THE APPLICATION OF AUTOMATED CORRELATION OPTIMIZED WARPING TO THE QUALITY EVALUATION OF Radix Puerariae thomsonii: CORRECTING RETENTION TIME SHIFT IN THE CHROMATOGRAPHIC FINGERPRINTS

The application of automated correlation optimized warping (ACOW) to the correction of retention time shift in the chromatographic fingerprints of Radix Puerariae thomsonii (RPT) was investigated. Twenty-seven samples were extracted from 9 batches of RPT products. The fingerprints of the 27 samples were established by the HPLC method. Because there is a retention time shift in the established fingerprints, the quality of these samples cannot be correctly evaluated by using similarity estimation and principal component analysis (PCA). Thus, the ACOW method was used to align these fingerprints. In the ACOW procedure, the warping parameters, which have a significant influence on the alignment result, were optimized by an automated algorithm. After correcting the retention time shift, the quality of these RPT samples was correctly evaluated by similarity estimation and PCA. It is demonstrated that ACOW is a practical method for aligning the chromatographic fingerprints of RPT. The combination of ACOW, similarity estimation, and PCA is shown to be a promising method for evaluating the quality of Traditional Chinese Medicine.

Small-area estimation with spatial similarity

A class of composite estimators of small area quantities that exploit spatial (distancerelated)similarity is derived. It is based on a distribution-free model for the areas, but theestimators are aimed to have optimal design-based properties. Composition is applied alsoto estimate some of the global parameters on which the small area estimators depend.It is shown that the commonly adopted assumption of random effects is not necessaryfor exploiting the similarity of the districts (borrowing strength across the districts). Themethods are applied in the estimation of the mean household sizes and the proportions ofsingle-member households in the counties (comarcas) of Catalonia. The simplest version ofthe estimators is more efficient than the established alternatives, even though the extentof spatial similarity is quite modest.

Software development for estimation of optical clearing agent’s diffusion coefficients in biological tissues

The study of chemical diffusion in biological tissues is a research field of high importance and with application in many clinical, research and industrial areas. The evaluation of diffusion and viscosity properties of chemicals in tissues is necessary to characterize treatments or inclusion of preservatives in tissues or organs for low temperature conservation. Recently, we have demonstrated experimentally that the diffusion properties and dynamic viscosity of sugars and alcohols can be evaluated from optical measurements. Our studies were performed in skeletal muscle, but our results have revealed that the same methodology can be used with other tissues and different chemicals. Considering the significant number of studies that can be made with this method, it becomes necessary to turn data processing and calculation easier. With this objective, we have developed a software application that integrates all processing and calculations, turning the researcher work easier and faster. Using the same experimental data that previously was used to estimate the diffusion and viscosity of glucose in skeletal muscle, we have repeated the calculations with the new application. Comparing between the results obtained with the new application and with previous independent routines we have demonstrated great similarity and consequently validated the application. This new tool is now available to be used in similar research to obtain the diffusion properties of other chemicals in different tissues or organs.

A test of long memory hypothesis based on self-similarity

This paper develops a new test of true versus spurious long memory, based on log-periodogram estimation of the long memory parameter using skip-sampled data. A correction factor is derived to overcome the bias in this estimator due to aliasing. The procedure is designed to be used in the context of a conventional test of significance of the long memory parameter, and composite test procedure described that has the properties of known asymptotic size and consistency. The test is implemented using the bootstrap, with the distribution under the null hypothesis being approximated using a dependent-sample bootstrap technique to approximate short-run dependence following fractional differencing. The properties of the test are investigated in a set of Monte Carlo experiments. The procedure is illustrated by applications to exchange rate volatility and dividend growth series.

