Tools and collaborative environments for bioinformatics research

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies.     

高阶线性泛函方程解的振动性

考虑一类高阶线性泛函方程解的振动性,我们获得一些新的振动准则.这些振动准则,推广或改进了一些文献中的某些结果.     

Is 'big biology' a commercial enterprise?

Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, in the USA, Europe and Japan, and highlights some issues to be considered when deciding whether particular research belongs in a company rather than an academic setting.     

Antibacterial substances from lichens

Crude extracts of many lichens and some lichen acids have considerable antibacterial activity, suggesting their possible value in chemotherapy and providing some justification for their folk-lore use in some countries against pulmonary disorders.     

Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.     

What makes a mitochondrion?

Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.     

侵染细胞质膜附近小泡的来源及其作用

箭舌豌豆根瘤幼龄侵染细胞的壁和质膜比较光滑,成熟侵染细胞与此不同,不仅细胞壁厚薄均,有较多的胞间连丝,而且质膜常常内陷形成各种突起,然后离质膜形成小泡。这些位于质膜附近的小泡体积较小,多呈圆形,既可单独存在,也可多个聚在一起。在向细胞中央移动中,有的小泡靠近细胞质膜,甚至与细菌周期融合,有的小泡不民附近的小液泡融合变为较大液泡,并常用降解程度不同的细菌位于其中,在衰老侵染细胞中,细胞壁附近有小泡,     

Modeling the Citation Network by Network Cosmology

Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well.     

On the HIV Incubation Distribution Under AZT Treatment

Assuming some general models for the HIV epidemic, in this paper I derive the HIV incubation distributions under AZT treatment. It is shown that under some conditions, these probability distributions are mixtures of some generalized Gamma distributions and products of generalized Gamma distributions.     

Histochemical and electrophoretic studies of lactate dehydrogenase (LDH/E.C. 1.1.1.27/) activity in the rat liver following the administration of Biseptol 480 (co-trimoxazole)

The present experiments are stimulated by some reports suggesting disturbances in the liver metabolism after application of Biseptol 480. 10 a ago, Biseptol has been widely used in the treatment of some inflammatory states of the respiratory and urinary systems, the alimentary canal, the genitals, and of some bacterial skin infection. The examinations were carried out on 15 white male rats of Wistar strain which were treated by 80 mg of the sulphonamide Biseptol 480 for 7 consecutive days, by stomach tube. Histochemical activity of lactate dehydrogenase (LDH) and isoenzymatic composition of LDH were estimated in the liver's experimental sections. The results show a decrease of LDH activity in the liver tissue and the absence of LDH-5 and LDH-1 fractions in the experimental electrophoregrams. They confirm some authors' supposition of some disturbances in the liver metabolism following application of Biseptol 480.     

呼吸中枢发育的基因调控研究进展

脑干呼吸中枢组成一个复杂的网络系统,产生和调控节律性呼吸。近年来,人们利用分子生物学技术研究发现,小鼠某些基因突变可影响呼吸中枢特定神经元的发育,并由此导致特殊的呼吸表型。最近,在人类某些中枢性呼吸疾病中,也发现了相应的基因突变。因此,基因水平的研究为深入认识节律性呼吸活动的产生和调控机制提供了新的研究途径。本文就目前研究较多、相对较深入的一些呼吸中枢发育调节基因的研究进展作一综述。     

Dendritic protein synthesis, synaptic plasticity, and memory

Considerable evidence suggests that the formation of long-term memories requires a critical period of new protein synthesis. Recently, the notion that some of these newly synthesized proteins originate through local translation in neuronal dendrites has gained some traction. Here, we review the experimental support for this idea and highlight some of the key questions outstanding in this area.     

Neuronal basis of behavior

In addition to describing behavior in terms of neuronal properties and interconnections, some studies are using these well defined neuronal circuits to see how the circuits interact, how they develop, and how they are modified by experience, hormones and neuromodulators. The ready availability of computers and computational techniques has helped in some efforts, as have improvements in physiological and morphological techniques. The major insights, however, still come from experiments that ask clear and direct questions. This review highlights some of the promising approaches and suggests some general features of how neuronal circuits produce behavior.     

THE FLAVONOIDS OF ONAGRACEAE,TRIBE EPILOBIEAE: EPILOBIUM SECT. EPILOBIUM

An analysis of about 100 populations of 39 taxa of Epilobium sect. Epilobium showed quercetin 3-0-rhamnoside and glucoside and myricetin 3-0-rhamnoside and glucoside to be present in most species, with the arabinosides present in some and in much smaller quantities. Kaempferol 3-0-rhamnoside was also present in some populations of some entities in small quantities. Variability, particularly in the presence of myricetin 3-0-rhamnoside and quercetin 3-0-glucoside, was characteristic of some species, especially those of Australia and New Zealand.     

Clonal structure of tumors: difference between clones based on the ability to secrete growth-regulating factors and to react to them

Conditioned medium isolated from different clones of tumour cell culture PS-103 (sarcoma induced in CBA mouse by plastic film implantation) varied in the ability to stimulate cell proliferation in semi-solid medium. The clones differed also in their response to the medium conditioned by culture PS-103: some clones responded by increased proliferation in semi-solid medium, some were inhibited and some failed to respond.     

蜜露对天敌昆虫生长繁殖及搜寻行为的影响

已有研究表明:同翅目昆虫蜜露对一些天敌昆虫有着特殊的作用。一方面,蜜露可用来补充营养,从而促进天敌若虫死亡率下降、成虫寿命延长以及繁殖力提高;另一方面,蜜露作为天敌搜寻行为的信息物质。而人工蜜露在很多情况下对部分天敌也具有上述2方面的作用。文章就此内容的研究进展作一概述,以期促进蜜露在天敌昆虫人工饲养、害虫综合防治以及其他方面发挥作用。     

The heart's Da Vinci code: a Renaissance at Keystone

At a recent Keystone symposium on "Molecular Pathways in Cardiac Development and Disease" in Colorado, significant advances in the understanding of heart development were discussed. The identification and isolation of cardiovascular progenitors, their modulation by secreted factors, and some tantalizing insights into cardiac regeneration were some of the highlights of what was characterized by some as a renaissance in cardiovascular development.     

Neuropsychology: time out of mind.

We have always known that some form of clock is needed to measure time. It now seems that a variety of different neural clocks are involved in determining our temporal perceptions, some specialised for shorter and some for longer durations.     

我国煤矿矿山医疗救护工作的SWOT分析

运用SWOT方法分析了目前我国矿山医疗救护工作的整体优势，认识到当前矿山医疗救护工作创新能力不足是面临的主要劣势，剖析了创新发展的机遇和一些结构性威胁，并提出了相应的发展策略。     

Sequence-based analysis of enzymatically amplified DNA fragments by mutation detection techniques.

The accurate analysis of molecular variation is important in a range of disciplines of parasitology. Although conventional DNA techniques have overcome some of the limitations of traditional approaches, some can be relatively expensive and/or cumbersome to use when large sample sizes require analysis, and some cannot accurately resolve or define nucleotide variation. Using selected examples of applications to parasites, Robin Gasser and Xingquan Zhu discuss some PCR-based mutation detection techniques and their advantages over conventional analytical methods.