ALBERT

Description: Postdisaster search and rescue is an important application of ultrawideband (UWB) radar systems, which mainly detect trapped victims by their respiratory-motion response. The development of a respiratory-motion detection (RMD) algorithm that can eliminate nonstationary clutter and noise is a challenging task for the application. A new algorithm is proposed to deal with the task in this letter. It uses the multichannel singular spectrum analysis (MSSA) technique to reconstruct the respiratory-motion response detected by a UWB radar. During the reconstruction, the periodicity and range interrelation characteristics of the response are exploited to adaptively identify signal subspaces. The performance of the algorithm is verified both by simulated and real data. The results show its improved performance over the reference algorithms, e.g., a singular-value-decomposition-based algorithm. The adaptive-MSSA-based RMD algorithm has great promise not only in practical use but also for future research of UWB-radar-based human being remote sensing.

Description: Land–sea contamination observed in Soil Moisture and Ocean Salinity (SMOS) brightness temperature images is found to have two main contributions: the floor error inherent of image reconstruction and a multiplicative error either in the antenna temperature or in the visibility samples measured by the correlator. The origin of this last one is traced down to SMOS calibration parameters to yield a simple correction scheme, which is validated against several geophysical scenarios. Autoconsistency rules in interferometric synthesis together with redundant and complementary calibration procedures provide a robust SMOS calibration scheme.

Description: This letter proposes a novel algorithm, which is based on the generalized method of moments (GMM), for the estimation and correction of phase errors induced in synthetic aperture radar (SAR) imagery. The GMM algorithm is used to replace the original phase-estimation kernel in the basic structure of the phase-gradient-autofocus algorithm. Since this novel algorithm does not require the observed signal to be a certain distribution model, it is able to estimate arbitrary phase errors. The GMM algorithm has the ability of estimating range-dependent phase errors, which makes it an efficient estimator. As a result, higher accuracy of the estimated phase errors and a better focused image can be achieved. Excellent results have been obtained in autofocusing and imaging experiments on real SAR data.

Description: Strong clutter reflections of terrain and marine surfaces obscure the contrast between the target-of-interest and clutter (terrain and marine surface reflections) in synthetic aperture radar (SAR) images and consequently hinder the efficiency of image interpretation and analysis. To overcome this problem, this letter proposes an efficient clutter suppression method in SAR images, which is named shedding irrelevant patterns (SIP). The essence is to construct a regression function that can suppress clutter and preserve the target patterns concurrently. We assume that the clutter is irrelevant to the target-of-interest and distinguishable in patterns in terms of image-pixel distribution and intensity (spatial information). Experimental results show the efficiency of the proposed method in both clutter suppression and target pattern preservation.

Description: A concern in hyperspectral image classification is the high number of required training samples. When traditional classifiers are applied, feature reduction (FR) techniques are the most common approaches to deal with this problem. Subspace-based classifiers, which are developed based on high-dimensional space characteristics, are another way to handle the high dimension of hyperspectral images. In this letter, a novel subspace-based classification approach is proposed and compared with basic and improved subspace-based classifiers. The proposed classifier is also compared with traditional classifiers that are accompanied by an FR technique and the well-known support vector machine classifier. Experimental results prove the efficiency of the proposed method, especially when a limited number of training samples are available. Furthermore, the proposed method has a very high level of automation and simplicity, as it has no parameters to be set.

Description: To improve the spatial density of measurement points of persistent-scatterer interferometry, distributed scatterer (DS) should be considered and processed. An important procedure in DS interferometry is the phase triangulation (PT). This letter introduces two modified PT algorithms (i.e., equal-weighted PT and coherence-weighted PT) and analyzes the mathematical relations between different published PT methods (i.e., the maximum-likelihood phase estimator, least squares estimator, and eigendecomposition-based phase estimators). The analysis shows that the above five PT methods share very similar mathematical forms with different weight values in the estimation procedure.

Description: Sparse representation-based classifier and its variants have been widely adopted for hyperspectral image (HSI) classification recently. However, sparse representation is unstable so that similar features might obtain significantly different sparse codes. Despite the instability, we find that the sparse codes follow a class-dependent distribution under the structured dictionary consisting of training samples from all classes. Based on this observation, a novel discriminative feature, sparse code histogram (SCH), is developed for HSI classification. By counting the SCH of each sample from the sparse codes of its spatial neighbors, we can statistically obtain the distribution pattern of sparse codes of the class to which the sample belongs, and then treat the SCH as a new feature for classification. To reduce the possible outliers among the neighbors, a shape-adaptive neighborhood extractor is also employed to enhance the stability of the histogram feature. Experimental results demonstrate that SCH enjoys a strong discriminative power, which can achieve notably better performance than several state-of-the-art methods for HSI classification with limited training samples.

Description: Several detection statistics have been proposed for detecting fine ground disturbances between two synthetic aperture radar (SAR) images, such as vehicle tracks. The standard method involves estimating a local correlation coefficient between images. Other methods have been proposed using various statistical hypothesis tests. One of these alternative methods is a generalized likelihood ratio test (GLRT), which compares a full-correlation image model to a no-correlation image model. In this letter, we expand the GLRT to polarimetric SAR data and derive the appropriate GLRT detection statistics. Additionally, we explore relaxing the equal variance/equal polarimetric covariance assumptions used in previous results and find improved performance on macroscopic scene changes.

Description: For downward-looking linear array 3-D synthetic aperture radar, the resolution in cross-track direction is much lower than the ones in range and azimuth. Hence, superresolution reconstruction algorithms are desired. Since the cross-track signal to be reconstructed is sparse in the object domain, compressive sensing algorithm has been used. However, the imaging processing on the 3-D scene brings large computational loads, which renders challenges in both data acquisition and processing. To cover this shortage, truncated singular value decomposition is utilized to reconstruct a reduced-redundancy spatial measurement matrix. The proposed algorithm provides advantages in terms of computational time while maintaining the quality of the scene reconstructions. Moreover, our results on uniform linear array are generally applicable to sparse nonuniform linear array. Superresolution properties and reconstruction accuracies are demonstrated using simulations under the noise and clutter scenarios.

Description: This letter proposes a signal processing method of passive bistatic radar (PBR) exploiting an uncooperative radar as an illuminator. Compared with other opportunity illuminators, the transmitting signal of a radar usually has a better ambiguity function, which leads to a higher range resolution. Two channels are needed in PBR system. The reference channel is used to estimate radar signal parameters and reconstruct directly propagated signal. The surveillance channel is used to receive scattered wave. An array antenna and a simultaneous multibeam algorithm are necessary in the surveillance channel due to the flexible beam scanning of the uncooperative radar. The procedure of the proposed method is explained in detail, which is then followed by a field experiment. Preliminary results from the field experiment show that the proposed method can be applied to target angle and bistatic range measurement successfully.

Description: In order to achieve 3-D imaging with an airborne down-looking linear-array synthetic aperture radar (LASAR), a uniform virtual antenna array may be obtained by aperture synthesis of the cross-track sparse multiple-input–multiple-output array. However, the actual 3-D imaging quality is unavoidably degraded by errors in the virtual element position. In this letter, we investigate the effects of these errors on the forms and the degrees of image quality degradation by decomposing the error-related stochastic processes via an orthogonal transform based on discrete Legendre polynomials. It should be noted that these analyses are helpful for designing a LASAR system and providing a reference for specifying the requisite precision of measurement devices and calibration methods. Finally, we briefly consider the use of calibration methods to eliminate the effects of errors.

Description: In problems where labeled data are scarce, semisupervised learning (SSL) techniques are an attractive framework that can exploit both labeled and unlabeled data. These approaches typically rely on a smoothness assumption such that examples that are similar in input space should also be similar in label space. In many domains, such as remotely sensed hyperspectral image (HSI) classification, the data violate this assumption. In response, we propose a general method by which a neighborhood graph used in SSL is learned using binary classifiers that are trained to predict whether a pair of pixels shares the same label. Working within the framework of semisupervised neural networks (SSNNs), we show that our approach improves on the performance of the SSNN on two HSI data sets.

Description: In this letter, new models for the spatial correlation of sea clutter texture and intensity are proposed as improved versions of current power law models or exponential decay model. The models for texture have three unknown parameters, and thus can be called triparametric models. The structure of the models is a weighted sum of two components, which can describe the decaying process of the correlation coefficient with spatial lags, as well as the periodic behavior due to the existence of transient coherent structures in sea clutter. Unknown parameters are optimized by the nonlinear least square fit method. Models for sea clutter intensity can be obtained through a linear transform for uncorrelated speckle based on the compound-Gaussian representation of sea clutter. The proposed models are validated and compared with current models using S- and C-band measured sea clutter data. Analysis results indicate the effectiveness of the proposed models in that they can describe the behavior of spatial correlation coefficients with higher accuracy.

Description: Terrestrial laser scanning (TLS) has become a popular tool for acquiring source data points which can be used to construct digital elevation models (DEMs) for a wide number of applications. A TLS point cloud often has a very fine spatial resolution, which can represent well the spatial variation of a terrain surface. However, the uncertainty in DEMs created from this relatively new type of source data is not well understood, which forms the focus of this letter. TLS survey data representing four terrain surfaces of different characteristics were used to explore the effects of surface complexity and typical TLS data density (in terms of data point spacing) on DEM accuracy. The spatial variation in TLS data can be decomposed into parts corresponding to the signal of spatial variation (of terrain surfaces) and noise due to measurement error. We found a linear relation between the DEM error and the typical TLS data spacings considered (30–100 mm) which arises as a function of the interpolation error, and a constant contribution from the propagated data noise. This letter quantifies these components for each of the four surfaces considered and shows that, for the interpolation method considered here, higher density sampling would not be beneficial.