Temporal diffeomorphic free-form deformation: application to motion and strain estimation from 3D echocardiography

This paper presents a new registration algorithm, called Temporal Di eomorphic Free Form Deformation (TDFFD), and its application to motion and strain quanti cation from a sequence of 3D ultrasound (US) images. The originality of our approach resides in enforcing time consistency by representing the 4D velocity eld as the sum of continuous spatiotemporal B-Spline kernels. The spatiotemporal displacement eld is then recovered through forward Eulerian integration of the non-stationary velocity eld. The strain tensor iscomputed locally using the spatial derivatives of the reconstructed displacement eld. The energy functional considered in this paper weighs two terms: the image similarity and a regularization term. The image similarity metric is the sum of squared di erences between the intensities of each frame and a reference one. Any frame in the sequence can be chosen as reference. The regularization term is based on theincompressibility of myocardial tissue. TDFFD was compared to pairwise 3D FFD and 3D+t FFD, bothon displacement and velocity elds, on a set of synthetic 3D US images with di erent noise levels. TDFFDshowed increased robustness to noise compared to these two state-of-the-art algorithms. TDFFD also proved to be more resistant to a reduced temporal resolution when decimating this synthetic sequence. Finally, this synthetic dataset was used to determine optimal settings of the TDFFD algorithm. Subsequently, TDFFDwas applied to a database of cardiac 3D US images of the left ventricle acquired from 9 healthy volunteers and 13 patients treated by Cardiac Resynchronization Therapy (CRT). On healthy cases, uniform strain patterns were observed over all myocardial segments, as physiologically expected. On all CRT patients, theimprovement in synchrony of regional longitudinal strain correlated with CRT clinical outcome as quanti ed by the reduction of end-systolic left ventricular volume at follow-up (6 and 12 months), showing the potential of the proposed algorithm for the assessment of CRT.

Dynamic estimation of three-dimensional cerebrovascular deformation from rotational angiography

Purpose: The objective of this study is to investigate the feasibility of detecting and quantifying 3D cerebrovascular wall motion from a single 3D rotational x-ray angiography (3DRA) acquisition within a clinically acceptable time and computing from the estimated motion field for the further biomechanical modeling of the cerebrovascular wall. Methods: The whole motion cycle of the cerebral vasculature is modeled using a 4D B-spline transformation, which is estimated from a 4D to 2D + t image registration framework. The registration is performed by optimizing a single similarity metric between the entire 2D + t measured projection sequence and the corresponding forward projections of the deformed volume at their exact time instants. The joint use of two acceleration strategies, together with their implementation on graphics processing units, is also proposed so as to reach computation times close to clinical requirements. For further characterizing vessel wall properties, an approximation of the wall thickness changes is obtained through a strain calculation. Results: Evaluation on in silico and in vitro pulsating phantom aneurysms demonstrated an accurate estimation of wall motion curves. In general, the error was below 10% of the maximum pulsation, even in the situation when substantial inhomogeneous intensity pattern was present. Experiments on in vivo data provided realistic aneurysm and vessel wall motion estimates, whereas in regions where motion was neither visible nor anatomically possible, no motion was detected. The use of the acceleration strategies enabled completing the estimation process for one entire cycle in 5-10 min without degrading the overall performance. The strain map extracted from our motion estimation provided a realistic deformation measure of the vessel wall. Conclusions: The authors' technique has demonstrated that it can provide accurate and robust 4D estimates of cerebrovascular wall motion within a clinically acceptable time, although it has to be applied to a larger patient population prior to possible wide application to routine endovascular procedures. In particular, for the first time, this feasibility study has shown that in vivo cerebrovascular motion can be obtained intraprocedurally from a 3DRA acquisition. Results have also shown the potential of performing strain analysis using this imaging modality, thus making possible for the future modeling of biomechanical properties of the vascular wall.

Dense deformation field estimation for atlas-based segmentation of pathological MR brain images.

Atlas registration is a recognized paradigm for the automatic segmentation of normal MR brain images. Unfortunately, atlas-based segmentation has been of limited use in presence of large space-occupying lesions. In fact, brain deformations induced by such lesions are added to normal anatomical variability and they may dramatically shift and deform anatomically or functionally important brain structures. In this work, we chose to focus on the problem of inter-subject registration of MR images with large tumors, inducing a significant shift of surrounding anatomical structures. First, a brief survey of the existing methods that have been proposed to deal with this problem is presented. This introduces the discussion about the requirements and desirable properties that we consider necessary to be fulfilled by a registration method in this context: To have a dense and smooth deformation field and a model of lesion growth, to model different deformability for some structures, to introduce more prior knowledge, and to use voxel-based features with a similarity measure robust to intensity differences. In a second part of this work, we propose a new approach that overcomes some of the main limitations of the existing techniques while complying with most of the desired requirements above. Our algorithm combines the mathematical framework for computing a variational flow proposed by Hermosillo et al. [G. Hermosillo, C. Chefd'Hotel, O. Faugeras, A variational approach to multi-modal image matching, Tech. Rep., INRIA (February 2001).] with the radial lesion growth pattern presented by Bach et al. [M. Bach Cuadra, C. Pollo, A. Bardera, O. Cuisenaire, J.-G. Villemure, J.-Ph. Thiran, Atlas-based segmentation of pathological MR brain images using a model of lesion growth, IEEE Trans. Med. Imag. 23 (10) (2004) 1301-1314.]. Results on patients with a meningioma are visually assessed and compared to those obtained with the most similar method from the state-of-the-art.

