User-friendly Search Engine Research Articles

Search Engine on Vedas

The Search Engine on Vedas Project is an effort to create a comprehensive and user-friendly search engine for the vast corpus of Vedic literature. The project involves digitizing and indexing a diverse range of Vedic texts, including hymns, rituals, commentaries, and translations, and developing a user-friendly interface that allows efficient searching and browsing. The search engine employs advanced search algorithms, such as natural language processing and machine learning, to enable users to search for specific keywords, phrases, or concepts within the Vedic texts. The interface is designed to be intuitive and customizable, with options for filtering and sorting search results based on various criteria, such as author, type of text, language, and publication date. The project also includes interactive features, such as multimedia resources, glossaries, and forums, to facilitate a more engaging and immersive user experience. Additionally, the search engine aims to provide a platform for collaborative research and knowledge-sharing among scholars and enthusiasts of Vedic literature.

Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides.

As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described Saccharomyces cerevisiae transfer RNA and Bos taurus total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from Pseudomonas aeruginosa 70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.

Text Mining: Design of Interactive Search Engine Based Regular Expressions of Online Automobile Advertisements

Technology world has greatly evolved over the past decades, which led to inflated data volume. This progress of technology in the digital form generated scattered texts across millions of web pages. Unstructured texts contain a vast amount of textual data. Discover of useful and interesting relations from unstructured texts requires more processing by computers. Therefore, text mining and information extraction have become an exciting research field to get structured and valuable information. This paper focuses on text pre-processing of automotive advertisements domains to configure a structured database. The structured database was created by extract the information over unstructured automotive advertisements, which is an area of natural language processing. Information extraction deals with finding factual information in text using learning regular expressions. We manually craft rule-based specific approaches to extract structured information from unstructured web pages. Structured information will be provided by user-friendly search engine designed for topic-specific knowledge. Consequently, this information that extracted from these advertisements uses to perform a structured search over certain interesting attributes. Thus, the tuples are assigned a probability and indexed to support the efficiency of extraction and exploration via user queries.

Search Engine Optimization with Google-Web

Search engine optimization is a technique to take a web document in top search results of a search engine. Web presence Companies is not only an easy way to reach among the target users but it may be profitable for Business is exactly find the target users as of the reason that most of the time user search out with the keywords of their use rather than searching the Company name, and if the Company Website page come in the top positions then the page may be profitable. This work describes the tweaks of taking the page on top position in Google by increasing the Page rank which may result in the improved visibility and profitable deal for a Business. Google is most user-friendly search engine to prove for the all users which give user-oriented results. In addition ,most of other search engines use Google search patterns so we have concentrated on it. So, if a page is Register on Google it Is Display on most of the search engines.

MENDA: a comprehensive curated resource of metabolic characterization in depression.

Depression is a seriously disabling psychiatric disorder with a significant burden of disease. Metabolic abnormalities have been widely reported in depressed patients and animal models. However, there are few systematic efforts that integrate meaningful biological insights from these studies. Herein, available metabolic knowledge in the context of depression was integrated to provide a systematic and panoramic view of metabolic characterization. After screening more than 10 000 citations from five electronic literature databases and five metabolomics databases, we manually curated 5675 metabolite entries from 464 studies, including human, rat, mouse and non-human primate, to develop a new metabolite-disease association database, called MENDA (http://menda.cqmu.edu.cn:8080/index.php). The standardized data extraction process was used for data collection, a multi-faceted annotation scheme was developed, and a user-friendly search engine and web interface were integrated for database access. To facilitate data analysis and interpretation based on MENDA, we also proposed a systematic analytical framework, including data integration and biological function analysis. Case studies were provided that identified the consistently altered metabolites using the vote-counting method, and that captured the underlying molecular mechanism using pathway and network analyses. Collectively, we provided a comprehensive curation of metabolic characterization in depression. Our model of a specific psychiatry disorder may be replicated to study other complex diseases.

PalmXplore: oil palm gene database.

