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AGMAAS: a GIS integrated tool for modelling wind-borne spreading of FMD virus Nature Precedings
Judit Sábitz; Zoltán Barcza Solymosi; Norbert Solymosi.
The aim of our work was to develop a tool integrated into Quantum GIS (QGIS) that can help
the user estimate and visualize the possible infective areas around an outbreak based on HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model.
Tipo: Poster Palavras-chave: Ecology; Earth & Environment.
Ano: 2012 URL: http://precedings.nature.com/documents/7022/version/1
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Aligning the top-level of SNOMED-CT with Basic Formal Ontology Nature Precedings
William Hogan.
Effective translational research requires automated analysis of large datasets collected by multiple researchers working at multiple locations. Reliable, machine interpretation of-—and reasoning with—-large datasets assembled at different times and places by different researchers requires standard representations of data. These representations are controlled, structured vocabularies also known as ontologies. By far, the most successful ontology is the Gene Ontology (GO), used by bioinformatics researchers to annotate genomics data. However, to address the phenotype side of translational research will require annotation of electronic medical record data and clinical research data with a clinical-phenotype ontology analogous to GO....
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2373/version/1
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Allele-specific primer based identification of dimeric alpha-amylase inhibitor Nature Precedings
Pradeep Sharma; Pooja Sharma; Manoj Saini; S. S. Singh.
Wheat is one of the most important staple food crops cultivated over 200 mha in the range of environment throughout the world. Wheat production must continue to increase by 2% annually, more particularly in developing world including south-east Asia. Besides increasing the inherent productivity of wheat, it is important to minimize the losses caused to production by various abiotic and biotic factors. Alpha–amylase inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as the energy source. They play an important role in the carbohydrate metabolism of many heterotrophic and autotrophic organisms. In this study, we aimed to make sequence comparison and phylogenetic relationship among...
Tipo: Poster Palavras-chave: Biotechnology.
Ano: 2011 URL: http://precedings.nature.com/documents/5596/version/1
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Allergological and toxicological risk assessment of genetically modified (GM) plants - Development of a model system Nature Precedings
Alain Steinmann; Kristin Entzian; Birgit Grümmer; Udo Meyer.
Technical advances in biotechnology lead to a rising number of genetically modified plants and derived food and feed. Therefore, the international interest in adequate and standardized analytical methods increases to assess health risks in a rapid and low cost manner.
To address this issue a decision support system (DSS), which will be based on baseline data and thresholds of key parameters, is going to be established in the framework of a joint project (BioOK). Determination of the potential allergenicity or toxicity of novel proteins caused by the genetic modification compared to near isogenic variants (NIV) is a key issue in this context. For the development of DSS the model plant “potato” was used to compare...
Tipo: Poster Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4441/version/1
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Alpha band oscillations track temporal orienting of attention Nature Precedings
Gustavo Rohenkohl; Anna Christina Nobre.
Introduction: Recent investigations using field-potential recordings in visual and auditory cortices have shown that oscillatory activity in neuronal ensembles become entrained to the timing of rhythmically presented stimuli according to their modality and location (Lakatos, Chen et al. 2007; Lakatos, Karmos et al. 2008; Lakatos, O'Connell et al. 2009). In spite of the evidence showing the role of brain oscillations on forming predictions about forthcoming sensory events (for a review (Engel, Fries et al. 2001), little is known about the role of such oscillations in the temporal orienting of attention (Nobre 2001; Coull and Nobre 2008). To test the effect of temporal orienting of attention on early perceptual processing, motor selection, and...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2010 URL: http://precedings.nature.com/documents/4509/version/1
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An approach able to escape the most common problem during protein Crystallization i.e. formation of salt crystal Nature Precedings
K. Awaneesh Singh; Patrick Celie; G. R. K. Rao; M. V. Jagannatham.
Formation and differentiation of salt crystal is a most common as well as challenging problem during protein crystallography. Although there are some methods used for their differentiation i.e. physical manipulation, birefringence, dye absorption and run a gel but all of them are totally depends on own perception and expertise as well as also require a good crystal (final stage crystal). To escape this problem the screening was done with PACT, JCSG and other automated screens as everyone do. But during optimization the additives/salts were ignored at first and optimization screen was made just based on different buffers and precipitant. After selecting suitable buffer, the type and percentage of precipitant was optimized. We got some ugly crystals and with...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4725/version/1
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An Ontology To Represent Knowledge On Animal Testing Alternatives Nature Precedings
Thomas Wächter; Ursula G. Sauer; Andreas Doms; Barbara Grune; Michael R. Alvers; Horst Spielmann; Michael Schroeder.
EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R ("www.Go3R.org":http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3148/version/1
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Analysis of acceptance of bacillus to various heavy metals and antibiotics Nature Precedings
Yamini Singh Sisodia; Vivek Bajpai; Deeksha Gaur; Pankaj Kumar Jain.
The present study was carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from the Shekhawati region of Rajasthan. In this survey, 26 bacterial strains were isolated and identified using biochemical and molecular methods. Molecular identification of isolates was done by DNA isolation, PCR amplification using 16S rDNA primer and partial sequencing of purified product after sequencing, out of 26, 10 sequences were submitted to NCBI. Out of these 10 isolates Bacillus pumilis, Bacillus subtilis and Bacillus licheniformis were taken for further studies. There is growing awareness of the need for development of new antimicrobial agents for the treatment of human, animal and plant diseases. Keeping this fact in mind, we...
Tipo: Poster Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7073/version/1
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Analysis of Antarctic Ice Core Data (EPICA Dome C) with Flicker-Noise Spectroscopy Nature Precedings
Yuriy Polyakov; Jean Robert Petit; Serge Timashev.
Evolution of Earth’s climate system over the past 800,000 years represents a complex process with successions of uneven glacial and interglacial periods. The length, amplitudes, and development of each climate cycle depend on a number of different factors, including the orbital parameters attributed to insolation and the complex responses of the Earth system to solar radiation primarily through the amplification by Earth’s albedo and greenhouse gas and secondarily through a system of heat reservoirs, such as ice sheet and deep ocean, distributed throughout our planet. The purpose of this study is to analyze the transitions related to climate cycles in Antarctic ice core data (EPICA Dome C) of deuterium composition and dust...
Tipo: Poster Palavras-chave: Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3341/version/1
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Analysis of binding properties of VP2 protein of Human parvovirus B19 through in silico molecular docking Nature Precedings
Praneetha Amburu; Dibyabhaba Pradhan; Vani Priyadarshini; Munikumar Manne; Umamaheswari Amineni.
Human parvovirus B19, a member of the Parvoviridae family, is a pathogen associated with a wide variety of diseases. Most commonly, it causes childhood rash erythema infectiosum, but in some cases more serious symptoms such as persistent arthropathy, critical failures of red cell production causing transient aplastic crisis, this infection in pregnancy causes hydrops fetalis and myocarditis. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation would provide role of viral proteome in its survival and pathogenic mechanisms. SVMProt functional family annotations of VP2 protein had deciphered its zinc-binding, coat protein, outer membrane, chlorophyll biosynthesis, DNA repair and...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/5289/version/1
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Analysis of DNA structure as a 2D random walk by complex wavelet transform Nature Precedings
Eugene B. Postnikov; Alexander Y. Loskutov; Sergey A. Larionov; Evgeny V. Ryadchenko; Roman V. Kiseliov.
We propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex plane. Namely, we consider the mapping of two irreducible A − T and G − C sequences into a walk trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. 
 This function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based on the representation of the transform’s result as a solution of the specific Cauchy problem for the system of PDE. 
 As an example, we applied the described algorithm to a part of the telomer region of the 22 human chromosome and demonstated...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/1461/version/1
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Analysis of Human Spleen Contamination Nature Precedings
Martin Kopani; Martin Weis; Jan Jakubovsky.
