Large-Area Photo-Mosaics Using Global Alignment and Navigation Data

Seafloor imagery is a rich source of data for the study of biological and geological processes. Among several applications, still images of the ocean floor can be used to build image composites referred to as photo-mosaics. Photo-mosaics provide a wide-area visual representation of the benthos, and enable applications as diverse as geological surveys, mapping and detection of temporal changes in the morphology of biodiversity. We present an approach for creating globally aligned photo-mosaics using 3D position estimates provided by navigation sensors available in deep water surveys. Without image registration, such navigation data does not provide enough accuracy to produce useful composite images. Results from a challenging data set of the Lucky Strike vent field at the Mid Atlantic Ridge are reported

Monocular-based 3-D seafloor reconstruction and ortho-mosaicing by piecewise planar representation

Photo-mosaicing techniques have become popular for seafloor mapping in various marine science applications. However, the common methods cannot accurately map regions with high relief and topographical variations. Ortho-mosaicing borrowed from photogrammetry is an alternative technique that enables taking into account the 3-D shape of the terrain. A serious bottleneck is the volume of elevation information that needs to be estimated from the video data, fused, and processed for the generation of a composite ortho-photo that covers a relatively large seafloor area. We present a framework that combines the advantages of dense depth-map and 3-D feature estimation techniques based on visual motion cues. The main goal is to identify and reconstruct certain key terrain feature points that adequately represent the surface with minimal complexity in the form of piecewise planar patches. The proposed implementation utilizes local depth maps for feature selection, while tracking over several views enables 3-D reconstruction by bundle adjustment. Experimental results with synthetic and real data validate the effectiveness of the proposed approach

Streptococcus pneumoniae bacteremia: clinical and microbiological epidemiology in a health area of Southern Spain

Streptococcus pneumoniae remains an important cause of bacteremia worldwide. Last years, a decrease of S. pneumoniae penicillin-resistant isolates has been observed. The objective of this study was to describe the episodes of bacteremia due to S. pneumoniae during a period of 11 years. Epidemiological and clinical data, serotypes causing bacteremia, antibiotic susceptibility and prognosis factors were studied. Over a period of 11 years, all the episodes of S. pneumoniae bacteremia were analysed. Their clinical and microbiological features were recorded. Statistical analysis was carried out to determine risk factors for pneumococcal bacteremia and predictors of fatal outcome. Finally, 67 S. pneumoniae bacteremia episodes were included in this study. The majority of cases were produced in white men in the middle age of their life. The main predisposing factors observed were smoking, antimicrobial and/or corticosteroids administration, chronic pulmonary obstructive disease and HIV infection, and the most common source of bacteremia was the low respiratory tract. The main serotypes found were 19A, 1, 14 and 7F. Seventy-seven percent of these isolates were penicillin-susceptible, and the mortality in this serie was really low. Statistical significance was observed between age, sex and race factors and the presence of bacteremia, and there was relationship between the patient’s condition and the outcome. In our study, S. pneumoniae bacteremia is mainly from community-acquired origin mainly caused in men in the median age of the life. 40% of bacteremias were caused by serotypes 19A, 1, 7F and 14. During the period of study the incidence of bacteremia was stable and the mortality rate was very low.

The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

Domestic, peridomestic and wild hosts in the transmission of Trypanosoma cruzi in the Caatinga area colonised by Triatoma brasiliensis

The role played by different mammal species in the maintenance of Trypanosoma cruzi is not constant and varies in time and place. This study aimed to characterise the importance of domestic, wild and peridomestic hosts in the transmission of T. cruzi in Tauá, state of Ceará, Caatinga area, Brazil, with an emphasis on those environments colonised by Triatoma brasiliensis. Direct parasitological examinations were performed on insects and mammals, serologic tests were performed on household and outdoor mammals and multiplex polymerase chain reaction was used on wild mammals. Cytochrome b was used as a food source for wild insects. The serum prevalence in dogs was 38% (20/53), while in pigs it was 6% (2/34). The percentages of the most abundantly infected wild animals were as follows: Thrichomys laurentius 74% (83/112) and Kerodon rupestris 10% (11/112). Of the 749 triatomines collected in the household research, 49.3% (369/749) were positive for T. brasiliensis, while 6.8% were infected with T. cruzi (25/369). In captured animals, T. brasiliensis shares a natural environment with T. laurentius, K. rupestris, Didelphis albiventris, Monodelphis domestica, Galea spixii, Wiedomys pyrrhorhinos, Conepatus semistriatus and Mus musculus. In animals identified via their food source, T. brasiliensis shares a natural environment with G. spixii, K. rupestris, Capra hircus, Gallus gallus, Tropidurus oreadicus and Tupinambis merianae. The high prevalence of T. cruzi in household and peridomiciliar animals reinforces the narrow relationship between the enzootic cycle and humans in environments with T. brasiliensis and characterises it as ubiquitous.

JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

A hybrid method for sag source location in power network

The work presented in this paper belongs to the power quality knowledge area and deals with the voltage sags in power transmission and distribution systems. Propagating throughout the power network, voltage sags can cause plenty of problems for domestic and industrial loads that can financially cost a lot. To impose penalties to responsible party and to improve monitoring and mitigation strategies, sags must be located in the power network. With such a worthwhile objective, this paper comes up with a new method for associating a sag waveform with its origin in transmission and distribution networks. It solves this problem through developing hybrid methods which hire multiway principal component analysis (MPCA) as a dimension reduction tool. MPCA reexpresses sag waveforms in a new subspace just in a few scores. We train some well-known classifiers with these scores and exploit them for classification of future sags. The capabilities of the proposed method for dimension reduction and classification are examined using the real data gathered from three substations in Catalonia, Spain. The obtained classification rates certify the goodness and powerfulness of the developed hybrid methods as brand-new tools for sag classification

A strange foot not far from CRPS I

Introduction.- Since the work of the "International Association for the Study of Pain" (IASP), complex regional pain syndrome type 1 (CRPS I) or algodystrophy includes motor disorders (tremor, dystony, myoclony) as diagnosis criterion. This can lead to confusion with some neurologic disorders which can wrongly be considered as CRPS I. The following observation illustrates this problem.Observation.- A 31-year-old man was hospitalised in a rehabilitation clinic in April 2007 with suspected CRPS I with persistent pain in the left leg. In 2005, the patient underwent ligament reconstruction at the right ankle. In May 2006, a recurrence of his ankle sprain was treated conservatively. The course of this pathology was unfavourable with an extension of the pain areas (leg and foot) as well as an appearance of abnormal motion. Toe motion in abduction was observed (especially T5) followed by a flexion cramp; an hypoesthesia in the sural nerve area, a scar allodynia and discrete vasomotor disorders. The scintigraphy was compatible with a stage 2 algodystrophy. Lower limb electromyography was normal; measurement of pseudo periodic activity of the motor unit at the foot level (abductor of the 5th toe, 4th interosseous). A "Painful legs and moving toes syndrome" was diagnosed which was treated with gabapentin and carbamazepine with a partial improvement.Discussion.- The "Painful legs and moving toes syndrome" is a rare pathology rehabilitation specialists should recognize. The origin is often peripheral nerve damage. The medullar interneuron activation (between the dorsal and ventral horn) is considered as the source of the efferent motor nerves which are responsible for the abnormal movements. This observation illustrates the need for a demanding approach before establishing the diagnosis of CRPS I and the respect of the 4th criterion of the ASP (exclusion of this syndrome when another pathology may explain pain and dysfunction).

