Characterization of two isoforms of human SPRR3 from saliva of preterm human newborn and autoptic fetal oral mucosa, parotid and submandibular gland samples

RP-HPLC-ESI-MS profile of saliva samples from human preterm newborn showed a protein peak in the elution range 26.6-27.6 min. Deconvolution of ESI-MS spectra revealed the presence of two proteins with average molecular mass (Mav) values of 17,239 ± 3 Da and 18,065 ± 3 Da in 9 samples, with Mav value of 17,239 ± 3 Da in 4 samples and Mav value of 18,065 ± 3 Da in 2 samples. MALDI-TOF-MS analysis of tryptic digest allowed identifying the proteins as two isoforms of small proline-rich protein 3 and cDNA amplification of RNA extracts from oral mucosa, parotid and submandibular gland samples, obtained at fetal autopsy, provided two nucleotide sequences in agreement with those reported in the literature. The two proteins differ for an octapeptide repeat (GCTKVPEP) and the substitution Leu → Val, at position 148 and 140 of the mature form of the 18,065 and 17,239 Da protein, respectively. During maturation the two proteins undergo two post-translational modifications, corresponding to N-terminal acetylation and removal of the initiator methionine. cDNA amplification did not allow to clarify if the proteins found in saliva originated from cellular shedding of the epithelium and/or secretion.     

基于时间聚类分析和独立成分分析的癫痫fMRI盲分析方法

提出了一种基于时间聚类分析和独立成分分析的癫痫fMRI数据盲分析方法,并将两种方法有效联合,提取发作间期的癫痫fMRI激活时空信息.该方法首先由时间聚类分析得到与激活相关的时间峰度特征曲线,以此特征作为时间参考信息;再由空间独立成分分析分解fMRI信号得到空间独立成分;最后将每个独立成分所对应的时间曲线与参考曲线做相关分析提取相应脑激活图.提出的方法无需任何关于癫痫fMRI的先验假设信息,有效解决了独立成分的排序问题,实现了对数据的盲分析.仿真试验结果阐明了这一方法的有效性及可靠性,对癫痫数据的试验结果显示空间定位准确性优于统计参数图方法.     

Transcriptional Profiling of Gene Expression Changes in a PACE-Transfected CHO DUKX Cell Line Secreting High Levels of rhBMP-2

Chinese hamster ovary (CHO) cells are widely used in the biopharmaceutical industry for the production of recombinant human proteins including complex polypeptides such as recombinant human bone morphogenic protein 2 (rhBMP-2). Large-scale manufacture of rhBMP-2 has associated production difficulties resulting from incomplete processing of the recombinant human protein due to insufficient endogenous levels of the paired basic amino acid cleaving enzyme (PACE) in CHO. In order to resolve this issue, CHO DUKX cells expressing rhBMP-2 were transfected with the soluble version of human PACE (PACEsol) resulting in improved amino-terminal homogeneity and a fourfold increase in rhBMP-2 productivity. In this article, we present a microarray expression profile analysis comparing the parental lineage to the higher producing subclone co-expressing PACEsol using a proprietary CHO-specific microarray. Using this technology we observed 1,076 significantly different genes in the high-productivity cells co-expressing PACEsol. Following further analysis of the differentially expressed genes, the Unfolded Protein Response (UPR) component of the endoplasmic reticulum stress response pathway was identified as a key candidate for effecting increased productivity in this cell system. Several additional ER- and Golgi-localised proteins were identified which may also contribute to this effect. The results presented here support the use of large-scale microarray expression profiling as a viable and valuable route towards understanding the behaviour of bioprocess cultures in vitro.     

A DSRPCL-SVM approach to informative gene analysis

Microarray data based tumor diagnosis is a very interesting topic in bioinformatics. One of the key problems is the discovery and analysis of informative genes of a tumor. Although there are many elaborate approaches to this problem, it is still difficult to select a reasonable set of informative genes for tumor diagnosis only with microarray data. In this paper, we classify the genes expressed through microarray data into a number of clusters via the distance sensitive rival penalized competitive learning （DSRPCL） algorithm and then detect the informative gene cluster or set with the help of support vector machine （SVM）. Moreover, the critical or powerful informative genes can be found through further classifications and detections on the obtained informative gene clusters. It is well demonstrated by experiments on the colon, leukemia, and breast cancer datasets that our proposed DSRPCL-SVM approach leads to a reasonable selection of informative genes for tumor diagnosis.     

