Missing value imputation in a data matrix using the regularised singular value decomposition.

Some statistical analysis techniques may require complete data matrices, but a frequent problem in the construction of databases is the incomplete collection of information for different reasons. One option to tackle the problem is to estimate and impute the missing data. This paper describes a form of imputation that mixes regression with lower rank approximations. To improve the quality of the imputations, a generalisation is proposed that replaces the singular value decomposition (SVD) of the matrix with a regularised SVD in which the regularisation parameter is estimated by cross-validation. To evaluate the performance of the proposal, ten sets of real data from multienvironment trials were used. Missing values were created in each set at four percentages of missing not at random, and three criteria were then considered to investigate the effectiveness of the proposal. The results show that the regularised method proves very competitive when compared to the original method, beating it in several of the considered scenarios. As it is a very general system, its application can be extended to all multivariate data matrices. •The imputation method is modified through the inclusion of a stable and efficient computational algorithm that replaces the classical SVD least squares criterion by a penalised criterion. This penalty produces smoothed eigenvectors and eigenvalues that avoid overfitting problems, improving the performance of the method when the penalty is necessary. The size of the penalty can be determined by minimising one of the following criteria: the prediction errors, the Procrustes similarity statistic or the critical angles between subspaces of principal components.

A new cryptic species of Imparfinis (Siluriformes: Heptapteridae) from the Orinoco River basin, revealed by an iterative approach.

An iterative analysis of Imparfinis, combining phylogenetic analysis based on cytochrome oxidase gene and multivariate morphometrics, revealed a new cryptic species from the Andean tributaries of the Orinoco River basin, which is described here. The new species is sister to a clade constituted by Imparfinis hasemani and Imparfinis pijpersi, both from the river basins of the Guiana Shield, being also the most geographically proximate species. Nonetheless, the new species is most similar in general appearance to Imparfinis guttatus from the Madeira and Paraguay River drainages, being almost undistinguishable by conventional characters of external morphology, differing only by morphometric attributes overall. The new species can be distinguished from the remaining congeners by a unique combination of characters, including lower lobe of caudal fin darker than upper lobe, maxillary barbel reaching or surpassing pelvic-fin insertion, 12-15 gill rakers on first gill arch, 40-42 total vertebrae and 9-10 ribs. The new species constitutes the only representative from the Orinoco River basin belonging to Imparfinis sensu stricto.

Accuracy and Precision of Iodine Quantification in Subtracted Micro-Computed Tomography: Effect of Reconstruction and Noise Removal Algorithms.

PURPOSE: To evaluate the effect of reconstruction and noise removal algorithms on the accuracy and precision of iodine concentration (CI) quantified with subtracted micro-computed tomography (micro-CT). PROCEDURES: Two reconstruction algorithms were evaluated: a filtered backprojection (FBP) algorithm and a simultaneous iterative reconstruction technique (SIRT) algorithm. A 3D bilateral filter (BF) was used for noise removal. A phantom study evaluated and compared the image quality, and the accuracy and precision of CI in four scenarios: filtered FBP, filtered SIRT, non-filtered FBP, and non-filtered SIRT. In vivo experiments were performed in an animal model of chemically-induced mammary cancer. RESULTS: Linear relationships between the measured and nominal CI values were found for all the scenarios in the phantom study (R2 > 0.95). SIRT significantly improved the accuracy and precision of CI compared to FBP, as given by their lower bias (adj. p-value = 0.0308) and repeatability coefficient (adj. p-value < 0.0001). Noise removal enabled a significant decrease in bias in filtered SIRT images only; non-significant differences were found for the repeatability coefficient. The phantom and in vivo studies showed that CI is a reproducible imaging parameter for all the scenarios (Pearson r > 0.99, p-value < 0.001). The contrast-to-noise ratio showed non-significant differences among the evaluated scenarios in the phantom study, while a significant improvement was found in the in vivo study when SIRT and BF algorithms were used. CONCLUSIONS: SIRT and BF algorithms improved the accuracy and precision of CI compared to FBP and non-filtered images, which encourages their use in subtracted micro-CT imaging.

