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.     

兰属中若干分类群的订正

基于对许多活植物的观察,对兰科中兰属的若干种类进行了分类学考订,结果承认菅草兰Cymbidium　tortisepalum与峨眉春蕙C. omeiense为独立的种,将春剑C. longibracteatum移至菅草兰之下作为变种,送春C. szechuanicum移至莎叶兰C. cyperifolium之下作为变种。由于春剑、峨眉春蕙和送春的模式标本及引证标本已在30多年前全部丢失,本文指定了新模式。     

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...     

兰科虎舌兰属Epipogium种类增补与修订

报道日本虎舌兰Epipogium japonicum Makino在中国四川西部的新记录,并讨论了该种与虎舌兰E. roseum (D. Don) Lindl.的形态差异。过去将日本虎舌兰处理为虎舌兰的异名是不恰当的。日本虎舌兰间断分布于日本和中国的四川西部高海拔地区及台湾。     

A process model to estimate biodiesel production costs

'Biodiesel' is the name given to a renewable diesel fuel that is produced from fats and oils. It consists of the simple alkyl esters of fatty acids, most typically the methyl esters. We have developed a computer model to estimate the capital and operating costs of a moderately-sized industrial biodiesel production facility. The major process operations in the plant were continuous-process vegetable oil transesterification, and ester and glycerol recovery. The model was designed using contemporary process simulation software, and current reagent, equipment and supply costs, following current production practices. Crude, degummed soybean oil was specified as the feedstock. Annual production capacity of the plant was set at 37,854,118 l (10 x 10(6)gal). Facility construction costs were calculated to be US dollar 11.3 million. The largest contributors to the equipment cost, accounting for nearly one third of expenditures, were storage tanks to contain a 25 day capacity of feedstock and product. At a value of US dollar 0.52/kg (dollar 0.236/lb) for feedstock soybean oil, a biodiesel production cost of US dollar 0.53/l (dollar 2.00/gal) was predicted. The single greatest contributor to this value was the cost of the oil feedstock, which accounted for 88% of total estimated production costs. An analysis of the dependence of production costs on the cost of the feedstock indicated a direct linear relationship between the two, with a change of US dollar 0.020/l (dollar 0.075/gal) in product cost per US dollar 0.022/kg (dollar 0.01/lb) change in oil cost. Process economics included the recovery of coproduct glycerol generated during biodiesel production, and its sale into the commercial glycerol market as an 80% w/w aqueous solution, which reduced production costs by approximately 6%. The production cost of biodiesel was found to vary inversely and linearly with variations in the market value of glycerol, increasing by US dollar 0.0022/l (dollar 0.0085/gal) for every US dollar 0.022/kg (dollar 0.01/lb) reduction in glycerol value. The model is flexible in that it can be modified to calculate the effects on capital and production costs of changes in feedstock cost, changes in the type of feedstock employed, changes in the value of the glycerol coproduct, and changes in process chemistry and technology.     

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.     

兰科火烧兰属Epipactis若干种类的增补与修订

讨论了北美火烧兰 Epipactis gigantea、卵叶火烧兰 E．royleana和大叶火烧兰 E．mairei之间的异同。过去被许多作者认为是北美火烧兰 E．gigantea和卵叶火烧兰 E．royleana的中国植物实际上应是大叶火烧兰 E.mairei。卵叶火烧兰在中国仅局限于西藏东南部。     

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.     

Critical notes on the classification of the Liriope muscari complex

The presence of stolons is taxonomically significant in the genus Liriope Linn. However, probably due to a lapse of attention, F. T. Wang and T. Tang failed to recognize Ophiopogon muscari Decne., type of Liriope muscari (Decne.) Bailey, a nonstoloniferous taxon, and erroneously referred it as a synonym to the stoloniferous L. spicata Lour. At the same time, however, they described another non-stoloniferous species-L. platyphylla Wang et Tang (L. muscari Bailey) as new. What, then, is the difference between L. platyphylla Wang et Tang and L. muscari (Decne.) Bailey? A comparison of the type photo of Ophiopogon muscari Decne. with specimens of L. platyphylla Wang et Tang shows that the two forms are much alike, but the latter has longer scapes usually overtopping the foliage, as well as longer spikes and broader leaves. L. H. Bailey must had combined the two forms into one species. Furthermore. there are another two non-stoloniferous forms, both having scapes shorter than their foliage, but differing from L. muscari (Decne.) Bailey in their much narrower leaves. One of them has very short leaves and looks like L. minor Makino. Finally, what are the correlations among the above four forms? By using methods of quantitative analysis, such as pictorialized scatter diagram and histogram, on herbarium material, it has been found that the L. muscari complex can be separated into two parts: 1) muscari (M), and 2) platyphylla (P). But since these two parts display a continuous variation pattern as a whole, it seems advisable to treat both as varieties of the same species, i. e., L. muscari (Decne.) Bailey var. muscari, and L. muscari var. communis (Maxim.) Hsu et L. C. Li. (Ophiopogon spicatus Ker-Cawl. var. communis Maxim.) As to the other two narrow-leaved forms, they can hardly be regarded as sufficient for two distinct infraspecific units, for they are found to be inseparablefrom each other as well as from muscari.     

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 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 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 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.