Source wavelet estimation for waveform inversion of crosshole georadar data

AbstractFor a wide range of environmental, hydrological, and engineering applications there is a fast growing need for high-resolution imaging. In this context, waveform tomographic imaging of crosshole georadar data is a powerful method able to provide images of pertinent electrical properties in near-surface environments with unprecedented spatial resolution. In contrast, conventional ray-based tomographic methods, which consider only a very limited part of the recorded signal (first-arrival traveltimes and maximum first-cycle amplitudes), suffer from inherent limitations in resolution and may prove to be inadequate in complex environments. For a typical crosshole georadar survey the potential improvement in resolution when using waveform-based approaches instead of ray-based approaches is in the range of one order-of- magnitude. Moreover, the spatial resolution of waveform-based inversions is comparable to that of common logging methods. While in exploration seismology waveform tomographic imaging has become well established over the past two decades, it is comparably still underdeveloped in the georadar domain despite corresponding needs. Recently, different groups have presented finite-difference time-domain waveform inversion schemes for crosshole georadar data, which are adaptations and extensions of Tarantola's seminal nonlinear generalized least-squares approach developed for the seismic case. First applications of these new crosshole georadar waveform inversion schemes on synthetic and field data have shown promising results. However, there is little known about the limits and performance of such schemes in complex environments. To this end, the general motivation of my thesis is the evaluation of the robustness and limitations of waveform inversion algorithms for crosshole georadar data in order to apply such schemes to a wide range of real world problems.One crucial issue to making applicable and effective any waveform scheme to real-world crosshole georadar problems is the accurate estimation of the source wavelet, which is unknown in reality. Waveform inversion schemes for crosshole georadar data require forward simulations of the wavefield in order to iteratively solve the inverse problem. Therefore, accurate knowledge of the source wavelet is critically important for successful application of such schemes. Relatively small differences in the estimated source wavelet shape can lead to large differences in the resulting tomograms. In the first part of my thesis, I explore the viability and robustness of a relatively simple iterative deconvolution technique that incorporates the estimation of the source wavelet into the waveform inversion procedure rather than adding additional model parameters into the inversion problem. Extensive tests indicate that this source wavelet estimation technique is simple yet effective, and is able to provide remarkably accurate and robust estimates of the source wavelet in the presence of strong heterogeneity in both the dielectric permittivity and electrical conductivity as well as significant ambient noise in the recorded data. Furthermore, our tests also indicate that the approach is insensitive to the phase characteristics of the starting wavelet, which is not the case when directly incorporating the wavelet estimation into the inverse problem.Another critical issue with crosshole georadar waveform inversion schemes which clearly needs to be investigated is the consequence of the common assumption of frequency- independent electromagnetic constitutive parameters. This is crucial since in reality, these parameters are known to be frequency-dependent and complex and thus recorded georadar data may show significant dispersive behaviour. In particular, in the presence of water, there is a wide body of evidence showing that the dielectric permittivity can be significantly frequency dependent over the GPR frequency range, due to a variety of relaxation processes. The second part of my thesis is therefore dedicated to the evaluation of the reconstruction limits of a non-dispersive crosshole georadar waveform inversion scheme in the presence of varying degrees of dielectric dispersion. I show that the inversion algorithm, combined with the iterative deconvolution-based source wavelet estimation procedure that is partially able to account for the frequency-dependent effects through an "effective" wavelet, performs remarkably well in weakly to moderately dispersive environments and has the ability to provide adequate tomographic reconstructions.

Body surface area and body weight predict total liver volume in Western adults.

Computed tomography (CT) is used increasingly to measure liver volume in patients undergoing evaluation for transplantation or resection. This study is designed to determine a formula predicting total liver volume (TLV) based on body surface area (BSA) or body weight in Western adults. TLV was measured in 292 patients from four Western centers. Liver volumes were calculated from helical computed tomographic scans obtained for conditions unrelated to the hepatobiliary system. BSA was calculated based on height and weight. Each center used a different established method of three-dimensional volume reconstruction. Using regression analysis, measurements were compared, and formulas correlating BSA or body weight to TLV were established. A linear regression formula to estimate TLV based on BSA was obtained: TLV = -794.41 + 1,267.28 x BSA (square meters; r(2) = 0.46; P <.0001). A formula based on patient weight also was derived: TLV = 191.80 + 18.51 x weight (kilograms; r(2) = 0.49; P <.0001). The newly derived TLV formula based on BSA was compared with previously reported formulas. The application of a formula obtained from healthy Japanese individuals underestimated TLV. Two formulas derived from autopsy data for Western populations were similar to the newly derived BSA formula, with a slight overestimation of TLV. In conclusion, hepatic three-dimensional volume reconstruction based on helical CT predicts TLV based on BSA or body weight. The new formulas derived from this correlation should contribute to the estimation of TLV before liver transplantation or major hepatic resection.

Posterior auricular perichondrial cutaneous graft combined with cartilage strip in nostril reconstruction.

Objective: Reconstruction of alar structures of the nose remains difficult. The result has to be not only functional but also aesthetic. Different solutions to reconstruct alar defects are feasible. A good result that meets the specific demands on stability, aesthetics, and stable architecture without shrinkage of the area is not easily achieved. Method: A perichondrial cutaneous graft (PCCG), a graft consisting of a perichondral layer, fatty tissue, and skin that is harvested retroauriculary, is combined with an attached cartilage strip. Case Result: A 72-year-old patient suffering from basal cell carcinoma of the ala of the nose underwent the reconstructive procedure with a good result in 1 year in terms of stability, color match, and graft take. Conclusion: First, a strip of cartilage had been included in a PCCG where tumor resection required sacrifice of more than 50% of the alar rim. The case shows that one can consider a cartilage strip-enhanced PCCG graft to reconstruct alar defects.

