基于区域相似性测量的CT／PET图像配准

图像配准在临床诊断中有重要意义,针对这一问题已经提出了许多方法。本文以区域相似性匹配测度,运用改进的分割方法,结合Powell寻优算法实现了CT／PET多模医学图像配准。实验结果表明,该算法易于实现,配准速度快、精度高,鲁棒性较好。     

Scaling species dynamics in Pinus palustris communities: Effects of pine straw raking

Abstract. In the southeastern USA, harvest of pine straw sometimes involves mechanical raking of natural Pinus palustris (longleaf pine) communities. Little is known about the effects of raking nor how these effects may vary in time and space. In a two yr experiment, we examined the effects of mechanized raking on Pinus palustris dominated communities (scrub oak, dry savanna, and mesic savanna) by monitoring vegetation at seven spatial scales (0.01–100 m²). We measured floristic similarity and the proportion of species initially present that were gained (i.e. new species) or lost during four sampling periods. Relationships between spatial scale and these community attributes were analyzed using a repeated measures approach and functional response curves. Spatial scale clearly affected observed rates of species loss and floristic similarity; losses declined and floristic similarity increased as scale increased. We relate these patterns to expanding population sizes with scale and our inability to detect species reductions in large populations. Scale had little influence on species gains. The effects of raking did not differ across scales, but raking caused greater mean losses of species and greater mean changes in floristic similarity when mean values were calculated over all scales. Raking also increased the mean rate of species gains in the mesic savanna during one period. Otherwise, interaction effects of community and raking were largely absent from both mean values and response curves. Despite significant short‐term effects of raking, changes in species richness were minor.     

Identifying miRNA-disease association based on integrating miRNA topological similarity and functional similarity

Background: MicroRNAs (miRNAs) are a significant type of non-coding RNAs, which usually were encoded by endogenous genes with about ~22 nt nucleotides. Accumulating biological experiments have shown that miRNAs have close associations with various human diseases. Although traditional experimental methods achieve great successes in miRNA-disease interaction identification, these methods also have some limitations. Therefore, it is necessary to develop computational method to predict miRNA-disease interactions. Methods: Here, we propose a computational framework (MDVSI) to predict interactions between miRNAs and diseases by integrating miRNA topological similarity and functional similarity. Firstly, the CosRA index is utilized to measure miRNA similarity based on network topological feature. Then, in order to enhance the reliability of miRNA similarity, the functional similarity and CosRA similarity are integrated based on linear weight method. Further, the potential miRNA-disease associations are predicted by using recommendation method. In addition, in order to overcome limitation of recommendation method, for new disease, a new strategy is proposed to predict potential interactions between miRNAs and new disease based on disease functional similarity. Results: To evaluate the performance of different methods, we conduct ten-fold cross validation and de novo test in experiment and compare MDVSI with two the-state-of-art methods. The experimental result shows that MDVSI achieves an AUC of 0.91, which is at least 0.012 higher than other compared methods. Conclusions: In summary, we propose a computational framework (MDSVI) for miRNA-disease interaction prediction. The experiment results demonstrate that it outperforms other the-state-of-the-art methods. Case study shows that it can effectively identify potential miRNA-disease interactions.     

燕麦孢囊线虫孢囊定殖菌物的多样性

为揭示燕麦孢囊线虫孢囊定殖菌物的多样性,从青岛市选择3个罹患燕麦孢囊线虫病的冬小麦地,在返青期至成熟期,定时采集小麦根际燕麦孢囊线虫病土样,采用孢囊刺破法、单孢分离法或单菌丝分离法对定殖菌物进行分离纯化,并对定殖菌物进行形态鉴定和分子鉴定以及多样性分析。结果表明,从3个地点分离得到1 072个菌株,这些菌株归属于19目（含3个未定目）28科（含10个未定科）35属（含3个未定属）,其中轮枝孢属Verticillium的相对多度最高,为25.2%,是优势属;镰孢菌属Fusarium、黑团孢属Periconia及链格孢属Alternaria的相对多度分别为14.9%、13.5%及13.4%。示范园样品的Margalef’s丰富度指数,Shannon-Wiener多样性指数及Pielou均匀度指数均最高,分别为4.30、2.516及0.755;家属区样品的Margalef’s丰富度指数最低,为3.18;而葛家屯样品的Shannon-Wiener多样性指数和Pielou均匀度指数最低,分别为2.077和0.654。3个地点定殖菌物群落组成的Jaccard相似性指数在0.486-0.607之间。     

Concordance of Species Composition Patterns among Microcrustaceans,Rotifers and Testate Amoebae in a Shallow Pond