ARACAM: A RGB-D Multi-View Photogrammetry System for Lower Limb 3D Reconstruction Applications.

In the world, there is a growing need for lower limb prostheses due to a rising number of amputations caused primarily, by diabetic foot. Researchers enable functional and comfortable prostheses through prosthetic design by integrating new technologies applied to the traditional handcrafted method for prosthesis fabrication that is still current. That is why computer vision shows to be a promising tool for the integration of 3D reconstruction that may be useful for prosthetic design. This work has the objective to design, prototype, and test a functional system to scan plaster cast molds, which may serve as a platform for future technologies for lower limb reconstruction applications. The image capture system comprises 5 stereoscopic color and depth cameras, each with 4 DOF mountings on an enveloping frame, as well as algorithms for calibration, segmentation, registration, and surface reconstruction. The segmentation metrics of dice coefficient and Hausdorff distance (HD) show strong visual similarity with an average similarity of 87% and average error of 6.40 mm, respectively. Moving forward, the system was tested on a known 3D printed model obtained from a computer tomography scan to which comparison results via HD show an average error of ≤1.93 mm thereby making the system competitive against the systems reviewed from the state-of-the-art.

Missing value imputation using least squares techniques in contaminated matrices.

This paper describes strategies to reduce the possible effect of outliers on the quality of imputations produced by a method that uses a mixture of two least squares techniques: regression and lower rank approximation of a matrix. To avoid the influence of discrepant data and maintain the computational speed of the original scheme, pre-processing options were explored before applying the imputation method. The first proposal is to previously use a robust singular value decomposition, the second is to detect outliers and then treat the potential outliers as missing. To evaluate the proposed methods, a cross-validation study was carried out on ten complete matrices of real data from multi-environment trials. The imputations were compared with the original data using three statistics: a measure of goodness of fit, the squared cosine between matrices and the prediction error. The results show that the original method should be replaced by one of the options presented here because outliers can cause low quality imputations or convergence problems.•The imputation algorithm based on Gabriel's cross-validation method uses two least squares techniques that can be affected by the presence of outliers. The inclusion of a robust singular value decomposition allows both to robustify the procedure and to detect outliers and consider them later as missing. These forms of pre-processing ensure that the algorithm performs well on any dataset that has a matrix form with suspected contamination.

Uniaxial Partitioning Strategy for Efficient Point Cloud Registration.

In 3D reconstruction applications, an important issue is the matching of point clouds corresponding to different perspectives of a particular object or scene, which is addressed by the use of variants of the Iterative Closest Point (ICP) algorithm. In this work, we introduce a cloud-partitioning strategy for improved registration and compare it to other relevant approaches by using both time and quality of pose correction. Quality is assessed from a rotation metric and also by the root mean square error (RMSE) computed over the points of the source cloud and the corresponding closest ones in the corrected target point cloud. A wide and plural set of experimentation scenarios was used to test the algorithm and assess its generalization, revealing that our cloud-partitioning approach can provide a very good match in both indoor and outdoor scenes, even when the data suffer from noisy measurements or when the data size of the source and target models differ significantly. Furthermore, in most of the scenarios analyzed, registration with the proposed technique was achieved in shorter time than those from the literature.

Information Theory Based Evaluation of the RC4 Stream Cipher Outputs.

This paper presents a criterion, based on information theory, to measure the amount of average information provided by the sequences of outputs of the RC4 on the internal state. The test statistic used is the sum of the maximum plausible estimates of the entropies H(jt|zt), corresponding to the probability distributions P(jt|zt) of the sequences of random variables (jt)t∈T and (zt)t∈T, independent, but not identically distributed, where zt are the known values of the outputs, while jt is one of the unknown elements of the internal state of the RC4. It is experimentally demonstrated that the test statistic allows for determining the most vulnerable RC4 outputs, and it is proposed to be used as a vulnerability metric for each RC4 output sequence concerning the iterative probabilistic attack.

