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Item 1-bit Phase Shifters for Large-Antenna Full-Duplex mmWave Communications(IEEE, 2020) da Silva, José Mairton Barros Jr.; Sabharwal, Ashutosh; Fodor, Gábor; Fischione, CarloMillimeter-wave using large-antenna arrays is a key technological component for the future cellular systems, where it is expected that hybrid beamforming along with quantized phase shifters will be used due to their implementation and cost efficiency. In this paper, we investigate the efficacy of full-duplex mmWave communication with hybrid beamforming using low-resolution phase shifters. We assume that the self-interference can be sufficiently cancelled by a combination of propagation domain and digital self-interference techniques, without any analog self-interference cancellation. We formulate the problem of joint self-interference suppression and downlink beamforming as a mixed-integer nonconvex joint optimization problem. We propose LowRes, a near-to-optimal solution using penalty dual decomposition. Numerical results indicate that LowRes using low-resolution phase shifters perform within 3% of the optimal solution that uses infinite phase shifter resolution. Moreover, even a single quantization bit outperforms half-duplex transmissions, respectively by 29% and 10% for both low and high residual self-interference scenarios, and for a wide range of practical antenna to radio-chain ratios. Thus, we conclude that 1-bit phase shifters suffice for full-duplex millimeter-wave communications, without requiring any additional new analog hardware.Item The 2nu-SVM: A Cost-Sensitive Extension of the nu-SVM(2005-12-01) Davenport, Mark A.; Digital Signal Processing (http://dsp.rice.edu/)Standard classification algorithms aim to minimize the probability of making an incorrect classification. In many important applications, however, some kinds of errors are more important than others. In this report we review cost-sensitive extensions of standard support vector machines (SVMs). In particular, we describe cost-sensitive extensions of the C-SVM and the nu-SVM, which we denote the 2C-SVM and 2nu-SVM respectively. The C-SVM and the nu-SVM are known to be closely related, and we prove that the 2C-SVM and 2nu-SVM share a similar relationship. This demonstrates that the 2C-SVM and 2nu-SVM explore the same space of possible classifiers, and gives us a clear understanding of the parameter space for both versions.Item 3-D Local Radon Power Spectra for Seismic Attribute Extraction(1998-01-15) Steeghs, Philippe; Fokkema, Jacob T; Diephuis, Gerhard; Digital Signal Processing (http://dsp.rice.edu/)In this paper we discuss a method for volume attribute extraction that is based on a new type of local Radon power spectrum. The new algorithm results in robust and geologically meaningful volume attributes, such as volume dip and azimuth. Seismic volume attribute analysis greatly facilitates the interpretation of large 3-D seismic data volumes. However, horizon attribute maps are generally more easy to interpret than volume attribute images, which are usually time slices or cross-sections. We show that, for dip estimation, the volume attribute image is very similar to the horizon dip map.Item 3D Geometry Coding using Mixture Models and the Estimation Quantization Algorithm(2002-09-01) Lavu, Sridhar; Lavu, Sridhar; Digital Signal Processing (http://dsp.rice.edu/)3D surfaces are used in applications such as animations, 3D object modeling and visualization. The geometries of such surfaces are often approximated using polygonal meshes. This thesis aims to compress 3D geometry meshes by using an algorithm based on normal meshes and the Estimation-Quantization (EQ) algorithm. Normal meshes are multilevel representations where finer level vertices lie in a direction normal to the local surface and therefore compress the vertex data to one scalar value per vertex. A mixture distribution model is used for the wavelet coefficients. The EQ algorithm uses the local neighborhood information and Rate-Distortion optimization to encode the wavelet coefficients. We achieve performance gains of 0.5-1dB compared to the zerotree coder for normal meshes.Item 3D microfabrication of single-wall carbon nanotube/polymer composites by two-photon polymerization lithography(Elsevier, 2013) Ushiba, Shota; Shoji, Satoru; Masui, Kyoko; Kuray, Preeya; Kono, Junichiro; Kawata, SatoshiWe present a method to develop single-wall carbon nanotube (SWCNT)/polymer composites into arbitrary three-dimensional micro/nano structures. Our approach, based on two-photon polymerization lithography, allows one to fabricate three-dimensional SWCNT/polymer composites with a minimum spatial resolution of a few hundreds nm. A