Extrapolation from ten sections can make CT-based quantification of lung aeration more practicable

Clinical applications of quantitative computed tomography (qCT) in patients with pulmonary opacifications are hindered by the radiation exposure and by the arduous manual image processing. We hypothesized that extrapolation from only ten thoracic CT sections will provide reliable information on the aeration of the entire lung. CTs of 72 patients with normal and 85 patients with opacified lungs were studied retrospectively. Volumes and masses of the lung and its differently aerated compartments were obtained from all CT sections. Then only the most cranial and caudal sections and a further eight evenly spaced sections between them were selected. The results from these ten sections were extrapolated to the entire lung. The agreement between both methods was assessed with Bland-Altman plots. Median (range) total lung volume and mass were 3,738 (1,311-6,768) ml and 957 (545-3,019) g, the corresponding bias (limits of agreement) were 26 (-42 to 95) ml and 8 (-21 to 38) g, respectively. The median volumes (range) of differently aerated compartments (percentage of total lung volume) were 1 (0-54)% for the nonaerated, 5 (1-44)% for the poorly aerated, 85 (28-98)% for the normally aerated, and 4 (0-48)% for the hyperaerated subvolume. The agreement between the extrapolated results and those from all CT sections was excellent. All bias values were below 1% of the total lung volume or mass, the limits of agreement never exceeded +/- 2%. The extrapolation method can reduce radiation exposure and shorten the time required for qCT analysis of lung aeration.

Squared Extrapolation Methods (SQUAREM): A New Class of Simple and Efficient Numerical Schemes for Accelerating the Convergence of the EM Algorithm

We derive a new class of iterative schemes for accelerating the convergence of the EM algorithm, by exploiting the connection between fixed point iterations and extrapolation methods. First, we present a general formulation of one-step iterative schemes, which are obtained by cycling with the extrapolation methods. We, then square the one-step schemes to obtain the new class of methods, which we call SQUAREM. Squaring a one-step iterative scheme is simply applying it twice within each cycle of the extrapolation method. Here we focus on the first order or rank-one extrapolation methods for two reasons, (1) simplicity, and (2) computational efficiency. In particular, we study two first order extrapolation methods, the reduced rank extrapolation (RRE1) and minimal polynomial extrapolation (MPE1). The convergence of the new schemes, both one-step and squared, is non-monotonic with respect to the residual norm. The first order one-step and SQUAREM schemes are linearly convergent, like the EM algorithm but they have a faster rate of convergence. We demonstrate, through five different examples, the effectiveness of the first order SQUAREM schemes, SqRRE1 and SqMPE1, in accelerating the EM algorithm. The SQUAREM schemes are also shown to be vastly superior to their one-step counterparts, RRE1 and MPE1, in terms of computational efficiency. The proposed extrapolation schemes can fail due to the numerical problems of stagnation and near breakdown. We have developed a new hybrid iterative scheme that combines the RRE1 and MPE1 schemes in such a manner that it overcomes both stagnation and near breakdown. The squared first order hybrid scheme, SqHyb1, emerges as the iterative scheme of choice based on our numerical experiments. It combines the fast convergence of the SqMPE1, while avoiding near breakdowns, with the stability of SqRRE1, while avoiding stagnations. The SQUAREM methods can be incorporated very easily into an existing EM algorithm. They only require the basic EM step for their implementation and do not require any other auxiliary quantities such as the complete data log likelihood, and its gradient or hessian. They are an attractive option in problems with a very large number of parameters, and in problems where the statistical model is complex, the EM algorithm is slow and each EM step is computationally demanding.

Establiment de bases científiques per al desenvolupament d'una estratègia integrada per avaluar toxicitat en reproducció

Report for the scientific sojourn at the National Institute for Public Health and the Environment (RIVM), Netherlands, from 2006 to 2008. This project aimed at creating scientific elements that could help deriving an integrated testing strategy for reproductive toxicity. Part of the project focused on the use of alternative tests for regulatory purposes. An in vitro-in vivo extrapolation method for embryotoxicity was proposed and evaluated. In vitro and in vivo dose descriptors were correlated; however, the scatter in the correlation was too large to allow an accurate estimation of an in vivo dose from an in vitro dose. The in vitro-in vivo extrapolation method together with toxicokinetic data was also applied to a category of substances (phthalates). Although based on a limited number of substances, the results suggested that in vitro-in vivo extrapolation for embryotoxicity is possible within a category of compounds if adequate toxicokinetic data is available. Because of the limitations that still remain in the use of alternative tests for reproductive toxicicity, other approaches to reduce animal testing were explored. Thus, a database of reproductive toxicity studies was created to retrospectively evaluate the comparative value of some studies or elements in a particular study. When compared to the subchronic toxicity study, the rat two-generation reproductive toxicity study had a considerable impact on the identification of hazard for reproductive toxicity, but not on the overall NOAEL. Among the two-generation studies included in our database, the second generation affected neither the overall NOAEL nor the critical effect. The rat and the rabbit developmental toxicity studies were, on average, similarly sensitive. However, for certain substances the developmental study in either one of the two species appeared to be more sensitive than in the other species.