Hydrography rather than lip morphology better explains the evolutionary relationship between Gymnogeophagus labiatus and G. lacustris in Southern Brazil (Cichlidae: Geophagini)

Gymnogeophagus labiatus and G. lacustris have been long recognized as sister species exhibiting different ecological requirements. Gymnogeophagus labiatus occurs in rock bottom rivers in the hydrographic basins of Patos Lagoon (HBP) and Tramandaí River (HBT), while G. lacustris is exclusive from sand bottom coastal lagoons of the HBT. In this study, we used molecular markers, morphological measurements and data from nuptial male coloration to investigate the evolutionary relationship between these species in each hydrographic basin. We found, for all data sets, a closer relationship between G. labiatus and G. lacustris from the HBT than between G. labiatus populations from HBT and HBP. In particular, lip area had a large intraspecific plasticity, being uninformative to diagnose G. lacustris from G. labiatus. Molecular clock-based estimates suggest a recent divergence between species in the HBT (17,000 years ago), but not between G. labiatus from HBP and HBT (3.6 millions of years ago). Finally, we also found a divergent G. labiatus genetic lineage from the Camaquã River, in the HBP. These results show that the current taxonomy of G. labiatus and G. lacustris does not properly represent evolutionary lineages in these species.(AU)

Gymnogeophagus labiatus e G. lacustris vêm sendo consideradas espécies irmãs que possuem diferentes exigências ecológicas. Gymnogeophagus labiatus ocorre em rios de fundo de pedra nas bacias hidrográficas da Laguna dos Patos (HBP) e do rio Tramandaí (HBT), enquanto G. lacustris é exclusivo da HBT, ocorrendo em lagoas costeiras de fundo de arenoso. Nesse estudo, foram usados marcadores moleculares, medidas morfológicas e dados sobre a coloração nupcial em machos para investigar a relação evolutiva entre estas espécies em cada bacia hidrográfica. Para todos os conjuntos de dados foi observada uma relação mais próxima entre G. labiatus e G. lacustris da HBT do que entre as populações de G. labiatus da HBP e HBT. Em particular, a área do lábio teve uma grande plasticidade intraespecífica, não sendo informativa para diagnosticar G. lacustris de G. labiatus. Estimativas baseadas no relógio molecular sugeriram uma divergência recente entre as espécies da HBT (17.000 anos atrás), mas não entre as populações de G. labiatus da HBP e HBT (3,6 milhões de anos atrás). Finalmente, também foi encontrada uma linhagem genética de G. labiatus divergente no rio Camaquã, na HBP. Esses resultados mostram que a taxonomia atual de G. labiatus e G. lacustris não representa adequadamente as linhagens evolutivas nessas espécies.(AU)

Hydrography rather than lip morphology better explains the evolutionary relationship between Gymnogeophagus labiatus and G. lacustris in Southern Brazil (Cichlidae: Geophagini)

Gymnogeophagus labiatus and G. lacustris have been long recognized as sister species exhibiting different ecological requirements. Gymnogeophagus labiatus occurs in rock bottom rivers in the hydrographic basins of Patos Lagoon (HBP) and Tramandaí River (HBT), while G. lacustris is exclusive from sand bottom coastal lagoons of the HBT. In this study, we used molecular markers, morphological measurements and data from nuptial male coloration to investigate the evolutionary relationship between these species in each hydrographic basin. We found, for all data sets, a closer relationship between G. labiatus and G. lacustris from the HBT than between G. labiatus populations from HBT and HBP. In particular, lip area had a large intraspecific plasticity, being uninformative to diagnose G. lacustris from G. labiatus. Molecular clock-based estimates suggest a recent divergence between species in the HBT (17,000 years ago), but not between G. labiatus from HBP and HBT (3.6 millions of years ago). Finally, we also found a divergent G. labiatus genetic lineage from the Camaquã River, in the HBP. These results show that the current taxonomy of G. labiatus and G. lacustris does not properly represent evolutionary lineages in these species.(AU)