near-infrared femtosecond pulsed laser beam was focused onto a SWCNT-dispersed photo resin, and the laser light solidified a nanometric volume of the resin. The focus spot was three-dimensionally scanned, resulting in the fabrication of arbitrary shapes of SWCNT/polymer composites. SWCNTs were uniformly distributed throughout the whole structures, even in a few hundreds nm thick nanowires. Furthermore, we also found an intriguing phenomenon that SWCNTs were self-aligned in polymer nanostructures, promising improvements in mechanical and electrical properties. Our method has great potential to open up a wide range of applications such as micro- and nanoelectromechanical systems, micro/nano actuators, sensors, and photonics devices based on CNTs.Item 3D printed fiber optic faceplates by custom controlled fused deposition modeling(Optical Society of America, 2018) Wang, Ye; Gawedzinski, John; Pawlowski, Michal E.; Tkaczyk, Tomasz S.A 3D printing technique for manufacturing air-clad coherent fiber optic faceplates is presented. The custom G-code programming is implemented on a fused deposition modeling (FDM) desktop printer to additively draw optical fibers using high-transparency thermoplastic filaments. The 3D printed faceplate consists of 20000 fibers and achieves spatial resolution 1.78 LP/mm. Transmission loss and crosstalk are characterized and compared among the faceplates printed from four kinds of transparent filaments as well as different faceplate thicknesses. The printing temperature is verified by testing the transmission of the faceplates printed under different temperatures. Compared with the conventional stack-and-draw fabrication, the FDM 3D printing technique simplifies the fabrication procedure. The ability to draw fibers with arbitrary organization, structure and overall shape provides additional degree of freedom to opto-mechanical design. Our results indicate a promising capability of 3D printing as the manufacturing technology for fiber optical devices.Item 802.11b Operating in a Mobile Channel: Performance and Challenges(2003-09-20) Steger, Christopher; Radosavljevic, Predrag; Frantz, Patrick; Center for Multimedia Communications (http://cmc.rice.edu/)In the past, the worlds of wireless voice and data transmission have been largely disjoint. Voice traffic has been carried over circuit-switched cellular links, and data has been largely restricted to packet-switched wireless LANs. Now, as consumers demand higher bandwidth connections without sacrificing mobility and traffic transitions from primarily voice to data, service providers must produce what is essentially a ubiquitous wireless LAN. To this end, we have studied the effects of a mobile channel on current generation 802.11 A, B, and G wireless LAN cards to see how readily they can be applied to more challenging environments. Not surprisingly, current WLAN technology suffers from significantly degraded performance when subjected to the rigors of a mobile channel. We created emulated bi-directional peer-to-peer links in which we were able to manipulate individual channel parameters. By isolating individual propagation effects and testing several different implementations of the standards, we have discovered which channel parameters have the most significant impact on performance. For instance, the large delay spreads typical of an outdoor channel seem to produce the most deleterious effect on throughput in 802.11b. We use our observations to evaluate the viability of direct-sequence spread-spectrum systems (similar to 802.11b) versus that of OFDM systems (like 802.11a and 802.11g). Then we offer suggestions for how future systems should be adapted in order to manage these effects, and we project the ultimate limitations and possibilities for subsequent 802.11-like systems.Item A Context-Aware Trust Framework for Resilient Distributed Cooperative Spectrum Sensing in Dynamic Settings(IEEE, 2017) Vosoughi, Aida; Cavallaro, Joseph R.; Marshall, AlanCognitive radios enable dynamic spectrum access where secondary users (SUs) are allowed to operate on the licensed spectrum bands on an opportunistic noninterference basis. Cooperation among the SUs for spectrum sensing is essential for environments with deep shadows. In this paper, we study the adverse effect of insistent spectrum sensing data falsification (ISSDF) attack on iterative distributed cooperative spectrum sensing. We show that the existing trust management schemes are not adequate in mitigating ISSDF attacks in dynamic settings where the primary user (PU) of the band frequently transitions between active and inactive states. We propose a novel context-aware distributed trust framework for cooperative spectrum sensing in mobile cognitive radio ad hoc