Description: A novel way to estimate the live fuel moisture content (LFMC) was explored from the ratio of canopy water content (CWC) and foliage dry biomass (FDB). The CWC was estimated using the PROSAIL (PROSPECT + SAIL) radiative transfer model from the Landsat 8 product. A weak constraint 4-D variational data assimilation method was employed to assimilate the temporally estimated leaf area index into a soil-water-atmosphere-plant (SWAP) model for optimizing the model control variables. Then, the SWAP model was reinitialized with this optimum set of control variables, and better prediction of FDB was obtained. Results showed that a high accuracy level was achieved for the estimated CWC ( $R^{2}=0.91$ , $mbox{RMSE}=84.74 mbox{g/m}^2$ ) and FDB ( $R^2=0.88$ , $mbox{RMSE}=48.54 mbox{g/m} ^2$ ) when compared with in situ measured values. However, the accuracy level of estimated LFMC was poor ( $R^2=0.59$ , $mbox{RMSE} =30.85%$ ) . Further analyses find that the estimated LFMC is reliable for low LFMC but challenged for high LFMC, which indicates that the presented method still makes sense to the assessment of wildfire risk since the wildfire generally occurs when the vegetation is in low LFMC condition.

Description: In this letter, we present the use of experimental human micro-Doppler signature data gathered by a multistatic radar system to discriminate between unarmed and potentially armed personnel walking along different trajectories. Different ways of extracting suitable features from the spectrograms of the micro-Doppler signatures are discussed, particularly empirical features such as Doppler bandwidth, periodicity, and others, and features extracted from singular value decomposition (SVD) vectors. High classification accuracy of armed versus unarmed personnel (between 90% and 97% depending on the walking trajectory of the people) can be achieved with a single SVD-based feature, in comparison with using four empirical features. The impact on classification performance of different aspect angles and the benefit of combining multistatic information is also evaluated in this letter.

Description: Automatic urban area detection in remote sensing images is an important application in the field of earth observation. Most of the existing methods employ feature classifiers and thereby contain a data training process. Moreover, some methods cannot detect urban areas in complex scenes accurately. This letter proposes an automatic urban area detection method that uses multiple features that have different resolutions. First, a downsampled low-resolution image is used to segment the candidate area. After the corner points of the urban area are extracted, a weighted Gaussian voting matrix technique is employed to integrate the corner points into the candidate area. Then, the edge features and homogeneous region are extracted by using the original high-resolution image. Using these results as the input, the processes of guided filtering and contrast enhancement can finally detect accurately the urban areas. This method combines multiple features, such as corner, edge, and regional characteristics, to detect the urban areas. The experimental results show that the proposed method has better detection accuracy for urban areas than the existing algorithms.

Description: In marine sciences, time series are often nonlinear and nonstationary. Adequate and specific methods are needed to analyze such series. In this letter, an application of the empirical mode decomposition method (EMD) associated to the Hilbert spectral analysis (HSA) is presented. Furthermore, EMD-based time-dependent intrinsic correlation (TDIC) analysis is applied to consider the correlation between two nonstationary time series. Four temperature time series obtained from automatic measurements in nearshore waters of the Réunion island are considered, recorded every 10 min from July 2011 to January 2012. The application of the EMD on these series and the estimation of their power spectra using the HSA are illustrated. The authors identify low-frequency tidal waves and display the pattern of correlations at different scales and different locations. By TDIC analysis, it was concluded that the high-frequency modes have small correlation, whereas the trends are perfectly correlated.

Description: Detecting vehicles in aerial images provides important information for traffic management and urban planning. Detecting the cars in the images is challenging due to the relatively small size of the target objects and the complex background in man-made areas. It is particularly challenging if the goal is near-real-time detection, i.e., within few seconds, on large images without any additional information, e.g., road database and accurate target size. We present a method that can detect the vehicles on a 21-MPixel original frame image without accurate scale information within seconds on a laptop single threaded. In addition to the bounding box of the vehicles, we extract also orientation and type (car/truck) information. First, we apply a fast binary detector using integral channel features in a soft-cascade structure. In the next step, we apply a multiclass classifier on the output of the binary detector, which gives the orientation and type of the vehicles. We evaluate our method on a challenging data set of original aerial images over Munich and a data set captured from an unmanned aerial vehicle (UAV).

Description: We compare five slope correction methods developed by Walter et al. , Montes et al. , Schleppi et al. , España et al. , and Gonsamo et al. (referred to as WAL, MON, SCH, ESP, and GON, respectively) using artificial fisheye pictures simulated by graphics software and a lookup table (LUT) retrieval method. The LUT is built by simulating the directional gap fraction as a function of leaf area index (LAI) and average leaf inclination angle (ALIA) using the Poisson law. LAI and ALIA estimates correspond to the case of the LUT that provides the lowest root-mean-square error between the observed gap fractions after slope correction and the simulated ones. Three LAI values (1.5, 3.5, and 5.5), four ALIA values (26.8°, 45°, 57.5°, and 63.2°), and three slope angles (0°, 20°, and 50°) constituted 36 samples of random scenes. ESP is recommended because its results are accurate and independent on the leaf angle distribution (LAD), while GON only performs well for spherical LAD. The three other methods present less good performances with underestimation or overestimation of LAI and/or ALIA depending on the LAD, and the recommended order for them is MON, SCH, and WAL.

Description: In this letter, an improved phase correlation (PC) method based on 2-D plane fitting and the maximum kernel density estimator (MKDE) is proposed, which combines the idea of Stone's method and robust estimator MKDE. The proposed PC method first utilizes a vector filter to minimize the noise errors of the phase angle matrix and then unwraps the filtered phase angle matrix by the use of the minimum cost network flow unwrapping algorithm. Afterward, the unwrapped phase angle matrix is robustly fitted via MKDE, and the slope coefficients of the 2-D plane indicate the subpixel shifts between images. The experiments revealed that the improved method can effectively avoid the impact of outliers on the phase angle matrix during the plane fitting and is robust to aliasing and noise. The matching accuracy can reach 1/50th of a pixel using simulated data. The real image sequence tracking experiment was also undertaken to demonstrate the effectiveness of the proposed PC method with a registration accuracy of root-mean-square error better than 0.1 pixels.

Description: Accurately mapping forest carbon density by combining sample plots and remotely sensed images has become popular because this method provides spatially explicit estimates. However, mixed pixels often impede the improvement of the estimation. In this letter, regression modeling and spectral unmixing analysis were integrated to improve the estimation of forest carbon density for the You County of Hunan, China, using Landsat Thematic Mapper images. Linear spectral unmixing with and without a constraint (LSUWC and LSUWOC) and nonlinear spectral unmixing (NSU) were compared to derive the fractions of five endmembers, particularly forests. Stepwise regression, logistic regression, and polynomial regression (PR) with and without the forest fraction used as an independent variable and the product of the forest fraction image and the map from the best model without the forest fraction were compared. The models were developed using 56 sample plots, and their results were validated using 26 test plots. The decomposition of mixed pixels was assessed using higher spatial resolution SPOT images and a corresponding land cover map. The results showed that 1) LSUWC more accurately estimated the endmember fractions than LSUWOC and NSU, 2) PR had the greatest estimation accuracy of forest carbon, and 3) combining regression modeling and spectral unmixing increased the estimation accuracy by 31%–39%, and introducing the forest fraction into the regressions performed better than the product of forest fraction image and the results from PR without the fraction. This implied that the integrations provided great potential in reducing the impacts of mixed pixels in mapping forest carbon.

Description: This letter proposes a multiresolution technique to address the high computational cost in remote sensing image registration. The scale-invariant feature transform is applied to detect keypoints and descriptors, and then, global information combined with descriptors is utilized to establish keypoint mappings. Keypoints are first classified according to their octaves. Then, in the lowest resolution, the keypoints of the largest octave are mapped with descriptors and the global information, giving an initial affine transformation $T_0$ . In the next octave, the keypoints of the second largest octave are mapped by employing $T_0$ to narrow the space of matching keypoints. By this means, the process of establishing keypoint correspondences is conducted from one resolution (octave) to the next as the obtained transformation gets finer until we get to the highest resolution. Due to the high computational expense of computing global information, the proposed technique is important for aligning large-size remote sensing imagery. Experimental results show that the proposed method can achieve a comparable registration accuracy but with a less computational cost than directly building keypoint mappings on images of large size.

Description: Gold nanorods (GNRs) with surface plasmon resonance peak at 1063.8 nm were fabricated and experimentally exploited as the single and combined saturable absorber (SA) in a $Q$ -switched Nd:YAG laser for the first time. In the situation using GNRs as a single SA, the maximum pulse energy of 19 $muhbox{J} $ was achieved at a pulse repetition rate of 20 kHz. However, due to the small effective modulation depth of the GNRs, microsecond pulses were generated in such a GNRs-based passively $Q$ -switched laser. A novel configuration using GNRs as a combined SA in an acoustooptic $Q$ -switched Nd:YAG laser was proposed. The small nonlinear loss modulation induced by the GNRs played a distinctive role in flexibly manipulating the nanosecond pulse waveforms. Our study demonstrated the feasibility of generating high-energy pulses by singly using GNRs-based SA in all solid-state lasers. Meanwhile, a new application mode incorporating GNRs as a combined SA was studied, providing an alternative method to take advantage of the nanomaterial-based SA with a relatively small modulation depth.

