A Mismatch-Based Model for Memory Reconsolidation and Extinction in Attractor Networks

OSAN, R. , TORT, A. B. L. , AMARAL, O. B. . A mismatch-based model for memory reconsolidation and extinction in attractor networks. Plos One, v. 6, p. e23113, 2011.

Efficient Image and Video Representations for Retrieval

Image (Video) retrieval is an interesting problem of retrieving images (videos) similar to the query. Images (Videos) are represented in an input (feature) space and similar images (videos) are obtained by finding nearest neighbors in the input representation space. Numerous input representations both in real valued and binary space have been proposed for conducting faster retrieval. In this thesis, we present techniques that obtain improved input representations for retrieval in both supervised and unsupervised settings for images and videos. Supervised retrieval is a well known problem of retrieving same class images of the query. We address the practical aspects of achieving faster retrieval with binary codes as input representations for the supervised setting in the first part, where binary codes are used as addresses into hash tables. In practice, using binary codes as addresses does not guarantee fast retrieval, as similar images are not mapped to the same binary code (address). We address this problem by presenting an efficient supervised hashing (binary encoding) method that aims to explicitly map all the images of the same class ideally to a unique binary code. We refer to the binary codes of the images as `Semantic Binary Codes' and the unique code for all same class images as `Class Binary Code'. We also propose a new class­ based Hamming metric that dramatically reduces the retrieval times for larger databases, where only hamming distance is computed to the class binary codes. We also propose a Deep semantic binary code model, by replacing the output layer of a popular convolutional Neural Network (AlexNet) with the class binary codes and show that the hashing functions learned in this way outperforms the state­ of ­the art, and at the same time provide fast retrieval times. In the second part, we also address the problem of supervised retrieval by taking into account the relationship between classes. For a given query image, we want to retrieve images that preserve the relative order i.e. we want to retrieve all same class images first and then, the related classes images before different class images. We learn such relationship aware binary codes by minimizing the similarity between inner product of the binary codes and the similarity between the classes. We calculate the similarity between classes using output embedding vectors, which are vector representations of classes. Our method deviates from the other supervised binary encoding schemes as it is the first to use output embeddings for learning hashing functions. We also introduce new performance metrics that take into account the related class retrieval results and show significant gains over the state­ of­ the art. High Dimensional descriptors like Fisher Vectors or Vector of Locally Aggregated Descriptors have shown to improve the performance of many computer vision applications including retrieval. In the third part, we will discuss an unsupervised technique for compressing high dimensional vectors into high dimensional binary codes, to reduce storage complexity. In this approach, we deviate from adopting traditional hyperplane hashing functions and instead learn hyperspherical hashing functions. The proposed method overcomes the computational challenges of directly applying the spherical hashing algorithm that is intractable for compressing high dimensional vectors. A practical hierarchical model that utilizes divide and conquer techniques using the Random Select and Adjust (RSA) procedure to compress such high dimensional vectors is presented. We show that our proposed high dimensional binary codes outperform the binary codes obtained using traditional hyperplane methods for higher compression ratios. In the last part of the thesis, we propose a retrieval based solution to the Zero shot event classification problem - a setting where no training videos are available for the event. To do this, we learn a generic set of concept detectors and represent both videos and query events in the concept space. We then compute similarity between the query event and the video in the concept space and videos similar to the query event are classified as the videos belonging to the event. We show that we significantly boost the performance using concept features from other modalities.