Gymnogeophagus labiatus e G. lacustris vêm sendo consideradas espécies irmãs que possuem diferentes exigências ecológicas. Gymnogeophagus labiatus ocorre em rios de fundo de pedra nas bacias hidrográficas da Laguna dos Patos (HBP) e do rio Tramandaí (HBT), enquanto G. lacustris é exclusivo da HBT, ocorrendo em lagoas costeiras de fundo de arenoso. Nesse estudo, foram usados marcadores moleculares, medidas morfológicas e dados sobre a coloração nupcial em machos para investigar a relação evolutiva entre estas espécies em cada bacia hidrográfica. Para todos os conjuntos de dados foi observada uma relação mais próxima entre G. labiatus e G. lacustris da HBT do que entre as populações de G. labiatus da HBP e HBT. Em particular, a área do lábio teve uma grande plasticidade intraespecífica, não sendo informativa para diagnosticar G. lacustris de G. labiatus. Estimativas baseadas no relógio molecular sugeriram uma divergência recente entre as espécies da HBT (17.000 anos atrás), mas não entre as populações de G. labiatus da HBP e HBT (3,6 milhões de anos atrás). Finalmente, também foi encontrada uma linhagem genética de G. labiatus divergente no rio Camaquã, na HBP. Esses resultados mostram que a taxonomia atual de G. labiatus e G. lacustris não representa adequadamente as linhagens evolutivas nessas espécies.(AU)

Species delimitation in a range-restricted group of cascudinhos (Loricariidae: Epactionotus) supports morphological and genetic differentiation across coastal rivers of southern Brazil.

Epactionotus species are known for inhabiting the rocky-bottom stretches of fast-flowing rivers in a limited geographic area along the Atlantic coast of southern Brazil. These species are endemic to single coastal river drainages (two neighbouring drainages for Epactionotus bilineatus) isolated from each other by the coastal lacustrine environments or the Atlantic Ocean. E. bilineatus is from the Maquiné and Três Forquilhas River basins, both tributaries of the Tramandaí River system, whereas E. itaimbezinho is endemic to the Mampituba River drainage and Epactionotus gracilis to the Araranguá River drainage. Recent fieldwork in the Atlantic coastal drainages of southern Brazil revealed new populations in the Urussanga, Tubarão, d'Una and Biguaçu River drainages. Iterative species delimitation using molecular data (cytochrome c oxidase subunit I) and morphology (morphometrics and meristics) was applied to evaluate species recognition of isolated populations. With regard to new data, the genus was re-diagnosed, the status of Epactionotus species/populations was re-evaluated, formerly described species were supported and population structure was recognized. As for the newly discovered populations, both morphological and molecular data strongly support the population from the Biguaçu River drainage, in Santa Catarina State, as a new species. Molecular data revealed strong per-basin population structure, which may be related to species habitat specificity and low or no dispersal among drainages.

A computational approach for the inverse problem of neuronal conductances determination.

The derivation by Alan Hodgkin and Andrew Huxley of their famous neuronal conductance model relied on experimental data gathered using the squid giant axon. However, the experimental determination of conductances of neurons is difficult, in particular under the presence of spatial and temporal heterogeneities, and it is also reasonable to expect variations between species or even between different types of neurons of the same species.We tackle the inverse problem of determining, given voltage data, conductances with non-uniform distribution in the simpler setting of a passive cable equation, both in a single or branched neurons. To do so, we consider the minimal error iteration, a computational technique used to solve inverse problems. We provide several numerical results showing that the method is able to provide reasonable approximations for the conductances, given enough information on the voltages, even for noisy data.