Therapeutic drug monitoring of imatinib: Bayesian and alternative methods to predict trough levels

Background: The imatinib trough plasma concentration (C(min)) correlates with clinical response in cancer patients. Therapeutic drug monitoring (TDM) of plasma C(min) is therefore suggested. In practice, however, blood sampling for TDM is often not performed at trough. The corresponding measurement is thus only remotely informative about C(min) exposure. Objectives: The objectives of this study were to improve the interpretation of randomly measured concentrations by using a Bayesian approach for the prediction of C(min), incorporating correlation between pharmacokinetic parameters, and to compare the predictive performance of this method with alternative approaches, by comparing predictions with actual measured trough levels, and with predictions obtained by a reference method, respectively. Methods: A Bayesian maximum a posteriori (MAP) estimation method accounting for correlation (MAP-ρ) between pharmacokinetic parameters was developed on the basis of a population pharmacokinetic model, which was validated on external data. Thirty-one paired random and trough levels, observed in gastrointestinal stromal tumour patients, were then used for the evaluation of the Bayesian MAP-ρ method: individual C(min) predictions, derived from single random observations, were compared with actual measured trough levels for assessment of predictive performance (accuracy and precision). The method was also compared with alternative approaches: classical Bayesian MAP estimation assuming uncorrelated pharmacokinetic parameters, linear extrapolation along the typical elimination constant of imatinib, and non-linear mixed-effects modelling (NONMEM) first-order conditional estimation (FOCE) with interaction. Predictions of all methods were finally compared with 'best-possible' predictions obtained by a reference method (NONMEM FOCE, using both random and trough observations for individual C(min) prediction). Results: The developed Bayesian MAP-ρ method accounting for correlation between pharmacokinetic parameters allowed non-biased prediction of imatinib C(min) with a precision of ±30.7%. This predictive performance was similar for the alternative methods that were applied. The range of relative prediction errors was, however, smallest for the Bayesian MAP-ρ method and largest for the linear extrapolation method. When compared with the reference method, predictive performance was comparable for all methods. The time interval between random and trough sampling did not influence the precision of Bayesian MAP-ρ predictions. Conclusion: Clinical interpretation of randomly measured imatinib plasma concentrations can be assisted by Bayesian TDM. Classical Bayesian MAP estimation can be applied even without consideration of the correlation between pharmacokinetic parameters. Individual C(min) predictions are expected to vary less through Bayesian TDM than linear extrapolation. Bayesian TDM could be developed in the future for other targeted anticancer drugs and for the prediction of other pharmacokinetic parameters that have been correlated with clinical outcomes.

Vibrational intensities VII: ethane and ethane-d6

Absolute intensity measurements have been made on the fundamental vibrations of C2H6 and C2D6, using the extrapolation method of Wilson and Wells and using nitrogen at pressures up to 50 atmospheres to broaden the bands. The absorption coefficient was integrated against the logarithm of the frequency. Normal coordinates were calculated from the potential function of Hansen and Dennison, and were used to interpret the results in terms of quantities (∂p/∂Si) giving the change of dipole moment with respect to the symmetry coordinates Si. Consistency of data between the isotopes was used both to eliminate ambiguities in the interpretation, and as a criterion in separating overlapping pairs of absorption bands. The results have been interpreted in terms of bond effective moments.

A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring lambda 6 Light-Chain Fibrillogenesis

Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although lambda chains, particularly those belonging to the lambda 6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the lambda 6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wildtype protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the V(L) (variable region of the light chain)-V(L) interface. This mutant crystallized in two orthorhombic polymorphs, P2(1)2(1)2(1) and C222(1). In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222(1) lattice showed the establishment of intermolecular beta-beta interactions that involved the N-terminus and beta-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the V(L) interface in lambda 6 LCs. (C) 2009 Elsevier Ltd. All rights reserved.