Multi-sensor Cloud and Aerosol Retrieval Simulator and Its Applications

Executing a cloud or aerosol physical properties retrieval algorithm from controlled synthetic data is an important step in retrieval algorithm development. Synthetic data can help answer questions about the sensitivity and performance of the algorithm or aid in determining how an existing retrieval algorithm may perform with a planned sensor. Synthetic data can also help in solving issues that may have surfaced in the retrieval results. Synthetic data become very important when other validation methods, such as field campaigns,are of limited scope. These tend to be of relatively short duration and often are costly. Ground stations have limited spatial coverage whilesynthetic data can cover large spatial and temporal scales and a wide variety of conditions at a low cost. In this work I develop an advanced cloud and aerosol retrieval simulator for the MODIS instrument, also known as Multi-sensor Cloud and Aerosol Retrieval Simulator (MCARS). In a close collaboration with the modeling community I have seamlessly combined the GEOS-5 global climate model with the DISORT radiative transfer code, widely used by the remote sensing community, with the observations from the MODIS instrument to create the simulator. With the MCARS simulator it was then possible to solve the long standing issue with the MODIS aerosol optical depth retrievals that had a low bias for smoke aerosols. MODIS aerosol retrieval did not account for effects of humidity on smoke aerosols. The MCARS simulator also revealed an issue that has not been recognized previously, namely,the value of fine mode fraction could create a linear dependence between retrieved aerosol optical depth and land surface reflectance. MCARS provided the ability to examine aerosol retrievals against “ground truth” for hundreds of thousands of simultaneous samples for an area covered by only three AERONET ground stations. Findings from MCARS are already being used to improve the performance of operational MODIS aerosol properties retrieval algorithms. The modeling community will use the MCARS data to create new parameterizations for aerosol properties as a function of properties of the atmospheric column and gain the ability to correct any assimilated retrieval data that may display similar dependencies in comparisons with ground measurements.

Nested Sampling and its Applications in Stable Compressive Covariance Estimation and Phase Retrieval with Near-Minimal Measurements

Compressed covariance sensing using quadratic samplers is gaining increasing interest in recent literature. Covariance matrix often plays the role of a sufficient statistic in many signal and information processing tasks. However, owing to the large dimension of the data, it may become necessary to obtain a compressed sketch of the high dimensional covariance matrix to reduce the associated storage and communication costs. Nested sampling has been proposed in the past as an efficient sub-Nyquist sampling strategy that enables perfect reconstruction of the autocorrelation sequence of Wide-Sense Stationary (WSS) signals, as though it was sampled at the Nyquist rate. The key idea behind nested sampling is to exploit properties of the difference set that naturally arises in quadratic measurement model associated with covariance compression. In this thesis, we will focus on developing novel versions of nested sampling for low rank Toeplitz covariance estimation, and phase retrieval, where the latter problem finds many applications in high resolution optical imaging, X-ray crystallography and molecular imaging. The problem of low rank compressive Toeplitz covariance estimation is first shown to be fundamentally related to that of line spectrum recovery. In absence if noise, this connection can be exploited to develop a particular kind of sampler called the Generalized Nested Sampler (GNS), that can achieve optimal compression rates. In presence of bounded noise, we develop a regularization-free algorithm that provably leads to stable recovery of the high dimensional Toeplitz matrix from its order-wise minimal sketch acquired using a GNS. Contrary to existing TV-norm and nuclear norm based reconstruction algorithms, our technique does not use any tuning parameters, which can be of great practical value. The idea of nested sampling idea also finds a surprising use in the problem of phase retrieval, which has been of great interest in recent times for its convex formulation via PhaseLift, By using another modified version of nested sampling, namely the Partial Nested Fourier Sampler (PNFS), we show that with probability one, it is possible to achieve a certain conjectured lower bound on the necessary measurement size. Moreover, for sparse data, an l1 minimization based algorithm is proposed that can lead to stable phase retrieval using order-wise minimal number of measurements.