Description: Presents corrections to the paper, "Estimation of forest biomass from two-level model inversion of single-pass InSAR data" (Soja, M.J., et al.,Trans. Geosci. Remote Sens., vol. 53, no. 9, pp. 5083???5099, Sep. 2015).

Description: In this letter, we present an efficient parallel implementation of composite kernels in support vector machines (SVMs) for hyperspectral image (HSI) classification. Our implementation makes effective use of commodity graphics processing units (GPUs). Specifically, we port the calculation of composite kernels to GPUs, perform intensive computations based on NVidia's compute unified device architecture, and execute the rest of the operations related with control and small data calculations in the CPU. Our experimental results, conducted using real hyperspectral data sets and NVidia GPU platforms, indicate significant improvements in terms of computational effectiveness, achieving near-real-time performance of spatial–spectral HSI classification for the first time in the literature.

Description: Compared with airborne laser scanning, terrestrial laser scanning (TLS) offers ground-based point cloud data of trees and provides greater potential to accurately estimate tree and stand parameters. However, there is a lack of effective methods to accurately identify locations of individual trees from TLS point cloud data. It is also unknown whether the estimation accuracy of the parameters, including tree height (H), diameter at breast height (DBH), and so on, using TLS can meet the requirement of forest management and planning. In this letter, a novel method to effectively process point cloud data and further determine the locations of individual trees in a stand based on the central coordinates of point cloud data on a defined grid according to the largest DBH was developed. Moreover, a point-cloud-data-based convex hull algorithm and the cylinder method were, respectively, used to estimate DBH and H of individual trees. This study was conducted in a pure Chinese fir plantation of 45 trees located in Huang-Feng-Qiao forest farm, You County of Hunan, China. The comparison of the estimated and observed values showed that the obtained tree locations had errors of less than 20 cm, and the relative root mean square errors for the estimates of both DBH and H were less than 5%. This implies that TLS is very promising for the retrieval of tree and stand parameters in forest stands. For the applications of these methods to mixed forests with a structure of multilayer canopies, further examination is needed.

Description: Commercial, industrial, and military aerospace designs are increasingly deploying MEMS micro inertial measurement unit (MIMU) for motion control, automation, and positioning applications, such as the unmanned aerial vehicle (UAV), robot, and smart phone. On the one hand, MIMU has the merit of low cost, small size, low-power consumption, and high shock resistance, but on the other hand, low-cost MIMU is affected by systematic error caused by the instability of the drift, scaling factors, and axes misalignment, which may lead to large errors in the position and attitude’s determination from time to time. That means calibration before use is an effective way to improve the practical precision of MIMU. However, many customers have no precise turntable to calibrate the MIMU before they use it. To address these problems, this paper presents an easy self-calibration method to implement calibration of the MIMU on a common table only with an inclined surface, no precise turntable is needed. The calibration method is based on the following principles. First, the module of the output vector of the orthogonal configured three-axis accelerometers is equal to unit gravity. Second, when IMU rotates to a known gesture with a stable axis, the angles can be calculated through integration. Third, when the accelerometers’ parameters are calculated, it can act as a level datum. Furthermore, the accelerometers on the inclined surface are used to determine the rotating heading datum. Finally, after a series static positions test and rotating test, the parameters can be extracted and estimated. To demonstrate the success and the convenience of the proposed method, comparison experiments with the precision turntable have been made on an ADI’s MIMU. The calibration results show that the accuracy and precision of this method is quite equivalent with the turntable-based calibration, and the scale factors error with an order of magnitude always equal or less than $10^{-5}$ . The observed static and dynamic yaw maximum angular error in a certain period is <0.8°, the pitch maximum angular error is <0.5°, and the roll maximum angular error is <0.3°.

Description: Time–frequency packing (TFP) transmission provides the highest achievable spectral efficiency with a constrained symbol alphabet and detector complexity. In this paper, the application of the TFP technique to fiber-optic systems is investigated and experimentally demonstrated. The main theoretical aspects, design guidelines, and implementation issues are discussed, focusing on those aspects which are peculiar to TFP systems. In particular, adaptive compensation of propagation impairments, matched filtering, and maximum a posteriori probability detection are obtained by a combination of a two-dimensional equalizer and four eight-state parallel Bahl–Cocke–Jelinek–Raviv (BCJR) detectors. A novel algorithm that ensures adaptive equalization, channel estimation, and a proper distribution of tasks between the equalizer and BCJR detectors is proposed. A set of irregular low-density parity-check codes with different rates is designed to operate at low error rates and approach the spectral efficiency limit achievable by TFP at different signal-to-noise ratios. An experimental demonstration of the designed system is finally provided with five dual-polarization QPSK-modulated optical carriers, densely packed in a 100-GHz bandwidth, employing a recirculating loop to test the performance of the system at different transmission distances.

Description: We investigated nonlinear optical characteristics of Tungsten disulfide (WS 2 ) films and experimentally demonstrated their high potential for application as nonlinear saturable absorbers in passively mode-locked fiber lasers. Side polished fiber (SPF) was fabricated and WS 2 film was overlaid to provide an efficient evanescent field interaction. The WS 2 film was prepared using two methods: liquid phase exfoliation to form few-layer nano-sheets, and chemical vapor deposition (CVD) to grow uniform multilayer WS 2 on a SiO 2 substrate. Two SPF saturable absorbers were prepared by either spin coating WS 2 solution or lifting off the multilayer CVD WS 2 on SPF. An all-fiber ring cavity was built and the WS 2 film overlaid on SPF was employed as a mode locker along with Er-doped fiber as a gain medium. Using the spin-coated WS 2 SPF, stable soliton-like pulses were generated with a spectral width of 5.6 nm and 467 fs pulse duration. The fiber laser cavity containing CVD WS2 SPF generated a transform-limited soliton pulse train with a spectral width of 8.23 nm and a pulse duration of 332 fs. Our study confirmed a high potential of WS 2 film as a novel 2-D nonlinear optical material for laser applications.

Description: We propose and experimentally demonstrate an on-chip all-optical differential-equation solver capable of solving second-order ordinary differential equations (ODEs) characterizing continuous-time linear time-invariant systems. The photonic device is implemented by a self-coupled microresonator on a silicon-on-insulator platform with mutual coupling between the cavity modes. Owing to the mutual mode coupling within the same resonant cavity, the resonance wavelengths induced by different cavity modes are self-aligned, thus avoiding precise wavelength alignment and unequal thermal wavelength drifts as in the case of cascaded resonators. By changing the mutual mode coupling strength, the proposed device can be used to solve second-order ODEs with tunable coefficients. System demonstration using the fabricated device is carried out for 10-Gb/s optical Gaussian and super-Gaussian input pulses. The experimental results are in good agreement with theoretical predictions of the solutions, which verify the feasibility of the fabricated device as a tunable second-order photonic ODE solver.

Description: We demonstrate a 100 Gb/s short reach system using a multicarrier transmitter based on a gain switched monolithically integrated laser. An optical comb source with 12.5-GHz free spectral range is achieved by gain-switching an integrated passive feedback laser. The 100 Gb/s wavelength division multiplexed, single sideband, direct detection, orthogonal frequency division multiplexed (WDM-SSB-DD-OFDM) system operates over 25 km standard single mode fiber exhibiting a spectral efficiency of 1.8 b/s/Hz. Receiver sensitivity of –14.2 dBm is achieved after 25 km transmission. Performance optimization with phase and amplitude precompensation is employed to improve the SSB OFDM modulation thereby reducing the interchannel interference and overcoming the power fading induced by the optical filter. We also present a theoretical analysis of the SSB-OFDM modulation.

Description: In this paper, narrow-band emission lines are generated by means of two random distributed feedback fiber laser schemes. Spectral line-widths as narrow as 3.2 pm have been measured, which significantly improves previous reported results. The laser is analyzed with the aim of obtaining a spectral line-width as narrow as possible. Additionally a variation of this setup for multi-wavelength operation is also validated. Both schemes present a simple topology that use a combination of phase-shifted fiber Bragg gratings and regular fiber Bragg gratings as filtering elements.

Description: We report on the fabrication and characterization of 19-cell hypocycloid-shape Kagome fibers with core size larger than 100 μm. These inhibited coupling fibers present low propagation loss (100 dB/km) over broad transmission range with low chromatic dispersion combined with ultra-low power overlap with silica surround, making them an efficient solution for ultra-high power laser handling, ultra-fast laser delivery, and plasma photonics applications.