Ultra-low-dose chest computed tomography without anesthesia in the assessment of pediatric pulmonary diseases / Tomografia computadorizada de tórax de ultrabaixa dosagem sem anestesia naavaliação de doenças pulmonares pediátricas

Abstract Objective To evaluate the feasibility of using ultra-low-dose computed tomography of the chest with iterative reconstruction without anesthesia for assessment of pulmonary diseases in children. Methods This prospective study enrolled 86 consecutive pediatric patients (ranging from 1 month to 18 years) that underwent ultra-low-dose computed tomography due to suspicion of pulmonary diseases, without anesthesia and contrast. Parameters used were: 80 kVp; 15-30 mA; acquisition time, 0.5 s; and pitch, 1.375. The adaptive statistical iterative reconstruction technique was used. Subjective visual evaluation and quantitative assessment of image quality were done using a 5-point scale in 12 different structures of the chest. Results Mean age was 66 months (interquartile range, 16-147). Final diagnosis was performed in all exams, and 44 (51.2%) were diagnosed with cystic fibrosis, 27 (31.4%) with bronchiolitis obliterans, and 15 (17.4%) with congenital pulmonary airways malformations. Diagnostic quality was achieved in 98.9%, of which 82.6% were considered excellent and 16.3% were slightly blurred but did not interfere with image evaluation. Only one case (1.2%) presented moderate blurring that slightly compromised the image, and previous examinations demonstrated findings compatible with bronchiolitis obliterans. Mean effective radiation dose was 0.39 ± 0.15 mSv. Percentages of images with motion artifacts were 0.3% for cystic fibrosis, 1.3% for bronchiolitis obliterans, and 1.1% for congenital pulmonary airways malformations. Conclusion Chest ultra-low-dose computed tomography without sedation or anesthesia delivering a sub-millisievert dose can provide image quality to allow identification of common pulmonary anatomy and diseases.

Resumo Objetivo Avaliar a viabilidade do uso de tomografia computadorizada com ultrabaixa dose com reconstrução iterativa sem anestesia para avaliação de doenças pulmonares em crianças. Métodos Este estudo prospectivo envolveu 86 pacientes pediátricos consecutivos (um mês a 18 anos) submetidos à tomografia computadorizada com ultrabaixa dose por suspeita de doenças pulmonares, sem anestesia e contraste. Os parâmetros utilizados foram: 80 kVp; 15-30 mA; tempo de aquisição, 0,5 s; e pitch de 1,375. Foi utilizada a técnica de reconstrução estatística adaptativa iterativa. A avaliação visual subjetiva e a avaliação quantitativa da qualidade da imagem foram feitas com uma escala de 5 pontos em 12 estruturas do tórax. Resultados A média de idade foi de 66 meses (intervalo interquartil, 16-147). O diagnóstico final foi feito em todos os exames e 44 (51,2%) foram diagnosticados com fibrose cística, 27 (31,4%) com bronquiolite obliterante e 15 (17,4%) com malformação congênita pulmonar das vias aéreas. A qualidade diagnóstica foi alcançada em 98,9% dos casos, dos quais 82,6% foram considerados excelentes e 16,3% alteração leve na definição, mas isso não interferiu na avaliação da imagem. Apenas um caso (1,2%) apresentou alteração moderada na definição, comprometeu discretamente a imagem, e exames prévios demonstraram achados compatíveis com bronquiolite obliterante. A dose de radiação média efetiva foi de 0,39 ± 0,15 mSv. As porcentagens de imagens com artefatos de movimento foram de 0,3% para fibrose cística, 1,3% para bronquiolite obliterante e 1,1% para malformação congênita pulmonar das vias aéreas. Conclusão É possível realizar a tomografia computadorizada com ultrabaixa dose torácica sem sedação ou anestesia, administrando uma dose de submilisievert, com qualidade de imagem suficiente para a identificação pulmonar anatômica e de doenças pulmonares comuns.

Ultra-low-dose chest computed tomography without anesthesia in the assessment of pediatric pulmonary diseases.