Versioning Concept Schemes for Persistent Retrieval

Things change. Words change, meaning changes and use changes both words and meaning. In information access systems this means concept schemes such as thesauri or clas- sification schemes change. They always have. Concept schemes that have survived have evolved over time, moving from one version, often called an edition, to the next. If we want to manage how words and meanings - and as a conse- quence use - change in an effective manner, and if we want to be able to search across versions of concept schemes, we have to track these changes. This paper explores how we might expand SKOS, a World Wide Web Consortium (W3C) draft recommendation in order to do that kind of tracking.The Simple Knowledge Organization System (SKOS) Core Guide is sponsored by the Semantic Web Best Practices and Deployment Working Group. The second draft, edited by Alistair Miles and Dan Brickley, was issued in November 2005. SKOS is a “model for expressing the basic structure and content of concept schemes such as thesauri, classification schemes, subject heading lists, taxonomies, folksonomies, other types of controlled vocabulary and also concept schemes embedded in glossaries and terminologies” in RDF. How SKOS handles version in concept schemes is an open issue. The current draft guide suggests using OWL and DCTERMS as mechanisms for concept scheme revision.As it stands an editor of a concept scheme can make notes or declare in OWL that more than one version exists. This paper adds to the SKOS Core by introducing a tracking sys- tem for changes in concept schemes. We call this tracking system vocabulary ontogeny. Ontogeny is a biological term for the development of an organism during its lifetime. Here we use the ontogeny metaphor to describe how vocabularies change over their lifetime. Our purpose here is to create a conceptual mechanism that will track these changes and in so doing enhance information retrieval and prevent document loss through versioning, thereby enabling persistent retrieval.

MARS (Media Asset Retrieval System): Puget Sound’s Digital Archive

The MARS (Media Asset Retrieval System) Project is the collaborative effort of public broadcasters,libraries and schools in the Puget Sound region to create a digital online resource that provides access to content produced by public broadcasters via the public libraries. Convergence ConsortiumThe Convergence Consortium is a model for community collaboration, including organizations such as public broadcasters, libraries, museums, and schools in the Puget Sound region to assess the needs of their constituents and pool resources to develop solutions to meet those needs. Specifically, the archives of public broadcasters have been identified as significant resources for the local communities and nationally. These resources can be accessed on the broadcasters websites, and through libraries and used by schools, and integrated with text and photographic archives from other partners.MARS’ goalCreate an online resource that provides effective access to the content produced locally by KCTS (Seattle PBS affiliate) and KUOW (Seattle NPR affiliate). The broadcasts will be made searchable using the CPB Metadata Element Set (under development) and controlled vocabularies (to be developed). This will ensure a user friendly search and navigation mechanism and user satisfaction.Furthermore, the resource can search the local public library’s catalog concurrently and provide the user with relevant TV material, radio material, and books on a given subject.The ultimate goal is to produce a model that can be used in cities around the country.The current phase of the project assesses the community’s need, analyzes the current operational systems, and makes recommendations for the design of the resource.Deliverables• Literature review of the issues surrounding the organization, description and representation of media assets• Needs assessment report of internal and external stakeholders• Profile of the systems in the area of managing and organizing media assetsfor public broadcasting nationwideActivities• Analysis of information seeking behavior• Analysis of collaboration within the respective organizations• Analysis of the scope and context of the proposed system• Examining the availability of information resources and exchangeof resources among users

Puget Sound’s MARS (Media Asset Retrieval System) Digital Library

The MARS (Media Asset Retrieval System) Project is a collaboration between public broadcasters, libraries and schools in the Puget Sound region to assess the needs of their constituents and pool resources to develop solutions to meet those needs. The Project’s ultimate goal is to create a digital online resource that will provide access to content produced by public broadcasters and libraries. The MARS Project is funded by a grant from the Corporation for Public Broadcasting (CPB) Television Future Fund. Convergence ConsortiumThe Convergence Consortium is a model for community collaboration, including representatives from public broadcasting, libraries and schools in the Puget Sound region. They meet regularly to consider collaborative efforts that will be mutually beneficial to their institutions and constituents. Specifically, the archives of public broadcasters have been identified as significant resources that can be accessed through libraries and used by schools, and integrated with text and photographic archives from other partners.Using the work-centered framework, we collected data through interviews with nine engineers and observation of their searching while they performed their regular, job-related searches on the Web. The framework was used to analyze the data on two levels: 1) the activities and organizational relationships and constrains of work domains, and 2) users’ cognitive and social activities and their subjective preferences during searching.