Estudo da eficácia do tensoativo sorbitano tween 80 veiculado em nanoemulsão contendo óleo de soja, como inibidor de corrosão

Nowadays, the use of chemicals that satisfactorily meet the needs of different sectors of the chemical industry is linked to the consumption of biodegradable materials. In this context, this work contemplated biotechnological aspects with the objective of developing a more environmentally-friendly corrosion inhibitor. In order to achieve this goal, nanoemulsion-type systems (NE) were obtained by varying the amount of Tween 80 (9 to 85 ppm) a sortitan surfactant named polyoxyethylene (20) monooleate. This NE-system was analyzed using phase diagrams in which the percentage of the oil phase (commercial soybean oil, codenamed as OS) was kept constant. By changing the amount of Tween 80, several polar NE-OS derived systems (O/W-type nanoemulsion) were obtained and characterized through light scattering, conductivity and pH, and further subjected to electrochemical studies. The interfacial behavior of these NE-OS derived systems (codenamed NE-OS1, S2, S3, S4 and S5) as corrosion inhibitors on carbon steel AISI 1020 in saline media (NaCl 3.5%) were evaluated by measurement of Open Circuit Potential (OCP), Polarization Curves (Tafel extrapolation method) and Electrochemical Impedance Spectroscopy (EIS). The analyzed NE-OS1 and NE-OS2 systems were found to be mixed inhibitors with quantitative efficacy (98.6% - 99.7%) for concentrations of Tween 80 ranging between 9 and 85 ppm. According to the EIS technique, maximum corrosion efficiency was observed for some tested NE-OS samples. Additionaly to the electrochemical studies, Analysis of Variance (ANOVA) and Principal Component Analysis (PCA) were used, characterization of the nanoemulsion tested systems and adsorption studies, respectively, which confirmed the results observed in the experimental analyses using diluted NE-OS samples in lower concentrations of Tween 80 (0.5 1.75 ppm)

Dinâmica populacional do pargo, Lutjanus purpureus Poey, 1875 (Pisces: Lutjanidae) na plataforma norte do Brasil

O crescimento, a mortalidade, biometria e a reprodução do pargo Lutjanus purpureus foram estudadas a partir de amostras obtidas nos desembarques da frota comercial capturadas com pargueira na costa norte do Brasil no âmbito do programa REVIZEE e do Projeto biologia e pesca do pargo no norte do Brasil do CEPNOR/IBAMA. Dados de comprimentos total e zoológico de aproximadamente 500 indivíduos foram coletados aleatoriamente e mensalmente nos desembarques dos municípios de Belém, Vigia e Bragança, no período de janeiro de 1999 a dezembro de 2000. E para realizar estudos de reprodução e biometria foram obtidas subamostras mensais de 150 indivíduos em abril de 1998 a janeiro de 2000. No laboratório do CEPNOR/IBAMA foram realizadas as biometrias, sexagem e identificados os estágios de maturação gonadal. As amostras totalizaram 16.733 indivíduos com percentuais superiores a 50% de indivíduos jovens. A amplitude de classe total variou de 13 a 112 cm de comprimento e as médias de comprimentos foram de 45,72 cm e 51,91 cm, respectivamente para o ano de 1999 e 2000. As relações morfométricas e as relações peso/comprimento apresentaram alometria positiva. E a relação peso/comprimento para macho e fêmea diferem significativamente entre si, pelo teste de Student, bilateral, com alfa = 0,05. A reprodução foi estudada determinando a proporção sexual através do teste quiquadrado, o tamanho de primeira maturação e o período de desova, que foi analisado pela variação temporal das freqüências dos estágios gonadais e relação gonadossomática. Para todo o período estudado foi verificada a predominância de fêmeas e nas análises mensais apenas nos meses de abril de 1998, maio e junho de 1999 não apresentaram diferenças significativas entre os sexos. Na proporção sexual por classe de comprimento a predominância de fêmeas foi altamente significativa de 28 a 45 cm. A classe de comprimento total do tamanho de primeira maturação foi estimado 43 a 46 cm para fêmeas pelo método da extrapolação gráfica e de 43,67 cm pelo ajuste da ogiva de Galton. E o período reprodutivo foi observado em dois picos, sendo um intenso no segundo trimestre, com maior amplitude no mês de maio/1998 e um mais reduzido no quarto trimestre. Os parâmetros de crescimento foram estimados pelo sistema ELEFAN I, método de Bhattacharya, Gulland & Holt e Appeldoorn no programa Fisat. O método de Appeldoorn apresentou o melhor ajuste para a espécie com o valor de L= 115 cm K= 0,091ano-1 , que determinou a equação do crescimento de von Bertalanffy Lt = 115 (1-e 0,091tto). A mortalidade natural foi estimada em 0,25 ano-1 e 0,31 ano-1 pelas equações de Pauly e Rikhter & Efanov respectivamente. A mortalidade total estimada pelos métodos do comprimento convertido em curva de captura linearizada e Berverton & Holt atingiu valores de 0,59; 0,664 respectivamente. A mortalidade por pesca e a taxa de explotação também foram calculados. Os resultados foram F = 0,34 ano 1 e E = 0,57. A longevidade estimada pela fórmula de Taylor foi de 33 anos. O pargo apresenta crescimento lento e vida longa com desova contínua e periódica. A pesca na costa norte do Brasil incide em percentuais elevados de jovens o que pode contribuir para um estado de sobrepesca de crescimento, comprometendo assim a sustentabilidade da espécie e da atividade pesqueira na região norte. É imprescindível adotar medidas de ordenamento para a pesca do pargo, principalmente no que diz respeito ao tamanho mínimo de captura.

