Similarity-based birdcall retrieval from environmental audio

Automated digital recordings are useful for large-scale temporal and spatial environmental monitoring. An important research effort has been the automated classification of calling bird species. In this paper we examine a related task, retrieval of birdcalls from a database of audio recordings, similar to a user supplied query call. Such a retrieval task can sometimes be more useful than an automated classifier. We compare three approaches to similarity-based birdcall retrieval using spectral ridge features and two kinds of gradient features, structure tensor and the histogram of oriented gradients. The retrieval accuracy of our spectral ridge method is 94% compared to 82% for the structure tensor method and 90% for the histogram of gradients method. Additionally, this approach potentially offers a more compact representation and is more computationally efficient.

Generalised features for bird vocalisation retrieval in acoustic recordings

Bioacoustic monitoring has become a significant research topic for species diversity conservation. Due to the development of sensing techniques, acoustic sensors are widely deployed in the field to record animal sounds over a large spatial and temporal scale. With large volumes of collected audio data, it is essential to develop semi-automatic or automatic techniques to analyse the data. This can help ecologists make decisions on how to protect and promote the species diversity. This paper presents generic features to characterize a range of bird species for vocalisation retrieval. In the implementation, audio recordings are first converted to spectrograms using short-time Fourier transform, then a ridge detection method is applied to the spectrogram for detecting points of interest. Based on the detected points, a new region representation are explored for describing various bird vocalisations and a local descriptor including temporal entropy, frequency bin entropy and histogram of counts of four ridge directions is calculated for each sub-region. To speed up the retrieval process, indexing is carried out and the retrieved results are ranked according to similarity scores. The experiment results show that our proposed feature set can achieve 0.71 in term of retrieval success rate which outperforms spectral ridge features alone (0.55) and Mel frequency cepstral coefficients (0.36).

Birdcall retrieval from environmental acoustic recordings using image processing

Acoustic recordings of the environment provide an effective means to monitor bird species diversity. To facilitate exploration of acoustic recordings, we describe a content-based birdcall retrieval algorithm. A query birdcall is a region of spectrogram bounded by frequency and time. Retrieval depends on a similarity measure derived from the orientation and distribution of spectral ridges. The spectral ridge detection method caters for a broad range of birdcall structures. In this paper, we extend previous work by incorporating a spectrogram scaling step in order to improve the detection of spectral ridges. Compared to an existing approach based on MFCC features, our feature representation achieves better retrieval performance for multiple bird species in noisy recordings.

The grand philosopher of the Commons: In memory of Elinor Ostrom

The grand philosopher of the Commons, Elinor Ostrom, passed away on the 12th June 2012. She was a brilliant, creative polymath; a theoretician of fine precision and great intellectual power; a deviser of masterful empirical studies; and an energetic collaborator and networker. Ostrom posed a formidable intellectual challenge to the fields of economics and the social sciences - and the advocates of central regulation, privatization, and enclosure.

Ultra-flexible nonvolatile memory based on donor-acceptor diketopyrrolopyrrole polymer blends

Flexible memory cell array based on high mobility donor-acceptor diketopyrrolopyrrole polymer has been demonstrated. The memory cell exhibits low read voltage, high cell-to-cell uniformity and good mechanical flexibility, and has reliable retention and endurance memory performance. The electrical properties of the memory devices are systematically investigated and modeled. Our results suggest that the polymer blends provide an important step towards high-density flexible nonvolatile memory devices.

IgE+ B cells are scarce, but allergen-specific B cells with a memory phenotype circulate in patients with allergic rhinitis

Background Despite the critical role of immunoglobulin E (IgE) in allergy, circulating IgE+ B cells are scarce. Here, we describe in patients with allergic rhinitis B cells with a memory phenotype responding to a prototypic aeroallergen. Methods Fifteen allergic rhinitis patients with grass pollen allergy and 13 control subjects were examined. Blood mononuclear cells stained with carboxyfluorescein diacetate succinimidyl ester (CFSE) were cultured with Bahia grass pollen. Proliferation and phenotype were assessed by multicolour flow cytometry. Results In blood of allergic rhinitis patients with high serum IgE to grass pollen, most IgEhi cells were CD123+ HLA-DR- basophils, with IgE for the major pollen allergen (Pas n 1). Both B and T cells from pollen-allergic donors showed higher proliferation to grass pollen than nonallergic donors (P = 0.002, and 0.010, respectively), whereas responses to vaccine antigens and mitogen did not differ between groups. Allergen-driven B cells that divided rapidly (CD19mid CD3- CFSElo) showed higher CD27 (P = 0.008) and lower CD19 (P = 0.004) and CD20 (P = 0.004) expression than B cells that were slow to respond to allergen (CD19hi CD3- CFSEmid). Moreover, rapidly dividing allergen-driven B cells (CD19mid CFSElo CD27hi) showed higher expression of the plasmablast marker CD38 compared with B cells (CD19hi CFSEmid CD27lo) that were slow to divide. Conclusion Patients with pollen allergy but not control donors have a population of circulating allergen-specific B cells with the phenotype and functional properties of adaptive memory B-cell responses. These cells could provide precursors for allergen-specific IgE production upon allergen re-exposure. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The enigma of IgE+ B-cell memory in human subjects