networks (CRAHN) that effectively alleviates different types of ISSDF attacks (Always-Yes, Always-No, and fabricating) in dynamic scenarios. In the proposed framework, the SU nodes evaluate the trustworthiness of one another based on the two possible contexts in which they make observations from each other: PU absent context and PU present context. We evaluate the proposed context-aware scheme and compare it against the existing context-oblivious trust schemes using theoretical analysis and extensive simulations of realistic scenarios of mobile CRAHNs operating in TV white space. We show that in the presence of a large set of attackers (as high as 60% of the network), the proposed context-aware trust scheme successfully mitigates the attacks and satisfy the false alarm and missed-detection rates of 10−2 and lower. Moreover, we show that the proposed scheme is scalable in terms of attack severity, SU network density, and the distance of the SU network to the PU transmitter.Item A CRISPR toolbox for generating intersectional genetic mouse models for functional, molecular, and anatomical circuit mapping(Springer Nature, 2022) Lusk, Savannah J.; McKinney, Andrew; Hunt, Patrick J.; Fahey, Paul G.; Patel, Jay; Chang, Andersen; Sun, Jenny J.; Martinez, Vena K.; Zhu, Ping Jun; Egbert, Jeremy R.; Allen, Genevera; Jiang, Xiaolong; Arenkiel, Benjamin R.; Tolias, Andreas S.; Costa-Mattioli, Mauro; Ray, Russell S.The functional understanding of genetic interaction networks and cellular mechanisms governing health and disease requires the dissection, and multifaceted study, of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic effector alleles represents a significant and powerful approach to delineate cell populations for functional, molecular, and anatomical studies. In addition to single recombinase systems, the expression of two recombinases in distinct, but partially overlapping, populations allows for more defined target expression. Although the application of this method is becoming increasingly popular, its experimental implementation has been broadly restricted to manipulations of a limited set of common alleles that are often commercially produced at great expense, with costs and technical challenges associated with production of intersectional mouse lines hindering customized approaches to many researchers. Here, we present a simplified CRISPR toolkit for rapid, inexpensive, and facile intersectional allele production.Item A distinct population of heterogeneously color-tuned neurons in macaque visual cortex(AAAS, 2021) Nigam, Sunny; Pojoga, Sorin; Dragoi, ValentinColor is a key feature of natural environments that higher mammals routinely use to detect food, avoid predators, and interpret social signals. The distribution of color signals in natural scenes is widely variable, ranging from uniform patches to highly nonuniform regions in which different colors lie in close proximity. Whether individual neurons are tuned to this high degree of variability of color signals is unknown. Here, we identified a distinct population of cells in macaque visual cortex (area V4) that have a heterogeneous receptive field (RF) structure in which individual subfields are tuned to different colors even though the full RF is only weakly tuned. This spatial heterogeneity in color tuning indicates a higher degree of complexity of color-encoding mechanisms in visual cortex than previously believed to efficiently extract chromatic information from the environment. Diverse color tuning in V4 receptive fields points to its possible role in encoding complex color stimuli in natural environment. Diverse color tuning in V4 receptive fields points to its possible role in encoding complex color stimuli in natural environment.Item A framework to identify structured behavioral patterns within rodent spatial trajectories(Springer Nature, 2021) Donnarumma, Francesco; Prevete, Roberto; Maisto, Domenico; Fuscone, Simone; Irvine, Emily M.; van der Meer, Matthijs A.A.; Kemere, Caleb; Pezzulo, GiovanniAnimal behavior is highly structured. Yet, structured behavioral patterns—or “statistical ethograms”—are not immediately apparent from the full spatiotemporal data that behavioral scientists usually collect. Here, we introduce a framework to quantitatively characterize rodent behavior during spatial (e.g., maze) navigation, in terms of movement building blocks or motor primitives. The hypothesis that we pursue is that rodent behavior is characterized by a small number of motor primitives, which are combined over time to produce open-ended movements. We assume motor primitives to be organized in terms of two sparsity principles: each movement is controlled using a limited subset of motor primitives (sparse