Critical assessment of a proposed model of Shaker

Detailed three-dimensional structures at atomic resolution are essential to understand how voltage-activated K(+) channels function. The X-ray crystallographic structure of the KvAP channel has offered the first view at atomic resolution of the molecular architecture of a voltage-activated K(+) channel. In the crystal, the voltage sensors are bound by monoclonal Fab fragments, which apparently induce a non-native conformation of the tetrameric channel. Thus, despite this significant advance our knowledge of the native conformation of a Kv channel in a membrane remains incomplete. Numerous results from different experimental approaches provide very specific constraints on the structure of K(+) channels in functional conformations. These results can be used to go further in trying to picture the native conformation of voltage-gated K(+) channels. However, the direct translation of all the available information into three-dimensional models is not straightforward and many questions about the structure of voltage-activated K(+) channels are still unanswered. Our aim in this review is to summarize the most important pieces of information currently available and to provide a critical assessment of the model of Shaker recently proposed by Lainé et al.     

A method to estimate the environmental impacts from genetic change in pig production systems

The International Journal of Life Cycle Assessment - The environmental impacts (EIs) of the global pig production sector are expected to increase with increasing global pork demand. Although the...     

Proposal for a method to estimate nutrient shock effects in bacteria

ABSTRACT: BACKGROUND: Plating methods are still the golden standard in microbiology; however, some studies have shown that these techniques can underestimate the microbial concentrations and diversity. A nutrient shock is one of the mechanisms proposed to explain this phenomenon. In this study, a tentative method to assess nutrient shock effects was tested. FINDINGS: To estimate the extent of nutrient shock effects, two strains isolated from tap water (Sphingomonas capsulata and Methylobacterium sp.) and two culture collection strains (E. coli CECT 434 and Pseudomonas fluorescens ATCC 13525) were exposed both to low and high nutrient conditions for different times and then placed in low nutrient medium (R2A) and rich nutrient medium (TSA). The average improvement (A.I.) of recovery between R2A and TSA for the different times was calculated to more simply assess the difference obtained in culturability between each medium. As expected, A.I. was higher when cells were plated after the exposition to water than when they were recovered from high-nutrient medium showing the existence of a nutrient shock for the diverse bacteria used. S. capsulata was the species most affected by this phenomenon. CONCLUSIONS: This work provides a method to consistently determine the extent of nutrient shock effects on different microorganisms and hence quantify the ability of each species to deal with sudden increases in substrate concentration.     

Accuracy of a transformation method to estimate muscle attachments based on three bony landmarks

In this work, the accuracy of a transformation method to estimate muscle attachments based on three bony landmarks was assessed. A concept of mathematical error was introduced and applied to a data-set of 17 muscles' attachment lines from the shoulders of seven cadavers. Within the muscles' attachment lines from the studied data-set, mathematical error and anatomical variability average percentage values were 37.3 and 62.7%, respectively, for the scapula, and 54.4 and 45.6%, respectively, for the humerus. To reduce mathematical error in the transformation method presented, the plane formed by the three landmarks of the segment corresponding to the scaled muscles should neither be too close to the origin of the global coordinate system, nor too far away from muscle attachment locations to be transformed. The procedure outlined in this work allows the researcher to analyse the anatomical variability within a data-set.     

A Bayesian method to estimate the optimal threshold of a longitudinal biomarker

The objective of this study was to develop methods to estimate the optimal threshold of a longitudinal biomarker and its credible interval when the diagnostic test is based on a criterion that reflects a dynamic progression of that biomarker. Two methods are proposed: one parametric and one non‐parametric. In both the cases, the Bayesian inference was used to derive the posterior distribution of the optimal threshold from which an estimate and a credible interval could be obtained. A numerical study shows that the bias of the parametric method is low and the coverage probability of the credible interval close to the nominal value, with a small coverage asymmetry in some cases. This is also true for the non‐parametric method in case of large sample sizes. Both the methods were applied to estimate the optimal prostate‐specific antigen nadir value to diagnose prostate cancer recurrence after a high‐intensity focused ultrasound treatment. The parametric method can also be applied to non‐longitudinal biomarkers.     

A simple method to estimate force plate inertial components in a moving surface

Support surface perturbations are a common paradigm for the study of balance and postural control. Forces and moments acquired from force plates mounted on, or within, the moving surface will contain components resulting from the inertia of the force plate itself. These force plate inertial components must be removed in order to accurately estimate forces resulting from contact with the force plate. This is particularly important when these contact forces are to be used in further calculations, such as an inverse dynamics analysis of joint kinetics. An estimate of the FPIC can be derived using the kinematics of the moving surface and the inertial properties of the force plate. This technique allowed for a reduction of up to 85% of the peak and integrated FPIC acquired from AMTI (OR6-7) force plates during translations of 0.1m, and surface rotations of 10 degrees, using a ramp stimulus of 150 ms duration.     

