Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

Joint Evaluation of Reduced Feedback Scheme, Scheduling, and Rate Adaptation in OFDMA Systems with Feedback Delays

Orthogonal frequency division multiple access (OFDMA) systems exploit multiuser diversity and frequency-selectivity to achieve high spectral efficiencies. However, they require considerable feedback for scheduling and rate adaptation, and are sensitive to feedback delays. We develop a comprehensive analysis of the OFDMA system throughput as a function of the feedback scheme, frequency-domain scheduler, and discrete rate adaptation rule in the presence of feedback delays. We analyze the popular best-n and threshold-based feedback schemes. We show that for both the greedy and round-robin schedulers, the throughput degradation, given a feedback delay, depends primarily on the fraction of feedback reduced by the feedback scheme and not the feedback scheme itself. Even small feedback delays at low vehicular speeds are shown to significantly degrade the throughput. We also show that optimizing the link adaptation thresholds as a function of the feedback delay can effectively counteract the detrimental effect of delays.

Characterization and Space-Time Downscaling of the Inundation Extent over the Inner Niger Delta Using GIEMS and MODIS Data

The objective in this work is to develop downscaling methodologies to obtain a long time record of inundation extent at high spatial resolution based on the existing low spatial resolution results of the Global Inundation Extent from Multi-Satellites (GIEMS) dataset. In semiarid regions, high-spatial-resolution a priori information can be provided by visible and infrared observations from the Moderate Resolution Imaging Spectroradiometer (MODIS). The study concentrates on the Inner Niger Delta where MODIS-derived inundation extent has been estimated at a 500-m resolution. The space-time variability is first analyzed using a principal component analysis (PCA). This is particularly effective to understand the inundation variability, interpolate in time, or fill in missing values. Two innovative methods are developed (linear regression and matrix inversion) both based on the PCA representation. These GIEMS downscaling techniques have been calibrated using the 500-m MODIS data. The downscaled fields show the expected space-time behaviors from MODIS. A 20-yr dataset of the inundation extent at 500 m is derived from this analysis for the Inner Niger Delta. The methods are very general and may be applied to many basins and to other variables than inundation, provided enough a priori high-spatial-resolution information is available. The derived high-spatial-resolution dataset will be used in the framework of the Surface Water Ocean Topography (SWOT) mission to develop and test the instrument simulator as well as to select the calibration validation sites (with high space-time inundation variability). In addition, once SWOT observations are available, the downscaled methodology will be calibrated on them in order to downscale the GIEMS datasets and to extend the SWOT benefits back in time to 1993.

Co-registration of speech production datasets from electromagnetic articulography and real-time magnetic resonance imaging

This paper describes a spatio-temporal registration approach for speech articulation data obtained from electromagnetic articulography (EMA) and real-time Magnetic Resonance Imaging (rtMRI). This is motivated by the potential for combining the complementary advantages of both types of data. The registration method is validated on EMA and rtMRI datasets obtained at different times, but using the same stimuli. The aligned corpus offers the advantages of high temporal resolution (from EMA) and a complete mid-sagittal view (from rtMRI). The co-registration also yields optimum placement of EMA sensors as articulatory landmarks on the magnetic resonance images, thus providing richer spatio-temporal information about articulatory dynamics. (C) 2014 Acoustical Society of America

Design and analysis of integrated optic quadrature phase shift keying modulator

Quadrature phase shift keying (QPSK) is one of the most popular modulation schemes in coherent optical communication systems for data rates in excess of 40 Gbps because of its high spectral efficiency. This paper proposes a simple method of implementing a QPSK modulator in integrated optic (IO) domain. The QPSK modulator is realized using standard IO components, such as Y-branches and electro-optic modulators (EOMs). Design optimization of EOM is carried out considering the fabrication constraints, miniaturization aspects, and simplicity. Also, the interdependency between electrode length, operating voltage, and electrode gap of an EOM has been captured in the form of a family of curves. These plots enable designing of EOMs for custom requirements. An innovative approach has been adopted in demonstrating the operation of IO QPSK modulator in terms of phase data extracted from beam propagation model. The results obtained by this approach have been verified using the conventional interferometric approach. The operation of the proposed IO QPSK modulator is experimentally demonstrated. The design of IO QPSK modulator is taken up as a part of a broader scheme that aims at generation of QPSK modulated microwave signal based on optical heterodyning. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)

Recent NMR Methodological Developments for Chiral Analysis in Isotropic Solutions