Description: The iterative demodulation and decoding algorithm introduced in 2005 by Colavolpe, Barbieri, and Caire to cope with channels affected by phase noise needs pilot symbols to bootstrap. However, pilot symbols reduce the spectral efficiency of the system and, consequently, system's throughput. The aim of this paper is to show that trellis-based demodulation can be used to bootstrap the iterative process without the need of pilot symbols. Also, the complexity issue of trellis-based demodulation is addressed in this paper. The result is that the performance of iterative demodulation and decoding after the iterations is virtually unaffected by complexity reduction, provided that the reduced-complexity demodulator guarantees cycle-slip-free operation. From the numerical results presented in this paper, we show that cycle-slip-free operation can be achieved with substantial complexity reduction also for phase noise associated with linewidths of practical interest.

Description: The optical pulse evolution in a highly nonlinear normal dispersion-increasing fiber has been considered, both experimentally and theoretically. It was found that large spectral broadening in tapered waveguides could occur without temporal instabilities and impose the linear frequency modulation, i.e., chirp, required for high-quality pulse compression. The pedestal-free pulses have been demonstrated after dechirping in a standard single-mode fiber.

Description: This work proposes a novel localized surface plasmon resonance (LSPR) biochemical sensor featuring high sensitivity and a high resolution. The sensor was divided into two subcomponents according to their distinct functions; namely, single-mode fiber and metal array. Single-mode fibers located on the left and right sides of the sensors function as the input and output for optical fiber signals. A metal array comprising an arrangement of cylindrical nanometal particles served as the detection area of the sensor. To effectively reduce the memory capacity and calculation time, two innovative techniques (i.e., object meshing and boundary meshing) were integrated with the finite element method. With the area of the triangular elements used as a basis, the object boundary, small object, medium object, and large objects were meshed at a ratio of 1:8:160:1600. The improved numerical simulation methods and six design procedures were adopted to develop and analyze the proposed LSPR biochemical sensor. The results show that the novel LSPR biochemical sensor outperformed two current high-performance biochemical sensors and provided additional advantages such as short length (approximately 430 μm), high resolution (approximately –120 dB), and high sensitivity (approximately 127 604 nm/RIU).

Description: We propose an ultra-broadband super light absorber by integrating different-sized tapered hyperbolic metamaterial (HMM) waveguides, each of which has a different and wide absorption band due to broadband slow-light response, into a unit cell. We numerically demonstrate that such an absorber is superior to a single-sized HMM absorber in terms of absorption bandwidth, while maintaining a comparable absorption efficiency. A three different-sized HMM absorber presents the capability of working with an ultra-wide frequency band ranging from 1 to 30 THz, which is much larger than previously proposed absorbers working in the same spectral region. Such a design shows great promise for a broad range of applications such as thermal emitters, photovoltaics, optical-chemical energy harvesting, and stealth technology, where ultra-wideband absorption is in very high demand.

Description: This paper proposes a ring-based integrated wireless optical network architecture and an associated protocol that involves Ethernet passive optical network (EPON) and long term evolution (LTE) wireless network. The architecture along with the proposed protocol is instrumental toward the reduction of handover delay. The proposed ring-based EPON architecture facilitates the implementation of the X2 interface for LTE network by enabling the optical network units of the EPON backhaul to directly communicate with each other. The work further discusses about an open access network architecture where a single EPON can be used by multiple mobile service providers without compromising information security. Extensive simulations have been carried out to evaluate the performance of the proposed network. An analytical model has been introduced to calculate the queuing delay experienced by the X2 interface. The model has been validated with the simulations results.

Description: High spectrum efficiency and fast restoration speed are highly desired for survivable elastic optical networks (EONs). In this paper, we take the advantages of failure-independent path-protecting preconfigured cycles (FIPP p -cycles) and investigate how to realize spectrum efficient resilience design with them. We first study the problem of offline service provisioning with FIPP p -cycles. We formulate an integer linear programming model and prove that the problem is $mathcal{NP}$ hard. Then, several time-efficient heuristics are designed for FIPP p -cycle formulation and related routing, modulation format, and spectrum assignment. Extensive simulations on offline provisioning verify that the heuristics can obtain near-optimal solutions. Next, we consider online service provisioning with FIPP p -cycles in dynamic EONs. In order to overcome the decrease of protection efficiency during dynamic network operation, we propose a p -cycle reconfiguration scheme to reoptimize protection structures on-the-fly. Simulation results demonstrate that the proposed algorithms can improve spectrum efficiency and reduce bandwidth blocking probability simultaneously.

Description: Photo-thermo-refractive (PTR) glasses are the class of polyfunctional materials that combine the properties of several monofunctional materials such as photo-refractive, laser, luminescent, and plasmonic ones. Based on PTR glasses, various diffractive holographic elements and photonic devices were developed in both the volume and fiber versions. In this paper, the fabrication of optical planar waveguides on PTR glass by low-temperature ion exchange is reported for the first time. Planar waveguides were fabricated through substituting the sodium ions in glass by silver, potassium, rubidium, and cesium ones from the nitrate melts. The silver waveguides were shown to have the largest depth (27 μm) and reveal no birefringence. For the silver waveguides, an increase in the refractive index is caused by differences in the polarizabilities of cations exchanged. The maximum increment of the refractive index was observed in the cesium waveguides (0.0512). An increase in the refractive index and also appearing the birefringence in potassium, rubidium, and cesium waveguides are found to be due to the compressive mechanical stresses and their relaxation. The potentialities of the ion exchange technology for fabricating, in PTR glasses, planar gradient waveguides with low losses (0.5 dB/cm) are demonstrated, the potentialities extending the application field of PTR glasses in photonics.

Description: Background: Cardiovascular disease (CVD) remains the major cause of excess mortality in patients with non-alcoholic fatty liver disease (NAFLD). The aim of this study was to investigate the individual contribution of NAFLD to CVD risk factors in the absence of pathogenic influences from other comorbidities often found in NAFLD patients, by using an established in-vitro model of hepatic steatosis. Methods: Histopathological events in non-alcoholic fatty liver disease were recapitulated by focused metabolic nutrient overload of hepatoblastoma C3A cells, using oleate-treated-cells and untreated controls for comparison. Microarray and proteomic data from cell culture experiments were integrated into a custom-built systems biology database and proteogenomics analysis performed. Candidate genes with significant dysregulation and concomitant changes in protein abundance were identified and STRING association and enrichment analysis performed to identify putative pathogenic pathways. Results: The search strategy yielded 3 candidate genes that were specifically and significantly up-regulated in nutrient-overloaded cells compared to untreated controls: fibrinogen alpha chain (2.2 fold), fibrinogen beta chain (2.3 fold) and fibrinogen gamma chain (2.1 fold) (all rank products pfp

Description: Background: Adaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an ‘early-burst’ process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus. Results: Our phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the ‘early-burst’ model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size. Conclusions: Liolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.

Description: Background: Recently, the Bayesian method becomes more popular for analyzing high dimensional gene expression data as it allows us to borrow information across different genes and provides powerful estimators for evaluating gene expression levels. It is crucial to develop a simple but efficient gene selection algorithm for detecting differentially expressed (DE) genes based on the Bayesian estimators. Results: In this paper, by extending the two-criterion idea of Chen et al. (Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. J Stat Plan Inference. 2008;138:387–404), we propose two new gene selection algorithms for general Bayesian models and name these new methods as the confident difference criterion methods. One is based on the standardized differences between two mean expression values among genes; the other adds the differences between two variances to it. The proposed confident difference criterion methods first evaluate the posterior probability of a gene having different gene expressions between competitive samples and then declare a gene to be DE if the posterior probability is large. The theoretical connection between the proposed first method based on the means and the Bayes factor approach proposed by Yu et al. (Yu F, Chen M-H, Kuo L. Detecting differentially expressed genes using alibrated Bayes factors. Statistica Sinica. 2008;18:783–802) is established under the normal-normal-model with equal variances between two samples. The empirical performance of the proposed methods is examined and compared to those of several existing methods via several simulations. The results from these simulation studies show that the proposed confident difference criterion methods outperform the existing methods when comparing gene expressions across different conditions for both microarray studies and sequence-based high-throughput studies. A real dataset is used to further demonstrate the proposed methodology. In the real data application, the confident difference criterion methods successfully identified more clinically important DE genes than the other methods. Conclusion: The confident difference criterion method proposed in this paper provides a new efficient approach for both microarray studies and sequence-based high-throughput studies to identify differentially expressed genes.

Description: Background: Spounavirinae viruses have received an increasing interest as tools for the control of harmful bacteria due to their relatively broad host range and strictly virulent phenotype. Results: In this study, we collected and analyzed the complete genome sequences of 61 published phages, either ICTV-classified or candidate members of the Spounavirinae subfamily of the Myoviridae. A set of comparative analyses identified a distinct, recently proposed Bastille-like phage group within the Spounavirinae. More importantly, type 1 thymidylate synthase (TS1) and dihydrofolate reductase (DHFR) genes were shown to be unique for the members of the proposed Bastille-like phage group, and are suitable as molecular markers. We also show that the members of this group encode beta-lactamase and/or sporulation-related SpoIIIE homologs, possibly questioning their suitability as biocontrol agents. Conclusions: We confirm the creation of a new genus—the “Bastille-like group”—in Spounavirinae, and propose that the presence of TS1- and DHFR-encoding genes could serve as signatures for the new Bastille-like group. In addition, the presence of metallo-beta-lactamase and/or SpoIIIE homologs in all members of Bastille-like group phages makes questionable their suitability for use in biocontrol.

