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1.
Effects of Biomimetic Surface Designs on Furrow Opener Performance   总被引:1,自引:0,他引:1  
The effects of biomimetic designs of tine furrow opener surface on equivalent pressure and pressure in the direction ofmotion on opener surface against soil were studied by finite element method (FEM) simulation and the effects of these designson tool force and power requirements were examined experimentally.Geometrical structures of the cuticle surfaces of dungbeetle (Copris ochus Motschulsky) were examined by stereoscopy.The structures of the cuticle surfaces and Ultra High Mo-lecular Weight Polyethylene (UHMWPE) material were modeled on surface of tine furrow opener as biomimetic designs.Sevenfurrow openers were analyzed in ANSYS program (a FEM simulation software).The biomimetic furrow opener surfaces withUHMWPE structures were found to have lower equivalent pressure and pressure in the direction of motion as compared to theconventional surface and to the biomimetic surfaces with textured steel-35 structures.It was found that the tool force and powerwere increased with the cutting depth and operating speed and the biomimetic furrow opener with UHMWPE tubular sectionridges showed the lowest resistance and power requirement against soil..  相似文献   

2.
3.
异型雄蕊植物花内雄蕊的分化   总被引:1,自引:0,他引:1  
Flowers that have heteromorphic stamens (heterantherous flowers) have intrigued many researchers ever since the phenomenon was discovered in the 19th century. The morphological differentiation in androecia has been suggested as a reflection of "labor division" in pollination in which one type of stamens attracts pollinators and satisfies their demand for pollen as food and the other satisfies the plant's need for safe gamete dispersal. The extent and patterns of stamen differentiation differ notably among taxa with heterantherous flowers. Seven species with heteromorphic stamens in three genera were sampled from Leguminosae and Melastomataceae, and the morphological difference of androecia, pollen content, pollen histochemistry and viability, pollen micro- morphology, as well as the main pollinators were examined and compared. Pollen number differs significantly between stamen sets of the same flower in most species investigated, and a correlation of pollen number and anther size was substantiated. Higher pollen viabilities were found in the long (pollinating) stamens of Senna alata (L.) Roxb. and S. bicapsularis (L.) Roxb. Dimorphic pollen exine ornamentation is reported here for the first time in Fordiophytonfaberi Stapf. The height of stigma and anther tips of the long stamens in natural conditions was proved to be highly correlated, supporting the hypothesis that they contact similar areas of the pollinator's body.  相似文献   

4.
The ability to predict the subcellular localization of a protein from its sequence is of great importance, as it provides information about the protein's function. We present a computational tool, PredSL, which utilizes neural networks, Markov chains, profile hidden Markov models, and scoring matrices for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence. It aims to classify proteins into five groups: chloroplast, thylakoid, mitochondrion, secretory pathway, and "other". When tested in a fivefold cross-validation procedure, PredSL demonstrates 86.7% and 87.1% overall accuracy for the plant and non-plant datasets, respectively. Compared with TargetP, which is the most widely used method to date, and LumenP, the results of PredSL are comparable in most cases. When tested on the experimentally verified proteins of the Saccharomyces cerevisiae genome, PredSL performs comparably if not better than any available algorithm for the same task. Furthermore, PredSL is the only method capable for the prediction of these subcellular localizations that is available as a stand-alone application through the URL: http://bioinformatics.biol.uoa.gr/PredSL/.  相似文献   

5.
The emergence of next-generation sequencing (NGS) technologies has significantly improved sequencing throughput and reduced costs. However, the short read length, duplicate reads and massive volume of data make the data processing much more difficult and complicated than the first-generation sequencing technology. Although there are some software packages developed to assess the data quality, those packages either are not easily available to users or require bioinformatics skills and computer resources. Moreover, almost all the quality assessment software currently available didn’t taken into account the sequencing errors when dealing with the duplicate assessment in NGS data. Here, we present a new user-friendly quality assessment software package called BIGpre, which works for both Illumina and 454 platforms. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well. BIGpre is primarily written in Perl and integrates graphical capability from the statistics package R. This package produces both tabular and graphical summaries of data quality for sequencing datasets from Illumina and 454 platforms. Processing hundreds of millions reads within minutes, this package provides immediate diagnostic information for user to manipulate sequencing data for downstream analyses. BIGpre is freely available at http://bigpre.sourceforge.net/.  相似文献   

6.
With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been gener-ated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research.  相似文献   