In this study, spatial concordance among microcrustaceans, rotifers and testate amoebae was examined in a small pond in Central Brazil. The main goal was to test how consistently different taxonomic groups ordinate 9 sites distributed along the pond's main axis. Microcrustaceans were more abundant during the dry season, characterized by waters with high transparency and dissolved oxygen concentration. An increase in species richness and densities of rotifers and testate amoebae was detected during rainy season, with low values of Secchi disk and concentrations of dissolved oxygen. However, the ordination patterns generated by these groups were different. Concordant patterns across sites were found only between cladocerans and copepods. These results suggest that great care should be taken when ordination patterns based on some taxonomic groups are extrapolated to other groups for detecting environmental changes. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

基于分块主成分分析的太行山猕猴面部相似性

2012 年4 ～8 月,在太行山猕猴国家级自然保护区济源管理局天坛山管护区(北纬35°05′ ～ 35°15′,东经112°12′ ～ 112°22′),对太行山猕猴王屋1 群(WW - 1)内的3 个母系单元(matrilineal unit) 中大于(等于)3 岁龄的26 只个体进行面部拍照,获取其面部特写照片,进而利用分块主成分分析(modular principal component analysis,MPCA)法,对个体进行面部识别分析,旨在探讨个体间面部相似度与亲缘关系的相关性。结果表明:(1)太行山猕猴个体间的面部相似度与亲缘类型有关,母亲与大于3 岁龄子代间的面部相似度为0.93 ±0. 00,显著高于单元内(0. 89 ± 0. 00)和单元间(0.84 ±0.01)的面部相似度;(2)太行山猕猴个体的面部特征随年龄增长而变化,4 岁(含4 岁)龄以上个体与母亲间的面部相似度较高(0.88 ～ 0. 95),依此值可准确地识别母子关系。本研究采用量化方法对非人灵长类个体间面部相似度进行分析,发现太行山猕猴个体间的面部相似度与亲缘关系密切相关;研究结果可为非人灵长类的个体识别提供较为客观的手段和方法。     

Establishment of optimal regulatory network of colorectal cancer based on p42.3 protein

Objective: to establish regulatory network of colorectal cancer involving p42.3 protein and to provide theoretical evidence for deep functional exploration of p42.3 protein in the onset and development of colorectal cancer. Methods: with protein similarity algorithm, reference protein set of p42.3 cell apoptosis was built according to structural features of p42.3. GO and KEGG databases were used to establish regulatory network of tumor cell apoptosis involving p42.3; meanwhile, the largest possible working pathway that involves p42.3 protein was screened out based on Bayesian network theory. Besides, GO and KEGG were used to build regulatory network on early diagnosis gene markers for colorectal cancer including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, at the same time, a regulatory network of colorectal cancer cell apoptosis which involves p42.3 was established. Results: cell apoptotic regulatory network that p42.3 participates in primarily consists of Bcl-2 family genes and the largest possible pathway is p42.3 → FKBP → Bcl-2 centered as FKBP protein. Combined with colorectal cancer regulatory network that involves early diagnosis gene markers, it can be predicted that p42.3 is most likely to regulate the colorectal cancer cell apoptosis through FKBP → Bcl-2 → Bax → caspase-9 → caspase-3 pathway. Conclusion: the colorectal cancer apoptosis network based on p42.3 established in the study provides theoretical evidence for deep exploration of p42.3 regulatory mechanism and molecular targeting treatment of colorectal cancer.     

Species packing in eco‐evolutionary models of seasonally fluctuating environments

As ecology and evolution become ever more entwined, many areas of ecological theory are being re‐examined. Eco‐evolutionary analyses of classic coexistence mechanisms are yielding new insights into the structure and stability of communities. We examine fluctuation‐dependent coexistence models, identifying communities that are both ecologically and evolutionarily stable. Members of these communities possess distinct environmental preferences, revealing widespread patterns of limiting similarity. This regularity leads to consistent changes in the structure of communities across fluctuation regimes. However, at high amplitudes, subtle differences in the form of fluctuations dramatically affect the collapse of communities. We also show that identical fluctuations can support multiple evolutionarily stable communities – a novel example of alternative stable states within eco‐evolutionary systems. Consequently, the configuration of communities will depend on historical contingencies, including details of the adaptive process. Integrating evolution into the study of coexistence offers new insights, while enriching our understanding of ecology.     

Opposing mechanisms affect taxonomic convergence between tree assemblages during tropical forest succession

Whether successional forests converge towards an equilibrium in species composition remains an elusive question, hampered by high idiosyncrasy in successional dynamics. Based on long‐term tree monitoring in second‐growth (SG) and old‐growth (OG) forests in Costa Rica, we show that patterns of convergence between pairs of forest stands depend upon the relative abundance of species exhibiting distinct responses to the successional gradient. For instance, forest generalists contributed to convergence between SG and OG forests, whereas rare species and old‐growth specialists were a source of divergence. Overall, opposing trends in taxonomic similarity among different subsets of species nullified each other, producing a net outcome of stasis over time. Our results offer an explanation for the limited convergence observed between pairwise communities and suggest that rare species and old‐growth specialists may be prone to dispersal limitation, while the dynamics of generalists and second‐growth specialists are more predictable, enhancing resilience in tropical secondary forests.