Description: Background: The transcription factor p63 belongs to the p53/p63/p73 family and plays key functional roles during normal epithelial development and differentiation and in pathological states such as squamous cell carcinomas. The human TP63 gene, located on chromosome 3q28 is driven by two promoters that generate the full-length transactivating (TA) and N-terminal truncated (ΔN) isoforms. Furthermore alternative splicing at the C-terminus gives rise to additional α, β, γ and likely several other minor variants. Teasing out the expression and biological function of each p63 variant has been both the focus of, and a cause for contention in the p63 field. Results: Here we have taken advantage of a burgeoning RNA-Seq based genomic data-sets to examine the global expression profiles of p63 isoforms across commonly utilized human cell-lines and major tissues and organs. Consistent with earlier studies, we find ΔNp63 transcripts, primarily that of the ΔNp63α isoforms, to be expressed in most cells of epithelial origin such as those of skin and oral tissues, mammary glands and squamous cell carcinomas. In contrast, TAp63 is not expressed in the majority of normal cell-types and tissues; rather it is selectively expressed at moderate to high levels in a subset of Burkitt’s and diffuse large B-cell lymphoma cell lines. We verify this differential expression pattern of p63 isoforms by Western blot analysis, using newly developed ΔN and TA specific antibodies. Furthermore using unsupervised clustering of human cell lines, tissues and organs, we show that ΔNp63 and TAp63 driven transcriptional networks involve very distinct sets of molecular players, which may underlie their different biological functions. Conclusions: In this study we report comprehensive and global expression profiles of p63 isoforms and their relationship to p53/p73 and other potential transcriptional co-regulators. We curate publicly available data generated in part by consortiums such as ENCODE, FANTOM and Human Protein Atlas to delineate the vastly different transcriptomic landscapes of ΔNp63 and TAp63. Our studies help not only in dispelling prevailing myths and controversies on p63 expression in commonly used human cell lines but also augur new isoform- and cell type-specific activities of p63.

Description: Background: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. Results: The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Conclusions: Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.

Description: In this letter, a novel algorithm for attitude measurement based on a 3-D electromagnetic model (3-D em-model) is proposed. The 3-D em-model is established offline based on the geometric structure of the target, and it can be used to predict the scattering features at different target attitudes. In order to measure the attitude of the air target, we design a bistatic step frequency radar system. The directions of the two radars' lines of sight (LOSs) relative to the target are acquired by matching the high-resolution range profiles (HRRPs) from the target echoes to the HRRPs generated from the 3-D em-model. Since the directions of two radars' LOSs relative to the Earth are already known, the absolute attitude of the target can be acquired. The innovative contributions of this letter are as follows: 1) A comprehensive theoretical analysis of air target attitude measurement based on its own 3-D em-model is proposed; 2) the method can be applied to different kinds of air targets such as aircraft, satellite, missile, etc.; 3) the proposed attitude measurement method does not require target motion model in advance; and 4) the proposed algorithm can be applied to any kind of step frequency waveforms. Experiments using both data predicted by a high-frequency electromagnetic code and data measured in the chamber verify the validity of the method.

Description: The Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) missions provide Level-1 brightness temperature (Tb) observations that are used for global soil moisture estimation. However, the nature of these Tb data differs: the SMOS Tb observations contain atmospheric and select reflected extraterrestrial (“Sky”) radiation, whereas the SMAP Tb data are corrected for these contributions, using auxiliary near-surface information. Furthermore, the SMOS Tb observations are multiangular, whereas the SMAP Tb is measured at 40° incidence angle only. This letter discusses how SMOS Tb, SMAP Tb, and radiative transfer modeling components can be aligned in order to enable a seamless exchange of SMOS and SMAP Tb data in soil moisture retrieval and assimilation systems. The aggregated contribution of the atmospheric and reflected Sky radiation is, on average, about 1 K for horizontally polarized Tb and 0.5 K for vertically polarized Tb at 40° incidence angle, but local and short-term values regularly exceed 5 K.

Description: Background: Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging. Results: We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies). Conclusions: An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated genome dynamics that characterize the wasp and ants.

Description: A multi-sensor addressing method for fiber Bragg grating aided fiber loop ringdown (FBG-FLRD) sensor array is proposed. It is capable of simultaneous measurement of temperature and force. Light from a wavelength-swept fiber laser (WSFL) is modulated into pulsed light to illuminate FBG-FLRD sensor array. Based on the time sequence of pulsed lights reflected by fiber Bragg grating array, each FBG-FLRD sensor can be distinguished. The time interval between the trigger signal of the WSFL and the pulsed light reflected by FBG offers temperature variation information. By measuring the ringdown time of each FBG-FLRD, the loss of fiber ring induced by temperature and force can be obtained. And then simultaneous measurement can be implemented in real time. To prove the validity of the proposed system, a six elements array is experimentally validated with interrogation frequency of 27.5 Hz.

Description: Background: Rhodococcus jostii RHA1 growing on different substrates is capable of accumulating simultaneously three types of carbon storage compounds: glycogen, polyhydroxyalkanoates (PHA), and triacylglycerols (TAG). Under nitrogen-limited (N-limited) condition, the level of storage increases as is commonly observed for other bacteria. The proportion of each storage compound changes with substrate, but it remains unclear what modelling approach should be adopted to predict the relative composition of the mixture of the storage compounds. We analyzed the growth of R. jostii RHA1 under N-limited conditions using a genome-scale metabolic modelling approach to determine which global metabolic objective function could be used for the prediction. Results: The R. jostii RHA1 model (iMT1174) produced during this study contains 1,243 balanced metabolites, 1,935 unique reactions, and 1,174 open reading frames (ORFs).Seven objective functions used with flux balance analysis (FBA) were compared for their capacity to predict the mixture of storage compounds accumulated after the sudden onset of N-limitation. Predictive abilities were determined using a Bayesian approach. Experimental data on storage accumulation mixture (glycogen, polyhydroxyalkanoates, and triacylglycerols) were obtained for batch cultures grown on glucose or acetate. The best FBA simulation results were obtained using a novel objective function for the N-limited condition which combined the maximization of the storage fluxes and the minimization of metabolic adjustments (MOMA) with the preceding non-limited conditions (max storage + environmental MOMA). The FBA solutions for the non-limited growth conditions were simply constrained by the objective function of growth rate maximization. Measurement of central metabolic fluxes by 13 C-labelling experiments of amino acids further supported the application of the environmental MOMA principle in the context of changing environment. Finally, it was found that the quantitative predictions of the storage mixture during N-limited storage accumulation were fairly sensitive to the biomass composition, as expected. Conclusions: The genome-scale metabolic model analysis of R. jostii RHA1 cultures suggested that the intracellular reaction flux profile immediately after the onset of N-limited condition are impacted by the values of the same fluxes during the period of non-limited growth. PHA turned out to be the main storage pool of the mixture in R. jostii RHA1.

Description: Background: Plant organ segmentation from 3D point clouds is a relevant task for plant phenotyping and plant growth observation. Automated solutions are required to increase the efficiency of recent high-throughput plant phenotyping pipelines. However, plant geometrical properties vary with time, among observation scales and different plant types. The main objective of the present research is to develop a fully automated, fast and reliable data driven approach for plant organ segmentation. Results: The automated segmentation of plant organs using unsupervised, clustering methods is crucial in cases where the goal is to get fast insights into the data or no labeled data is available or costly to achieve. For this we propose and compare data driven approaches that are easy-to-realize and make the use of standard algorithms possible. Since normalized histograms, acquired from 3D point clouds, can be seen as samples from a probability simplex, we propose to map the data from the simplex space into Euclidean space using Aitchisons log ratio transformation, or into the positive quadrant of the unit sphere using square root transformation. This, in turn, paves the way to a wide range of commonly used analysis techniques that are based on measuring the similarities between data points using Euclidean distance. We investigate the performance of the resulting approaches in the practical context of grouping 3D point clouds and demonstrate empirically that they lead to clustering results with high accuracy for monocotyledonous and dicotyledonous plant species with diverse shoot architecture. Conclusion: An automated segmentation of 3D point clouds is demonstrated in the present work. Within seconds first insights into plant data can be deviated – even from non-labelled data. This approach is applicable to different plant species with high accuracy. The analysis cascade can be implemented in future high-throughput phenotyping scenarios and will support the evaluation of the performance of different plant genotypes exposed to stress or in different environmental scenarios.

Description: Tim Hunt took an undergraduate degree in Natural Sciences at Cambridge in 1964, and his PhD and subsequent work focussed on the control of protein synthesis until 1982, when his adventitious discovery of the central cell cycle regulator cyclin, while he was teaching at the Marine Biological Laboratory in Woods Hole, redirected him to the study of cell cycle regulation. From 1990 to his retirement Tim worked in the Clare Hall Laboratories of Cancer Research UK. He shared the Nobel Prize in Physiology and Medicine with Lee Hartwell and Paul Nurse in 2001, and talked to us about the series of coincidences that led him to the prizewinning discovery.