Our understanding of the origin and fate of the IgE-switched B cell has been markedly improved by studies in mouse models. The immediate precursor of the IgE-switched B cell is either a relatively naive nonswitched B cell or a mature IgG-switched B cell. These 2 routes are referred to as the direct and indirect pathways, respectively. IgE responses derived from each pathway differ significantly, largely reflecting the difference in time spent in a germinal center and thus time for clonal expansion, somatic hypermutation, affinity maturation, and acquisition of a memory phenotype. The clinical and therapeutic implications for IgE responses in human subjects are still a matter of debate, largely because the immunization procedures used in the animal models are significantly different from classical atopic sensitization to allergens from pollen and mites. On the basis of the limited information available, it seems likely that these atopic IgE responses are characterized by a relatively low IgG/IgE ratio, low B-cell memory, and modest affinity maturation, which fits well with the direct switching pathway. It is still unresolved how the IgE response evolves to cover a wide epitope repertoire involving many epitopes per allergen, as well as many different allergens from a single allergen source. © 2013 American Academy of Allergy, Asthma & Immunology.

Medical free-text to concept mapping as an information retrieval problem

Concept mapping involves determining relevant concepts from a free-text input, where concepts are defined in an external reference ontology. This is an important process that underpins many applications for clinical information reporting, derivation of phenotypic descriptions, and a number of state-of-the-art medical information retrieval methods. Concept mapping can be cast into an information retrieval (IR) problem: free-text mentions are treated as queries and concepts from a reference ontology as the documents to be indexed and retrieved. This paper presents an empirical investigation applying general-purpose IR techniques for concept mapping in the medical domain. A dataset used for evaluating medical information extraction is adapted to measure the effectiveness of the considered IR approaches. Standard IR approaches used here are contrasted with the effectiveness of two established benchmark methods specifically developed for medical concept mapping. The empirical findings show that the IR approaches are comparable with one benchmark method but well below the best benchmark.

Fear memory reactivation after extinction activates plasticity in the lateral amygdala

Little is known about the neuronal changes that occur within the lateral amygdala (LA) following fear extinction. In fear extinction, the repeated presentation of a conditioned stimulus (CS), in the absence of a previously paired aversive unconditioned stimulus (US), reduces fear elicited by the CS. Fear extinction is an active learning process that leads to the formation of a consolidated extinction memory, however it is fragile and prone to spontaneous recovery and renewal under environmental changes such as context. Understanding the neural mechanisms underlying fear extinction is of great clinical relevance, as psychological treatments of several anxiety disorders rely largely on extinction-based procedures and relapse is major clinical problem. This study investigated plasticity in the LA following fear memory reactivation in rats with and without extinction training. Phosphorylated MAPK (p44/42 ERK/MAPK), a protein kinase required in the amygdala for fear learning and its extinction, was used as a marker for neuronal plasticity. Rats (N = 11) underwent a Pavlovian auditory fear conditioning and extinction paradigm, and later received a single conditioned stimulus presentation to reactivate the fear memory. Results showed more pMAPK+ expressing neurons in the LA following extinction-reactivation compared to control rats, with the largest number of pMAPK+ neurons counted in the ventral LA, especially including the ventro-lateral subdivision (LAvl). These findings indicate that LA subdivision specific plasticity occurs to the conditioned fear memory in the LAvl following extinction-reactivation. These findings provide important insight into the organisation of fear memories in the LA, and pave the way for future research in the memory mechanisms of fear extinction and its pathophysiology.

SPSA Based Feature Relevance Estimation For Video Retrieval

With the availability of a huge amount of video data on various sources, efficient video retrieval tools are increasingly in demand. Video being a multi-modal data, the perceptions of ``relevance'' between the user provided query video (in case of Query-By-Example type of video search) and retrieved video clips are subjective in nature. We present an efficient video retrieval method that takes user's feedback on the relevance of retrieved videos and iteratively reformulates the input query feature vectors (QFV) for improved video retrieval. The QFV reformulation is done by a simple, but powerful feature weight optimization method based on Simultaneous Perturbation Stochastic Approximation (SPSA) technique. A video retrieval system with video indexing, searching and relevance feedback (RF) phases is built for demonstrating the performance of the proposed method. The query and database videos are indexed using the conventional video features like color, texture, etc. However, we use the comprehensive and novel methods of feature representations, and a spatio-temporal distance measure to retrieve the top M videos that are similar to the query. In feedback phase, the user activated iterative on the previously retrieved videos is used to reformulate the QFV weights (measure of importance) that reflect the user's preference, automatically. It is our observation that a few iterations of such feedback are generally sufficient for retrieving the desired video clips. The novel application of SPSA based RF for user-oriented feature weights optimization makes the proposed method to be distinct from the existing ones. The experimental results show that the proposed RF based video retrieval exhibit good performance.

