Models and Analysis of Vocal Emissions for Biomedical Applications

The International Workshop on Models and Analysis of Vocal Emissions for Biomedical Applications (MAVEBA) came into being in 1999 from the particularly felt need of sharing know-how, objectives and results between areas that until then seemed quite distinct such as bioengineering, medicine and singing. MAVEBA deals with all aspects concerning the study of the human voice with applications ranging from the neonate to the adult and elderly. Over the years the initial issues have grown and spread also in other aspects of research such as occupational voice disorders, neurology, rehabilitation, image and video analysis. MAVEBA takes place every two years always in Firenze, Italy

The Telecommunications and Data Acquisition Report

Archival reports on developments in programs managed by JPL's Office of Telecommunications and Data Acquisition (TDA) are presented. Activities of the Deep Space Network (DSN) and its associated Ground Communications Facility (GCF) related to DSN advanced systems, systems implementation, and DSN operations are addressed. In addition, recent developments in the NASA SETI (Search for Extraterrestrial Intelligence) sky survey are summarized

MIMO underwater acoustic communications over time-varying channels: from theory to practice

Despite more than 70% of our planet surface is covered by water, today the underwater world can still be considered largely unknown. Rivers, lakes, seas and oceans have always been a fundamental resource for human life development, but at the same time they have often represented natural obstacles very hard to surmount. The most impressive example is probably given by the ocean, whose vastness severely limited geographical explorations and discoveries for tens of centuries. Anyway, the growing curiosity about what happens below the water surface has gradually led man to immerse in this unknown environment, trying to overcome its inaccessibility and figure out its secrets. Underwater investigation and exploring have been increasingly supported by technology, advanced over time for different purposes (military, commercial, scientific). In this regard, providing a communication link between remote users has been recognized as one of the main issues to be addressed. The first significant solutions derived from the radio-frequency world, subject of study since the 19th century. Unfortunately both wired and wireless RF inspired signal propagation strategies were not evaluated as successful. The former ones, since considering the deployment of meters (up to kilometers) of cable in depth, were too costly and difficult, while the latter ones did not offer good performance in terms of communication range due to signal attenuation. An alternative way, examined with particular interest from the beginning of the 20th century, has been that one offered by acoustics. Actually, the study of sound and its propagation through different media has been an intriguing topic since the Old World Age, hence the attempt of messaging underwater has seemed to be a great opportunity to convey theoretical principles in a real application. In addition, not only humans but also marine animals use acoustic waves to communicate, even over several kilometers distances as demonstrated by whales. So, since already existing in nature, acoustic communications have been considered as potentially successful, furthermore representing an effective trade-off between feasibility and performance, especially if compared to the other electromagnetic signals-based methods. Communication over RF channels has been extensively investigated so as to become a mature technology. The thorough knowledge about OSI (Open Systems Interconnection) model physical layer issues has allowed the researchers attention to be drawn to the upper layers. Following this direction, the recent advances in technology in this field have been accomplished mainly due to novelties in networks managing rather than to enhancements in the signal propagation study. Moving to acoustics, unfortunately this approach results to be failing if applied in the underwater scenario, as the major challenges rise indeed from physics matters. The underwater environment is varied and variable, so understanding the mechanisms that govern the propagation of sound in water is a key element for the design of a well-performing communication system. In this sense, the physical layer has therefore regained the centrality that has been diminished in other contexts. The underwater acoustic communications can be adopted in a wide range of applications. The best-known are coastal monitoring, target detection, AUVs (Autonomous Underwater Vehicles) remote control, tsunami alarm, environmental data collection and transmission. Those ones are very specific activities, so the devices to be employed must sometimes meet very strict requirements. In this regard, the solutions commercially available provide good performance (that are paid in terms of high costs). On the other hand, the fact that hardware and software are usually copyrighted leads to have a closed system. Having reconfigurable devices is instead an opportunity to match the technology with the environment features and variations, especially in real-time applications. Recently, the need to overcome these constraints has encouraged the debate about underwater technology challenges. The work by Demirors et al. [1] reports an interesting discussion about the implementation of software-defined underwater acoustic networks (UWANs), highlighting how this solution can provide enhancements in terms of software portability, computational capacity, energy efficiency and real-time reconfigurability. Furthermore, the authors propose the architecture of a software-defined acoustic modem and evaluate its performance and capabilities with tank and lake experiments. Considering the comments outlined above, the following dissertation deals with the design of an acoustic communication system. The preliminary theoretical analysis regarding physical layer concerns, such as signal propagation and channel behavior, represents the starting point from which several proposals regarding the implementation of UWANs are introduced. In particular the context of Multiple-Input Multiple-Output (MIMO) communications is investigated, presenting several solutions about transmission schemes and receiver implementation. Furthermore, concerning UWANs management, some strategies for access and error control, established at the data link layer level, are detailed. It is worth highlighting that the goal of this contribution is not to present a disjointed discussion about the topics just listed. The objective is instead to propose practical solutions developed hand in hand with theory, making choices firstly by looking at what nature allows