Description: Background: Hybridization between incipient species is expected to become progressively limited as their genetic divergence increases and reproductive isolation proceeds. Amphibian radiations and their secondary contact zones are useful models to infer the timeframes of speciation, but empirical data from natural systems remains extremely scarce. Here we follow this approach in the European radiation of tree frogs (Hyla arborea group). We investigated a natural hybrid zone between two lineages (Hyla arborea and Hyla orientalis) of Mio-Pliocene divergence (~5 My) for comparison with other hybrid systems from this group. Results: We found concordant geographic distributions of nuclear and mitochondrial gene pools, and replicated narrow transitions (~30 km) across two independent transects, indicating an advanced state of reproductive isolation and potential local barriers to dispersal. This result parallels the situation between H. arborea and H. intermedia, which share the same amount of divergence with H. orientalis. In contrast, younger lineages show much stronger admixture at secondary contacts. Conclusions: Our findings corroborate the negative relationship between hybridizability and divergence time in European tree frogs, where 5 My are necessary to achieve almost complete reproductive isolation. Speciation seems to progress homogeneously in this radiation, and might thus be driven by gradual genome-wide changes rather than single speciation genes. However, the timescale differs greatly from that of other well-studied amphibians. General assumptions on the time necessary for speciation based on evidence from unrelated taxa may thus be unreliable. In contrast, comparative hybrid zone analyses within single radiations such as our case study are useful to appreciate the advance of speciation in space and time.

Description: Background: Preterm birth is the leading cause of mortality and morbidity in newborn infants. Its etiology is multifactorial with genes and environmental factors, including chronic maternal stress, contributing to its risk. Our objective was to investigate whether single nucleotide polymorphisms (SNPs) in genes involved in the stress response are associated with spontaneous preterm birth using a candidate gene approach. Methods: A total of 210 cases (singleton spontaneous preterm birth at

Description: Background: Host genetic variability has been implicated in chemotherapy-induced peripheral neuropathy (CIPN). A dose-limiting toxicity for chemotherapy agents, CIPN is also a debilitating condition that may progress to chronic neuropathic pain. We utilized a bioinformatics approach, which captures the complexity of intracellular and intercellular interactions, to identify genes for CIPN. Methods: Using genes pooled from the literature as a starting point, we used Ingenuity Pathway Analysis (IPA) to generate gene networks for CIPN. Results: We performed IPA core analysis for genes associated with platinum-, taxane- and platinum-taxane–induced neuropathy. We found that IL6, TNF, CXCL8, IL1B and ERK1/2 were the top genes in terms of the number of connections in platinum-induced neuropathy and TP53, MYC, PARP1, P38 MAPK and TNF for combined taxane-platinum–induced neuropathy. Conclusion: Neurotoxicity is common in cancer patients treated with platinum compounds and anti-microtubule agents and CIPN is one of the debilitating sequela. The bioinformatic approach helped identify genes associated with CIPN in cancer patients.

Description: Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (α/β) 8 TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T m of 44 °C and a Gibbs free energy of unfolding (ΔG°) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C m of 1.6 M and a ΔG° of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Description: Background: Tumorigenesis is an evolutionary process by which tumor cells acquire mutations through successive diversification and differentiation. There is much interest in reconstructing this process of evolution due to its relevance to identifying drivers of mutation and predicting future prognosis and drug response. Efforts are challenged by high tumor heterogeneity, though, both within and among patients. In prior work, we showed that this heterogeneity could be turned into an advantage by computationally reconstructing models of cell populations mixed to different degrees in distinct tumors. Such mixed membership model approaches, however, are still limited in their ability to dissect more than a few well-conserved cell populations across a tumor data set. Results: We present a method to improve on current mixed membership model approaches by better accounting for conserved progression pathways between subsets of cancers, which imply a structure to the data that has not previously been exploited. We extend our prior methods, which use an interpretation of the mixture problem as that of reconstructing simple geometric objects called simplices, to instead search for structured unions of simplices called simplicial complexes that one would expect to emerge from mixture processes describing branches along an evolutionary tree. We further improve on the prior work with a novel objective function to better identify mixtures corresponding to parsimonious evolutionary tree models. We demonstrate that this approach improves on our ability to accurately resolve mixtures on simulated data sets and demonstrate its practical applicability on a large RNASeq tumor data set. Conclusions: Better exploiting the expected geometric structure for mixed membership models produced from common evolutionary trees allows us to quickly and accurately reconstruct models of cell populations sampled from those trees. In the process, we hope to develop a better understanding of tumor evolution as well as other biological problems that involve interpreting genomic data gathered from heterogeneous populations of cells.

Description: Background: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Description: Background: Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information. Results: We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported. Conclusion: IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/.

Description: Background: For faithful chromosome segregation during cell division, correct attachments must be established between sister chromosomes and microtubules from opposite spindle poles through kinetochores (chromosome bi-orientation). Incorrect attachments of kinetochore microtubules (kMTs) lead to chromosome mis-segregation and aneuploidy, which is often associated with developmental abnormalities such as Down syndrome and diseases including cancer. The interaction between kinetochores and microtubules is highly dynamic with frequent attachments and detachments. However, it remains unclear how chromosome bi-orientation is achieved with such accuracy in such a dynamic process. Results: To gain new insight into this essential process, we have developed a simple mathematical model of kinetochore–microtubule interactions during cell division in general, i.e. both mitosis and meiosis. Firstly, the model reveals that the balance between attachment and detachment probabilities of kMTs is crucial for correct chromosome bi-orientation. With the right balance, incorrect attachments are resolved spontaneously into correct bi-oriented conformations while an imbalance leads to persistent errors. In addition, the model explains why errors are more commonly found in the first meiotic division (meiosis I) than in mitosis and how a faulty conformation can evade the spindle assembly checkpoint, which may lead to a chromosome loss. Conclusions: The proposed model, despite its simplicity, helps us understand one of the primary causes of chromosomal instability—aberrant kinetochore–microtubule interactions. The model reveals that chromosome bi-orientation is a probabilistic self-organisation, rather than a sophisticated process of error detection and correction.

Description: Background: Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. It is highly prevalent and is characterized by symptoms including odor, discharge and irritation. No single microbe has been found to cause BV. In this paper we use random forests and logistic regression classifiers to model the relationship between the microbial community and BV. We use subsets of the microbial community features in order to determine which features are important to the classification models. Results: We find that models generated using logistic regression and random forests perform nearly identically and identify largely similar important features. Only a few features are necessary to obtain high BV classification accuracy. Additionally, there appears to be substantial redundancy between the microbial community features. Conclusions: These results are in contrast to a previous study in which the important features identified by the classifiers were dissimilar. This difference appears to be the result of using different feature importance measures. It is not clear whether machine learning classifiers are capturing patterns different from simple correlations.

Description: Background: Bacterial populations communicate through the cell density-dependent mechanism of quorum sensing (QS). Vibrio harveyi, one of the best studied model organisms for QS, was used to explore effects of the synthetic cannabinoid HU-210 on QS and different QS-regulated physiological processes in bacteria. Results: Analysis of QS-regulated bioluminescence in wild-type and mutant strains of V. harveyi revealed that HU-210 affects the autoinducer-2 (AI-2) pathway, one of three known QS cascades of V. harveyi. Furthermore, QS-mediated biofilm formation and swimming motility in the mutant strain BB152 (AI-1 − , AI-2 + ) were significantly reduced in the presence of HU-210. HU-210 inhibited QS-mediated virulence factor production without any inhibitory effect on bacterial growth. It also alters the expression of several genes, which are regulated by QS, specifically downregulating the genes of the AI-2 QS cascade. Conclusion: First evidence is being provided for interference of bacterial signal-transduction systems by a synthetic cannabinoid. The effect of HU-210 was specific to the AI-2 cascade in V. harveyi. AI-2 is known as a "universal autoinducer" and interference with its activity opens a broad spectrum of applications for synthetic cannabinoids in future research as a potential anti-QS agent.

Description: Background: Several studies described the phytochemical constituents of plants in relation with the free radical scavenging property and inhibition of lipid peroxidation. This study investigated the in vitro antioxidant property, and the protective effects of ethanolic and aqueous ethanol extract of the leaves and barks of Afrostyrax lepidophyllus (Huaceae) against ion mediated oxidative damages. Methods: Four extracts (ethanol and aqueous-ethanol) from the leaves and barks of A. lepidophyllus were used in this study. The total phenols content, the antiradical and antioxidant properties were determined using standard colorimetric methods. Results: The plant extracts had a significant scavenging potential on the 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl (OH), nitrite oxide (NO) and 2,2-azinobis (3-ethylbenzthiazoline)-6-sulfonic acid (ABTS) radicals with the IC 50 varied between 47 and 200 µg/mL depending on the part of plant and the type of extract. The ethanol extract of A. lepidophyllus bark (GEE) showed the highest polyphenolic (35.33 ± 0.29) and flavonoid (12.00 ± 0.14) content. All the tested extracts demonstrated a high protective potential with the increased of superoxide dismutase, catalase and peroxidase activities. Conclusion: Afrostyrax lepidophyllus extracts exhibited higher antioxidant potential and significant protective potential on liver enzymes.

