Assessment of cerebral hemodynamics during neurosurgical procedures using laser speckle image analysis

Aneurysmal subarachnoid hemorrhage (aSAH) is a severe medical condition associated with a significant cause of mortality throughout the world. Cisterna magna injection model is accepted widely to mimic clinical aSAH and is performed on small animal models to study aSAH during neurosurgery. Coherent light scattered from the surface of the rat brain is used to infer information about the variations in blood flow during this condition. We obtained speckle images from the exposed cortex during the entire experiment using an external tissue imaging system. Contrast and fractal analyses are carried out for the recorded speckle pattern time series. Correlation analysis based on Hurst exponent for these images is found to be a more sensitive tool in studying aSAH as compared to routinely used laser speckle contrast analysis for assessing the changes in blood flow velocity. Additionally, our studies provide improved blood flow detection sensitivity with image Hurst exponent in combination with computed fractal dimension, during an event of aSAH.     

苏北平原灌区小水利工程对沟渠水文连通结构的影响

平原灌区的水文情势复杂,且受农村小水利工程及人为管理影响强烈。本研究选取典型平原灌区——苏北阜东灌区作为研究区,构建沟渠网络连通指标及农村小水利工程的影响指标来定量分析水文连通程度,利用自组织特征映射(SOM)分析法,判断小水利工程对研究区沟渠网络结构连通性空间异质性的影响。结果表明: 阜东灌区各区域水文结构连通差异较大。其中,灌区北部连通性最好,灌区中南部连通性最差。研究区共有876个泵站、633个闸点和2420个涵洞。在没有小水利工程影响时,水文结构连通性极差的行政村共有13个,连通性较好和连通性最好的行政村共48个。在小水利工程的影响下,连通性极差的行政村减为8个,连通性较好和连通性最好的行政村增加为53个。由于闸点和涵洞的影响,阜东灌区共有26个行政村的水文结构连通性变差;由于泵站的影响,39个行政村的水文结构连通性得到改善。     

“三生空间”视角下三峡库区土地利用转型的生态系统服务价值效应

明晰社会经济快速转型背景下的“三生空间”演变过程及其生态系统服务效应,对国土空间优化和区域可持续发展具有重要意义。以1980、2000、2018年土地利用遥感监测数据为基础,基于“三生空间”视角,采用地学信息图谱刻画了三峡库区土地利用转型过程,并通过生态系统服务贡献值测度了土地利用转型的生态环境效应。结果表明: 1980—2018年,三峡库区工业生产空间和生活空间面积不断增加,而农业生产空间和生态空间面积逐渐减少;从图谱转移视角分析,1980—2000年间,土地利用格局相对稳定,以未发生转移的图谱单元占主导,而2000—2018年土地利用转型复杂,以农业生产空间与林地、草地生态空间相互转化占主导,城镇化、工业化进程加快是导致农业生产空间、生态空间面积萎缩的主要原因;三峡库区生态系统服务价值在时间上呈先缓慢降低后迅速增加的趋势,在空间上呈“东部高-西部低”的分布特征;生态保护修复工程促进了生态系统服务价值正效应,但经济社会快速发展挤占了大量的农业生产空间、生态空间,加之农田复耕等行为在一定程度上导致了生态系统服务价值负效应。     

An Improved Computational Prediction Model for Lysine Succinylation Sites Mapping on Homo sapiens by Fusing Three Sequence Encoding Schemes with the Random Forest Classifier

Background Lysine succinylation is one of the reversible protein post-translational modifications (PTMs), which regulate the structure and function of proteins. It plays a significant role in various cellular physiologies including some diseases of human as well as many other organisms. The accurate identification of succinylation site is essential to understand the various biological functions and drug development.Methods In this study, we developed an improved method to predict lysine succinylation sites mapping on Homo sapiens by the fusion of three encoding schemes such as binary, the composition of k-spaced amino acid pairs (CKSAAP) and amino acid composition (AAC) with the random forest (RF) classifier. The prediction performance of the proposed random forest (RF) based on the fusion model in a comparison of other candidates was investigated by using 20-fold cross-validation (CV) and two independent test datasets were collected from two different sources.Results The CV results showed that the proposed predictor achieves the highest scores of sensitivity (SN) as 0.800, specificity (SP) as 0.902, accuracy (ACC) as 0.919, Mathew correlation coefficient (MCC) as 0.766 and partial AUC (pAUC) as 0.163 at a false-positive rate (FPR) = 0.10 and area under the ROC curve (AUC) as 0.958. It achieved the highest performance scores of SN as 0.811, SP as 0.902, ACC as 0.891, MCC as 0.629 and pAUC as 0.139 and AUC as 0.921 for the independent test protein set-1 and SN as 0.772, SP as 0.901, ACC as 0.836, MCC as 0.677 and pAUC as 0.141 at FPR = 0.10 and AUC as 0.923 for the independent test protein set-2. It also outperformed all the other existing prediction models.Conclusion The prediction performances as discussed in this article recommend that the proposed method might be a useful and encouraging computational resource for lysine succinylation site prediction in the case of human population.     

