Dynamic population coding in primary visual cortex

More than a century ago Ramon y Cajal pioneered the description of neural circuits. Currently, new techniques are being developed to streamline the characterization of entire neural circuits. Even if this 'connectome' approach is successful, it will represent only a static description of neural circuits. Thus, a fundamental question in neuroscience is to understand how information is dynamically represented by neural populations. In this thesis, I studied two main aspects of dynamical population codes. ^ First, I studied how the exposure or adaptation, for a fraction of a second to oriented gratings dynamically changes the population response of primary visual cortex neurons. The effects of adaptation to oriented gratings have been extensively explored in psychophysical and electrophysiological experiments. However, whether rapid adaptation might induce a change in the primary visual cortex's functional connectivity to dynamically impact the population coding accuracy is currently unknown. To address this issue, we performed multi-electrode recordings in primary visual cortex, where adaptation has been previously shown to induce changes in the selectivity and response amplitude of individual neurons. We found that adaptation improves the population coding accuracy. The improvement was more prominent for iso- and orthogonal orientation adaptation, consistent with previously reported psychophysical experiments. We propose that selective decorrelation is a metabolically inexpensive mechanism that the visual system employs to dynamically adapt the neural responses to the statistics of the input stimuli to improve coding efficiency. ^ Second, I investigated how ongoing activity modulates orientation coding in single neurons, neural populations and behavior. Cortical networks are never silent even in the absence of external stimulation. The ongoing activity can account for up to 80% of the metabolic energy consumed by the brain. Thus, a fundamental question is to understand the functional role of ongoing activity and its impact on neural computations. I studied how the orientation coding by individual neurons and cell populations in primary visual cortex depend on the spontaneous activity before stimulus presentation. We hypothesized that since the ongoing activity of nearby neurons is strongly correlated, it would influence the ability of the entire population of orientation-selective cells to process orientation depending on the prestimulus spontaneous state. Our findings demonstrate that ongoing activity dynamically filters incoming stimuli to shape the accuracy of orientation coding by individual neurons and cell populations and this interaction affects behavioral performance. In summary, this thesis is a contribution to the study of how dynamic internal states such as rapid adaptation and ongoing activity modulate the population code accuracy. ^

POPULATION CODING IN LAMINAR CORTICAL CIRCUITS

One of the fundamental questions in neuroscience is to understand how encoding of sensory inputs is distributed across neuronal networks in cerebral cortex to influence sensory processing and behavioral performance. The fact that the structure of neuronal networks is organized according to cortical layers raises the possibility that sensory information could be processed differently in distinct layers. The goal of my thesis research is to understand how laminar circuits encode information in their population activity, how the properties of the population code adapt to changes in visual input, and how population coding influences behavioral performance. To this end, we performed a series of novel experiments to investigate how sensory information in the primary visual cortex (V1) emerges across laminar cortical circuits. First, it is commonly known that the amount of information encoded by cortical circuits depends critically on whether or not nearby neurons exhibit correlations. We examined correlated variability in V1 circuits from a laminar-specific perspective and observed that cells in the input layer, which have only local projections, encode incoming stimuli optimally by exhibiting low correlated variability. In contrast, output layers, which send projections to other cortical and subcortical areas, encode information suboptimally by exhibiting large correlations. These results argue that neuronal populations in different cortical layers play different roles in network computations. Secondly, a fundamental feature of cortical neurons is their ability to adapt to changes in incoming stimuli. Understanding how adaptation emerges across cortical layers to influence information processing is vital for understanding efficient sensory coding. We examined the effects of adaptation, on the time-scale of a visual fixation, on network synchronization across laminar circuits. Specific to the superficial layers, we observed an increase in gamma-band (30-80 Hz) synchronization after adaptation that was correlated with an improvement in neuronal orientation discrimination performance. Thus, synchronization enhances sensory coding to optimize network processing across laminar circuits. Finally, we tested the hypothesis that individual neurons and local populations synchronize their activity in real-time to communicate information about incoming stimuli, and that the degree of synchronization influences behavioral performance. These analyses assessed for the first time the relationship between changes in laminar cortical networks involved in stimulus processing and behavioral performance.