A new method to estimate relatedness from molecular markers

Four major problems can affect the efficiency of methods developed to estimate relatedness between individuals from information of molecular markers: (i) some of them are dependent on the knowledge of the true allelic frequencies in the base population; (ii) they assume that all loci are unlinked and in Hardy-Weinberg and linkage equilibrium; (iii) pairwise methods can lead to incongruous assignations because they take into account only two individuals at a time; (iv) most are usually constructed for particular structured populations (only consider a few relationship classes, e.g. full-sibs vs. unrelated). We have developed a new approach to estimate relatedness that is free from the above limitations. The method uses a 'blind search algorithm' (actually simulated annealing) to find the genealogy that yield a co-ancestry matrix with the highest correlation with the molecular co-ancestry matrix calculated using the markers. Thus (i and ii) it makes no direct assumptions about allelic frequencies or Hardy-Weinberg and linkage equilibrium; (iii) it always provide congruent relationships, as it considers all individuals at a time; (iv) degrees of relatedness can be as complex as desired just increasing the 'depth' (i.e. number of generations) of the proposed genealogies. Computer simulations have shown that the accuracy and robustness against genotyping errors of this new approach is comparable to that of other proposed methods in those particular situations they were developed for, but it is more flexible and can cope with more complex situations.     

A Bayesian phylogenetic method to estimate unknown sequence ages

Heterochronous data sets comprise molecular sequences sampled at different points in time. If the temporal range of the sampled sequences is large relative to the rate of mutation, the sampling times can directly calibrate evolutionary rates to calendar time. Here, we extend this calibration process to provide a full probabilistic method that utilizes temporal information in heterochronous data sets to estimate sampling times (leaf-ages) for sequenced for which this information unavailable. Our method is similar to relaxing the constraints of the molecular clock on specific lineages within a phylogenetic tree. Using a combination of synthetic and empirical data sets, we demonstrate that the method estimates leaf-ages reliably and accurately. Potential applications of our approach include incorporating samples of uncertain or radiocarbon-infinite age into ancient DNA analyses, evaluating the temporal signal in a particular sequence or data set, and exploring the reliability of sequence ages that are somehow contentious.     

A transformation method to estimate muscle attachments based on three bony landmarks

In order to create musculoskeletal models that can be scalable to different subject specificities the calculation of the exact locations of muscle attachment is required. For this purpose, a scaling method is presented that estimates muscle attachment locations in homologous segments using three bony landmarks per segment.A data-set of 17 muscles’ attachment lines from the shoulders of seven cadavers was used to assess the estimation quality of the scaling method. By knowing from the cadaver data the measured location of the muscles’ attachment lines it is possible to assess the quality of the estimated ones. The scaling results showed an overall mean RMSE for the scapula and humerus muscles of 7.6 and 11.1 mm, respectively. These results were then analyzed with an upper extremity model, in order to compute the influence of the RMSE in glenohumeral elevation muscle moment arms in the scapular plane.The results presented were considered to be satisfactory. Among other error contributors, the inter- and intra-subject variability should be further investigated, along with the sensitivity of a biomechanical model to these error variations.     

Application of a geographically-weighted regression analysis to estimate net primary production of Chinese forest ecosystems

Aim The objective of this paper is to obtain a net primary production (NPP) regression model based on the geographically weighted regression (GWR) method, which includes spatial non‐stationarity in the parameters estimated for forest ecosystems in China. Location We used data across China. Methods We examine the relationships between NPP of Chinese forest ecosystems and environmental variables, specifically altitude, temperature, precipitation and time‐integrated normalized difference vegetation index (TINDVI) based on the ordinary least squares (OLS) regression, the spatial lag model and GWR methods. Results The GWR method made significantly better predictions of NPP in simulations than did OLS, as indicated both by corrected Akaike Information Criterion (AIC_c) and R². GWR provided a value of 4891 for AIC_c and 0.66 for R², compared with 5036 and 0.58, respectively, by OLS. GWR has the potential to reveal local patterns in the spatial distribution of a parameter, which would be ignored by the OLS approach. Furthermore, OLS may provide a false general relationship between spatially non‐stationary variables. Spatial autocorrelation violates a basic assumption of the OLS method. The spatial lag model with the consideration of spatial autocorrelation had improved performance in the NPP simulation as compared with OLS (5001 for AIC_c and 0.60 for R²), but it was still not as good as that via the GWR method. Moreover, statistically significant positive spatial autocorrelation remained in the NPP residuals with the spatial lag model at small spatial scales, while no positive spatial autocorrelation across spatial scales can be found in the GWR residuals. Conclusions We conclude that the regression analysis for Chinese forest NPP with respect to environmental factors and based alternatively on OLS, the spatial lag model, and GWR methods indicated that there was a significant improvement in model performance of GWR over OLS and the spatial lag model.     