The Telecommunications and Data Acquisition

This quarterly publication provides archival reports on developments in programs managed by JPL's Office of Telecommunications and Data Acquisition (TDA). In space communications, radio navigation, radio science, and ground-based radio and radar astronomy, it reports on activities of the Deep Space Network (DSN) in planning, supporting research and technology, implementation, and operations. Also included are standards activity at JPL for space data and information systems and reimbursable DSN work performed for other space agencies through NASA. The preceding work is all performed for NASA's Office of Space Communications (OSC)

Generating Pictures from Waves: Aspects of Image Formation

Thesis Supervisor: Gregory W. Wornell Title: Professor of Electrical Engineering and Computer ScienceThe research communities, technologies, and tools for image formation are diverse. On the one hand, computer vision and graphics researchers analyze incoherent light using coarse geometric approximations from optics. On the other hand, array signal processing and acoustics researchers analyze coherent sound waves using stochastic estimation theory and diffraction formulas from physics. The ability to inexpensively fabricate analog circuitry and digital logic for millimeter-wave radar and ultrasound creates opportunities in comparing diverse perspectives on image formation, and presents challenges in implementing imaging systems that scale in size. We present algorithms, architectures, and abstractions for image formation that relate the different communities, technologies, and tools. We address practical technical challenges in operating millimeter-wave radar and ultrasound systems in the presence of phase noise and scattering. We model a broad class of physical phenomena with isotropic point sources. We show that the optimal source location estimator for coherent waves reduces to processing an image produced by a conventional camera, provided the sources are wellseparated relative to the system resolution, and in the limit of small wavelength and globally incoherent light. We introduce quasi light fields to generalize the incoherent image formation process to coherent waves, offering resolution tradeoffs that surpass the traditional Fourier uncertainty principle by leveraging time-frequency distributions. We show that the number of sensors in a coherent imaging array defines a stable operating point relative to the phase noise. We introduce a digital phase tightening algorithm to reduce phase noise. We present a system identification framework for multiple-input multiple-output (MIMO) ultrasound imaging that generalizes existing approaches with time-varying filters. Our theoretical results enable the application of traditional techniques in incoherent imaging to coherent imaging, and vice versa. Our practical results suggest a methodology for designing millimeter-wave imaging systems. Our conclusions reinforce architectural principles governing transmitter and receiver design, the role of analog and digital circuity, and the tradeoff between data rate and data precision.Microsoft Research, MIT Lincoln Laboratory, and the C2S2 Focus Center, one of six research centers funded under the Focus Center Research Program (FCRP), a Semiconductor Research Corporation entity