Cardiac motion estimation by joint alignment of tagged MRI sequences

Image registration has been proposed as an automatic method for recovering cardiac displacement fields from Tagged Magnetic Resonance Imaging (tMRI) sequences. Initially performed as a set of pairwise registrations, these techniques have evolved to the use of 3D+t deformation models, requiring metrics of joint image alignment (JA). However, only linear combinations of cost functions defined with respect to the first frame have been used. In this paper, we have applied k-Nearest Neighbors Graphs (kNNG) estimators of the -entropy (H ) to measure the joint similarity between frames, and to combine the information provided by different cardiac views in an unified metric. Experiments performed on six subjects showed a significantly higher accuracy (p < 0.05) with respect to a standard pairwise alignment (PA) approach in terms of mean positional error and variance with respect to manually placed landmarks. The developed method was used to study strains in patients with myocardial infarction, showing a consistency between strain, infarction location, and coronary occlusion. This paper also presentsan interesting clinical application of graph-based metric estimators, showing their value for solving practical problems found in medical imaging.

Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.

MOTIVATION: Comparative analyses of gene expression data from different species have become an important component of the study of molecular evolution. Thus methods are needed to estimate evolutionary distances between expression profiles, as well as a neutral reference to estimate selective pressure. Divergence between expression profiles of homologous genes is often calculated with Pearson's or Euclidean distance. Neutral divergence is usually inferred from randomized data. Despite being widely used, neither of these two steps has been well studied. Here, we analyze these methods formally and on real data, highlight their limitations and propose improvements. RESULTS: It has been demonstrated that Pearson's distance, in contrast to Euclidean distance, leads to underestimation of the expression similarity between homologous genes with a conserved uniform pattern of expression. Here, we first extend this study to genes with conserved, but specific pattern of expression. Surprisingly, we find that both Pearson's and Euclidean distances used as a measure of expression similarity between genes depend on the expression specificity of those genes. We also show that the Euclidean distance depends strongly on data normalization. Next, we show that the randomization procedure that is widely used to estimate the rate of neutral evolution is biased when broadly expressed genes are abundant in the data. To overcome this problem, we propose a novel randomization procedure that is unbiased with respect to expression profiles present in the datasets. Applying our method to the mouse and human gene expression data suggests significant gene expression conservation between these species. CONTACT: marc.robinson-rechavi@unil.ch; sven.bergmann@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Efficient topology estimation for large scale optical mapping

Large scale image mosaicing methods are in great demand among scientists who study different aspects of the seabed, and have been fostered by impressive advances in the capabilities of underwater robots in gathering optical data from the seafloor. Cost and weight constraints mean that lowcost Remotely operated vehicles (ROVs) usually have a very limited number of sensors. When a low-cost robot carries out a seafloor survey using a down-looking camera, it usually follows a predetermined trajectory that provides several non time-consecutive overlapping image pairs. Finding these pairs (a process known as topology estimation) is indispensable to obtaining globally consistent mosaics and accurate trajectory estimates, which are necessary for a global view of the surveyed area, especially when optical sensors are the only data source. This thesis presents a set of consistent methods aimed at creating large area image mosaics from optical data obtained during surveys with low-cost underwater vehicles. First, a global alignment method developed within a Feature-based image mosaicing (FIM) framework, where nonlinear minimisation is substituted by two linear steps, is discussed. Then, a simple four-point mosaic rectifying method is proposed to reduce distortions that might occur due to lens distortions, error accumulation and the difficulties of optical imaging in an underwater medium. The topology estimation problem is addressed by means of an augmented state and extended Kalman filter combined framework, aimed at minimising the total number of matching attempts and simultaneously obtaining the best possible trajectory. Potential image pairs are predicted by taking into account the uncertainty in the trajectory. The contribution of matching an image pair is investigated using information theory principles. Lastly, a different solution to the topology estimation problem is proposed in a bundle adjustment framework. Innovative aspects include the use of fast image similarity criterion combined with a Minimum spanning tree (MST) solution, to obtain a tentative topology. This topology is improved by attempting image matching with the pairs for which there is the most overlap evidence. Unlike previous approaches for large-area mosaicing, our framework is able to deal naturally with cases where time-consecutive images cannot be matched successfully, such as completely unordered sets. Finally, the efficiency of the proposed methods is discussed and a comparison made with other state-of-the-art approaches, using a series of challenging datasets in underwater scenarios