superposition) and each primitive is active only for time-limited, time-contiguous portions of movements (sparse activity). We formalize this hypothesis using a sparse dictionary learning method, which we use to extract motor primitives from rodent position and velocity data collected during spatial navigation, and successively to reconstruct past trajectories and predict novel ones. Three main results validate our approach. First, rodent behavioral trajectories are robustly reconstructed from incomplete data, performing better than approaches based on standard dimensionality reduction methods, such as principal component analysis, or single sparsity. Second, the motor primitives extracted during one experimental session generalize and afford the accurate reconstruction of rodent behavior across successive experimental sessions in the same or in modified mazes. Third, in our approach the number of motor primitives associated with each maze correlates with independent measures of maze complexity, hence showing that our formalism is sensitive to essential aspects of task structure. The framework introduced here can be used by behavioral scientists and neuroscientists as an aid for behavioral and neural data analysis. Indeed, the extracted motor primitives enable the quantitative characterization of the complexity and similarity between different mazes and behavioral patterns across multiple trials (i.e., habit formation). We provide example uses of this computational framework, showing how it can be used to identify behavioural effects of maze complexity, analyze stereotyped behavior, classify behavioral choices and predict place and grid cell displacement in novel environments.Item A hyperspectral projector for simultaneous 3D spatial and hyperspectral imaging via structured illumination(Optical Society of America, 2020) Xu, Yibo; Giljum, Anthony; Kelly, Kevin F.Both 3D imaging and hyperspectral imaging provide important information of the scene and combining them is beneficial in helping us perceive and understand real-world structures. Previous hyperspectral 3D imaging systems typically require a hyperspectral imaging system as the detector suffers from complicated hardware design, high cost, and high acquisition and reconstruction time. Here, we report a low-cost, high-frame rate, simple-design, and compact hyperspectral stripe projector (HSP) system based on a single digital micro-mirror device, capable of producing hyperspectral patterns where each row of pixels has an independently programmable spectrum. We demonstrate two example applications using the HSP via hyperspectral structured illumination: hyperspectral 3D surface imaging and spectrum-dependent hyperspectral compressive imaging of volume density of participating medium. The hyperspectral patterns simultaneously encode the 3D spatial and spectral information of the target, requiring only a grayscale sensor as the detector. The reported HSP and its applications provide a solution for combining structured illumination techniques with hyperspectral imaging in a simple, efficient, and low-cost manner. The work presented here represents a novel structured illumination technique that provides the basis and inspiration of future variations of hardware systems and software encoding schemes.Item A microfluidic-induced C. elegans sleep state(Springer Nature, 2019) Gonzales, Daniel L.; Zhou, Jasmine; Fan, Bo; Robinson, Jacob T.An important feature of animal behavior is the ability to switch rapidly between activity states, however, how the brain regulates these spontaneous transitions based on the animal’s perceived environment is not well understood. Here we show a C. elegans sleep-like state on a scalable platform that enables simultaneous control of multiple environmental factors including temperature, mechanical stress, and food availability. This brief quiescent state, which we refer to as microfluidic-induced sleep, occurs spontaneously in microfluidic chambers, which allows us to track animal movement and perform whole-brain imaging. With these capabilities, we establish that microfluidic-induced sleep meets the behavioral requirements of C. elegans sleep and depends on multiple factors, such as satiety and temperature. Additionally, we show that C. elegans sleep can be induced through mechanosensory pathways. Together, these results establish a model system for studying how animals process multiple sensory pathways to regulate behavioral states.Item A Miniaturized QEPAS Trace Gas Sensor with a 3D-Printed Acoustic Detection Module(MDPI, 2017) Yang, Xiaotao; Xiao, Youhong; Ma, Yufei; He, Ying; Tittel, Frank K.A 3D printing technique was introduced to a quartz-enhanced photoacoustic spectroscopy (QEPAS) sensor and is reported