DTFLOW: Inference and Visualization of Single-cell Pseudotime Trajectory Using Diffusion Propagation

One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data. Although substantial studies have been conducted in recent years, more effective methods are still strongly needed to infer the developmental processes accurately. This work devises a new method, named DTFLOW, for determining the pseudotemporal trajectories with multiple branches. DTFLOW consists of two major steps: a new method called Bhattacharyya kernel feature decomposition(BKFD) to reduce the data dimensions, and a novel approach named Reverse Searching on k-nearest neighbor graph(RSKG) to identify the multi-branching processes of cellular differentiation. In BKFD, we first establish a stationary distribution for each cell to represent the transition of cellular developmental states based on the random walk with restart algorithm, and then propose a new distance metric for calculating pseudotime of single cells by introducing the Bhattacharyya kernel matrix. The effectiveness of DTFLOW is rigorously examined by using four single-cell datasets. We compare the efficiency of DTFLOW with the published state-of-the-art methods. Simulation results suggest that DTFLOW has superior accuracy and strong robustness properties for constructing pseudotime trajectories. The Python source code of DTFLOW can be freely accessed at https://github.com/statway/DTFLOW.     

Rotationally resliced 3D prostate segmentation of MR images using Bhattacharyya similarity and active band theory

PurposeIn this article, we propose a novel, semi-automatic segmentation method to process 3D MR images of the prostate using the Bhattacharyya coefficient and active band theory with the goal of providing technical support for computer-aided diagnosis and surgery of the prostate.MethodsOur method consecutively segments a stack of rotationally resectioned 2D slices of a prostate MR image by assessing the similarity of the shape and intensity distribution in neighboring slices. 2D segmentation is first performed on an initial slice by manually selecting several points on the prostate boundary, after which the segmentation results are propagated consecutively to neighboring slices. A framework of iterative graph cuts is used to optimize the energy function, which contains a global term for the Bhattacharyya coefficient with the help of an auxiliary function. Our method does not require previously segmented data for training or for building statistical models, and manual intervention can be applied flexibly and intuitively, indicating the potential utility of this method in the clinic.ResultsWe tested our method on 3D T2-weighted MR images from the ISBI dataset and PROMISE12 dataset of 129 patients, and the Dice similarity coefficients were 90.34 ± 2.21% and 89.32 ± 3.08%, respectively. The comparison was performed with several state-of-the-art methods, and the results demonstrate that the proposed method is robust and accurate, achieving similar or higher accuracy than other methods without requiring training.ConclusionThe proposed algorithm for segmenting 3D MR images of the prostate is accurate, robust, and readily applicable to a clinical environment for computer-aided surgery or diagnosis.     

Study on specificity of colon carcinoma-associated serum markers and establishment of SVM prediction model

We aimed to evaluate the specificity of 12 tumor markers related to colon carcinoma and identify the most sensitive index. Logistic regression and Bhattacharyya distance were used to evaluate the index. Then, different index combinations were used to establish a support vector machine (SVM) diagnosis model of malignant colon carcinoma. The accuracy of the model was checked. High accuracy was assumed to indicate the high specificity of the index. Through Logistic regression, three indexes, CEA, HSP60 and CA199, were screened out. Using Bhattacharyya distance, four indexes with the largest Bhattacharyya distance were screened out, including CEA, NSE, AFP, and CA724. The specificity of the combination of the above six indexes was higher than that of other combinations, so did the accuracy of the established SVM identification model. Using Logistic regression and Bhattacharyya distance for detection and establishing an SVM model based on different serum marker combinations can increase diagnostic accuracy, providing a theoretical basis for application of mathematical models in cancer diagnosis.     

WEBnm@ v2.0: Web server and services for comparing protein flexibility

Background

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins.

Results

We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma.

Conclusion

WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0427-6) contains supplementary material, which is available to authorized users.     