Chiral auxiliaries are used for NMR spectroscopic study of enantiomers. Often the presence of impurities, severe overlap of peaks, excessive line broadening and complex multiplicity pattern restricts the chiral analysis using 1D H-1 NMR spectrum. There are few approaches to resolve the overlapped peaks. One approach is to use suitable chiral auxiliary, which induces large chemical shift difference between the discriminated peaks (Delta delta(R,S)) and minimize the overlap. Another direction of approach is to design appropriate NMR experiments to circumvent some of these problems, viz, enhancing spectral resolution, unravelling the superimposed spectra of enantiomers, and reduction of spectral complexity. Large number of NMR techniques, such as two dimensional selective F-1 decoupling, RES-TOCSY, multiple quantum detection, frequency selective homodecoupling, band selective homodecoupling, broadband homodecoupling, etc. have been reported for such a purpose. Many of these techniques have aided in chiral analysis for molecules of diverse functionality in the presence of chiral auxiliaries. The present review summarizes the recently reported NMR experimental methodologies, with a special emphasis on the work carried out in authors' laboratory.

Real-time maximum a-posteriori image reconstruction for fluorescence microscopy

Rapid reconstruction of multidimensional image is crucial for enabling real-time 3D fluorescence imaging. This becomes a key factor for imaging rapidly occurring events in the cellular environment. To facilitate real-time imaging, we have developed a graphics processing unit (GPU) based real-time maximum a-posteriori (MAP) image reconstruction system. The parallel processing capability of GPU device that consists of a large number of tiny processing cores and the adaptability of image reconstruction algorithm to parallel processing (that employ multiple independent computing modules called threads) results in high temporal resolution. Moreover, the proposed quadratic potential based MAP algorithm effectively deconvolves the images as well as suppresses the noise. The multi-node multi-threaded GPU and the Compute Unified Device Architecture (CUDA) efficiently execute the iterative image reconstruction algorithm that is similar to 200-fold faster (for large dataset) when compared to existing CPU based systems. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Reconstruction of the Disassembly Pathway of an Icosahedral Viral Capsid and Shape Determination of Two Successive Intermediates

Viral capsids derived from an icosahedral plant virus widely used in physical and nanotechnological investigations were fully dissociated into dimers by a rapid change of pH. The process was probed in vitro at high spatiotemporal resolution by time-resolved small-angle X-ray scattering using a high brilliance synchrotron source. A powerful custom-made global fitting algorithm allowed us to reconstruct the most likely pathway parametrized by a set of stoichiometric coefficients and to determine the shape of two successive intermediates by ab initio calculations. None of these two unexpected intermediates was previously identified in self-assembly experiments, which suggests that the disassembly pathway is not a mirror image of the assembly pathway. These findings shed new light on the mechanisms and the reversibility of the assembly/disassembly of natural and synthetic virus-based systems. They also demonstrate that both the structure and dynamics of an increasing number of intermediate species become accessible to experiments.

A real-time coherent dedispersion pipeline for the giant metrewave radio telescope

A fully real-time coherent dedispersion system has been developed for the pulsar back-end at the Giant Metrewave Radio Telescope (GMRT). The dedispersion pipeline uses the single phased array voltage beam produced by the existing GMRT software back-end (GSB) to produce coherently dedispersed intensity output in real time, for the currently operational bandwidths of 16 MHz and 32 MHz. Provision has also been made to coherently dedisperse voltage beam data from observations recorded on disk. We discuss the design and implementation of the real-time coherent dedispersion system, describing the steps carried out to optimise the performance of the pipeline. Presently functioning on an Intel Xeon X5550 CPU equipped with a NVIDIA Tesla C2075 GPU, the pipeline allows dispersion free, high time resolution data to be obtained in real-time. We illustrate the significant improvements over the existing incoherent dedispersion system at the GMRT, and present some preliminary results obtained from studies of pulsars using this system, demonstrating its potential as a useful tool for low frequency pulsar observations. We describe the salient features of our implementation, comparing it with other recently developed real-time coherent dedispersion systems. This implementation of a real-time coherent dedispersion pipeline for a large, low frequency array instrument like the GMRT, will enable long-term observing programs using coherent dedispersion to be carried out routinely at the observatory. We also outline the possible improvements for such a pipeline, including prospects for the upgraded GMRT which will have bandwidths about ten times larger than at present.

