Hiding the Rabbit: Using a genetic algorithm to investigate shape guidance in visual search.

During visual search, attention is guided by specific features, including shape. Our understanding of shape guidance is limited to specific attributes (closures and line terminations) that do not fully explain the richness of preattentive shape processing. We used a novel genetic algorithm method to explore shape space and to stimulate hypotheses about shape guidance. Initially, observers searched for targets among 12 random distractors defined, in radial frequency space, by the amplitude and phase of 10 radial frequencies. Reaction time (RT) was the measure of "fitness." To evolve toward an easier search task, distractors with faster RTs survived to the next generation, "mated," and produced offspring (new distractors for the next generation of search). To evolve a harder search, surviving distractors were those yielding longer RTs. Within eight generations of evolution, the method succeeds in producing visual searches either harder or easier than the starting search. In radial frequency space, easy distractors evolve amplitude × frequency spectra that are dissimilar to the target, whereas hard distractors evolve spectra that are more similar to the target. This method also works with naturally shaped targets (e.g., rabbit silhouettes). Interestingly, the most inefficient distractors featured a combination of a body and ear distractors that did not resemble the rabbit (visually or in spectrum). Adding extra ears to these distractors did not impact the search spectrally and instead made it easier to confirm a rabbit, once it was found. In general, these experiments show that shapes that are clearly distinct when attended are similar to each other preattentively.

Simulation of the song motor pathway in birds: A single neuron initiates a chain of events that produces birdsong with realistic spectra properties.

Birdsong is a complex learned behavior regulated by Neuromuscular coordination of different muscle sets necessary for producing relevant sounds. We developed a heterogeneous and stochastically connected neural network representing the pathway from the high vocal center (HVC) to the robust nucleus of the arcopallium (RA) neurons that drive the muscles to generate sounds. We show that a single active neuron is sufficient to initiate a chain of spiking events that results to excite the entire network system. The network could synthesize realistic bird sounds spectra, with spontaneous generation of intermittent sound bursts typical of birdsong (song syllables). This study confirms experiments on animals and on humans, where results have shown that single neurons are responsible for the activation of complex behavior or are associated with high-level perception events.

Surface exciton polaritons supported by a J-aggregate-dye/air interface at room temperature.

Surface exciton polaritons (SEPs) are very important for the realization of novel sensors and next-generation optical devices. Here we propose for the first time, to the best of our knowledge, a Kretschmann-Raether device that is able to induce SEPs propagating along the interface between a J-aggregate cyanine dye and air at room temperature. This configuration has the advantages of being straightforward to realize and easy to study because the Kretschmann-Raether approach is the most simple and fundamental from the theoretical point of view. Here a J-aggregate cyanine dye produces strong binding energy due to Frenkel excitons, and this enables the observation of SEPs easily at room temperature. One of the advantages of the use of the J-aggregate cyanine dye is the simple device preparation. This is because the J-aggregate cyanine dye can be easily deposited on any arbitrary substrates with a spincoating or dip-coating technique from its aqueous solution in ambient condition. We observed SEPs at room temperature, and the deepest resonant peak was obtained for a 94 nm thick 5,6-dichloro-2-[[5,6-dichloro-1-ethyl-3-(4-sulfobutyl)-benzimidazol-2-ylidene]-propenyl]-1-ethyl-3-(4-sulfobutyl)-benzimidazolium hydroxide film at 532 nm wavelength. Our results may pave the way for the realization of novel SEP biosensors in a simple and straightforward way at room temperature.

Near-field surface plasmon field enhancement induced by rippled surfaces.

The occurrence of plasmon resonances on metallic nanometer-scale structures is an intrinsically nanoscale phenomenon, given that the two resonance conditions (i.e., negative dielectric permittivity and large free-space wavelength in comparison with system dimensions) are realized at the same time on the nanoscale. Resonances on surface metallic nanostructures are often experimentally found by probing the structures under investigation with radiation of various frequencies following a trial-and-error method. A general technique for the tuning of these resonances is highly desirable. In this paper we address the issue of the role of local surface patterns in the tuning of these resonances as a function of wavelength and electric field polarization. The effect of nanoscale roughness on the surface plasmon polaritons of randomly patterned gold films is numerically investigated. The field enhancement and relation to specific roughness patterns is analyzed, producing many different realizations of rippled surfaces. We demonstrate that irregular patterns act as metal-dielectric-metal local nanogaps (cavities) for the resonant plasmonic field. In turn, the numerical results are compared to experimental data obtained via aperture scanning near-field optical microscopy.

Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22.

Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2'-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H](+) > [M + H - 116](+) transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work.

Transient memory effect in the photoluminescence of InGaN single quantum wells.

The transition to maximum photoluminescence of InGaN single quantum wells is a phenomena that has time constants in the range of few seconds. Using a systematic illumination/darkening procedure we found that these characteristics are related to previous stimulations as if the sample has a memory of past illumination events. Choosing opportune time sequences, time constants were observed to vary more than 100%. These facts suggest the presence of carrier trapping/de-trapping processes that act beyond the single illumination event, accumulating over time in a complex effect.