OBJECTIVE: To evaluate the feasibility of using ultra-low-dose computed tomography of the chest with iterative reconstruction without anesthesia for assessment of pulmonary diseases in children. METHODS: This prospective study enrolled 86 consecutive pediatric patients (ranging from 1 month to 18 years) that underwent ultra-low-dose computed tomography due to suspicion of pulmonary diseases, without anesthesia and contrast. Parameters used were: 80kVp; 15-30mA; acquisition time, 0.5s; and pitch, 1.375. The adaptive statistical iterative reconstruction technique was used. Subjective visual evaluation and quantitative assessment of image quality were done using a 5-point scale in 12 different structures of the chest. RESULTS: Mean age was 66 months (interquartile range, 16-147). Final diagnosis was performed in all exams, and 44 (51.2%) were diagnosed with cystic fibrosis, 27 (31.4%) with bronchiolitis obliterans, and 15 (17.4%) with congenital pulmonary airways malformations. Diagnostic quality was achieved in 98.9%, of which 82.6% were considered excellent and 16.3% were slightly blurred but did not interfere with image evaluation. Only one case (1.2%) presented moderate blurring that slightly compromised the image, and previous examinations demonstrated findings compatible with bronchiolitis obliterans. Mean effective radiation dose was 0.39±0.15mSv. Percentages of images with motion artifacts were 0.3% for cystic fibrosis, 1.3% for bronchiolitis obliterans, and 1.1% for congenital pulmonary airways malformations. CONCLUSION: Chest ultra-low-dose computed tomography without sedation or anesthesia delivering a sub-millisievert dose can provide image quality to allow identification of common pulmonary anatomy and diseases.

Methods for Reducing Metal Artifacts in Computerized Tomography / Métodos para reducir los artefactos metálicos en la tomografía computarizada

Abstract Metal artifacts are common in clinical images. Many methods for artifact reduction have been published to overcome this problem. In this work, animage smoothing method for artifact reduction (ISMAR) is proposed for image quality improvement in patients with hip prosthesis and dental fillings, which caused metal artifacts. ISMAR was evaluated and compared with three well-known methods for metal artifact reduction (linear interpolation (LI), normalized metal artifact reduction (NMAR) and frequency split metal artifact reduction (FSMAR)). The new method is based on edge-preserving smoothing via L0 Gradient Minimization filter. Image quality was evaluated by two experienced radiologists completely blinded to the information about if the image was processed or not to suppress the artifacts. They graded image quality in a five points-scale, where zero is an index of clear artifact presence, and five, a whole artifact suppression. The new method had the best results and it was statistically significant respect to the other tested methods (p < 0.05). This new method has a better performance in artifact suppression and tissue feature preservation.

Resumen Los artefactos metálicos son comunes en las imágenes clínicas. Muchos métodos para la reducción de los artefactos han sido publicados para superar este problema. En el presente trabajo, un método de suavizado de imágenes para la reducción de artefactos (ISMAR) es propuesto para mejorar la calidad de la imagen en pacientes con prótesis de cadera y empastes dentales, los cuales causaron artefactos metálicos. ISMAR fue evaluado y comparado con otros tres métodos reconocidos por su desempeño en la reducción de los artefactos metálicos (Interpolación lineal (LI), reducción de artefactos de metal normalizados (NMAR) y reducción de artefactos de metal divididos en frecuencia (FSMAR)). El nuevo método se basa en el suavizado y conservación de bordes, utilizando para ello el filtro de minimización de gradiente L0. La calidad de la imagen fue evaluada por dos radiólogos experimentados completamente ciegos a la información sobre si la imagen fue procesada o no para suprimir los artefactos. Ellos calificaron la calidad de la imagen en una escala de cinco puntos, donde el cero indica la presencia de artefactos, y el cinco, una supresión total de los artefactos. El nuevo método tuvo los mejores resultados y fue estadísticamente significativo con respecto a los otros métodos probados (p < 0.05). Este nuevo método tiene un mejor rendimiento en la supresión de artefactos y en la conservación de las características de los tejidos.