A critical revision of the estimation of the latent heat flux from two-wavelength scintillometry

Simultaneous scintillometer measurements at multiple wavelengths (pairing visible or infrared with millimetre or radio waves) have the potential to provide estimates of path-averaged surface fluxes of sensible and latent heat. Traditionally, the equations to deduce fluxes from measurements of the refractive index structure parameter at the two wavelengths have been formulated in terms of absolute humidity. Here, it is shown that formulation in terms of specific humidity has several advantages. Specific humidity satisfies the requirement for a conserved variable in similarity theory and inherently accounts for density effects misapportioned through the use of absolute humidity. The validity and interpretation of both formulations are assessed and the analogy with open-path infrared gas analyser density corrections is discussed. Original derivations using absolute humidity to represent the influence of water vapour are shown to misrepresent the latent heat flux. The errors in the flux, which depend on the Bowen ratio (larger for drier conditions), may be of the order of 10%. The sensible heat flux is shown to remain unchanged. It is also verified that use of a single scintillometer at optical wavelengths is essentially unaffected by these new formulations. Where it may not be possible to reprocess two-wavelength results, a density correction to the latent heat flux is proposed for scintillometry, which can be applied retrospectively to reduce the error.

Patch-based local histograms and contour estimation for static foreground classification

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Development of a physically-based method for delineation of hydrologically homogeneous regions and flood quantile estimation in ungauged basins via the index flood method

Regional flood frequency techniques are commonly used to estimate flood quantiles when flood data is unavailable or the record length at an individual gauging station is insufficient for reliable analyses. These methods compensate for limited or unavailable data by pooling data from nearby gauged sites. This requires the delineation of hydrologically homogeneous regions in which the flood regime is sufficiently similar to allow the spatial transfer of information. It is generally accepted that hydrologic similarity results from similar physiographic characteristics, and thus these characteristics can be used to delineate regions and classify ungauged sites. However, as currently practiced, the delineation is highly subjective and dependent on the similarity measures and classification techniques employed. A standardized procedure for delineation of hydrologically homogeneous regions is presented herein. Key aspects are a new statistical metric to identify physically discordant sites, and the identification of an appropriate set of physically based measures of extreme hydrological similarity. A combination of multivariate statistical techniques applied to multiple flood statistics and basin characteristics for gauging stations in the Southeastern U.S. revealed that basin slope, elevation, and soil drainage largely determine the extreme hydrological behavior of a watershed. Use of these characteristics as similarity measures in the standardized approach for region delineation yields regions which are more homogeneous and more efficient for quantile estimation at ungauged sites than those delineated using alternative physically-based procedures typically employed in practice. The proposed methods and key physical characteristics are also shown to be efficient for region delineation and quantile development in alternative areas composed of watersheds with statistically different physical composition. In addition, the use of aggregated values of key watershed characteristics was found to be sufficient for the regionalization of flood data; the added time and computational effort required to derive spatially distributed watershed variables does not increase the accuracy of quantile estimators for ungauged sites. This dissertation also presents a methodology by which flood quantile estimates in Haiti can be derived using relationships developed for data rich regions of the U.S. As currently practiced, regional flood frequency techniques can only be applied within the predefined area used for model development. However, results presented herein demonstrate that the regional flood distribution can successfully be extrapolated to areas of similar physical composition located beyond the extent of that used for model development provided differences in precipitation are accounted for and the site in question can be appropriately classified within a delineated region.