基于统计建模的系统发育谱方法研究

系统发育谱算法作为一种有效的大规模基因组功能注释方法,已经被成功的应用到原核生物基因组的功能注释中去。通过对系统发育谱方法中的一个关键环节——相似谱的聚类进行分析,提出了一种基于统计建模的方法来对相似的系统发育谱进行聚类。实验表明,该方法在保证较高的覆盖率的同时,还有效的提高了算法的整体速度,且当参与建模的系统发育谱的数目越大时,算法的精确度越高。     

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach （Prunus persica）

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.     

Homogeneous Agent-Based Distributed Information Filtering

Recent advances in processor, networking and software technologies have made distributed computing a reality in today's world. Distributed systems offer many advantages, ranging from a higher performance to the effective utilization of physically dispersed resources. Many diverse application domains can benefit by exploiting principles of distributed computing. Information filtering is one such application domain. In this article, we present a design of a homogeneous distributed multi-agent information filtering system, called D-SIFTER. D-SIFTER is based on the language-dependent model of Java RMI. The detailed design process and various experiments carried out using D-SIFTER are also described. The results indicate that the distributed inter-agent collaboration improves the overall filtering performance.     

节肢动物群落稳定性测度的灰色模型及其应用

证明了累加生成可增大两单调递增序列的协方差,意味着累加生成有可能提高两正相关序列的线性相关性,使之达到线性拟合的要求。在一个节肢动物群落中总个体数与种类数、天敌总个体数与害虫总个体数具有灰正相关关系。以各样本中总个体数m与种类数S及天敌总个体数mn与害虫总个体数mp为变量,利用累加生成和线性回归的方法建立节肢动物群落稳定性测度灰色模型。通过模型求出比值S/m和mn/mp作为测度群落稳定性的指标,其值愈大表明群落稳定性愈好。将该模型应用于福州、安溪、武夷山、福安等四地茶园节肢动物群落稳定性的测度,对所得结果应用灰色聚类法按“好”、“中”、“差”3类对4地茶园节肢动物群落稳定性状况进行灰色聚类评估。评估结果为:福州、安溪茶园为“好”,武夷山茶园为“中”,福安茶园为“差”。这一结果与实际基本相符,表明建立的灰色模型是可行的,并验证了生物多样性可导致群落稳定性这一假说。     

Indices of bird-habitat preference from field surveys of birds and remote sensing of land cover: a study of south-eastern England with wider implications for conservation and biodiversity assessment

Aim This paper describes the development of novel indices of bird‐habitat preference to examine bird species’ use of habitats and their distributions relative to habitats. It assesses the implications for bird conservation regionally and the scope for biodiversity assessments generally. Location A 200 km by 400 km area of farmland with seminatural and urban areas, covering south‐eastern England. Methods Cluster analysis was used to link birds to landscapes. Cluster centroid coordinate values were processed to derive indices of bird‐habitat preference. Further developments assessed the relative values of individual habitats for birds. Results Clustering objectively linked birds to landscapes. Maps of the clusters showed strong regional patterns associated with distinctive habitat assemblages. Derived indices related bird species directly to individual habitats and habitats to birds. Even rare species and scarce habitats showed successful linkages, often to each other. Objective corroboration strongly supported the associations of coastal, wetland, urban and woodland birds and habitats; but, it suggested that farmland birds, whose numbers have nearly halved since 1977, may prefer alternative habitats. Main conclusions Land cover maps from remote sensing provide an effective way to link birds to habitats and vice versa. Thus, generalized habitat maps might be used to extrapolate localized or sample‐based bird observations or the results of autecological studies, helping to predict and understand bird distributions in the wider countryside. The weak links between farmland birds and farmland habitats in a region dominated by farming, suggests that reasons for the decline in farmland birds may be deep seated and thus hard to reverse. The procedures described are repeatable elsewhere and applicable more generally to evaluate landscapes and biodiversity. It is suggested that remote sensing could rarely be bettered as a means of assessing habitats, comprehensively, over wide areas, in most parts of the world.     

多维协变量具有测量误差的结构回归模型

提出具有测量误差的结构回归模型,研究可交换条件下多维协变量的测量误差对平均处理效应估计的影响,在没有其它的附加条件下,尽管大多数模型参数不可识别,平均处理效应仍可识别,由于平均处理效应的极大似然估计求解困难,建议在实际中使用拟极大似然估计作为替代。