Open Database for Accurate Upper-Limb Intent Detection Using Electromyography and Reliable Extreme Learning Machines.

Surface Electromyography (sEMG) signal processing has a disruptive technology potential to enable a natural human interface with artificial limbs and assistive devices. However, this biosignal real-time control interface still presents several restrictions such as control limitations due to a lack of reliable signal prediction and standards for signal processing among research groups. Our paper aims to present and validate our sEMG database through the signal classification performed by the reliable forms of our Extreme Learning Machines (ELM) classifiers, used to maintain a more consistent signal classification. To perform the signal processing, we explore the use of a stochastic filter based on the Antonyan Vardan Transform (AVT) in combination with two variations of our Reliable classifiers (denoted R-ELM and R-Regularized ELM (RELM), respectively), to derive a reliability metric from the system, which autonomously selects the most reliable samples for the signal classification. To validate and compare our database and classifiers with related papers, we performed the classification of the whole of Databases 1, 2, and 6 (DB1, DB2, and DB6) of the NINAProdatabase. Our database presented consistent results, while the reliable forms of ELM classifiers matched or outperformed related papers, reaching average accuracies higher than 99 % for the IEEdatabase, while average accuracies of 75 . 1 % , 79 . 77 % , and 69 . 83 % were achieved for NINAPro DB1, DB2, and DB6, respectively.

Biochemical characterization of the minimal domains of an iterative eukaryotic polyketide synthase.

Iterative type I polyketide synthases (PKS) are megaenzymes essential to the biosynthesis of an enormously diverse array of bioactive natural products. Each PKS contains minimally three functional domains, ß-ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP), and a subset of reducing domains such as ketoreductase (KR), dehydratase (DH), and enoylreductase (ER). The substrate selection, condensation reactions, and ß-keto processing of the polyketide growing chain are highly controlled in a programmed manner. However, the structural features and mechanistic rules that orchestrate the iterative cycles, processing domains functionality, and chain termination in this kind of megaenzymes are often poorly understood. Here, we present a biochemical and functional characterization of the KS and the AT domains of a PKS from the mallard duck Anas platyrhynchos (ApPKS). ApPKS belongs to an animal PKS family phylogenetically more related to bacterial PKS than to metazoan fatty acid synthases. Through the dissection of the ApPKS enzyme into mono- to didomain fragments and its reconstitution in vitro, we determined its substrate specificity toward different starters and extender units. ApPKS AT domain can effectively transfer acetyl-CoA and malonyl-CoA to the ApPKS ACP stand-alone domain. Furthermore, the KS and KR domains, in the presence of Escherichia coli ACP, acetyl-CoA, and malonyl-CoA, showed the ability to catalyze the chain elongation and the ß-keto reduction steps necessary to yield a 3-hydroxybutyryl-ACP derivate. These results provide new insights into the catalytic efficiency and specificity of this uncharacterized family of PKSs.

Complete 1H NMR assignment of cholesteryl benzoate.

The 750 MHz 1H NMR spectrum of cholesteryl benzoate (1b) could be assigned completely, which means all chemical shifts and all coupling constants, including some long-range values, were established. This task was possible by extracting many approximate coupling constant values in the overlapped spectrum region from an HSQC experiment, and using these values in the 1H iterative full spin analysis integrated in the PERCH NMR software. The task was facilitated using our published data for 3ß-acetoxypregna-5,16-dien-20-one (3), the assignment data of the sesquiterpene benzoquinone dihydroperezone (2), also performed in the present study, which contains the same carbon atoms chain than cholesterol (1a), and an HSQC study of (25R)-27-deuteriocholesterol (1c) we prepared some 40 years ago. The HSQC values of 1c in combination with the coupling constants of 1b also allowed to completely assigning the spectrum of 1c. The complete assignment of 1b and 1c further provided the opportunity to estimate the hydrogen shifts induced upon benzoylation of cholesterol. Comparison of the experimental vicinal coupling constants of 1b with the values calculated using the Altona software provides an excellent correlation. In addition, a single crystal X-ray diffraction study of 1b provided the molecular conformation in the solid state, which revealed the side chain adopts an extended conformation.

