How the owl resolves auditory coding ambiguity

The barn owl (Tyto alba) uses interaural time difference (ITD) cues to localize sounds in the horizontal plane. Low-order binaural auditory neurons with sharp frequency tuning act as narrow-band coincidence detectors; such neurons respond equally well to sounds with a particular ITD and its phase equivalents and are said to be phase ambiguous. Higher-order neurons with broad frequency tuning are unambiguously selective for single ITDs in response to broad-band sounds and show little or no response to phase equivalents. Selectivity for single ITDs is thought to arise from the convergence of parallel, narrow-band frequency channels that originate in the cochlea. ITD tuning to variable bandwidth stimuli was measured in higher-order neurons of the owl’s inferior colliculus to examine the rules that govern the relationship between frequency channel convergence and the resolution of phase ambiguity. Ambiguity decreased as stimulus bandwidth increased, reaching a minimum at 2–3 kHz. Two independent mechanisms appear to contribute to the elimination of ambiguity: one suppressive and one facilitative. The integration of information carried by parallel, distributed processing channels is a common theme of sensory processing that spans both modality and species boundaries. The principles underlying the resolution of phase ambiguity and frequency channel convergence in the owl may have implications for other sensory systems, such as electrolocation in electric fish and the computation of binocular disparity in the avian and mammalian visual systems.

GeneSplicer: a new computational method for splice site prediction

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.

Mapping the universe in three dimensions

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble’s law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin.

Determination of the Hubble constant

Establishing accurate extragalactic distances has provided an immense challenge to astronomers since the 1920s. The situation has improved dramatically as better detectors have become available, and as several new, promising techniques have been developed. For the first time in the history of this difficult field, relative distances to galaxies are being compared on a case-by-case basis, and their quantitative agreement is being established. New instrumentation, the development of new techniques for measuring distances, and recent measurements with the Hubble Space telescope all have resulted in new distances to galaxies with precision at the ±5–20% level. The current statistical uncertainty in some methods for measuring H0 is now only a few percent; with systematic errors, the total uncertainty is approaching ±10%. Hence, the historical factor-of-two uncertainty in the value of the H0 is now behind us.

Detection of synchrony in the activity of auditory nerve fibers by octopus cells of the mammalian cochlear nucleus

The anatomical and biophysical specializations of octopus cells allow them to detect the coincident firing of groups of auditory nerve fibers and to convey the precise timing of that coincidence to their targets. Octopus cells occupy a sharply defined region of the most caudal and dorsal part of the mammalian ventral cochlear nucleus. The dendrites of octopus cells cross the bundle of auditory nerve fibers just proximal to where the fibers leave the ventral and enter the dorsal cochlear nucleus, each octopus cell spanning about one-third of the tonotopic array. Octopus cells are excited by auditory nerve fibers through the activation of rapid, calcium-permeable, α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate receptors. Synaptic responses are shaped by the unusual biophysical characteristics of octopus cells. Octopus cells have very low input resistances (about 7 MΩ), and short time constants (about 200 μsec) as a consequence of the activation at rest of a hyperpolarization-activated mixed-cation conductance and a low-threshold, depolarization-activated potassium conductance. The low input resistance causes rapid synaptic currents to generate rapid and small synaptic potentials. Summation of small synaptic potentials from many fibers is required to bring an octopus cell to threshold. Not only does the low input resistance make individual excitatory postsynaptic potentials brief so that they must be generated within 1 msec to sum but also the voltage-sensitive conductances of octopus cells prevent firing if the activation of auditory nerve inputs is not sufficiently synchronous and depolarization is not sufficiently rapid. In vivo in cats, octopus cells can fire rapidly and respond with exceptionally well-timed action potentials to periodic, broadband sounds such as clicks. Thus both the anatomical specializations and the biophysical specializations make octopus cells detectors of the coincident firing of their auditory nerve fiber inputs.