A földrajzi távolság, a kulturális hasonlóság és a szabadkereskedelem hatása a borkereskedelemre = Effects on the global wine trade of geographical distance, cultural and linguistic similarity, and free trade

A globalizálódó világgazdaságban a vezető bortermelő országok egyre jelentősebb borkereskedelmet bonyolítanak le egymás között. Míg Európában a fogyasztók egyre kevesebb bort vásárolnak, addig Amerikában és Ázsiában a bor iránti kereslet folyamatosan bővül: a borkereskedelem földrajzi átrendeződése zajlik. A kulturális hasonlóság és a földrajzi távolság kereskedelemre gyakorolt hatását gyakran a kereskedelemelméletek gravitációs modelljével elemzik. E tanulmány azt vizsgálja, hogy a fő borexportáló országok közötti földrajzi távolság, kulturális hasonlóság és szabadkereskedelem milyen hatással van a nemzetközi borkereskedelemre, annak költségeire. A regressziós becslés eredményei alátámasztják, hogy a borkereskedelem költségei alacsonyabbak, ha a kereskedelmi partnerek kulturálisan hasonlók, földrajzilag közel helyezkednek el egymáshoz, vagy van tengeri kikötőjük, tagjai a WTO-nak, illetve ha kötöttek egymással regionális kereskedelmi megállapodást. Ezenkívül megállapítható, hogy az angolszász, a latin-amerikai és az európai kulturális klaszterek elsősorban egymással kereskednek. A kutatás számos kulturális változó alkalmazásával és több ökonometriai modell, illetve becslési eljárás nagymintás tesztelésével gazdagítja a szakirodalmat. ____ In a globalizing world, major wine-producing countries export considerable quantities to the global wine market and turn over a notable trade, but in what happens European wine regions differ markedly from the New World. Here major wine producers suffered a remarkable fall in domestic wine consumption in recent decades, while New World wine producers increased their production potential and generated new foreign demand. The changes have been joined by geographical relocation of wine consumption and exports. The gravity equation can be derived from demand-side or supply-side theory-consistent estimation methods that suggest relationships between the size of the economies, geographical distances, cultural similarities, and size of their trade. The paper analyses the effects of cultural and geographical proximity, free trade, and linguistic similarity on bilateral trade in the main wine-producing countries, using a cross-section gravity model for 2012. The results suggest that larger countries export more wine, while transport costs rise in line with geographical distance and are higher for landlocked trading partners. Wine export costs are lower if trading partners are culturally similar, share a dominant religion, or are both WTO members with regional trade agreements. Anglo-Saxon, Germanic, Latin American and Latin European countries mainly trade wines within their groups. The paper looks to extend the number of trading partners, investigate the effect of language clusters, and confirm that the results are robust by different econometric methodologies.

Stopping rules in Bayesian adaptive threshold estimation

Threshold estimation with sequential procedures is justifiable on the surmise that the index used in the so-called dynamic stopping rule has diagnostic value for identifying when an accurate estimate has been obtained. The performance of five types of Bayesian sequential procedure was compared here to that of an analogous fixed-length procedure. Indices for use in sequential procedures were: (1) the width of the Bayesian probability interval, (2) the posterior standard deviation, (3) the absolute change, (4) the average change, and (5) the number of sign fluctuations. A simulation study was carried out to evaluate which index renders estimates with less bias and smaller standard error at lower cost (i.e. lower average number of trials to completion), in both yes–no and two-alternative forced-choice (2AFC) tasks. We also considered the effect of the form and parameters of the psychometric function and its similarity with themodel function assumed in the procedure. Our results show that sequential procedures do not outperform fixed-length procedures in yes–no tasks. However, in 2AFC tasks, sequential procedures not based on sign fluctuations all yield minimally better estimates than fixed-length procedures, although most of the improvement occurs with short runs that render undependable estimates and the differences vanish when the procedures run for a number of trials (around 70) that ensures dependability. Thus, none of the indices considered here (some of which are widespread) has the diagnostic value that would justify its use. In addition, difficulties of implementation make sequential procedures unfit as alternatives to fixed-length procedures.