Estimation of spectral similarities utilizing segmented regions' probability distribution in the block-optimized pan-sharpened image for material classification

Pan-sharpening is an image fusion approach that combines the spectral information in multispectral (MS) images with the spatial properties of PAN (Panchromatic) images. This vital technique is used in categorization, detection, and other remote sensing applications. In the first step, the article focuses on increasing the finer spatial details in the MS image with PAN images using two levels of fusion without causing spectral deterioration. The suggested fusion method efficiently utilizes image transformation techniques and spatial domain image fusion methods. The luminance component of MS images typically contains spatial features that are not as detailed as the PAN images. A multiscale transform is applied to the intensity/luminance component and PAN image to introduce features into the intensity component. In the first level of processing, coefficients obtained from the non-subsampled contourlet transform are subjected to particle swarm optimization weighted block-based fusion. The second level of fusion is carried out using the concept of spatial frequency to reduce spectral distortion. Numerous reference and non-reference parameters are used to evaluate the sharpened image's quality. In the next step, the article focuses on designing an evaluation metric for analysing spectral distortion based on the Bhattacharyya coefficient and distance. The Bhattacharyya coefficient and distance are calculated for each segmented region to assess the sharpened images' quality. Spectral degradation analysis using proposed techniques can also be useful for analysing materials in the segmented regions. The research findings demonstrate that the spatial features of fused images obtained from the proposed technique increased with the least spectral degradation.     

枇杷花茶水提物的镇咳、抗炎与抗氧化作用研究

采用小鼠氨水致咳法研究枇杷花茶水提物镇咳效果,以二甲苯致小鼠耳肿胀法研究其抗炎效果,并从枇杷花茶的还原能力及对超氧阴离子和羟自由基的清除作用分析枇杷花茶水提物的抗氧化效果。结果表明,枇杷花茶的水提物高剂量组(3000 mg·kg-1)、低剂量组(700 mg·kg-1)均有镇咳抗炎效果,水提物的浓度越高,效果越好。各浓度枇杷花茶水提物均表现出一定的还原能力,对于羟基自由基和超氧阴离子都有一定的清除效果。其中,20 mg·mL-1水提物还原效果最好(吸光值0.903),超过0.2 mg·mL-1抗坏血酸(吸光值0.814);10 mg·mL-1的水提物对超氧阴离子的清除率为47.32%;20 mg·mL-1水提物对于羟基自由基的清除效果非常明显,清除率为91.62%。枇杷花茶水提物镇咳、抗炎、抗氧化效果明显。     

基因功能研究方法的新进展

随着生命科学的发展,研究领域的不断开拓,越来越多的未知新基因和基因的新功能被科学家们发现,研究这些未知新基因的功能和已知基因的新功能成为了极其重要的一项内容。本文对基因功能研究的最新方法进行了介绍。     

Nonparametric Tests for Interval‐Censored Failure Time Data

This paper discusses two sample nonparametric comparison of survival functions when only interval‐censored failure time data are available. The problem considered often occurs in, for example, biological and medical studies such as medical follow‐up studies and clinical trials. For the problem, we present and study several nonparametric test procedures that include methods based on both absolute and squared survival differences as well as simple survival differences. The presented tests provide alternatives to existing methods, most of which are rank‐based tests and not sensitive to nonproportional or nonmonotone alternatives. Simulation studies are performed to evaluate and compare the proposed methods with existing methods and suggest that the proposed tests work well for nonmonotone alternatives as well as monotone alternatives. An illustrative example is presented.     

Flavonoids and cognitive function: a review of human randomized controlled trial studies and recommendations for future studies

Evidence in support of the neuroprotective effects of flavonoids has increased significantly in recent years, although to date much of this evidence has emerged from animal rather than human studies. Nonetheless, with a view to making recommendations for future good practice, we review 15 existing human dietary intervention studies that have examined the effects of particular types of flavonoid on cognitive performance. The studies employed a total of 55 different cognitive tests covering a broad range of cognitive domains. Most studies incorporated at least one measure of executive function/working memory, with nine reporting significant improvements in performance as a function of flavonoid supplementation compared to a control group. However, some domains were overlooked completely (e.g. implicit memory, prospective memory), and for the most part there was little consistency in terms of the particular cognitive tests used making across study comparisons difficult. Furthermore, there was some confusion concerning what aspects of cognitive function particular tests were actually measuring. Overall, while initial results are encouraging, future studies need to pay careful attention when selecting cognitive measures, especially in terms of ensuring that tasks are actually sensitive enough to detect treatment effects.     