Simple neural networks for the amplification and utilization of small changes in neuron firing rates

I describe physiologically plausible “voter-coincidence” neural networks such that secondary “coincidence” neurons fire on the simultaneous receipt of sufficiently large sets of input pulses from primary sets of neurons. The networks operate such that the firing rate of the secondary, output neurons increases (or decreases) sharply when the mean firing rate of primary neurons increases (or decreases) to a much smaller degree. In certain sensory systems, signals that are generally smaller than the noise levels of individual primary detectors, are manifest in very small increases in the firing rates of sets of afferent neurons. For such systems, this kind of network can act to generate relatively large changes in the firing rate of secondary “coincidence” neurons. These differential amplification systems can be cascaded to generate sharp, “yes–no” spike signals that can direct behavioral responses.

Microfabricated structures for integrated DNA analysis.

Photolithographic micromachining of silicon is a candidate technology for the construction of high-throughput DNA analysis devices. However, the development of complex silicon microfabricated systems has been hindered in part by the lack of a simple, versatile pumping method for integrating individual components. Here we describe a surface-tension-based pump able to move discrete nanoliter drops through enclosed channels using only local heating. This thermocapillary pump can accurately mix, measure, and divide drops by simple electronic control. In addition, we have constructed thermal-cycling chambers, gel electrophoresis channels, and radiolabeled DNA detectors that are compatible with the fabrication of thermocapillary pump channels. Since all of the components are made by conventional photolithographic techniques, they can be assembled into more complex integrated systems. The combination of pump and components into self-contained miniaturized devices may provide significant improvements in DNA analysis speed, portability, and cost. The potential of microfabricated systems lies in the low unit cost of silicon-based construction and in the efficient sample handling afforded by component integration.

Limits to dark matter annihilation cross-section from a combined analysis of MAGIC and Fermi-LAT observations of dwarf satellite galaxies

We present the first joint analysis of gamma-ray data from the MAGIC Cherenkov telescopes and the Fermi Large Area Telescope (LAT) to search for gamma-ray signals from dark matter annihilation in dwarf satellite galaxies. We combine 158 hours of Segue 1 observations with MAGIC with 6-year observations of 15 dwarf satellite galaxies by the Fermi-LAT. We obtain limits on the annihilation cross-section for dark matter particle masses between 10 GeV and 100 TeV – the widest mass range ever explored by a single gamma-ray analysis. These limits improve on previously published Fermi-LAT and MAGIC results by up to a factor of two at certain masses. Our new inclusive analysis approach is completely generic and can be used to perform a global, sensitivity-optimized dark matter search by combining data from present and future gamma-ray and neutrino detectors.

Azimuthal asymmetry in the risetime of the surface detector signals of the Pierre Auger Observatory.

The azimuthal asymmetry in the risetime of signals in Auger surface detector stations is a source of information on shower development. The azimuthal asymmetry is due to a combination of the longitudinal evolution of the shower and geometrical effects related to the angles of incidence of the particles into the detectors. The magnitude of the effect depends upon the zenith angle and state of development of the shower and thus provides a novel observable, (sec theta)(max), sensitive to the mass composition of cosmic rays above 3 x 10(18) eV. By comparing measurements with predictions from shower simulations, we find for both of our adopted models of hadronic physics (QGSJETII-04 and EPOS-LHC) an indication that the mean cosmic-ray mass increases slowly with energy, as has been inferred from other studies. However, the mass estimates are dependent on the shower model and on the range of distance from the shower core selected. Thus the method has uncovered further deficiencies in our understanding of shower modeling that must be resolved before the mass composition can be inferred from (sec theta)(max).

Resonant elements contactless coupled to bolometric micro-stripes

One of the main technical difficulties in the fabrication of optical antennas working as light detectors is the proper design and manufacture of auxiliary elements as load lines and signal extraction structures. These elements need to be quite small to reach the location of the antennas and should have a minimal effect on the response of the device. Unfortunately this is not an easy task and signal extraction lines resonate along with the antenna producing a complex signal that usually masks the one given by the antenna. In order to decouple the resonance from the transduction we present in this contribution a parametric analysis of the response of a bolometric stripe that is surrounded by resonant dipoles with different geometries and orientations. We have checked that these elements should provide a signal proportional to the polarization state of the incoming light.