Processing of Ex-Situ Acquired Signals from Magnetic Disks

The ubiquity and high performance of hard disk drives for nonvolatile digital data storage cannot be denied. As the magnetic recording industry continues to develop new techniques for increasing storage density and reducing cost per bit, diagnostic and forensic tools for characterizing and interpreting the magnetic patterns recorded onto disk drive media become increasingly important. Therefore, this dissertation presents developments to the uniquely suitable spin-stand-based method of imaging magnetization patterns on media extracted from commercial hard disk drives. The emphasis of the presented research is placed on the following three areas: microscopy enhancement techniques for longitudinal magnetic recording media, "drive-independent" characterization and reconstruction of disk data, and the exploration of spin-stand microscopy in the novel context of perpendicular magnetic recording. First, it is known that, while the spin-stand microscopy technique offers high-speed and massive scale imaging capabilities, the images obtained are corrupted by distortion due to the non-local sensing or finite spatial resolution of the imaging sensor. Two techniques for mitigating this distortion, one based on characterizing the head by means of its linear response function, and a new method based on spatial Hilbert transforms, are described and demonstrated. Furthermore, a two-dimensional extension of the Hilbert transform in the context of magnetic recording is derived based on physical arguments and its application to spin-stand imaging is demonstrated. Second, although magnetic media imaging is interesting in its own right, an extension of this capability is the identification of commercial hard disk drive write channels and the subsequent reconstruction of the data written to the associated disks in a "drive-independent" manner on the spin-stand. For fundamental and practical reasons, a multilayered encoding process is performed on digital data before it is written to the disk; the presented work details the theoretical and experimental results obtained in characterizing and reversing these codes. Finally, because perpendicular recording technology has recently come on the market in consumer disk drives, the spin-stand microscopy technique is extended to imaging the media employing this new mode of recording. In particular, the novel aspects of perpendicular recording are discussed and their impact on spin-stand microscopy is demonstrated

The Telecommunications and Data Acquisition Report

Developments in programs managed by the Jet Propulsion Laboratory's Office of Telecommunications and Data acquisition are discussed. Space communications, radio antennas, the Deep Space Network, antenna design, Project SETI, seismology, coding, very large scale integration, downlinking, and demodulation are among the topics covered

Efficient homology search for genomic sequence databases

Genomic search tools can provide valuable insights into the chemical structure, evolutionary origin and biochemical function of genetic material. A homology search algorithm compares a protein or nucleotide query sequence to each entry in a large sequence database and reports alignments with highly similar sequences. The exponential growth of public data banks such as GenBank has necessitated the development of fast, heuristic approaches to homology search. The versatile and popular blast algorithm, developed by researchers at the US National Center for Biotechnology Information (NCBI), uses a four-stage heuristic approach to efficiently search large collections for analogous sequences while retaining a high degree of accuracy. Despite an abundance of alternative approaches to homology search, blast remains the only method to offer fast, sensitive search of large genomic collections on modern desktop hardware. As a result, the tool has found widespread use with millions of queries posed each day. A significant investment of computing resources is required to process this large volume of genomic searches and a cluster of over 200 workstations is employed by the NCBI to handle queries posed through the organisation's website. As the growth of sequence databases continues to outpace improvements in modern hardware, blast searches are becoming slower each year and novel, faster methods for sequence comparison are required. In this thesis we propose new techniques for fast yet accurate homology search that result in significantly faster blast searches. First, we describe improvements to the final, gapped alignment stages where the query and sequences from the collection are aligned to provide a fine-grain measure of similarity. We describe three new methods for aligning sequences that roughly halve the time required to perform this computationally expensive stage. Next, we investigate improvements to the first stage of search, where short regions of similarity between a pair of sequences are identified. We propose a novel deterministic finite automaton data structure that is significantly smaller than the codeword lookup table employed by ncbi-blast, resulting in improved cache performance and faster search times. We also discuss fast methods for nucleotide sequence comparison. We describe novel approaches for processing sequences that are compressed using the byte packed format already utilised by blast, where four nucleotide bases from a strand of DNA are stored in a single byte. Rather than decompress sequences to perform pairwise comparisons, our innovations permit sequences to be processed in their compressed form, four bases at a time. Our techniques roughly halve average query evaluation times for nucleotide searches with no effect on the sensitivity of blast. Finally, we present a new scheme for managing the high degree of redundancy that is prevalent in genomic collections. Near-duplicate entries in sequence data banks are highly detrimental to retrieval performance, however existing methods for managing redundancy are both slow, requiring almost ten hours to process the GenBank database, and crude, because they simply purge highly-similar sequences to reduce the level of internal redundancy. We describe a new approach for identifying near-duplicate entries that is roughly six times faster than the most successful existing approaches, and a novel approach to managing redundancy that reduces collection size and search times but still provides accurate and comprehensive search results. Our improvements to blast have been integrated into our own version of the tool. We find that our innovations more than halve average search times for nucleotide and protein searches, and have no signifcant effect on search accuracy. Given the enormous popularity of blast, this represents a very significant advance in computational methods to aid life science research