A polarization-modulation method for the near-field mapping of laterally grown InGaN samples.

Epitaxial Laterally overgrown (ELOG) InGaN materials are investigated using a polarization modulated scanning near-field optical microscope. The authors found that luminescence has spatial inhomogeneities and it is partially polarized. Near-field photoluminescence shows polarization phase fluctuation up to 45 degrees over adjacent domains. These results point toward the existence of asymmetries in carrier confinement due to structural anisotropic strain within the framework of the ELOG structure.

Acoustical nanometre-scale vibrations of live cells detected by a near-field optical setup.

The Scanning Near-field Optical Microscope (SNOM) is able to detect tiny vertical movement on the cell membrane in the range of only 1 nanometer or less, about 3 orders of magnitude better than conventional optical microscopes. Here we show intriguing data of cell membrane nanometer-scale dynamics associated to different phenomena of the cell's The Scanning Near-field Optical Microscope (SNOM) is able to detect tiny vertical movement on the cell membrane in the range of only 1 nanometer or less, about 3 orders of magnitude better than conventional optical microscopes. Here we show intriguing data of cell membrane nanometer-scale dynamics associated to different phenomena of the cell's life, such as cell cycle and cell death, on rat pheochromocytoma line PC12. Working in culture medium with alive and unperturbed samples, we could detect nanometer-sized movements; Fourier components revealed a clear distinct behavior associated to regulation of neurite outgrowth and changes on morphology after necrotic stimulus.

Fabrication of an atomic resolution low cost STM-SNOM hybrid probe.

We derived a simple method to fabricate STM-SNOM hybrid probes obtained from commercial cheap communication optical fibers. The tips are fabricated by a methodology that combines two well-known techniques: the selective attack by a buffered solution and the protected layer chemical etching, in a single new one-step technique. The tailored probes are then sputtered by metal and mounted on a STM setup. The usual difficulties of integrating the optical fiber in the STM head are solved originally with a particular home made mount described in details. We will show that the resulting probes reach atomic resolution on both vertical and horizontal scale, and that the optical imaging is free of artifacts and satisfactory with a lateral resolution in the order of lamda/20, as far as we know the finest resolution obtained with a system based on a hybrid fiber probe. We believe that our methodology is very interesting for its simplicity of realization and for the good resolving power in both SNOM and STM modes.

Index-of-refraction sensors: virtually unlimited sensing power at the critical angle.

In an effort to improve and simplify refractive index sensors, we identified a basic operation mode at the critical angle. Sensitivity to the refractive index is higher than in standard surface plasmon resonance sensors, and we have been able to demonstrate analytically that it is virtually an unbounded value. We describe this approach and submit a complete analytical study demonstrating its unlimited sensing power. To test the approach, we constructed an economical and basic sensor. Despite its simplicity, we demonstrated the discrimination capability to be of the order of 10(-6), as far as we know close to the best sensitivity ever recorded. This detection method is generally applicable to any optical system and may pave the way for the next generation of optical sensing devices.

Nano-probing of the membrane dynamics of rat pheochromocytoma by near-field optics.

High-resolution analysis of activities of live cells is limited by the use of non-invasive methods. Apparatuses such as SEM, STM or AFM are not practicable because the necessary treatment or the harsh contact with system probe will disturb or destroy the cell. Optical methods are purely non-invasive, but they are usually diffraction limited and then their resolution is limited to approximately 1 microm. To overcome these restrictions, we introduce here the study of membrane activity of a live cell sample using a Scanning Near-field Optical Microscope (SNOM). A near field optical microscope is able to detect tiny vertical movement on the cell membrane in the range of only 1 nm or less, about 3 orders of magnitude better than conventional optical microscopes. It is a purely non-invasive, non-contact method, so the natural life activity of the sample is unperturbed. In this report, we demonstrated the nanometer-level resolving ability of our SNOM system analyzing cardiomyocytes samples of which membrane movement is known, and then we present new intriguing data of sharp 40 nm cell membrane sudden events on rat pheochromocytoma cell line PC12. All the measurements are carried out in culture medium with alive and unperturbed samples. We believe that this methodology will open a new approach to investigate live samples. The extreme sensitivity of SNOM allows measurements that are not possible with any other method on live biomaterial paving the way for a broad range of novel studies and applications.

Biological imaging with a near-field optical setup.

Noncontact scanning near-field optical microscope (SNOM) systems can be used to optically resolve samples in atmospheric conditions at theoretical resolutions comparable to those of transmission electron microscope and atomic force microscope systems. SNOM systems are also increasingly used to image biological samples. In this study we custom built a SNOM system with the aim of further demonstrating the potential applications of near-field optical examination of biological material. In this study we were able to image both fixed whole-cell samples in air and liquid environments and live whole-cell samples in liquids. The images acquired were of a relatively low resolution, but this work has shown that SNOM systems can be used to monitor the dynamics of living cells at subnanometric resolutions in the z axis and for fluorescent imaging of whole cells in a liquid medium.