Post-transcriptional Regulation of Mammalian Gene Expression in Non-coding Region of Target RNA

Tumor Suppressor Candidate 2 (TUSC2) is a novel tumor suppressor gene located in the human chromosome 3p21.3 region. TUSC2 mRNA transcripts could be detected on Northern blots in both normal lung and some lung cancer cell lines, but no endogenous TUSC2 protein could be detected in a majority of lung cancer cell lines. Mechanisms regulating TUSC2 protein expression and its inactivation in primary lung cancer cells are largely unknown. We investigated the role of the 5’- and 3’-untranslated regions (UTRs) of the TUSC2 gene in the regulation of TUSC2 protein expression. We found that two small upstream open-reading frames (uORFs) in the 5’UTR of TUSC2 could markedly inhibit the translational initiation of TUSC2 protein by interfering with the “scanning” of the ribosome initiation complexes. Site-specific stem-loop array reverse transcription-polymerase chain reaction (SLA-RT-PCR) verified several micoRNAs (miRNAs) targeted at 3’UTR and directed TUSC2 cleavage and degradation. In addition, we used the established let-7-targeted high mobility group A2 (Hmga2) mRNA as a model system to study the mechanism of regulation of target mRNA by miRNAs in mammalian cells under physiological conditions. There have been no evidence of direct link between mRNA downregulation and mRNA cleavages mediated by miRNAs. Here we showed that the endonucleolytic cleavages on mRNAs were initiated by mammalian miRNA in seed pairing style. Let-7 directed cleavage activities among the eight predicted potential target sites have varied efficiency, which are influenced by the positional and the structural contexts in the UTR. The 5’ cleaved RNA fragments were mostly oligouridylated at their 3’-termini and accumulated for delayed 5’–3’ degradation. RNA fragment oligouridylation played important roles in marking RNA fragments for delayed bulk degradation and in converting RNA degradation mode from 3’–5’ to 5’–3’ with cooperative efforts from both endonucleolytic and non-catalytic miRNA-induced silencing complex (miRISC). Our findings point to a mammalian miRNA-mediated mechanism for the regulation of mRNA that miRNA can decrease target mRNA through target mRNA cleavage and uridine addition

Mechanism of translationally coupled mRNA turnover mediated by c-fos protein-coding-region determinant

Proto-oncogene c-fos is a member of the class of early-response genes whose transient expression plays a crucial role in cell proliferation, differentiation, and apoptosis. Degradation of c- fos mRNA is an important mechanism for controlling c-fos expression. Rapid mRNA turnover mediated by the protein-coding-region determinant (mCRD) of the c-fos transcript illustrates a functional interplay between mRNA turnover and translation that coordinately influences the fate of cytoplasmic mRNA. It is suggested that mCRD communicates with the 3′ poly(A) tail via an mRNP complex comprising mCRD-associated proteins, which prevents deadenylation in the absence of translation. Ribosome transit as a result of translation is required to alter the conformation of the mRNP complex, thereby eliciting accelerated deadenylation and mRNA decay. To gain further insight into the mechanism of mCRD-mediated mRNA turnover, Unr was identified as an mCRD-binding protein, and its binding site within mCRD was characterized. Moreover, the functional role for Unr in mRNA decay was demonstrated. The result showed that elevation of Unr protein level in the cytoplasm led to inhibition of mRNA destabilization by mCRD. In addition, GST pull-down assay and immuno-precipitation analysis revealed that Unr interacted with PABP in an RNA-independent manner, which identified Unr as a novel PABP-interacting protein. Furthermore, the Unr interacting domain in PABP was characterized. In vivo mRNA decay experiments demonstrated a role for Unr-PABP interaction in mCRD-mediated mRNA decay. In conclusion, the findings of this study provide the first evidence that Unr plays a key role in mCRD-mediated mRNA decay. It is proposed that Unr is recruited by mCRD to initiate the formation of a dynamic mRNP complex for communicating with poly(A) tail through PABP. This unique mRNP complex may couple translation to mRNA decay, and perhaps to recruit the responsible nuclease for deadenylation. ^

Plant protein-coding gene families: emerging bioinformatics approaches

Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is.

A Novel Scalable Deblocking-Filter Architecture for H.264/AVC and SVC Video Codecs

A highly parallel and scalable Deblocking Filter (DF) hardware architecture for H.264/AVC and SVC video codecs is presented in this paper. The proposed architecture mainly consists on a coarse grain systolic array obtained by replicating a unique and homogeneous Functional Unit (FU), in which a whole Deblocking-Filter unit is implemented. The proposal is also based on a novel macroblock-level parallelization strategy of the filtering algorithm which improves the final performance by exploiting specific data dependences. This way communication overhead is reduced and a more intensive parallelism in comparison with the existing state-of-the-art solutions is obtained. Furthermore, the architecture is completely flexible, since the level of parallelism can be changed, according to the application requirements. The design has been implemented in a Virtex-5 FPGA, and it allows filtering 4CIF (704 × 576 pixels @30 fps) video sequences in real-time at frequencies lower than 10.16 Mhz.