Generating pictures from waves : aspects of image formation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 171-177).The research communities, technologies, and tools for image formation are diverse. On the one hand, computer vision and graphics researchers analyze incoherent light using coarse geometric approximations from optics. On the other hand, array signal processing and acoustics researchers analyze coherent sound waves using stochastic estimation theory and diffraction formulas from physics. The ability to inexpensively fabricate analog circuitry and digital logic for millimeter-wave radar and ultrasound creates opportunities in comparing diverse perspectives on image formation, and presents challenges in implementing imaging systems that scale in size. We present algorithms, architectures, and abstractions for image formation that relate the different communities, technologies, and tools. We address practical technical challenges in operating millimeter-wave radar and ultrasound systems in the presence of phase noise and scattering. We model a broad class of physical phenomena with isotropic point sources. We show that the optimal source location estimator for coherent waves reduces to processing an image produced by a conventional camera, provided the sources are well separated relative to the system resolution, and in the limit of small wavelength and globally incoherent light. We introduce quasi light fields to generalize the incoherent image formation process to coherent waves, offering resolution tradeoffs that surpass the traditional Fourier uncertainty principle by leveraging time-frequency distributions. We show that the number of sensors in a coherent imaging array defines a stable operating point relative to the phase noise. We introduce a digital phase tightening algorithm to reduce phase noise. We present a system identification framework for multiple-input multiple-output (MIMO) ultrasound imaging that generalizes existing approaches with time-varying filters. Our theoretical results enable the application of traditional techniques in incoherent imaging to coherent imaging, and vice versa. Our practical results suggest a methodology for designing millimeter-wave imaging systems. Our conclusions reinforce architectural principles governing transmitter and receiver design, the role of analog and digital circuity, and the tradeoff between data rate and data precision.by Anthony Accardi.Ph.D

Computational and Imaging Methods for Studying Neuronal Populations during Behavior

One of the central questions in neuroscience is how the nervous system generates and regulates behavior. To understand the neural code for any behavior, an ideal experiment would entail (i) quantitatively defining that behavior, (ii) recording neuronal activity in relevant brain regions to identify the underlying neuronal circuits and eventually (iii) manipulating them to test their function. Novel methods in neuroscience have greatly advanced our abilities to conduct such experiments but are still insufficient. In this thesis, I developed methods for these three goals. In Chapter 2, I describe an automatic behavior identification and classification method for the cnidarian Hydra vulgaris using machine learning. In Chapter 3, I describe a fast volumetric two-photon microscope with dual-color laser excitation that can image in 3D the activity of populations of neurons from visual cortex of awake mice. In Chapter 4, I present a machine learning method that identifies cortical ensembles and pattern completion neurons in mouse visual cortex, using two-photon calcium imaging data. These methods advance current technologies, providing opportunities for new discoveries