Disaggregation of LST over India: comparative analysis of different vegetation indices

The non-availability of high-spatial-resolution thermal data from satellites on a consistent basis led to the development of different models for sharpening coarse-spatial-resolution thermal data. Thermal sharpening models that are based on the relationship between land-surface temperature (LST) and a vegetation index (VI) such as the normalized difference vegetation index (NDVI) or fraction vegetation cover (FVC) have gained much attention due to their simplicity, physical basis, and operational capability. However, there are hardly any studies in the literature examining comprehensively various VIs apart from NDVI and FVC, which may be better suited for thermal sharpening over agricultural and natural landscapes. The aim of this study is to compare the relative performance of five different VIs, namely NDVI, FVC, the normalized difference water index (NDWI), soil adjusted vegetation index (SAVI), and modified soil adjusted vegetation index (MSAVI), for thermal sharpening using the DisTrad thermal sharpening model over agricultural and natural landscapes in India. Multi-temporal LST data from Landsat-7 Enhanced Thematic Mapper Plus (ETM+) and Moderate Resolution Imaging Spectroradiometer (MODIS) sensors obtained over two different agro-climatic grids in India were disaggregated from 960 m to 120 m spatial resolution. The sharpened LST was compared with the reference LST estimated from the Landsat data at 120 m spatial resolution. In addition to this, MODIS LST was disaggregated from 960 m to 480 m and compared with ground measurements at five sites in India. It was found that NDVI and FVC performed better only under wet conditions, whereas under drier conditions, the performance of NDWI was superior to other indices and produced accurate results. SAVI and MSAVI always produced poorer results compared with NDVI/FVC and NDWI for wet and dry cases, respectively.

Visualization of molecule interaction between antigen and antibody - One of ellipsometric imaging applications

It is to investigate molecule interactions between antigen and antibody with ellipsometric imaging technique and demonstrate some features and possibilities offered by applications of the technique. Molecule interaction is an important interest for molecule biologist and immunologist. They have used some established methods such as immufluorcence, radioimmunoassay and surface plasma resonance, etc, to study the molecule interaction. At the same time, experimentalists hope to use some updated technique with more direct visual results. Ellipsometric imaging is non-destructive and exhibits a high sensitivity to phase transitions with thin layers. It is capable of imaging local variations in the optical properties such as thickness due to the presence of different surface concentration of molecule or different deposited molecules. If a molecular mono-layer (such as antigen) with bio-activity were deposited on a surface to form a sensing surface and then incubated in a solution with other molecules (such as antibody), a variation of the layer thickness when the molecules on the sensing surface reacted with the others in the solution could be observed with ellipsometric imaging. Every point on the surface was measured at the same time with a high sensitivity to distinguish the variation between mono-layer and molecular complexes. Ellipsometric imaging is based on conventional ellipsometry with charge coupled device (CCD) as detector and images are caught with computer with image processing technique. It has advantages of high sensitivity to thickness variation (resolution in the order of angstrom), big field of view (in square centimeter), high sampling speed (a picture taken within one second), and high lateral resolution (in the order of micrometer). Here it has just shown one application in study of antigen-antibody interaction, and it is possible to observe molecule interaction process with an in-situ technique.

Optical Remote Sensing of Coastal Habitats, Moss Landing, California, 9-11 January, 2006: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop on Optical Remote Sensing of Coastal Habitats was convened January 9-11, 2006 at Moss Landing Marine Laboratories in Moss Landing, California, sponsored by the ACT West Coast regional partnership comprised of the Moss Landing Marine Laboratories (MLML) and the Monterey Bay Aquarium Research Institute (MBARI). The "Optical Remote Sensing of Coastal Habitats" (ORS) Workshop completes ACT'S Remote Sensing Technology series by building upon the success of ACT'S West Coast Regional Partner Workshop "Acoustic Remote Sensing Technologies for Coastal Imaging and Resource Assessment" (ACT 04-07). Drs. Paul Bissett of the Florida Environmental Research Institute (FERI) and Scott McClean of Satlantic, Inc. were the ORS workshop co-chairs. Invited participants were selected to provide a uniform representation of the academic researchers, private sector product developers, and existing and potential data product users from the resource management community to enable development of broad consensus opinions on the role of ORS technologies in coastal resource assessment and management. The workshop was organized to examine the current state of multi- and hyper-spectral imaging technologies with the intent to assess the current limits on their routine application for habitat classification and resource monitoring of coastal watersheds, nearshore shallow water environments, and adjacent optically deep waters. Breakout discussions focused on the capabilities, advantages ,and limitations of the different technologies (e.g., spectral & spatial resolution), as well as practical issues related to instrument and platform availability, reliability, hardware, software, and technical skill levels required to exploit the data products generated by these instruments. Specifically, the participants were charged to address the following: (1) Identify the types of ORS data products currently used for coastal resource assessment and how they can assist coastal managers in fulfilling their regulatory and management responsibilities; (2) Identify barriers and challenges to the application of ORS technologies in management and research activities; (3) Recommend a series of community actions to overcome identified barriers and challenges. Plenary presentations by Drs. Curtiss 0. Davis (Oregon State University) and Stephan Lataille (ITRES Research, Ltd.) provided background summaries on the varieties of ORS technologies available, deployment platform options, and tradeoffs for application of ORS data products with specific applications to the assessment of coastal zone water quality and habitat characterization. Dr. Jim Aiken (CASIX) described how multiscale ground-truth measurements were essential for developing robust assessment of modeled biogeochemical interpretations derived from optically based earth observation data sets. While continuing improvements in sensor spectral resolution, signal to noise and dynamic range coupled with sensor-integrated GPS, improved processing algorithms for georectification, and atmospheric correction have made ORS data products invaluable synoptic tools for oceanographic research, their adoption as management tools has lagged. Seth Blitch (Apalachicola National Estuarine Research Reserve) described the obvious needs for, yet substantial challenges hindering the adoption of advanced spectroscopic imaging data products to supplement the current dominance of digital ortho-quad imagery by the resource management community, especially when they impinge on regulatory issues. (pdf contains 32 pages)