Reconstruction fronto-orbitaire complexe avec prothèse en PEEK et expansion cutanée : à propos d'un cas [Complex fronto-orbital reconstruction with a PEEK prosthesis and skin expansion: about a case].

INTRODUCTION: Reconstructions of the fronto-orbital area remain a challenge to the reconstructive surgeon, due to the functional and esthetic impact. OBSERVATION: The authors present a case of a complex fronto-orbital reconstruction with a PEEK (PolyEtherEtherKetone) implant, associated with a skin expansion. DISCUSSION: With a follow-up of over three years, the cosmetic result is excellent. The authors believe that this technique is reliable, fast with long-term good results.

Direct Fourier Tomographic Reconstruction Image-To-Image Filter

We present an open-source ITK implementation of a directFourier method for tomographic reconstruction, applicableto parallel-beam x-ray images. Direct Fourierreconstruction makes use of the central-slice theorem tobuild a polar 2D Fourier space from the 1D transformedprojections of the scanned object, that is resampled intoa Cartesian grid. Inverse 2D Fourier transform eventuallyyields the reconstructed image. Additionally, we providea complex wrapper to the BSplineInterpolateImageFunctionto overcome ITKâeuro?s current lack for image interpolatorsdealing with complex data types. A sample application ispresented and extensively illustrated on the Shepp-Loganhead phantom. We show that appropriate input zeropaddingand 2D-DFT oversampling rates together with radial cubicb-spline interpolation improve 2D-DFT interpolationquality and are efficient remedies to reducereconstruction artifacts.

A fast Bayesian reconstruction algorithm for emission tomography with entropy prior converging to feasible images

The development and tests of an iterative reconstruction algorithm for emission tomography based on Bayesian statistical concepts are described. The algorithm uses the entropy of the generated image as a prior distribution, can be accelerated by the choice of an exponent, and converges uniformly to feasible images by the choice of one adjustable parameter. A feasible image has been defined as one that is consistent with the initial data (i.e. it is an image that, if truly a source of radiation in a patient, could have generated the initial data by the Poisson process that governs radioactive disintegration). The fundamental ideas of Bayesian reconstruction are discussed, along with the use of an entropy prior with an adjustable contrast parameter, the use of likelihood with data increment parameters as conditional probability, and the development of the new fast maximum a posteriori with entropy (FMAPE) Algorithm by the successive substitution method. It is shown that in the maximum likelihood estimator (MLE) and FMAPE algorithms, the only correct choice of initial image for the iterative procedure in the absence of a priori knowledge about the image configuration is a uniform field.

The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection.

OBJECTIVES: To monitor HIV-1 transmitted drug resistance (TDR) in a well defined urban area with large access to antiretroviral therapy and to assess the potential source of infection of newly diagnosed HIV individuals. METHODS: All individuals resident in Geneva, Switzerland, with a newly diagnosed HIV infection between 2000 and 2008 were screened for HIV resistance. An infection was considered as recent when the positive test followed a negative screening test within less than 1 year. Phylogenetic analyses were performed by using the maximum likelihood method on pol sequences including 1058 individuals with chronic infection living in Geneva. RESULTS: Of 637 individuals with newly diagnosed HIV infection, 20% had a recent infection. Mutations associated with resistance to at least one drug class were detected in 8.5% [nucleoside reverse transcriptase inhibitors (NRTIs), 6.3%; non-nucleoside reverse transcriptase inhibitors (NNRTIs), 3.5%; protease inhibitors, 1.9%]. TDR (P-trend = 0.015) and, in particular, NNRTI resistance (P = 0.002) increased from 2000 to 2008. Phylogenetic analyses revealed that 34.9% of newly diagnosed individuals, and 52.7% of those with recent infection were linked to transmission clusters. Clusters were more frequent in individuals with TDR than in those with sensitive strains (59.3 vs. 32.6%, respectively; P < 0.0001). Moreover, 84% of newly diagnosed individuals with TDR were part of clusters composed of only newly diagnosed individuals. CONCLUSION: Reconstruction of the HIV transmission networks using phylogenetic analysis shows that newly diagnosed HIV infections are a significant source of onward transmission, particularly of resistant strains, thus suggesting an important self-fueling mechanism for TDR.