for the first time. The acoustic detection module (ADM) was designed and fabricated using the 3D printing technique and the ADM volume was compressed significantly. Furthermore, a small grin lens was used for laser focusing and facilitated the beam adjustment in the 3D-printed ADM. A quartz tuning fork (QTF) with a low resonance frequency of 30.72 kHz was used as the acoustic wave transducer and acetylene (C2H2) was chosen as the analyte. The reported miniaturized QEPAS trace gas sensor is useful in actual sensor applications.Item A NDIR Mid-Infrared Methane Sensor with a Compact Pentahedron Gas-Cell(MDPI, 2020) Ye, Weilin; Tu, Zihan; Xiao, Xupeng; Simeone, Alessandro; Yan, Jingwen; Wu, Tao; Wu, Fupei; Zheng, Chuantao; Tittel, Frank K.In order to improve the performance of the large divergence angle mid-infrared source in gas sensing, this paper aims at developing a methane (CH4) sensor with non-dispersive infrared (NDIR) technology using a compact pentahedron gas-cell. A paraboloid concentrator, two biconvex lenses and five planar mirrors were used to set up the pentahedron structure. The gas cell is endowed with a 170 mm optical path length with a volume of 19.8 mL. The mathematical model of the cross-section and the three-dimension spiral structure of the pentahedron gas-cell were established. The gas-cell was integrated with a mid-infrared light source and a detector as the optical part of the sensor. Concerning the electrical part, a STM32F429 was employed as a microcontroller to generate the driving signal for the IR source, and the signal from the detector was sampled by an analog-to-digital converter. A static volumetric method was employed for the experimental setup, and 20 different concentration CH4 samples were prepared to study the sensor’s evaluation, which revealed a 1σ detection limit of 2.96 parts-per-million (ppm) with a 43 s averaging time.Item A novel automated junctional ectopic tachycardia detection tool for children with congenital heart disease(Elsevier, 2022) Waugh, Jamie L. S.; Patel, Raajen; Ju, Yilong; Patel, Ankit B.; Rusin, Craig G.; Jain, Parag N.Background Junctional ectopic tachycardia (JET) is a prevalent life-threatening arrhythmia in children with congenital heart disease (CHD), with marked resemblance to normal sinus rhythm (NSR) often leading to delay in diagnosis. Objective To develop a novel automated arrhythmia detection tool to identify JET. Methods A single-center retrospective cohort study of children with CHD was performed. Electrocardiographic (ECG) data produced by bedside monitors is captured automatically by the Sickbay platform. Based on the detection of R and P wave peaks, 2 interpretable ECG features are calculated: P prominence median and PR interval interquartile range (IQR). These features are used as input to a simple logistic regression classification model built to distinguish JET from NSR. Results This study analyzed a total of 64.5 physician-labeled hours consisting of 509,833 cardiac cycles (R-R intervals), from 40 patients with CHD. The extracted P prominence median feature is much smaller in JET compared to NSR, whereas the PR interval IQR feature is larger in JET compared to NSR. The area under the receiver operating characteristic curve for the unseen patient test cohort was 93%. Selecting a threshold of 0.73 results in a true-positive rate of 90% and a false-positive rate of 17%. Conclusion This novel arrhythmia detection tool identifies JET, using 2 distinctive features of JET in ECG—the loss of a normal P wave and PR relationship—allowing for early detection and timely intervention.Item A novel mathematical method for disclosing oscillations in gene transcription: A comparative study(Public Library of Science, 2018) Antoulas, Athanasios C.; Zhu, Bokai; Zhang, Qiang; York, Brian; O'Malley, Bert W.; Dacso, Clifford C.Circadian rhythmicity, the 24-hour cycle responsive to light and dark, is determined by periodic oscillations in gene transcription. This phenomenon has broad ramifications in physiologic function. Recent work has disclosed more cycles in gene transcription, and to the uncovering of these we apply a novel signal processing methodology known as the pencil method and compare it to conventional parametric, nonparametric, and statistical methods. Methods: In order to assess periodicity of gene expression over time, we analyzed a database derived from livers of mice entrained to a 12-hour light/12-hour dark cycle. We also analyzed artificially generated signals to identify differences between the pencil decomposition and other alternative methods. Results: The pencil decomposition revealed hitherto-unsuspected oscillations in gene transcription with 12-hour periodicity. The pencil method was robust