Comparisons of an aerosol transport model with a 4-year analysis of summer aerosol optical depth retrievals over the Canadian Arctic

Abstract : This is a study concerning comparisons between the Dubovik Aerosol optical depth (AOD) retrievals from AEROCAN (ARONET) stations and AOD estimates from simulations provided by a chemical transport model (GEOS-Chem : Goddard Earth Observing System Chemistry). The AOD products associated with the Dubovik product are divided into total, fine and coarse mode components. The retrieval period is from January 2009 to January 2013 for 5 Arctic stations (Barrow, Alaska; Resolute Bay, Nunavut; 0PAL and PEARL (Eureka), Nunavut; and Thule, Greenland). We also employed AOD retrievals from 10 other mid-latitude Canadian stations for comparisons with the Arctic stations. The results of our investigation were submitted to Atmosphere-Ocean. To briefly summarize those results, the model generally but not always tended to underestimate the (monthly) averaged AOD and its components. We found that the subdivision into fine and coarse mode components could provide unique signatures of particular events (Asian dust) and that the means of characterizing the statistics (log-normal frequency distributions versus normal distributions) was an attribute that was common to both the retrievals and the model.

Self-supervised information retrieval: a novel approach based on Deep Metric Learning and Neural Language Models

Most of the existing open-source search engines, utilize keyword or tf-idf based techniques to find relevant documents and web pages relative to an input query. Although these methods, with the help of a page rank or knowledge graphs, proved to be effective in some cases, they often fail to retrieve relevant instances for more complicated queries that would require a semantic understanding to be exploited. In this Thesis, a self-supervised information retrieval system based on transformers is employed to build a semantic search engine over the library of Gruppo Maggioli company. Semantic search or search with meaning can refer to an understanding of the query, instead of simply finding words matches and, in general, it represents knowledge in a way suitable for retrieval. We chose to investigate a new self-supervised strategy to handle the training of unlabeled data based on the creation of pairs of ’artificial’ queries and the respective positive passages. We claim that by removing the reliance on labeled data, we may use the large volume of unlabeled material on the web without being limited to languages or domains where labeled data is abundant.

Integrated Proteomics Identified Up-regulated Focal Adhesion-mediated Proteins In Human Squamous Cell Carcinoma In An Orthotopic Murine Model.

Understanding the molecular mechanisms of oral carcinogenesis will yield important advances in diagnostics, prognostics, effective treatment, and outcome of oral cancer. Hence, in this study we have investigated the proteomic and peptidomic profiles by combining an orthotopic murine model of oral squamous cell carcinoma (OSCC), mass spectrometry-based proteomics and biological network analysis. Our results indicated the up-regulation of proteins involved in actin cytoskeleton organization and cell-cell junction assembly events and their expression was validated in human OSCC tissues. In addition, the functional relevance of talin-1 in OSCC adhesion, migration and invasion was demonstrated. Taken together, this study identified specific processes deregulated in oral cancer and provided novel refined OSCC-targeting molecules.

Electronic And Structural Study Of Pt-modified Au Vicinal Surfaces: A Model System For Pt-au Catalysts.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

The Soluble Guanylyl Cyclase Activator Bay 60-2770 Potently Relaxes The Pulmonary Artery On Congenital Diaphragmatic Hernia Rabbit Model.

Congenital diaphragmatic hernia (CDH) is associated with pulmonary hypertension which is often difficult to manage, and a significant cause of morbidity and mortality. In this study, we have used a rabbit model of CDH to evaluate the effects of BAY 60-2770 on the in vitro reactivity of left pulmonary artery. CDH was performed in New Zealand rabbit fetuses (n = 10 per group) and compared to controls. Measurements of body, total and left lung weights (BW, TLW, LLW) were done. Pulmonary artery rings were pre-contracted with phenylephrine (10 μM), after which cumulative concentration-response curves to glyceryl trinitrate (GTN; NO donor), tadalafil (PDE5 inhibitor) and BAY 60-2770 (sGC activator) were obtained as well as the levels of NO (NO3/NO2). LLW, TLW and LBR were decreased in CDH (p < 0.05). In left pulmonary artery, the potency (pEC50) for GTN was markedly lower in CDH (8.25 ± 0.02 versus 9.27 ± 0.03; p < 0.01). In contrast, the potency for BAY 60-2770 was markedly greater in CDH (11.7 ± 0.03 versus 10.5 ± 0.06; p < 0.01). The NO2/NO3 levels were 62 % higher in CDH (p < 0.05). BAY 60-2770 exhibits a greater potency to relax the pulmonary artery in CDH, indicating a potential use for pulmonary hypertension in this disease.

