paleo-NAO pattern during the Holocene. Additionally, increased South Alpine flood activity contrasts to low precipitation in tropical Central America (Cariaco Basin) on the Holocene and centennial time scale. This observation is consistent with a Holocene southward migration of the Atlantic circulation system, and hence of the ITCZ, driven by decreasing summer insolation in the Northern hemisphere, as well as with shorter-term fluctuations probably driven by solar activity.

Modeling & Analysis of Small Hydroelectric Generation and Battery Energy Storage Connected as a Microgrid

Thesis (Master's)--University of Washington, 2016-06

CCR5-Delta 32 mutation is strongly associated with primary sclerosing cholangitis

CCR5 plays a key role in the distribution of CD45RO+ T cells and contributes to generation of a T helper 1 immune response. CCR5-Delta32 is a 32-bp deletion associated with significant reduction in cell surface expression of the receptor. We investigated the role of CCR5-Delta32 on susceptibility to ulcerative colitis (UC), Crohn's disease ( CD) and primary sclerosing cholangitis (PSC). Genotype and allelic association analyses were performed in 162 patients with UC, 131 with CD, 71 with PSC and 419 matched controls. There was a significant difference in CCR5 genotype (OR 2.27, P = 0.003) between patients with sclerosing cholangitis and controls. Similarly, CCR5-Delta32 allele frequency was significantly higher in sclerosing cholangitis (17.6%) compared to controls (9.9%, OR 2.47, P = 0.007) and inflammatory bowel disease patients without sclerosing cholangitis ( 11.3%, OR 1.9, P = 0.027). There were no significant differences in CCR5 genotype or allele frequency between those with either UC or CD and controls. Genotypes with the CCR5-Delta32 variant were increased in patients with severe liver disease defined by portal hypertension and/or transplantation (45%) compared to those with mild liver disease (21%, OR 3.17, P = 0.03). The CCR5-Delta32 mutation may influence disease susceptibility and severity in patients with PSC.

Deterministic generation of tailored-optical-coherent-state superpositions

Pulsed coherent excitation of a two-level atom strongly coupled to a resonant cavity mode will create a superposition of two coherent states of opposite amplitudes in the field. By choosing proper parameters of interaction time and pulse shape the field after the pulse will be almost disentangled from the atom and can be efficiently outcoupled through cavity decay. The fidelity of the generation approaches unity if the atom-field coupling strength is much larger than the atomic and cavity decay rates. This implies a strong difference between even and odd output photon number counts. Alternatively, the coherence of the two generated field components can be proven by phase-dependent annihilation of the generated nonclassical superposition state by a second pulse.

An inverse methodology for high-frequency RF coil design for MRI with de-emphasized B-1 fields

An inverse methodology for the design of biologically loaded radio-frequency (RF) coils for magnetic resonance imaging applications is described. Free space time-harmonic electromagnetic Green's functions and de-emphasized B-1 target fields are used to calculate the current density on the coil cylinder. In theory, with the B-1 field de-emphasized in the middle of the RF transverse plane, the calculated current distribution can generate an internal magnetic field that can reduce the central overemphasis effect caused by field/tissue interactions at high frequencies. The current distribution of a head coil operating at 4 T (170 MHz) is calculated using an inverse methodology with de-emphasized B-1. target fields. An in-house finite-difference time-domain routine is employed to evaluate B-1 field and signal intensity inside a homogenous cylindrical phantom and then a complete human head model. A comparison with a conventional RF birdcage coil is carried out and demonstrates that this method can help in decreasing the normal bright region caused by field/tissue interactions in head images at 170 MHz and higher field strengths.

Analysis of transient eddy currents in MRI using a cylindrical FDTD method

Most magnetic resonance imaging (MRI) spatial encoding techniques employ low-frequency pulsed magnetic field gradients that undesirably induce multiexponentially decaying eddy currents in nearby conducting structures of the MRI system. The eddy currents degrade the switching performance of the gradient system, distort the MRI image, and introduce thermal loads in the cryostat vessel and superconducting MRI components. Heating of superconducting magnets due to induced eddy currents is particularly problematic as it offsets the superconducting operating point, which can cause a system quench. A numerical characterization of transient eddy current effects is vital for their compensation/control and further advancement of the MRI technology as a whole. However, transient eddy current calculations are particularly computationally intensive. In large-scale problems, such as gradient switching in MRI, conventional finite-element method (FEM)-based routines impose very large computational loads during generation/solving of the system equations. Therefore, other computational alternatives need to be explored. This paper outlines a three-dimensional finite-difference time-domain (FDTD) method in cylindrical coordinates for the modeling of low-frequency transient eddy currents in MRI, as an extension to the recently proposed time-harmonic scheme. The weakly coupled Maxwell's equations are adapted to the low-frequency regime by downscaling the speed of light constant, which permits the use of larger FDTD time steps while maintaining the validity of the Courant-Friedrich-Levy stability condition. The principal hypothesis of this work is that the modified FDTD routine can be employed to analyze pulsed-gradient-induced, transient eddy currents in superconducting MRI system models. The hypothesis is supported through a verification of the numerical scheme on a canonical problem and by analyzing undesired temporal eddy current effects such as the B-0-shift caused by actively shielded symmetric/asymmetric transverse x-gradient head and unshielded z-gradient whole-body coils operating in proximity to a superconducting MRI magnet.