A set of Elaeis guineensis genes had been generated by combining two gene prediction pipelines: Fgenesh++ developed by Softberry and Seqping by the Malaysian Palm Oil Board. PalmXplore was developed to provide a scalable data repository and a user-friendly search engine system to efficiently store, manage and retrieve the oil palm gene sequences and annotations. Information deposited in PalmXplore includes predicted genes, their genomic coordinates, as well as the annotations derived from external databases, such as Pfam, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Information about genes related to important traits, such as those involved in fatty acid biosynthesis (FAB) and disease resistance, is also provided. The system offers Basic Local Alignment Search Tool homology search, where the results can be downloaded or visualized in the oil palm genome browser (MYPalmViewer). PalmXplore is regularly updated offering new features, improvements to genome annotation and new genomic sequences. The system is freely accessible at http://palmxplore.mpob.gov.my.

BioCarian: search engine for exploratory searches in heterogeneous biological databases

BackgroundThere are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community.ResultsWe present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com.ConclusionsWe have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Databases of Conformations and NMR Structures of Glycan Determinants.

The present study reports a comprehensive nuclear magnetic resonance (NMR) characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large-scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B and O), core structures (Types 1, 2 and 4), fucosylated oligosaccharides (core and lacto-series), sialylated oligosaccharides (Types 1 and 2), Lewis antigens, GPI-anchors and globosides. A complementary set of about 100 glycan determinants occurring in glycoproteins and glycosaminoglycans has also been structurally characterized using molecular mechanics-based computation. The experimental and computational data generated are organized in two relational databases that can be queried by the user through a user-friendly search engine. The NMR ((1)H and (13)C, COSY, TOCSY, HMQC, HMBC correlation) spectra and 3D structures are available for visualization and download in commonly used structure formats. Emphasis has been given to the use of a common nomenclature for the structural encoding of the carbohydrates and each glycan molecule is described by four different types of representations in order to cope with the different usages in chemistry and biology. These web-based databases were developed with non-proprietary software and are open access for the scientific community available at http://glyco3d.cermav.cnrs.fr.

Structure and Location of the Regulatory β Subunits in the (αβγδ)4 Phosphorylase Kinase Complex

Phosphorylase kinase (PhK) is a hexadecameric (αβγδ)(4) complex that regulates glycogenolysis in skeletal muscle. Activity of the catalytic γ subunit is regulated by allosteric activators targeting the regulatory α, β, and δ subunits. Three-dimensional EM reconstructions of PhK show it to be two large (αβγδ)(2) lobes joined with D(2) symmetry through interconnecting bridges. The subunit composition of these bridges was unknown, although indirect evidence suggested the β subunits may be involved in their formation. We have used biochemical, biophysical, and computational approaches to not only address the quaternary structure of the β subunits within the PhK complex, i.e. whether they compose the bridges, but also their secondary and tertiary structures. The secondary structure of β was determined to be predominantly helical by comparing the CD spectrum of an αγδ subcomplex with that of the native (αβγδ)(4) complex. An atomic model displaying tertiary structure for the entire β subunit was constructed using chemical cross-linking, MS, threading, and ab initio approaches. Nearly all this model is covered by two templates corresponding to glycosyl hydrolase 15 family members and the A subunit of protein phosphatase 2A. Regarding the quaternary structure of the β subunits, they were directly determined to compose the four interconnecting bridges in the (αβγδ)(4) kinase core, because a β(4) subcomplex was observed through both chemical cross-linking and top-down MS of PhK. The predicted model of the β subunit was docked within the bridges of a cryoelectron microscopic density envelope of PhK utilizing known surface features of the subunit.

Development of a Novel Cross-linking Strategy for Fast and Accurate Identification of Cross-linked Peptides of Protein Complexes

Knowledge of elaborate structures of protein complexes is fundamental for understanding their functions and regulations. Although cross-linking coupled with mass spectrometry (MS) has been presented as a feasible strategy for structural elucidation of large multisubunit protein complexes, this method has proven challenging because of technical difficulties in unambiguous identification of cross-linked peptides and determination of cross-linked sites by MS analysis. In this work, we developed a novel cross-linking strategy using a newly designed MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). DSSO contains two symmetric collision-induced dissociation (CID)-cleavable sites that allow effective identification of DSSO-cross-linked peptides based on their distinct fragmentation patterns unique to cross-linking types (i.e. interlink, intralink, and dead end). The CID-induced separation of interlinked peptides in MS/MS permits MS(3) analysis of single peptide chain fragment ions with defined modifications (due to DSSO remnants) for easy interpretation and unambiguous identification using existing database searching tools. Integration of data analyses from three generated data sets (MS, MS/MS, and MS(3)) allows high confidence identification of DSSO cross-linked peptides. The efficacy of the newly developed DSSO-based cross-linking strategy was demonstrated using model peptides and proteins. In addition, this method was successfully used for structural characterization of the yeast 20 S proteasome complex. In total, 13 non-redundant interlinked peptides of the 20 S proteasome were identified, representing the first application of an MS-cleavable cross-linker for the characterization of a multisubunit protein complex. Given its effectiveness and simplicity, this cross-linking strategy can find a broad range of applications in elucidating the structural topology of proteins and protein complexes.