The DLMT. An alternative to the DCT

In the last recent years, with the popularity of image compression techniques, many architectures have been proposed. Those have been generally based on the Forward and Inverse Discrete Cosine Transform (FDCT, IDCT). Alternatively, compression schemes based on discrete “wavelets” transform (DWT), used, both, in JPEG2000 coding standard and in the next H264-SVC (Scalable Video Coding), do not need to divide the image into non-overlapping blocks or macroblocks. This paper discusses the DLMT (Discrete Lopez-Moreno Transform). It proposes a new scheme intermediate between the DCT and the DWT (Discrete Wavelet Transform). The DLMT is computationally very similar to the DCT and uses quasi-sinusoidal functions, so the emergence of artifact blocks and their effects have a relative low importance. The use of quasi-sinusoidal functions has allowed achieving a multiresolution control quite close to that obtained by a DWT, but without increasing the computational complexity of the transformation. The DLMT can also be applied over a whole image, but this does not involve increasing computational complexity. Simulation results in MATLAB show that the proposed DLMT has significant performance benefits and improvements comparing with the DCT

Scalable software architecture for on-line multi-camera video processing

In this paper we present a scalable software architecture for on-line multi-camera video processing, that guarantees a good trade off between computational power, scalability and flexibility. The software system is modular and its main blocks are the Processing Units (PUs), and the Central Unit. The Central Unit works as a supervisor of the running PUs and each PU manages the acquisition phase and the processing phase. Furthermore, an approach to easily parallelize the desired processing application has been presented. In this paper, as case study, we apply the proposed software architecture to a multi-camera system in order to efficiently manage multiple 2D object detection modules in a real-time scenario. System performance has been evaluated under different load conditions such as number of cameras and image sizes. The results show that the software architecture scales well with the number of camera and can easily works with different image formats respecting the real time constraints. Moreover, the parallelization approach can be used in order to speed up the processing tasks with a low level of overhead

Multi-Resolution Texture Coding for Multi-Resolution 3D Meshes

We present an innovative system to encode and transmit textured multi-resolution 3D meshes in a progressive way, with no need to send several texture images, one for each mesh LOD (Level Of Detail). All texture LODs are created from the finest one (associated to the finest mesh), but can be re- constructed progressively from the coarsest thanks to refinement images calculated in the encoding process, and transmitted only if needed. This allows us to adjust the LOD/quality of both 3D mesh and texture according to the rendering power of the device that will display them, and to the network capacity. Additionally, we achieve big savings in data transmission by avoiding altogether texture coordinates, which are generated automatically thanks to an unwrapping system agreed upon by both encoder and decoder.