7.
Fruit and leaf shoot of litchi (Litchi chinensis) infestation by naturally occurring populations of the fruit bprer, Conopomorpha sinensis larvae and C. sinensis parasitization rates were determined in litchi orchards in northern Thailand at high (ca. 1 400 m ASL) and low (ca. 800 m ASL) elevations with different, non-overlapping fruiting seasons. In addition, spray applications of Bacillus thuringiensis var. aizawai, the natural compound spinosad and the chemical pesticide imidacloprid were conducted in the field to test the effects of these agents on C. sinensis fruit infestation rate. Fruit infestation rate and fruit growth, studied in a low elevation orchard, were sigmoidal and showed a highly significant positive correlation (P ≤ 0.01). Leaf shoot infestation rate in the low elevation orchard decreased in the course of the fruiting season (March until May), but increased in the high elevation orchard, where no fruits were present within the same period of time. Together, these results indicate that females of C. sinensis clearly prefer fruits over shoots for oviposition. If no fruits are available, which was the case in the high elevation orchard during that time, they are constrained to lay their eggs on shoots. The parasitization rate of C. sinensis larvae in untreated fruits was 54.3%. The parasitoid species were Chelonus chailini (90.8%) and Phanerotoma sp. (9.2%). In the leaf shoots, C. sinensis was found to be parasitized by Phanerotoma sp. and Apanteles briareus. The applications of the different active agents had no significant effect on C. sinensis fruit infestation compared to the untreated control. Besides the cryptic life of the larvae, this is most probably explained by the fact that C. sinensis has several generations during the fruiting season. Because of the high parasitization rates recorded, an alternative and more effective control measure than the application of pesticides might be the augmentative release of parasitoids.  相似文献   

8.
In order to amplify the complete genome of enJSRV from the strain of Inner Mongolia (enJSRV-NM), we used enJSRV-specific and JSRV-specific DNA probes in dot blot hybridization. Seven pairs of primers were designed based on Genbank sequences. Seven fragments were obtained by PCR and were cloned into the PMD19-T vectors. The recombinant plasmids were sequenced and analyzed. The results showed that the genome was 7 942 bp in length and contained four overlapping open reading frames corresponding to the gag, pro, pol and env genes as well as an additional open reading frame (orf-x) that overlaps the 3' end of the pol gene. The nucleotide acid sequences of the enJSRV-NM loci were compared with the sequences of South Africa enJS56A1 strain (Accession No.AF153615) and USA JSRV21 strain (Accession No. AF105220). The nucleotide acid identities were 99.2% and 92.3% respectively. Two zinc fingers were found in the NC region in the predicted amino acid sequence. However, the YXXM motif, which is a reliable molecular marker for the infectious exogenous virus, was not found in the TM region. It was found that the enJSRV-NM region was 90%-98% identical at the amino acid level to its exogenous infectious counterparts in most of the retroviral genome. This is the first nucleotide sequence of enJSRV reported in P.R China. The resource work has provided a wide range of information useful not only for expression genomics and annotation of genomic DNA sequence, but also for further research on the clinical diagnosis of OPA.  相似文献   

9.
We studied the process of offspring production in queenless colonies of Acromyrmex subterraneus brunneus, and particularly evaluated the ovary development of workers as a function of their age. For this, subcolonies were set up and evaluated at different periods of isolation from the queen (2, 4 and 6 months), besides individually labeled age groups. The subcolonies were assessed according to offspring production and ovaries containing oocytes or not. The evaluations showed worker oviposition and development of males originating from worker-laid eggs. At 2 months' absence of the queen, eggs and larvae were found, with eggs in a higher proportion than larvae. After 4 months, the proportion of eggs had reduced while larvae had increased, and a pupa was found in one subcolony. At 6 months, besides a higher share of larvae, one pupa and one adult male were found. Dissection of workers revealed ovaries containing oocytes during the periods of evaluation. Only a group of medium-sized and large workers, 23.3%, 20.9% and 37.5% of the population from each period assessed in queenless subcolonies respectively, presented developed oocytes in the ovary. The same was observed in colonies with a queen, with 17.6%, 19.6% and 7.8% of the group of dissected workers from each time period, respectively. With respect to worker age, we observed by dissection of the ovary, that the greatest percentage of individuals with ovarioles containing oocytes occurred at 45 days (6 weeks) up to 90 days (12 weeks). These results probably are associated with the workers reproduction and the laying of trophic and reproductive eggs in colonies with and without a queen; these eggs have distinct functions in each situation.  相似文献   