Magnetic properties of ODP Hole 109-648B

Seventeen samples from pillow or massive "zero age" fresh basalts from ODP Legs 106 and 109 were studied in order to examine their magnetic properties and oxidation degree. Thermomagnetic analyses of studied samples show Curie temperatures from 127°C to 220°C with reversible heating and cooling curves. Hysteresis parameters indicate the contribution of large Pseudo-Single Domain (PSD) grain of titanomagnetites with saturation magnetization between 0.4 and 0.7 emu/g which is almost twice that those of other recent mid-oceanic dredged basalts (e.g., FAMOUS and CYAMEX-RISE). The large grain sizes and higher magnetic mineral concentration may suggest a slower cooling of these basalts compared to those previously studied. Electron microprobe analyses of titanomagnetite grains combined with Curie point determinations give z = 0.3 for the degree of low temperature oxidation, which is close to the other values reported for low temperature oxidation of mid-oceanic ridge basalts.

Umbrella pine above ground biomass estimation with very high spatial resolution satellite images

Above ground biomass is frequently estimated with forest inventory data and an extrapolation method for the per unit area evaluations. This procedure is labour demanding and costly. In this study above ground biomass functions, whose independent variable is crown horizontal projection, were developed. Multi-resolution segmentation method and object-oriented classification, based on very high spatial resolution satellite images, were used to obtain the area of tree crown horizontal projection for umbrella pine (Pinus pinea L.). A set of inventory plots were measured and with existing allometric functions for this species above ground biomass per tree and per plot were calculated. The two data sets were used to fit linear functions both for individual plot and their cumulative values. The results show a good performance of the models. Errors smaller than 10% are obtained for stand areas greater than 1.4 ha. These functions have the advantages of estimating above ground biomass for all the area under study or surveillance, not requiring forest inventory; allow monitoring in short time periods; and are easily implemented in a geographical information system environment.

Above ground biomass estimation in Mediterranean multiple use systems with high spatial resolution satellite images

Forest biomass has been having an increasing importance in the world economy and in the evaluation of the forests development and monitoring. It was identified as a global strategic reserve, due to its applications in bioenergy, bioproduct development and issues related to reducing greenhouse gas emissions. The estimation of above ground biomass is frequently done with allometric functions per species with plot inventory data. An adequate sampling design and intensity for an error threshold is required. The estimation per unit area is done using an extrapolation method. This procedure is labour demanding and costly. The mail goal of this study is the development of allometric functions for the estimation of above ground biomass with ground cover as independent variable, for forest areas of holm aok (Quercus rotundifolia), cork oak (Quercus suber) and umbrella pine (Pinus pinea) in multiple use systems. Ground cover per species was derived from crown horizontal projection obtained by processing high resolution satellite images, orthorectified, geometrically and atmospheric corrected, with multi-resolution segmentation method and object oriented classification. Forest inventory data were used to estimate plot above ground biomass with published allometric functions at tree level. The developed functions were fitted for monospecies stands and for multispecies stands of Quercus rotundifolia and Quercus suber, and Quercus suber and Pinus pinea. The stand composition was considered adding dummy variables to distinguish monospecies from multispecies stands. The models showed a good performance. Noteworthy is that the dummy variables, reflecting the differences between species, originated improvements in the models. Significant differences were found for above ground biomass estimation with the functions with and without the dummy variables. An error threshold of 10% corresponds to stand areas of about 40 ha. This method enables the overall area evaluation, not requiring extrapolation procedures, for the three species, which occur frequently in multispecies stands.