in detecting the 24-hour circadian cycle that was known to exist, as well as confirming the existence of shorter-period oscillations. A key consequence of this approach is that orthogonality of the different oscillatory components can be demonstrated. thus indicating a biological independence of these oscillations, that has been subsequently confirmed empirically by knocking out the gene responsible for the 24-hour clock. Conclusion: System identification techniques can be applied to biological systems and can uncover important characteristics that may elude visual inspection of the data. Significance: The pencil method provides new insights on the essence of gene expression and discloses a wide variety of oscillations in addition to the well-studied circadian pattern. This insight opens the door to the study of novel mechanisms by which oscillatory gene expression signals exert their regulatory effect on cells to influence human diseases.Item A Probabilistic Framework for Deep Learning(Neural Information Processing Systems Foundation, Inc., 2016) Patel, Ankit B.; Nguyen, Tan; Baraniuk, Richard G.We develop a probabilistic framework for deep learning based on the Deep Rendering Mixture Model (DRMM), a new generative probabilistic model that explicitly capture variations in data due to latent task nuisance variables. We demonstrate that max-sum inference in the DRMM yields an algorithm that exactly reproduces the operations in deep convolutional neural networks (DCNs), providing a first principles derivation. Our framework provides new insights into the successes and shortcomings of DCNs as well as a principled route to their improvement. DRMM training via the Expectation-Maximization (EM) algorithm is a powerful alternative to DCN back-propagation, and initial training results are promising. Classification based on the DRMM and other variants outperforms DCNs in supervised digit classification, training 2-3x faster while achieving similar accuracy. Moreover, the DRMM is applicable to semi-supervised and unsupervised learning tasks, achieving results that are state-of-the-art in several categories on the MNIST benchmark and comparable to state of the art on the CIFAR10 benchmark.Item A review of ultrawide bandgap materials: properties, synthesis and devices(Oxford University Press, 2022) Xu, Mingfei; Wang, Dawei; Fu, Kai; Mudiyanselage, Dinusha Herath; Fu, Houqiang; Zhao, YujiUltrawide bandgap (UWBG) materials such as diamond, Ga2O3, hexagonal boron nitride (h-BN) and AlN, are a new class of semiconductors that possess a wide range of attractive properties, including very large bandgap, high critical electric field, high carrier mobility and chemical inertness. Due to these outstanding characteristics, UWBG materials are promising candidates to enable high-performance devices for power electronics, ultraviolet photonics, quantum sensing and quantum computing applications. Despite their great potential, the research of UWBG semiconductors is still at a nascent stage and represents a challenging interdisciplinary research area of physics, materials science and devices engineering. In this review, the material properties, synthesis methods and device applications of UWBG semiconductors diamond, Ga2O3, h-BN and AlN will be presented and their recent progress, challenges and research opportunities will be discussed.Item A room-temperature mid-infrared photodetector for on-chip molecular vibrational spectroscopy(AIP Publishing, 2018) Zheng, Bob; Zhao, Hangqi; Cerjan, Ben; Yazdi, Sadegh; Ringe, Emilie; Nordlander, Peter; Halas, Naomi J.; Laboratory for NanophotonicsInfrared (IR) photodetection is of major scientific and technical interest since virtually all molecules exhibit characteristic vibrational modes in the mid-infrared region of the spectrum, giving rise to molecular spectroscopy and chemical imaging in this wavelength range. High-resolution IR spectroscopies, such as Fourier Transform IR spectroscopy, typically require large, bulky optical measurement systems and expensive photodetector components. Here, we present a high-responsivity photodetector for the mid-IR spectral region which operates at room temperature. Fabricated from silicon and aluminum, the photodetection mechanism is based on free carrier absorption, giving rise to a photoresponse rivalling commercially available cooled IR photodetectors. We demonstrate that infrared spectra of molecules deposited on this detector can be obtained by a direct electrical read-out. This work could pave the way for simple, fully integrated chemical sensors and other applications, such as chemical imaging, which would benefit from the combination of mid-IR detection, room-temperature operation, and ultracompact portability.