Scalable document hashing and retrieval

This thesis studies document signatures, which are small representations of documents and other objects that can be stored compactly and compared for similarity. This research finds that document signatures can be effectively and efficiently used to both search and understand relationships between documents in large collections, scalable enough to search a billion documents in a fraction of a second. Deliverables arising from the research include an investigation of the representational capacity of document signatures, the publication of an open-source signature search platform and an approach for scaling signature retrieval to operate efficiently on collections containing hundreds of millions of documents.

Improved assessment of aerosol absorption using OMI-MODIS joint retrieval

The Ozone Monitoring Instrument (OMI) aboard EOS-Aura and the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard EOS-Aqua fly in formation as part of the A-train. Though OMI retrieves aerosol optical depth (AOD) and aerosol absorption, it must assume aerosol layer height. The MODIS cannot retrieve aerosol absorption, but MODIS aerosol retrieval is not sensitive to aerosol layer height and with its smaller pixel size is less affected by subpixel clouds. Here we demonstrate an approach that uses MODIS-retrieved AOD to constrain the OMI retrieval, freeing OMI from making an a priori estimate of aerosol height and allowing a more direct retrieval of aerosol absorption. To predict near-UV optical depths using MODIS data we rely on the spectral curvature of the MODIS-retrieved visible and near-IR spectral AODs. Application of an OMI-MODIS joint retrieval over the north tropical Atlantic shows good agreement between OMI and MODIS-predicted AODs in the UV, which implies that the aerosol height assumed in the OMI-standard algorithm is probably correct. In contrast, over the Arabian Sea, MODIS-predicted AOD deviated from the OMI-standard retrieval, but combined OMI-MODIS retrievals substantially improved information on aerosol layer height (on the basis of validation against airborne lidar measurements). This implies an improvement in the aerosol absorption retrieval, but lack of UV absorption measurements prevents a true validation. Our study demonstrates the potential of multisatellite analysis of A-train data to improve the accuracy of retrieved aerosol products and suggests that a combined OMI-MODIS-CALIPSO retrieval has large potential to further improve assessments of aerosol absorption.

Structural basis for the function of anti-idiotypic antibody in immune memory

We had earlier proposed a hypothesis to explain the mechanism of perpetuation of immunological memory based on the operation of idiotypic network in the complete absence of antigen. Experimental evidences were provided for memory maintenance through anti-idiotypic antibody (Ab2) carrying the internal image of the antigen. In the present work, we describe a structural basis for such memory perpetuation by molecular modeling and structural analysis studies. A three-dimensional model of Ab2 was generated and the structure of the antigenic site on the hemagglutinin protein H of Rinderpest virus was modeled using the structural template of hemagglutinin protein of Measles virus. Our results show that a large portion of heavy chain containing the CDR regions of Ab2 resembles the domain of the hemagglutinin housing the epitope regions. The similarity demonstrates that an internal image of the H antigen is formed in Ab2, which provides a structural basis for functional mimicry demonstrated earlier. This work brings out the importance of the structural similarity between a domain of hemagglutinin protein to that of its corresponding Ab2. It provides evidence that Ab2 is indeed capable of functioning as surrogate antigen and provides support to earlier proposed relay hypothesis which has provided a mechanism for the maintenance of immunological memory.

Compact features for birdcall retrieval from environmental acoustic recordings

Bioacoustic data can be used for monitoring animal species diversity. The deployment of acoustic sensors enables acoustic monitoring at large temporal and spatial scales. We describe a content-based birdcall retrieval algorithm for the exploration of large data bases of acoustic recordings. In the algorithm, an event-based searching scheme and compact features are developed. In detail, ridge events are detected from audio files using event detection on spectral ridges. Then event alignment is used to search through audio files to locate candidate instances. A similarity measure is then applied to dimension-reduced spectral ridge feature vectors. The event-based searching method processes a smaller list of instances for faster retrieval. The experimental results demonstrate that our features achieve better success rate than existing methods and the feature dimension is greatly reduced.

Secondary attribute retrieval using tree data structures

Several techniques are known for searching an ordered collection of data. The techniques and analyses of retrieval methods based on primary attributes are straightforward. Retrieval using secondary attributes depends on several factors. For secondary attribute retrieval, the linear structures—inverted lists, multilists, doubly linked lists—and the recently proposed nonlinear tree structures—multiple attribute tree (MAT), K-d tree (kdT)—have their individual merits. It is shown in this paper that, of the two tree structures, MAT possesses several features of a systematic data structure for external file organisation which make it superior to kdT. Analytic estimates for the complexity of node searchers, in MAT and kdT for several types of queries, are developed and compared.