IMB-ASYNC: a revised method and benchmark to estimate MPI-3 asynchronous progress efficiency

The article presents design and methodology of a novel benchmark suite named IMB-ASYNC. The presented suite and method are aimed at measuring and comparing practical communication-computation overlap levels for Message Passing Interface standard (MPI) implementations with a special accent to some applicable use cases. Some typical MPI communication patterns implying communication-computation overlap are analyzed, and their reflection on a benchmark structure is proposed. We also analyze the previous works on overlap benchmarking and their best practices. We present a new benchmarking approach for non-blocking neighborhood collectives overlap and clarify the overlap estimation methodology. After a short overview of some technical details of currently available MPI asynchronous progress implementations, two benchmarking case studies are presented to illustrate the relevance of the methodology.

     

Economic feasibility of a new method to estimate mortality in crisis-affected and resource-poor settings

Introduction

Mortality data provide essential evidence on the health status of populations in crisis-affected and resource-poor settings and to guide and assess relief operations. Retrospective surveys are commonly used to collect mortality data in such populations, but require substantial resources and have important methodological limitations. We evaluated the feasibility of an alternative method for rapidly quantifying mortality (the informant method). The study objective was to assess the economic feasibility of the informant method.

Methods

The informant method captures deaths through an exhaustive search for all deaths occurring in a population over a defined and recent recall period, using key community informants and next-of-kin of decedents. Between July and October 2008, we implemented and evaluated the informant method in: Kabul, Afghanistan; Mae La camp for Karen refugees, Thai-Burma border; Chiradzulu District, Malawi; and Lugufu and Mtabila refugee camps, Tanzania. We documented the time and cost inputs for the informant method in each site, and compared these with projections for hypothetical retrospective mortality surveys implemented in the same site with a 6 month recall period and with a 30 day recall period.

Findings

The informant method was estimated to require an average of 29% less time inputs and 33% less monetary inputs across all four study sites when compared with retrospective surveys with a 6 month recall period, and 88% less time inputs and 86% less monetary inputs when compared with retrospective surveys with a 1 month recall period. Verbal autopsy questionnaires were feasible and efficient, constituting only 4% of total person-time for the informant method''s implementation in Chiradzulu District.

Conclusions

The informant method requires fewer resources and incurs less respondent burden. The method''s generally impressive feasibility and the near real-time mortality data it provides warrant further work to develop the method given the importance of mortality measurement in such settings.     

A method to estimate the effect of weather changes on the growing rat

Summary A method is described by which the effect of weather changes on growing rats can be estimated. The number of weight deviations per day of the mean individual weight increase per period of groups of male and female rats, kept in closed or open rooms is correlated with the temperature-humidity milieu of the outside climate.Results obtained with the method are mentioned.

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Zusammenfassung Es wird eine Methode beschrieben mit der die Wirkung von aperiodischen Wetteränderungen auf Hatten bestimmt werden kann.Die Anzahl Gewichts Abweichungen pro Tag vom mittleren individuellen Gewichtsanstieg pro Periode in einer Gruppe männlicher oder weiblicher Tiere, die in offenen oder geschlossenen Räumen gehalten werden,wird mit dem Temperatur-Feuchte Milieu des Aussenklimas korreliert. Ergebnisse,die bisher mit der Methode gewonnen wurden, werden berichtet.

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Résumé Une méthode permettant d'évaluer l'effet de changements de temps apériodiques sur le rat est décrite. Dans un groupe d'animaux mâles ou femelles gardés dans des espaces fermés ou ouverts, le nombre des déviations de poids, déterminé chaque jour à partir de la moyenne d'une période de croissance est mis en corrélation, avec le milieu températurehumidité résultant du climat ambiant externe.Les résultats déjà obtenus à l'aide de cette méthode sont rapportés.

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Hochalpine Forschungsstation Jungfraujoch Internationale Stiftung,Präsident:Prof.Dr. A.v. Muralt.