Description: Background: The internalization of Aspergillus fumigatus into alveolar epithelial cells (AECs) is tightly controlled by host cellular actin dynamics, which require close modulation of the ADF (actin depolymerizing factor)/cofilin family. However, the role of cofilin in A. fumigatus internalization into AECs remains unclear. Results: Here, we demonstrated that germinated A. fumigatus conidia were able to induce phosphorylation of cofilin in A549 cells during the early stage of internalization. The modulation of cofilin activity by overexpression, knockdown, or mutation of the cofilin gene in A549 cells decreased the efficacy of A. fumigatus internalization. Reducing the phosphorylation status of cofilin with BMS-5 (LIM kinase inhibitor) or overexpression of the slingshot phosphatases also impeded A. fumigatus internalization. Both the C. botulimun C3 transferase (a specific RhoA inhibitor) and Y27632 (a specific ROCK inhibitor) reduced the internalization of A. fumigatus and the level of phosphorylated cofilin. β-1,3-glucan (the major component of the conidial cell wall) and its host cell receptor dectin-1 did not seem to be associated with cofilin phosphorylation during A. fumigatus infection. Conclusion: These results indicated that cofilin might be involved in the modulation of A. fumigatus internalization into type II alveolar epithelial cells through the RhoA-ROCK-LIM kinase pathway.

Description: Background: With the introduction and implementation of a variety of government programs and policies to encourage adoption of electronic medical records (EMRs), EMRs are being increasingly adopted in North America. We sought to evaluate the completeness of a variety of EMR fields to determine if family physicians were comprehensively using their EMRs and the suitability of use of the data for secondary purposes in Ontario, Canada. Methods: We examined EMR data from a convenience sample of family physicians distributed throughout Ontario within the Electronic Medical Record Administrative data Linked Database (EMRALD) as extracted in the summer of 2012. We identified all physicians with at least one year of EMR use. Measures were developed and rates of physician documentation of clinical encounters, electronic prescriptions, laboratory tests, blood pressure and weight, referrals, consultation letters, and all fields in the cumulative patient profile were calculated as a function of physician and patient time since starting on the EMR. Results: Of the 167 physicians with at least one year of EMR use, we identified 186,237 patients. Overall, the fields with the highest level of completeness were for visit documentations and prescriptions (〉70 %). Improvements were observed with increasing trends of completeness overtime for almost all EMR fields according to increasing physician time on EMR. Assessment of the influence of patient time on EMR demonstrated an increasing likelihood of the population of EMR fields overtime, with the largest improvements occurring between the first and second years. Conclusions: All of the data fields examined appear to be reasonably complete within the first year of adoption with the biggest increase occurring the first to second year. Using all of the basic functions of the EMR appears to be occurring in the current environment of EMR adoption in Ontario. Thus the data appears to be suitable for secondary use.

Description: Background: Recognising the limitations of a paper-based approach to documenting vital sign observations and responding to national clinical guidelines, we have explored the use of an electronic solution that could improve the quality and safety of patient care. We have developed a system for recording vital sign observations at the bedside, automatically calculating an Early Warning Score, and saving data such that it is accessible to all relevant clinicians within a hospital trust. We have studied current clinical practice of using paper observation charts, and attempted to streamline the process. We describe our user-focussed design process, and present the key design decisions prior to describing the system in greater detail. Results: The system has been deployed in three pilot clinical areas over a period of 9 months. During this time, vital sign observations were recorded electronically using our system. Analysis of the number of observations recorded (21,316 observations) and the number of active users (111 users) confirmed that the system is being used for routine clinical observations. Feedback from clinical end-users was collected to assess user acceptance of the system. This resulted in a System Usability Scale score of 77.8, indicating high user acceptability. Conclusions: Our system has been successfully piloted, and is in the process of full implementation throughout adult inpatient clinical areas in the Oxford University Hospitals. Whilst our results demonstrate qualitative acceptance of the system, its quantitative effect on clinical care is yet to be evaluated.

Description: ObjectivesExcess adiposity (obesity and excess gestational weight gain, GWG) during pregnancy (EADP) increases risk for gestational diabetes, preeclampsia, and child and maternal obesity. Personal GWG goals predict total GWG. Some estimates suggest only 30% of pregnant women have personal GWG goals that are congruent with Institute of Medicine GWG recommendations. The primary purpose of this study was to determine the extent to which perceived pre-pregnancy weight status, healthcare provider advice, knowledge of EADP risks, and value for healthy GWG predicted knowledge of GWG recommendations. The secondary purpose was to determine sources of GWG information among pregnant women. Methods: Pregnant women with a confirmed singleton pregnancy completed a one-time survey in obstetric clinic waiting rooms. Logistic regression analysis was used. Results: 246 predominantly African American, low income, overweight/obese women completed surveys. Average age was 25 (SD 5.3) and gestation age ranged from 7 to 40 weeks. Knowledge of pre-pregnancy weight status was the only unique predictor of GWG recommendation knowledge (B = .642, p = .03). The top three sources of GWG information were physicians, internet, and books. The least frequently reported sources of GWG information were other healthcare providers, community programs, and television. Conclusion: In low income diverse overweight/obese pregnant women, accurate pre-pregnancy weight status perception was the only significant unique predictor of knowledge of GWG recommendations. Physicians were the preferred source of GWG information. Clinicians should have frequent, ongoing conversations about weight status with women before, during, and after pregnancy.

Description: Background: In Morocco, families play a major role in caring for elderly cancer patients. Methods: We conducted a prospective descriptive study, in the National Institute of Oncology in Morocco. The study aimed to include family members who are caregivers for patients aged ≥70 years old.FindingsAfter obtaining IRB approval, a total of 150 caregivers responded to the questionnaire. Mean age was 44.7 years. The majority were females (59.3%), living in urban areas (66.7%), and educated (62.7%).Offspring (sons or daughters) represented 56.7, 54% lived with their relatives in the same house. Most of the participants were married and have familial responsibilities. In relatives, anxiety was found in 79.3%, it was related to fear of losing the patient in 57% and resulted in the use of anxiolytics in 10%. Guilt feeling towards patients regarding neglecting their early symptoms was reported in 38%. Depression and anxiety were more frequent among female relatives and among those of urban origin. Obsession of dying from cancer was present in about 30% and fear of contagion was more common among those from rural areas and illiterate. Economic resources were exceeded in 78.7 and 56% have used banking credits, and sale of properties. Work lay-off was recorded in 54%. Relatives participated in treatment making decisions in 86% of patients. Conclusion: Even there was a great impact on elderly cancerous patients relatives, the benefits of caregiving was observed in 80%. More studies have to be conducted, especially in developing countries where the lack of resources majors the impact on family caregivers.

Description: Background: Leptospirosis and dengue are endemic in countries with subtropical or tropical climates and have epidemic potential. The incidence of both these diseases peaks during monsoons and both diseases present with similar clinical manifestations making differentiation of leptospirosis from dengue difficult. It is important to distinguish leptospirosis from dengue as early antibiotic therapy in leptospirosis leads to a favourable outcome, while dengue has no specific treatment, yet early recognition is vital for close monitoring and careful fluid management. Despite the high prevalence of both these infections, co-infection of leptospirosis and dengue has not been reported previously in Sri Lanka. We present the first case of co-infection with leptospirosis and dengue in a Sri Lankan male.Case presentationA 52 year old previously healthy Sri Lankan male was admitted to our facility with a history of fever for 4 days associated with headache, generalized myalgia, reduced urine output. On examination, he was rational, hypotensive, tacycardic, tacypneic and he did not have clinical evidence of fluid leakage or pneumonitis. His serology showed high titre of dengue IgG and IgM and rising titre of leptospirosis antibody. His course of illness was complicated with septic shock, acute renal failure, acute respiratory distress syndrome and disseminated intravascular coagulation and he succumbed to his illness on the eighth day of admission. Conclusion: In areas where both leptospirosis and dengue are endemic, both infections should be include in the differential diagnosis when evaluating patients with acute febrile illness and should consider the possibility of co-infection. Leptospirosis, being a condition having definitive antibiotic therapy, should always be ruled out even if the patient is positive for dengue serology in regions endemic to both these diseases as early initiation of antibiotic therapy can reduce mortality significantly.

Description: In this paper, the classification via sprepresentation and multitask learning is presented for target recognition in SAR image. To capture the characteristics of SAR image, a multidimensional generalization of the analytic signal, namely the monogenic signal, is employed. The original signal can be then orthogonally decomposed into three components: 1) local amplitude; 2) local phase; and 3) local orientation. Since the components represent the different kinds of information, it is beneficial by jointly considering them in a unifying framework. However, these components are infeasible to be directly utilized due to the high dimension and redundancy. To solve the problem, an intuitive idea is to define an augmented feature vector by concatenating the components. This strategy usually produces some information loss. To cover the shortage, this paper considers three components into different learning tasks, in which some common information can be shared. Specifically, the component-specific feature descriptor for each monogenic component is produced first. Inspired by the recent success of multitask learning, the resulting features are then fed into a joint sparse representation model to exploit the intercorrelation among multiple tasks. The inference is reached in terms of the total reconstruction error accumulated from all tasks. The novelty of this paper includes 1) the development of three component-specific feature descriptors; 2) the introduction of multitask learning into sparse representation model; 3) the numerical implementation of proposed method; and 4) extensive comparative experimental studies on MSTAR SAR dataset, including target recognition under standard operating conditions, as well as extended operating conditions, and the capability of outliers rejection.

Description: Offsets of synthetic aperture radar (SAR) images have played an important role in deriving complete three-dimensional (3-D) surface displacement fields in geoscientific applications. However, offset maps often suffer from multiple outliers and patch-like artifacts, because the standard offset-measurement method is a regular moving-window operation that does not consider the scattering characteristics of the ground. Here, we show that by focusing the offset measurements on predetected strong reflectors, the reliability and accuracy of SAR offsets can be significantly improved. Application to the 2011 Van (Turkey) earthquake reveals a clear deformation signal from an otherwise decorrelated interferogram, making derivation of the 3-D coseismic displacement field possible. Our proposed method can improve mapping of coseismic deformation and other ground displacements, such as glacier flow and landslide movement when strong reflectors exist.