Physical and MAC layer techniques for next generation satellite communications

In this thesis, we consider four different scenarios of interest in modern satellite communications. For each scenario, we will propose the use of advanced solutions aimed at increasing the spectral efficiency of the communication links. First, we will investigate the optimization of the current standard for digital video broadcasting. We will increase the symbol rate of the signal and determine the optimal signal bandwidth. We will apply the time packing technique and propose a specifically design constellation. We will then compare some receiver architectures with different performance and complexity. The second scenario still addresses broadcast transmissions, but in a network composed of two satellites. We will compare three alternative transceiver strategies, namely, signals completely overlapped in frequency, frequency division multiplexing, and the Alamouti space-time block code, and, for each technique, we will derive theoretical results on the achievable rates. We will also evaluate the performance of said techniques in three different channel models. The third scenario deals with the application of multiuser detection in multibeam satellite systems. We will analyze a case in which the users are near the edge of the coverage area and, hence, they experience a high level of interference from adjacent cells. Also in this case, three different approaches will be compared. A classical approach in which each beam carries information for a user, a cooperative solution based on time division multiplexing, and the Alamouti scheme. The information theoretical analysis will be followed by the study of practical coded schemes. We will show that the theoretical bounds can be approached by a properly designed code or bit mapping. Finally, we will consider an Earth observation scenario, in which data is generated on the satellite and then transmitted to the ground. We will study two channel models, taking into account one or two transmit antennas, and apply techniques such as time and frequency packing, signal predistortion, multiuser detection and the Alamouti scheme.

Fibre-based devices for next generation photonics communication systems

The future broadband information network will undoubtedly integrate the mobility and flexibility of wireless access systems with the huge bandwidth capacity of photonics solutions to enable a communication system capable of handling the anticipated demand for interactive services. Towards wide coverage and low cost implementations of such broadband wireless photonics communication networks, various aspects of the enabling technologies are continuingly generating intense research interest. Among the core technologies, the optical generation and distribution of radio frequency signals over fibres, and the fibre optic signal processing of optical and radio frequency signals, have been the subjects for study in this thesis. Based on the intrinsic properties of single-mode optical fibres, and in conjunction with the concepts of optical fibre delay line filters and fibre Bragg gratings, a number of novel fibre-based devices, potentially suitable for applications in the future wireless photonics communication systems, have been realised. Special single-mode fibres, namely, the high birefringence (Hi-Bi) fibre and the Er/Yb doped fibre have been employed so as to exploit their merits to achieve practical and cost-effective all-fibre architectures. A number of fibre-based complex signal processors for optical and radio frequencies using novel Hi-Bi fibre delay line filter architectures have been illustrated. In particular, operations such as multichannel flattop bandpass filtering, simultaneous complementary outputs and bidirectional nonreciprocal wavelength interleaving, have been demonstrated. The proposed configurations featured greatly reduced environmental sensitivity typical of coherent fibre delay line filter schemes, reconfigurable transfer functions, negligible chromatic dispersions, and ease of implementation, not easily achievable based on other techniques. A number of unique fibre grating devices for signal filtering and fibre laser applications have been realised. The concept of the superimposed fibre Bragg gratings has been extended to non-uniform grating structures and into Hi-Bi fibres to achieve highly useful grating devices such as overwritten phase-shifted fibre grating structure and widely/narrowly spaced polarization-discriminating filters that are not limited by the intrinsic fibre properties. In terms of the-fibre-based optical millimetre wave transmitters, unique approaches based on fibre laser configurations have been proposed and demonstrated. The ability of the dual-mode distributed feedback (DFB) fibre lasers to generate high spectral purity, narrow linewidth heterodyne signals without complex feedback mechanisms has been illustrated. A novel co-located dual DFB fibre laser configuration, based on the proposed superimposed phase-shifted fibre grating structure, has been further realised with highly desired operation characteristics without the need for costly high frequency synthesizers and complex feedback controls. Lastly, a novel cavity mode condition monitoring and optimisation scheme for short length, linear-cavity fibre lasers has been proposed and achieved. Based on the concept and simplicity of the superimposed fibre laser cavities structure, in conjunction with feedback controls, enhanced output performances from the fibre lasers have been achieved. The importance of such cavity mode assessment and feedback control for optimised fibre laser output performance has been illustrated.