Haemodynamics using transthoracic echocardiography in healthy pregnant and non-pregnant baboons (Papio hamadryas)

Background To determine systolic and diastolic function using transthoracic echocardiography in the baboon (Papio hamadryas). Methods Transthoracic echocardiography was performed in eight non‐pregnant female and six pregnant baboons according to American Society of Echocardiography recommendations. Results Haemodynamic measurements were obtained from fourteen baboons. Compared to non‐pregnant baboons, pregnant baboons demonstrated: (mean ± SD, pregnant vs. healthy) increased cardiac output (1615 ± 121 ml/minutes vs. 1317 ± 134 ml/minutes P = 0.001) due to an increased heart rate [120 ± 11 beats per minute (BPM) vs. 105 ± 6 BPM P = 0.018]. The inter‐observer and intra‐observer variability (mean difference ± SD) for the left ventricular outflow tract diameter was 0.05 ± 0.07 cm and 0.01 ± 0.03 cm respectively. There was minimal impact to the animal’s daily activities. Conclusions Transthoracic echocardiography was applicable and reproducible for the assessment of haemodynamics in baboons thus enabling translation of animal results to human studies.     

Quantifying protein function specificity in the gene ontology

Quantitative or numerical metrics of protein function specificity made possible by the Gene Ontology are useful in that they enable development of distance or similarity measures between protein functions. Here we describe how to calculate four measures of function specificity for GO terms: 1) number of ancestor terms; 2) number of offspring terms; 3) proportion of terms; and 4) Information Content (IC). We discuss the relationship between the metrics and the strengths and weaknesses of each.     

Enamel microstructure and molar wear in the greater galago,Otolemur crassicaudatus (mammalia,primates)

This study describes the molar enamel microstructure of the greater galago, based on SEM study of four individuals. Galago molar enamel consists primarily of radially oriented Pattern 1 prisms. However, the most superficial enamel is characterized by regions of poorly developed prisms or nonprismatic enamel, and Pattern 3 prisms can be found at depths intermediate and deep to the enamel surface. Orientations of prism long axes relative to wear surfaces differ among functionally distinct regions (cuspal facets, Phase I/II facets, and crushing basins). Consequently, orientations of enamel crystallites relative to these surfaces also differ. Because crystallites are the structural unit involved in enamel abrasion, these differences in orientation may have important effects on molar wear patterns. Crystallite orientations differ most between cuspal facets and Phase I/II facet surfaces. Cuspal facets are characterized by near surface-parallel interprismatic and surface-oblique prismatic crystallites. Previous experimental studies suggest that this arrangement is most resistant to wear when surface-normal (compressive) loads predominate. In contrast, prismatic and interprismatic crystallites intercept Phase I/II facet surfaces obliquely, an arrangement expected to resist abrasion when surface-parallel (shearing) loads predominate. Superficial enamel is preserved at most basin surfaces, indicating that these regions are subject to comparatively little abrasive wear. These results support the hypothesis that galago occlusal enamel is organized so as to resist abrasion of different functional regions, a property that may prove important in maintaining functional efficiency. However, this largely reflects constraints of occlusal topography on a microstructure typical of many mammals and thus does not appear to represent a structural innovation. © 1993 Wiley-Liss, Inc.     

Systematic analysis of residual density suggests that a major limitation in well‐refined X‐ray structures of proteins is the omission of ordered solvent

In the residual electron density map of a fully refined X‐ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e., some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x + dx. It is found that P(x) is single‐exponential and symmetric for both positive and negative peaks. Thus, P(x) can be used to discriminate residual peaks contributed by random noise in complete models from residual peaks being attributable to modeling errors in incomplete models. For a number of representative structures in the PDB it is found that P(x) has far more large (greater than 5 sigma) positive peaks than large negative peaks. This excess of large positive peaks suggests that the main defect in these refined structures is the omission of ordered water molecules.     

Charge effect on the colchicine binding-site of tubulin

Poly(L-lysine) was found to enhance colchicine binding activity of brain tubulin to a several folds. Bases of biological interests that were tested and found to be inactive were spermine, spermidine and even L-lysine. Part of this enhance binding is due to the increase in the affinity of colchicine-tubulin interaction in the presence of poly(L-lysine). Moreover, poly(L-lysine) stabilized the colchicine binding site of tubulin against thermal denaturation.