蛙皮抗菌肽促胰岛素分泌功能研究进展

随着对蛙皮抗菌肽功能研究的不断深入,陆续发现部分肽具有促胰岛素分泌活性,该活性对于2型糖尿病治疗具有较好的应用前景。蛙皮抗菌肽即可以通过克服注射胰岛素产生的低血糖反应,又能改善2型糖尿病胰岛素抵抗的问题,这使其有希望成为安全、高效治疗2型糖尿病药物的新药物。本文综述了具有促胰岛素分泌功能的蛙皮抗菌肽的序列特征和工作机制的研究进展,为进一步开展相关研究提供参考。     

Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules

Multivariate statistical methods are widely used to extract functional collective motions from macromolecular molecular dynamics (MD) simulations. In principal component analysis (PCA), a covariance matrix of positional fluctuations is diagonalized to obtain orthogonal eigenvectors and corresponding eigenvalues. The first few eigenvectors usually correspond to collective modes that approximate the functional motions in the protein. However, PCA representations are globally coherent by definition and, for a large biomolecular system, do not converge on the time scales accessible to MD. Also, the forced orthogonalization of modes leads to complex dependencies that are not necessarily consistent with the symmetry of biological macromolecules and assemblies. Here, we describe for the first time the application of local feature analysis (LFA) to construct a topographic representation of functional dynamics in terms of local features. The LFA representations are low dimensional, and like PCA provide a reduced basis set for collective motions, but they are sparsely distributed and spatially localized. This yields a more reliable assignment of essential dynamics modes across different MD time windows. Also, the intrinsic dynamics of local domains is more extensively sampled than that of globally coherent PCA modes.     

Specificity of molecular interactions in transient protein-protein interaction interfaces

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody-antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease-inhibitors and sig-naling proteins have optimized their interfaces to suit their biological functions, antibody-antigen interactions are the happenstance, implying that antibody-antigen complexes do not show distinctive interaction types. Persistent interaction types such as pi...pi, amide-carbonyl, and hydroxyl-carbonyl interaction, are also investigated. Analyzing the structural orientations of the pi...pi stacking interactions, we find that herringbone shape is a major configuration in transient protein-protein interfaces. This result is different from that of protein core, where parallel-displaced configurations are the major configuration. We also analyze overall trend of amide-carbonyl and hydroxyl-carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl-carbonyl interactions.     

警惕外来害虫暗梗天牛入侵为害

暗梗天牛Arhopalus tristis(F.)是一种重要的林业害虫,我国目前尚无分布,但已被我国口岸截获多次,必须对该虫的入侵保持警惕。该虫在新西兰危害严重,主要寄主是辐射松等松树,喜入侵火灾危害后的树木;还传播真菌病害,致使木材变色,降低木材质量。对暗梗天牛的形态特征、分布、寄主、危害特点、生物学特性及预防对策等作了简要介绍。     

Sequencing and analysis of a genomic fragment provide an insight into the Dunaliella viridis genomic sequence

Dunaliella is a genus of wall-less unicellular eukaryotic green alga.Its exceptional resistancesto salt and various other stresses have made it an ideal model for stress tolerance study.However,very littleis known about its genome and genomic sequences.In this study,we sequenced and analyzed a 29,268 bpgenomic fragment from DunalieIla viridis.The fragment showed low sequence homology to the GenBankdatabase.At the nucleotide level,only a segment with significant sequence homology to 18S rRNA wasfound.The fragment contained six putative genes,but only one gene showed significant homology at theprotein level to GenBank database.The average GC content of this sequence was 51.1%,which was muchlower than that of close related green algae Chlamydomonas (65.7%).Significant segmental duplicationswere found within this fragment.The duplicated sequences accounted for about 35.7% of the entireregion.Large amounts of simple sequence repeats (microsatellites) were found,with strong bias towards(AC)_n type (76%).Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749bp) was in agreement with these findings.These sequence features made it difficult to sequence Dunaliellagenomic sequences.Further investigation should be made to reveal the biological significance of these uniquesequence features.     

Prolegomena to a typology of morphological features

Morphological features characterize variations in morphological form which are independent of syntactic context. They contrast with morphosyntactic features, which characterize variations in form correlated with different syntactic contexts. Morphological features account for formal variation across lexemes (inflectional class), as well as morphosyntactically incoherent alternations within the paradigm of a single lexeme. Such morphological features are not available to the syntax, as is made explicit in the principle of ‘morphology-free syntax’. Building on work on stress patterns in Network Morphology and on stems in Paradigm Function Morphology, we take initial steps towards a typology of these morphological features. We identify four types: inflectional class features (affixal and prosodic), stem indexing features, syncretic index features and morphophonological features. Then we offer a first list of criteria for distinguishing them from morphosyntactic features (independently of the principle of morphology-free syntax). Finally we review the arguments demonstrating the need to recognize morphological features.