A CE/SE Scheme for Flows in Porous Media and Its Applications

In this paper, a new computational scheme for solving flows in porous media was proposed. The scheme was based on an improved CE/SE method (the space-time Conservation Element and Solution Element method). We described porous flows by adopting DFB (Brinkman-Forchheimer extended Darcy) equation. The comparison between our computational results and Ghia's confirmed the high accuracy, resolution, and efficiency of our CE/SE scheme. The proposed first-order CE/SE scheme is a new reliable way for numerical simulations of flows in porous media. After investigation of effects of Darcy number on porous flow, it shows that Darcy number has dominant influence on porous flow for the Reynolds number and porosity considered.

石英波片偏光干涉谱的研究

根据石英晶体双折射率的色散特性,对石英波片的偏光干涉谱进行了理论分析和数值模拟,提出了一种石英波片延迟量和厚度的偏光干涉标定法。即由偏光干涉谱,可以得出石英波片在200～2000 nm宽光谱范围内的延迟量；通过对长波段的偏光干涉谱极值波长的精确判断,可以准确地计算出该石英波片的厚度。利用Lambda 900 紫外可见近红外分光光度计对一片石英波片的偏光干涉谱进行了测量。在波长精度为0.1 nm的情况下,测量的厚度精度为0.1 μm。误差分析结果表明,通过提高光谱的最小分辨力及选择较长的光谱波段进行测量计算

Volatiles in Protoplanetary Disks

Planets are assembled from the gas, dust, and ice in the accretion disks that encircle young stars. Ices of chemical compounds with low condensation temperatures (<200 K), the so-called volatiles, dominate the solid mass reservoir from which planetesimals are formed and are thus available to build the protoplanetary cores of gas/ice giant planets. It has long been thought that the regions near the condensation fronts of volatiles are preferential birth sites of planets. Moreover, the main volatiles in disks are also the main C-and O-containing species in (exo)planetary atmospheres. Understanding the distribution of volatiles in disks and their role in planet-formation processes is therefore of great interest.

This thesis addresses two fundamental questions concerning the nature of volatiles in planet-forming disks: (1) how are volatiles distributed throughout a disk, and (2) how can we use volatiles to probe planet-forming processes in disks? We tackle the first question in two complementary ways. We have developed a novel super-resolution method to constrain the radial distribution of volatiles throughout a disk by combining multi-wavelength spectra. Thanks to the ordered velocity and temperature profiles in disks, we find that detailed constraints can be derived even with spatially and spectrally unresolved data -- provided a wide range of energy levels are sampled. We also employ high-spatial resolution interferometric images at (sub)mm frequencies using the Atacama Large Millimeter Array (ALMA) to directly measure the radial distribution of volatiles.

For the second question, we combine volatile gas emission measurements with those of the dust continuum emission or extinction to understand dust growth mechanisms in disks and disk instabilities at planet-forming distances from the central star. Our observations and models support the idea that the water vapor can be concentrated in regions near its condensation front at certain evolutionary stages in the lifetime of protoplanetary disks, and that fast pebble growth is likely to occur near the condensation fronts of various volatile species.