Calculating particle pair potentials from fluid-state pair correlations: Iterative ornstein-zernike inversion.

An iterative Monte Carlo inversion method for the calculation of particle pair potentials from given particle pair correlations is proposed in this article. The new method, which is best referred to as Iterative Ornstein-Zernike Inversion, represents a generalization and an improvement of the established Iterative Boltzmann Inversion technique (Reith, Pütz and Müller-Plathe, J. Comput. Chem. 2003, 24, 1624). Our modification of Iterative Boltzmann Inversion consists of replacing the potential of mean force as an approximant for the pair potential with another, generally more accurate approximant that is based on a trial bridge function in the Ornstein-Zernike integral equation formalism. As an input, the new method requires the particle pair correlations both in real space and in the Fourier conjugate wavenumber space. An accelerated iteration method is included in the discussion, by which the required number of iterations can be greatly reduced below that of the simple Picard iteration that underlies most common implementations of Iterative Boltzmann Inversion. Comprehensive tests with various pair potentials show that the new method generally surpasses the Iterative Boltzmann Inversion method in terms of reliability of the numerical solution for the particle pair potential. © 2018 Wiley Periodicals, Inc.

Comparison of Radiation Dose and Image Quality of Abdominopelvic CT Using Iterative (AIDR 3D) and Conventional Reconstructions.

OBJECTIVE: The purpose of this study is to compare radiation dose and image quality of abdominopelvic CT studies reconstructed with iterative and conventional techniques. MATERIALS AND METHODS: This retrospective study enrolled 99 patients who underwent abdominopelvic CT examinations with the portal venous phase images reconstructed with both filtered back projection and Adaptive Iterative Dose Reduction 3D (AIDR 3D) at different time points. Subjective assessment of image quality was performed by two radiologists who scored axial images for overall quality, sharpness, noise, and acceptability in a blinded fashion. The SD of the mean attenuation of the liver, aorta, and paraspinal muscle (as a measurement of image noise) and contrast-to-noise and signal-to-noise ratios for liver and aorta were used as objective parameters of image quality. Radiation dose parameters included CT dose index volume (CTDIvol), dose-length product, effective dose (ED), and size-specific dose estimate (SSDE). Results were compared for different body mass index (BMI; weight in kilograms divided by the square of height in meters) categories. Paired t test and McNemar paired tests for noninferiority were used, with p < 0.05 considered statistically significant. RESULTS: We obtained a 62.5% mean reduction in CTDIvol, a 58% mean reduction in ED, and a 63% mean reduction in SSDE when AIDR 3D was used (p < 0.001). Subjective parameters of image quality were considered noninferior for AIDR 3D studies compared with filtered back projection (p < 0.001), except for the sharpness of images of patients with BMI 20-24.9. Variable results were found regarding objective assessment of image quality. CONCLUSION: AIDR 3D allowed a significant reduction in radiation dose of abdominopelvic CT examinations without a loss of image quality in general.

Fast projection/backprojection and incremental methods applied to synchrotron light tomographic reconstruction.

Iterative methods for tomographic image reconstruction have the computational cost of each iteration dominated by the computation of the (back)projection operator, which take roughly O(N3) floating point operations (flops) for N × N pixels images. Furthermore, classical iterative algorithms may take too many iterations in order to achieve acceptable images, thereby making the use of these techniques unpractical for high-resolution images. Techniques have been developed in the literature in order to reduce the computational cost of the (back)projection operator to O(N2logN) flops. Also, incremental algorithms have been devised that reduce by an order of magnitude the number of iterations required to achieve acceptable images. The present paper introduces an incremental algorithm with a cost of O(N2logN) flops per iteration and applies it to the reconstruction of very large tomographic images obtained from synchrotron light illuminated data.