CrossSearch, a User-friendly Search Engine for Detecting Chemically Cross-linked Peptides in Conjugated Proteins

Chemical cross-linking and high resolution MS have been integrated successfully to capture protein interactions and provide low resolution structural data for proteins that are refractive to analyses by NMR or crystallography. Despite the versatility of these combined techniques, the array of products that is generated from the cross-linking and proteolytic digestion of proteins is immense and generally requires the use of labeling strategies and/or data base search algorithms to distinguish actual cross-linked peptides from the many side products of cross-linking. Most strategies reported to date have focused on the analysis of small cross-linked protein complexes (<60 kDa) because the number of potential forms of covalently modified peptides increases dramatically with the number of peptides generated from the digestion of such complexes. We report herein the development of a user-friendly search engine, CrossSearch, that provides the foundation for an overarching strategy to detect cross-linked peptides from the digests of large (>or=170-kDa) cross-linked proteins, i.e. conjugates. Our strategy combines the use of a low excess of cross-linker, data base searching, and Fourier transform ion cyclotron resonance MS to experimentally minimize and theoretically cull the side products of cross-linking. Using this strategy, the (alpha beta gamma delta)(4) phosphorylase kinase model complex was cross-linked to form with high specificity a 170-kDa betagamma conjugate in which we identified residues involved in the intramolecular cross-linking of the 125-kDa beta subunit between its regulatory N terminus and its C terminus. This finding provides an explanation for previously published homodimeric two-hybrid interactions of the beta subunit and suggests a dynamic structural role for the regulatory N terminus of that subunit. The results offer proof of concept for the CrossSearch strategy for analyzing conjugates and are the first to reveal a tertiary structural element of either homologous alpha or beta regulatory subunit of phosphorylase kinase.

The role of a resource center in national development: The Namibian context

The role of a resource center in national development: The Namibian context

Evaluating internet for extension in agriculture

Summary Effective adoption of Internet for extension in agriculture is elusive despite substantial investments in human capital and other resources. To better understand the process EUNITA (a concerted EU project www.eclipse.it/EUNITA/main.html), INEA (the Italian National Institute of Agricultural Economics - www.inea.it) and the Toscana Extension service sponsored a workshop in Alberese, Italy, to evaluate its adoption's critical success factors and failures. A summary of participant's opinions indicated general agreement on benefits such as: Updated and comprehensive information; availability of new types, “Just in time”, more and competing information sources; “One stop information shopping”; ease of exchange of information and/or ideas and facilities to discuss them; easier collaboration and/or access to peers, other farmers and experts; a ranked list of useful information such as updated market lists, weather information, plant protection regulations, recommendations and products, news, bulletins, and more. There was general agreement relating to critical success factors such as: Internet accessibility on individual farms or at farmer-gathering locations; inputting of information that farmers/extension want and/or need; identifying a tangible benefit to information users; defining and serving target audiences; packaging information in a way that it can be understood and applied; a simple, user-friendly search engine and interface design; responsibility for the information quality and reliability; revealed preference as a guiding factor for Internet development. The going deeper into the summary of detailed participant's opinions provided a practical, baseline, reference for Internet adoption planning, program implementation and goal achievement evaluation.

PEDro: a database of randomised controlled trials in physiotherapy.

PEDro is a database of clinical trials designed to assist the practice of evidence-based physiotherapy. When complete, it will contain bibliographic details, abstracts and quality assessment scores of all published randomised controlled trials in physiotherapy. Trials on the database will be rated on the basis of their methodological quality, so that users of the database can be guided to those trials which provide the most methodologically sound sources of evidence. The database has been made freely available on the world wide web, where it can be searched with a powerful and user-friendly search engine.