Bay 41-2272, A Soluble Guanylate Cyclase Stimulator, Relaxes Isolated Human Ureter In A Standardized In Vitro Model.

To characterize the relaxation induced by BAY 41-2272 in human ureteral segments. Ureter specimens (n = 17) from multiple organ human deceased donors (mean age 40 ± 3.2 years, male/female ratio 2:1) were used to characterize the relaxing response of BAY 41-2272. Immunohistochemical analysis for endothelial and neuronal nitric oxide synthase, guanylate cyclase stimulator (sGC) and type 5 phosphodiesterase was also performed. The potency values were determined as the negative log of the molar to produce 50% of the maximal relaxation in potassium chloride-precontracted specimens. The unpaired Student t test was used for the comparisons. Immunohistochemistry revealed the presence of endothelial nitric oxide synthase in vessel endothelia and neuronal nitric oxide synthase in urothelium and nerve structures. sGC was expressed in the smooth muscle and urothelium layer, and type 5 phosphodiesterase was present in the smooth muscle only. BAY 41-2272 (0.001-100 μM) relaxed the isolated ureter in a concentration dependent manner, with a potency and maximal relaxation value of 5.82 ± 0.14 and 84% ± 5%, respectively. The addition of nitric oxide synthase and sGC inhibitors reduced the maximal relaxation values by 21% and 45%, respectively. However, the presence of sildenafil (100 nM) significantly potentiated (6.47 ± 0.10, P <.05) this response. Neither glibenclamide or tetraethylammonium nor ureteral urothelium removal influenced the relaxation response by BAY 41-2272. BAY 41-2272 relaxes the human isolated ureter in a concentration-dependent manner, mainly by activating the sGC enzyme in smooth muscle cells rather than in the urothelium, although a cyclic guanosine monophosphate-independent mechanism might have a role. The potassium channels do not seem to be involved.

Atomic Charge Transfer-counter Polarization Effects Determine Infrared Ch Intensities Of Hydrocarbons: A Quantum Theory Of Atoms In Molecules Model.

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Mesenchymal Stromal Cells From Adipose Tissue Attached To Suture Material Enhance The Closure Of Enterocutaneous Fistulas In A Rat Model.

Surgical treatment for enterocutaneous fistulas (EF) frequently fails. Cell therapy may represent a new approach to treatment. Mesenchymal stromal cells (MSCs) have high proliferative and differentiation capacity. This study aimed to investigate whether MSCs could adhere to suture filament (SF), promoting better EF healing. MSCs, 1 × 10(6), from adipose tissue (ATMSCs) were adhered to a Polyvicryl SF by adding a specific fibrin glue formulation. Adhesion was confirmed by confocal and scanning electron microscopy (SEM). A cecal fistula was created in 22 Wistar rats by incising the cecum and suturing the opening to the surgical wound subcutaneously with four separate stitches. The animals were randomly allocated to three groups: control (CG)-five animals, EF performed; injection (IG)-eight animals 1 × 10(6) ATMSCs injected around EF borders; and suture filament (SG): nine animals, sutured with 1 × 10(6) ATMSCs attached to the filaments with fibrin glue. Fistulas were photographed on the operation day and every 3 days until the 21st day and analyzed by two observers using ImageJ Software. Confocal and SEM results demonstrated ATMSCs adhered to SF (ATMSCs-SF). The average reduction size of the fistula area at 21st day was greater for the SG group (90.34%, P < 0.05) than the IG (71.80%) and CG (46.54%) groups. ATMSCs adhered to SF maintain viability and proliferative capacity. EF submitted to ATMSCs-SF procedure showed greater recovery and healing. This approach might be a new and effective tool for EF treatment.