Description: We present an accelerated probabilistic learning concept and its prototype implementation for mining heterogeneous Earth observation images, e.g., multispectral images, synthetic aperture radar (SAR) images, image time series, or geographical information systems (GIS) maps. The system prototype combines, at pixel level, the unsupervised clustering results of different features, extracted from heterogeneous satellite images and geographical information resources, with user-defined semantic annotations in order to calculate the posterior probabilities that allow the final probabilistic searches. The system is able to learn different semantic labels based on a newly developed Bayesian networks algorithm and allows different probabilistic retrieval methods of all semantically related images with only a few user interactions. The new algorithm reduces the computational cost, overperforming existing conventional systems, under certain conditions, by several orders of magnitude. The achieved speed-up allows the introduction of new feature models improving the learning capabilities of knowledge-driven image information mining systems and opening them to Big Data environments.

Description: The mineralogy and environmental history of Mars are being extensively studied through remote sensing observations paired with laboratory and in situ experiments. A significant portion of these experiments is being devoted to the identification and mapping of different iron oxides present in the Martian terrains. Among these compounds, goethite has been an object of great interest since its occurrence can be interpreted as mineralogical evidence of past aqueous activity on those landscapes. Although such experiments can provide valuable information regarding the presence of these minerals, the scope of the resulting observations may be hindered by logistics and cost-related constraints. We believe that predictive computer simulations can be employed to mitigate some of these constraints and contribute to the generation and validation of hypotheses in this area. Accordingly, we propose the use of SPLITS ( Sp ectral Li ght T ransport Model for S and) in investigations involving the spectral signatures of iron-bearing regions of Mars. In this paper, we initially demonstrate the predictive capabilities of the SPLITS model in this context through qualitative comparisons of modeled results with actual observations and measured data. Using the resulting modeled reflectance curves as our baseline data, we then perform a series of controlled computational experiments to investigate how variations on goethite and hematite content affect the spectral responses of Martian sand-textured soils.

Description: Thermal infrared (TIR) time series are exploited by many methods based on Earth observation (EO), for such applications as agriculture, forest management, and meteorology. However, due to physical limitations, data acquired by a single sensor are often unsatisfactory in terms of spatial or temporal resolution. This issue can be tackled by using remotely sensed data acquired by multiple sensors with complementary features. When nonreal-time functioning or at least near real-time functioning is admitted, the measurements can be profitably fed to a sequential Bayesian algorithm, which allows to account for the correlation embedded in the successive acquisitions. In this work, we focus on applications that allow the batch processing of the whole data sequences acquired in a fixed time interval. In this case, multiple options for improving the final product are offered by the Bayesian framework, based on both sequential and smoothing techniques. We consider several such Bayesian strategies and comparatively assess their performances in practical applications and through real thermal data acquired by the SEVIRI and MODIS sensors, encompassing the presence of multiple disturbance source, e.g., the cloud coverage of the illuminated scene.

Description: Land surface albedo, qualifying the ratio of the radiant flux reflected from the land surface to the incident flux, is a key forcing parameter controlling the Earth’s energy budget. Previously, several BRDF archetypes were distilled from high-quality MODIS BRDF/Albedo products. In this study, we propose a method that largely relies on matching observed multiangular reflectances with the most appropriate of these prior BRDF archetypes to determine the amplitude and shape of the actual surface BRDFs, when directional signatures are insufficient. This method is first evaluated using an assortment of multisource BRDF data sets to demonstrate its viability for surface albedo estimates, and then is applied to airborne wide-angle infrared dual-mode line/area array scanner (WIDAS) from the Watershed Allied Telemetry Experimental Research (WATER) campaign in the Heihe River Basin of China in 2008. This algorithm makes use of the linear MODIS BRDF model to determine the BRDF archetypes needed as prior knowledge for intrinsic spectral albedo estimates. The intrinsic spectral albedos are then used to estimate actual spectral albedos by considering the proportion of direct and diffuse solar radiation. A spectral-to-broadband conversion is performed to generate the broadband albedo at shortwave regimes through the use of conversion coefficients derived from extensive radiative transfer simulations. A further validation confirms that the estimated albedos are consistent with in situ field measured albedos over available corn crop sites. This method provides a major advantage on utilizing generalized BRDF information derived from MODIS in conjunction with other instrument data that are acquired with less angular variation.

Description: Ocean current is highly related to the interaction between ocean and atmosphere. By measuring the speed and direction of the ocean current from space, we can investigate the ocean–atmosphere interaction on a global scale. The ocean–atmosphere interaction helps to maintain the balance that is essential for planet habitability. However, the conventional scatterometer is unable to measure the ocean current vector. To achieve this, a potentially feasible approach is to use a bigger antenna, a higher PRF, and measure the interferometric phase of two successive echoes. This paper derives four decorrelation factors, and provides the phase error model first. Then, an end-to-end simulation model is established, and it is used to analyze the feasibility of ocean surface current measurement from space. Based on the simulation model, the system parameters are optimized. The simulation results show that the current speed standard deviation (Std), which means the measurement accuracy, in along-track and cross-track direction is smaller than 0.1 m/s when the wind speed is larger than 4 m/s. The swath can be used for current vector inversion that is greater than 70% when the wind speed is larger than 7 m/s. Meanwhile, ${{bf K}_{{bf pc}}}$ of the modified scatterometer is computed and the results show that ${{bf K}_{{bf pc}}}$ is better than the traditional pencil-beam rotating scatterometer when the wind speed is larger than 6 m/s.

Description: High-resolution three-dimensional (3-D) radar imaging of space targets in micromotion plays a significant role in space target recognition and space situation awareness; thus, it has attracted extensive attention in recent years. Because of the fast rotation, some scattering centers are occluded by others, i.e., the scattering centers cannot be continuously illuminated by radar in the imaging interval, and their radar echoes are discontinuous. In this paper, a nonparametric 3-D imaging method based on scattering center trajectory association is proposed. It deals with target occlusion using the Riemannian manifold optimization and obtains focused imaging of targets in complex micromotion. The effectiveness of the proposed method is validated using simulated data.

Description: Recently, satellite-based systems have been introduced that utilize angle-of-arrival (AOA) measurements to geo-locate objects of interest. In the previous work, we considered the application of nonlinear optimization to AoA-based geolocation to these systems. This previous work, however, assumed that all noise sources were independent. In the case of fast-moving objects, however, there is a significant source of error due to the propagation time inherent in satellite-based observation of objects due to the difference between the location of the object when it is observed by a satellite, and the location of the object when it emitted the signal that is being measured. This introduces a systematic error into the system that cannot be resolved by the system proposed by Burchett et al. In this paper, we extend our prior work to account for the time-delay inherent in satellite-based geolocation systems, making this system accurate for fast-movers as well as fixed or slow-moving objects. Results demonstrating significant improvement in geolocation performance both in terms of accuracy and estimated error bounds are presented.

Description: Most of existing change detection methods could be classified into three groups, the traditional pixel-based change detection (PBCD), the object-based change detection (OBCD), and the hybrid change detection (HCD). Nevertheless, both PBCD and OBCD have disadvantages, and classical HCD methods belong to intuitive decision-level fusion schemes of PBCD and OBCD. There is no optimum HCD method as of yet. Analyzing the complementarities of PBCD and OBCD method, we propose a new unsupervised algorithm-level fusion scheme (UAFS-HCD) in this paper to improve the accuracy of PBCD using spatial context information through: 1) getting the preliminary change mask with PBCD at first to estimate some parameters for OBCD; 2) deriving the unchanged area mask to eliminate the areas without changes, reducing error amplification phenomenon of OBCD; and 3) obtaining the final change mask by means of OBCD method. Taking flood detection with multitemporal SAR data as an example, we compared the new scheme with some classical methods, including PBCD, OBCD, and HCD method and supervised manual trial-and-error procedure (MTEP). The experimental results of flood detection showed that the new scheme was efficient and robust, and its accuracy sometimes can even exceed MTEP.

Description: Low-energy technologies in the Internet of Things (IoTs) era are still unable to provide the reliability needed by the industrial world, particularly in terms of the wireless operation that pervasive deployments demand. While the industrial wireless performance has achieved an acceptable degree in communications, it is no easy task to determine an efficient energy-dimensioning of the device in order to meet the application requirements. This is especially true in the face of the uncertainty inherent in energy harvesting. Thus, it is of utmost importance to model and dimension the energy consumption of the IoT applications at the pre-deployment or pre-production stages, especially when considering critical factors, such as reduced cost, life-time, and available energy. This paper presents a comprehensive model for the power consumption of wireless sensor nodes. The model takes a system-level perspective to account for all energy expenditures: communications, acquisition and processing. Furthermore, it is based only on parameters that can empirically be quantified once the platform (i.e., technology) and the application (i.e., operating conditions) are defined. This results in a new framework for studying and analyzing the energy life-cycles in applications, and it is suitable for determining in advance the specific weight of application parameters, as well as for understanding the tolerance margins and tradeoffs in the system.