Extrapolation theory for the real interpolation method

We develop an abstract extrapolation theory for the real interpolation method that covers and improves the most recent versions of the celebrated theorems of Yano and Zygmund. As a consequence of our method, we give new endpoint estimates of the embedding Sobolev theorem for an arbitrary domain Omega

Method of determining the coefficient of storage from straight-line plots without extrapolation /

Mode of access: Internet.

Spatial relationship between the atmospheric circulation and the precipitation measured in the western Swiss Alps by means of the analogue method

An adaptation technique based on the synoptic atmospheric circulation to forecast local precipitation, namely the analogue method, has been implemented for the western Swiss Alps. During the calibration procedure, relevance maps were established for the geopotential height data. These maps highlight the locations were the synoptic circulation was found of interest for the precipitation forecasting at two rain gauge stations (Binn and Les Marécottes) that are located both in the alpine Rhône catchment, at a distance of about 100 km from each other. These two stations are sensitive to different atmospheric circulations. We have observed that the most relevant data for the analogue method can be found where specific atmospheric circulation patterns appear concomitantly with heavy precipitation events. Those skilled regions are coherent with the atmospheric flows illustrated, for example, by means of the back trajectories of air masses. Indeed, the circulation recurrently diverges from the climatology during days with strong precipitation on the southern part of the alpine Rhône catchment. We have found that for over 152 days with precipitation amount above 50 mm at the Binn station, only 3 did not show a trajectory of a southerly flow, meaning that such a circulation was present for 98% of the events. Time evolution of the relevance maps confirms that the atmospheric circulation variables have significantly better forecasting skills close to the precipitation period, and that it seems pointless for the analogue method to consider circulation information days before a precipitation event as a primary predictor. Even though the occurrence of some critical circulation patterns leading to heavy precipitation events can be detected by precursors at remote locations and 1 week ahead (Grazzini, 2007; Martius et al., 2008), time extrapolation by the analogue method seems to be rather poor. This would suggest, in accordance with previous studies (Obled et al., 2002; Bontron and Obled, 2005), that time extrapolation should be done by the Global Circulation Model, which can process atmospheric variables that can be used by the adaptation method.

A modified structural stress method for fatigue assessment of welded structures

Fatigue life assessment of weldedstructures is commonly based on the nominal stress method, but more flexible and accurate methods have been introduced. In general, the assessment accuracy is improved as more localized information about the weld is incorporated. The structural hot spot stress method includes the influence of macro geometric effects and structural discontinuities on the design stress but excludes the local features of the weld. In this thesis, the limitations of the structural hot spot stress method are discussed and a modified structural stress method with improved accuracy is developed and verified for selected welded details. The fatigue life of structures in the as-welded state consists mainly of crack growth from pre-existing cracks or defects. Crack growth rate depends on crack geometry and the stress state on the crack face plane. This means that the stress level and shape of the stress distribution in the assumed crack path governs thetotal fatigue life. In many structural details the stress distribution is similar and adequate fatigue life estimates can be obtained just by adjusting the stress level based on a single stress value, i.e., the structural hot spot stress. There are, however, cases for which the structural stress approach is less appropriate because the stress distribution differs significantly from the more common cases. Plate edge attachments and plates on elastic foundations are some examples of structures with this type of stress distribution. The importance of fillet weld size and weld load variation on the stress distribution is another central topic in this thesis. Structural hot spot stress determination is generally based on a procedure that involves extrapolation of plate surface stresses. Other possibilities for determining the structural hot spot stress is to extrapolate stresses through the thickness at the weld toe or to use Dong's method which includes through-thickness extrapolation at some distance from the weld toe. Both of these latter methods are less sensitive to the FE mesh used. Structural stress based on surface extrapolation is sensitive to the extrapolation points selected and to the FE mesh used near these points. Rules for proper meshing, however, are well defined and not difficult to apply. To improve the accuracy of the traditional structural hot spot stress, a multi-linear stress distribution is introduced. The magnitude of the weld toe stress after linearization is dependent on the weld size, weld load and plate thickness. Simple equations have been derived by comparing assessment results based on the local linear stress distribution and LEFM based calculations. The proposed method is called the modified structural stress method (MSHS) since the structural hot spot stress (SHS) value is corrected using information on weld size andweld load. The correction procedure is verified using fatigue test results found in the literature. Also, a test case was conducted comparing the proposed method with other local fatigue assessment methods.