10.
Production of high titers of an alkaline, extracellular and thermo-tolerant pectinase by a newly isolated yeast Pseudozyma sp. SPJ was carried out under solid state fermentation. Citrus peel, the inexpensive agro-industrial residue used as substrate, was experienced to be unsurpassed. Response surface methodology was conducted to optimize the culture conditions for Pseudozyma sp. SPJ for hyper production of pectinase. Plackett Burman design was applied to identify the most effective culture variables. Out of nine variables studied, incubation time, moisture content and ammonium sulfate were detected as most important. A full factorial Central Composite Design was used to optimize the levels of these variables, which resulted in 17-fold increase (71.19 IU/g to 1215.66 IU/g dry substrate) in the enzyme yield. The results of analysis of variance and multiple regression analysis implies that the effect of incubation time (p 〈 0.000) and moisture content (p 〈 0.018) is more than ammonium sulfate. And also the interaction of moisture content with ammonium sulfate (p 〈 0.002) is more significant.  相似文献   

11.
Bioinformatics software resources   总被引:1,自引:0,他引:1  
This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts.  相似文献   

12.
With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services.  相似文献   

13.
Pise is interface construction software for bioinformatics applications that run by command-line operations. It creates common, easy-to-use interfaces to these applications for the Web, or other uses. It is adaptable to new bioinformatics tools, and offers program chaining, Unix system batch and other controls, making it an attractive method for building and using your own bioinformatics web services.  相似文献   

14.
SUMMARY: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.  相似文献   

15.
Jemboss reloaded     
Bioinformatics tools are freely available from websites all over the world. Often they are presented as web services, although there are many tools for download and use on a local machine. This tutorial section looks at Jemboss, a Java-based graphical user interface (GUI) for the EMBOSS bioinformatics suite, which combines the advantages of both web service and downloaded software.  相似文献   

16.
One of the most tedious steps in genetic data analyses is the reformatting data generated with one program for use with other applications. This conversion is necessary because comprehensive evaluation of the data may be based on different algorithms included in diverse software, each requiring a distinct input format. A platform‐independent and freely available program or a web‐based tool dedicated to such reformatting can save time and efforts in data processing. Here, we report widgetcon , a website and a program which has been developed to quickly and easily convert among various molecular data formats commonly used in phylogenetic analysis, population genetics, and other fields. The web‐based service is available at https://www.widgetcon.net . The program and the website convert the major data formats in four basic steps in less than a minute. The resource will be a useful tool for the research community and can be updated to include more formats and features in the future.  相似文献   

17.
SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de  相似文献   

18.
The development of glycan-related databases and bioinformatics applications is considerably lagging behind compared with the wealth of available data and software tools in genomics and proteomics. Because the encoding of glycan structures is more complex, most of the bioinformatics approaches cannot be applied to glycan structures. No standard procedures exist where glycan structures found in various species, organs, tissues or cells can be routinely deposited. In this article the concepts of the GLYCOSCIENCES.de portal are described. It is demonstrated how an efficient structure-based cross-linking of various glycan-related data originating from different resources can be accomplished using a single user interface. The structure oriented retrieval options-exact structure, substructure, motif, composition and sugar components-are discussed. The types of available data-references, composition, spatial structures, nuclear magnetic resonance (NMR) shifts (experimental and estimated), theoretically calculated fragments and Protein Database (PDB) entries-are exemplified for Man(3.) The free availability and unrestricted use of glycan-related data is an absolute prerequisite to efficiently share distributed resources. Additionally, there is an urgent need to agree to a generally accepted exchange format as well as to a common software interface. An open access repository for glyco-related experimental data will secure that the loss of primary data will be considerably reduced.  相似文献   

19.
404 not found: the stability and persistence of URLs published in MEDLINE   总被引:8,自引:0,他引:8  
MOTIVATION: The advent of the World Wide Web has enabled unprecedented supplementation of traditional journal publications, allowing access to resources, such as video, sound, software, databases, datasets too large to publish, and even supplementary information and discussion. However, unlike traditional publications, continued availability of these online resources is not guaranteed. An automated survey was conducted to quantify the growth in Uniform Resource Locators (URLs) published to date in MEDLINE abstracts, their current availability and distribution by journal. RESULTS: Of 1630 unique URLs identified, formatting and/or spelling errors were detected within 201 (12%) of them as published. After corrections were made, a survey revealed that approximately 63% of these URLs were consistently available, and another 19% were available intermittently. The rate of failure was far worse for anonymous login to FTP sites, with only 12 of 33 sites (36%) responding. This survey also shows that journals vary disproportionately in the number of web citations published, suggesting policy implementation among a few could have a profound impact overall. Out of the 306 journals with a URL published in an abstract, Bioinformatics published the most (12% of total). AVAILABILITY: URL database and program available by request.  相似文献   

20.

Background  

The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources.  相似文献   

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