Detectivity comparison of bolometric optical antennas

The practical application of optical antennas in detection devices strongly depends on its ability to produce an acceptable signal-to-noise ratio for the given task. It is known that, due to the intrinsic problems arising from its sub-wavelength dimensions, optical antennas produce very small signals. The quality of these signals depends on the involved transduction mechanism. The contribution of different types of noise should be adapted to the transducer and to the signal extraction regime. Once noise is evaluated and measured, the specific detectivity, D*, becomes the parameter of interest when comparing the performance of antenna coupled devices with other detectors. However, this parameter involves some magnitudes that can be defined in several ways for optical antennas. In this contribution we are interested in the evaluation and comparison of D_ values for several bolometric optical antennas working in the infrared and involving two materials. At the same time, some material and geometrical parameters involved in the definition of noise and detectivity will be discussed to analyze the suitability of D_ to properly account for the performance of optical antennas.

Sistema para monitoramento e análise de paisagens acústicas submarinas.

O Monitoramento Acústico Passivo (PAM) submarino refere-se ao uso de sistemas de escuta e gravação subaquática, com o intuito de detectar, monitorar e identificar fontes sonoras através das ondas de pressão que elas produzem. Se diz que é passivo já que tais sistemas unicamente ouvem, sem perturbam o meio ambiente acústico existente, diferentemente de ativos, como os sonares. O PAM submarino tem diversas áreas de aplicação, como em sistemas de vigilância militar, seguridade portuária, monitoramento ambiental, desenvolvimento de índices de densidade populacional de espécies, identificação de espécies, etc. Tecnologia nacional nesta área é praticamente inexistente apesar da sua importância. Neste contexto, o presente trabalho visa contribuir com o desenvolvimento de tecnologia nacional no tema através da concepção, construção e operação de equipamento autônomo de PAM e de métodos de processamento de sinais para detecção automatizada de eventos acústicos submarinos. Foi desenvolvido um equipamento, nomeado OceanPod, que possui características como baixo custo de fabrica¸c~ao, flexibilidade e facilidade de configuração e uso, voltado para a pesquisa científica, industrial e para controle ambiental. Vários protótipos desse equipamento foram construídos e utilizados em missões no mar. Essas jornadas de monitoramento permitiram iniciar a criação de um banco de dados acústico, o qual permitiu fornecer a matéria prima para o teste de detectores de eventos acústicos automatizados e em tempo real. Adicionalmente também é proposto um novo método de detecção-identificação de eventos acústicos, baseado em análise estatística da representação tempo-frequência dos sinais acústicos. Este novo método foi testado na detecção de cetáceos, presentes no banco de dados gerado pelas missões de monitoramento.

Fabricação e caracterização de detector de Barreira de superfície a partir de substrato de silício comercial

Neste trabalho foram desenvolvidos detectores de radiação Barreira de superfície de silício que fossem capazes de detectar a presença da radiação gama de baixa energia proveniente de sementes de iodo-125 utilizada em tratamentos de braquiterapia. A partir de substratos comerciais de silício foram desenvolvidos os detectores, de uma sequência que partiu de tratamentos químicos nas superfícies destes substratos com a intenção de minimizar os possíveis ruídos gerados, validação das amostras obtidas como diodos, assegurando características detectoras, e a efetiva utilização como detector para fontes radioativas de iodo-125 com energia em torno de 25 kev e amerício-251 com energia na ordem de 59 kev. Finalizou realizando a análise dos espectros de energia obtidos e assim foi possível observar a capacidade destes detectores para mensuração da energia proveniente destas sementes.

Search for ultrahigh energy neutrinos in highly inclined events at the Pierre Auger Observatory

The Surface Detector of the Pierre Auger Observatory is sensitive to neutrinos of all flavors above 0.1 EeV. These interact through charged and neutral currents in the atmosphere giving rise to extensive air showers. When interacting deeply in the atmosphere at nearly horizontal incidence, neutrinos can be distinguished from regular hadronic cosmic rays by the broad time structure of their shower signals in the water-Cherenkov detectors. In this paper we present for the first time an analysis based on down-going neutrinos. We describe the search procedure, the possible sources of background, the method to compute the exposure and the associated systematic uncertainties. No candidate neutrinos have been found in data collected from 1 January 2004 to 31 May 2010. Assuming an E-2 differential energy spectrum the limit on the single-flavor neutrino is E(2)dN/dE < 1.74 x 10(-7)GeVcm(-2)s(-1)sr(-1) at 90% C.L. in the energy range 1 x 10(17) eV < E < 1 x 10(20)eV.