Integración MPlayer-OpenSVC en el procesador multinúcleo OMAP3530

La constante evolución de dispositivos portátiles multimedia que se ha producido en la última década ha provocado que hoy en día se disponga de una amplia variedad de dispositivos con capacidad para reproducir contenidos multimedia. En consecuencia, la reproducción de esos contenidos en dichos terminales lleva asociada disponer de procesadores que soporten una alta carga computacional, ya que las tareas de descodificación y presentación de video así lo requieren. Sin embargo, un procesador potente trabajando a elevadas frecuencias provoca un elevado consumo de la batería, y dado que se pretende trabajar con dispositivos portátiles, la vida útil de la batería se convierte en un asunto de especial importancia. La problemática que se plantea se ha convertido en una de las principales líneas de investigación del Grupo de Investigación GDEM (Grupo de Diseño Electrónico y Microelectrónico). En esta línea de trabajo, se persigue cómo optimizar el consumo de energía en terminales portables desde el punto de vista de la reducción de la calidad de experiencia del usuario a cambio de una mayor autonomía del terminal. Por tanto, para lograr esa reducción de la calidad de experiencia mencionada, se requiere un estándar de codificación de vídeo que así lo permita. El Grupo de Investigación GDEM cuenta con experiencia en el estándar de vídeo escalable H.264/SVC, el cual permite degradar la calidad de experiencia en función de las necesidades/características del dispositivo. Más concretamente, un video escalable contiene embebidas distintas versiones del video original que pueden ser descodificadas en diferentes resoluciones, tasas de cuadro y calidades (escalabilidades espacial, temporal y de calidad respectivamente), permitiendo una adaptación rápida y muy flexible. Seleccionado el estándar H.264/SVC para las tareas de vídeo, se propone trabajar con Mplayer, un reproductor de vídeos de código abierto (open source), al cual se le ha integrado un descodificador para vídeo escalable denominado OpenSVC. Por último, como dispositivo portable se trabajará con la plataforma de desarrollo BeagleBoard, un sistema embebido basado en el procesador OMAP3530 que permite modificar la frecuencia de reloj y la tensión de alimentación dinámicamente reduciendo de este modo el consumo del terminal. Este procesador a su vez contiene integrados un procesador de propósito general (ARM Cortex-A8) y un procesador digital de señal (DSP TMS320C64+TM). Debido a la alta carga computacional de la descodificación de vídeos escalables y la escasa optimización del ARM para procesamiento de datos, se propone llevar a cabo la ejecución de Mplayer en el ARM y encargar la tarea de descodificación al DSP, con la finalidad de reducir el consumo y por tanto aumentar la vida útil del sistema embebido sobre el cual se ejecutará la aplicación desarrollada. Una vez realizada esa integración, se llevará a cabo una caracterización del descodificador alojado en el DSP a través de una serie de medidas de rendimiento y se compararán los resultados con los obtenidos en el proceso de descodificación realizado únicamente en el ARM. ABSTRACT During the last years, the multimedia portable terminals have gradually evolved causing that nowadays a several range of devices with the ability of playing multimedia contents are easily available for everyone. Consequently, those multimedia terminals must have high-performance processors to play those contents because the coding and decoding tasks demand high computational load. However, a powerful processor performing to high frequencies implies higher battery consumption, and this issue has become one of the most important problems in the development cycle of a portable terminal. The power/energy consumption optimization on multimedia terminals has become in one the most significant work lines in the Electronic and Microelectronic Research Group of the Universidad Politécnica de Madrid. In particular, the group is researching how to reduce the user‟s Quality of Experience (QoE) quality in exchange for increased battery life. In order to reduce the Quality of Experience (QoE), a standard video coding that allows this operation is required. The H.264/SVC allows reducing the QoE according to the needs/characteristics of the terminal. Specifically, a scalable video contains different versions of original video embedded in an only one video stream, and each one of them can be decoded in different resolutions, frame rates and qualities (spatial, temporal and quality scalabilities respectively). Once the standard video coding is selected, a multimedia player with support for scalable video is needed. Mplayer has been proposed as a multimedia player, whose characteristics (open-source, enormous flexibility and scalable video decoder called OpenSVC) are the most suitable for the aims of this Master Thesis. Lastly, the embedded system BeagleBoard, based on the multi-core processor OMAP3530, will be the development platform used in this project. The multimedia terminal architecture is based on a commercial chip having a General Purpose Processor (GPP – ARM Cortex A8) and a Digital Signal Processor (DSP, TMS320C64+™). Moreover, the processor OMAP3530 has the ability to modify the operating frequency and the supply voltage in a dynamic way in order to reduce the power consumption of the embedded system. So, the main goal of this Master Thesis is the integration of the multimedia player, MPlayer, executed at the GPP, and scalable video decoder, OpenSVC, executed at the DSP in order to distribute the computational load associated with the scalable video decoding task and to reduce the power consumption of the terminal. Once the integration is accomplished, the performance of the OpenSVC decoder executed at the DSP will be measured using different combinations of scalability values. The obtained results will be compared with the scalable video decoding performed at the GPP in order to show the low optimization of this kind of architecture for decoding tasks in contrast to DSP architecture.

CumuloNimbo: A highly-scalable transaction processing platform as a service.

One of the main challenges facing next generation Cloud platform services is the need to simultaneously achieve ease of programming, consistency, and high scalability. Big Data applications have so far focused on batch processing. The next step for Big Data is to move to the online world. This shift will raise the requirements for transactional guarantees. CumuloNimbo is a new EC-funded project led by Universidad Politécnica de Madrid (UPM) that addresses these issues via a highly scalable multi-tier transactional platform as a service (PaaS) that bridges the gap between OLTP and Big Data applications.