Desenvolvimento e caracterização do filtro óptico de interferência variável para detectores de alta resolução espectral e biossensores.

O presente trabalho está fundamentado no desenvolvimento de uma metodologia e/ou uma tecnologia de obtenção e caracterização de filtros ópticos de interferência de banda passante variável [C.M. da Silva, 2010] e de banda de corte variáveis, constituídos por refletores dielétricos multicamadas de filmes finos intercalados por cavidades de Fabry-Perot não planares com espessuras linearmente variáveis, que apresentam a propriedade do deslocamento linear da transmitância máxima espectral em função da posição, isto é, um Filtro de Interferência Variável (FIV). Este método apresenta novas e abrangentes possibilidades de confecção de filtros ópticos de interferência variável: lineares ou em outras formas desejadas, de comprimento de onda de corte variável (passa baixa ou alta) e filtros de densidade neutra variável, através da deposição de metais, além de aplicações em uma promissora e nova área de pesquisa na deposição de filmes finos não uniformes. A etapa inicial deste desenvolvimento foi o estudo da teoria dos filtros ópticos dielétricos de interferência para projetar e construir um filtro óptico banda passante convencional de um comprimento de onda central com camadas homogêneas. A etapa seguinte, com base na teoria óptica dos filmes finos já estabelecida, foi desenvolver a extensão destes conhecimentos para determinar que a variação da espessura em um perfil inclinado e linear da cavidade entre os refletores de Bragg é o principal parâmetro para produzir o deslocamento espacial da transmitância espectral, possibilitando o uso de técnicas especiais para se obter uma variação em faixas de bandas de grande amplitude, em um único filtro. Um trabalho de modelagem analítica e análise de tolerância de espessuras dos filmes depositados foram necessários para a seleção da estratégia do \"mascaramento\" seletivo do material evaporado formado na câmara e-Beam (elétron-Beam) com o objetivo da obtenção do filtro espectral linear variável de características desejadas. Para tanto, de acordo com os requisitos de projeto, foram necessárias adaptações em uma evaporadora por e-Beam para receber um obliterador mecânico especialmente projetado para compatibilizar os parâmetros das técnicas convencionais de deposição com o objetivo de se obter um perfil inclinado, perfil este previsto em processos de simulação para ajustar e calibrar a geometria do obliterador e se obter um filme depositado na espessura, conformação e disposição pretendidos. Ao final destas etapas de modelagem analítica, simulação e refinamento recorrente, foram determinados os parâmetros de projeto para obtenção de um determinado FIV (Filtro de Interferência Variável) especificado. Baseadas nos FIVs muitas aplicações são emergentes: dispositivos multi, hiper e ultra espectral para sensoriamento remoto e análise ambiental, sistemas Lab-on-Chip, biossensores, detectores chip-sized, espectrofotometria de fluorescência on-chip, detectores de deslocamento de comprimento de onda, sistemas de interrogação, sistemas de imageamento espectral, microespectrofotômetros e etc. No escopo deste trabalho se pretende abranger um estudo de uma referência básica do emprego do (FIV) filtro de interferência variável como detector de varredura de comprimento de ondas em sensores biológicos e químicos compatível com pós processamento CMOS. Um sistema básico que é constituído por um FIV montado sobre uma matriz de sensores ópticos conectada a um módulo eletrônico dedicado a medir a intensidade da radiação incidente e as bandas de absorção das moléculas presentes em uma câmara de detecção de um sistema próprio de canais de microfluidos, configurando-se em um sistema de aquisição e armazenamento de dados (DAS), é proposto para demonstrar as possibilidades do FIV e para servir de base para estudos exploratórios das suas diversas potencialidades que, entre tantas, algumas são mencionadas ao longo deste trabalho. O protótipo obtido é capaz de analisar fluidos químicos ou biológicos e pode ser confrontado com os resultados obtidos por equipamentos homologados de uso corrente.