Besides carbon, oxygen and nitrogen, numerous other elements and their compounds are significant in the body of humans and other animals. Accumulation of some elements and their compounds is recognized by clinical and biochemical evaluation. The physical-chemical properties and topical characteristics of elements in tissues may play a crucial role in evaluation their effect on human body. The ^57^Fe Mössbauer measurement was used for evaluation of iron–oxide biomagnetic nanoparticles composition and properties. Absorption spectra of the powdered spleen recorded at 77K and 300K were measured and subsequently analyzed. From fitted data it is possible to obtain material composition as well as discuss the mean particle size (received from...
Tipo: Poster Palavras-chave: Chemistry; Earth & Environment.
Ano: 2007 URL: http://precedings.nature.com/documents/1408/version/1
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Analysis of N-Glycosylation Sites in HIV glycoprotein 160 Nature Precedings
Rajendra Mandage.
HIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system, which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that there are...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/5571/version/1
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Analysis of plant metabolites – the baseline-threshold principle Nature Precedings
Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.

The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4439/version/1
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Analysis of plant metabolites – the baseline-threshold principle Nature Precedings
Katja Neubauer; Jenny Bandomir; Anett Grunenberg; Andreas Müller; Udo Kragl; Kerstin Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.

The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4439/version/2
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Analyzing local image statistics via maximum-entropy constructions Nature Precedings
Jonathan D. Victor; Daniel J. Thengone; Mary M. Conte.
Because the space of signals that the visual system encounters is high-dimensional, investigations of visual processing and perception must utilize a sampling strategy. One kind of approach begins with a class of models for input-output relations, and then chooses a stimulus ensemble such as white noise that enables efficient determination of model parameters. A second kind of approach begins with the explicit recognition that it is important to understand the visual system in the context of the inputs under which it functions and evolves; this motivates the use of naturalistic stimulus ensembles. Neither approach alone is sufficient: models built from ensembles such as white noise provide only a fair account of responses to natural scenes, and the...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2011 URL: http://precedings.nature.com/documents/5794/version/1
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ANN Based Virtual Classification Model for Discriminating Active and Inactive Withanolide E Analogs against Human Breast Cancer Cell Line MCF-7 Nature Precedings
Om Prakash; Feroz Khan; R.S. Sangwan.
Withanolides are a group of natural C-28 steroids built on an ergostane skeleton and classified into two major groups according to their structural skeleton: (a) compounds with a beta-oriented side chain and (b) compounds with an alpha-oriented side chain. Withanolide E represents one of the members of the latter group. Classification of active compounds on the basis of pharmacophore against specific cancer cell line poses a serious concern at the primary stage of virtual screening. To overcome this problem we have developed an artificial neural network based virtual screening model for discriminating active and non-active Withanolide-E-like derivatives or analogs against human breast cancer cell line MCF-7. In the present work, a 2D chemical descriptors...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6616/version/1
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Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer) Nature Precedings
C Y Kok; S A Forbes; N Bindal; S Bamford; C G Cole; M Jia; D Breare; R Shepherd; A Menzies; K Leung; J Teague; M R Stratton; P A Futreal.
"COSMIC, the Catalogue Of Somatic Mutations In Cancer":http://www.sanger.ac.uk/cosmic is designed to store and display somatic mutation information relating to human cancers, combining detailed information on publications, samples and mutation types. The information is curated both from the primary literature and the laboratories at the Cancer Genome Project, Sanger Institute, UK, and then semi-automatically entered into the COSMIC database. The v47 release (May 2010) contained the curation of 9202 papers describing 116,977 mutations across 466,851 samples. In order to provide consistent annotation of the data, COSMIC has developed a classification system for cancer histology and tissue ontology, and adapted HGVS mutation nomenclature...
Tipo: Poster Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5106/version/1
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Annotation and Curation of the Protein Data Bank Nature Precedings
Jasmine Young; RCSB PDBj PDBe Protein Data Bank.
The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological macromolecules. Established in 1971 with just seven structures, it presently includes more than 56,000 entries. To maintain the highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data annotation and the development of procedures, tools, and resources. Annotation-related issues, particularly those impacted by new developments
in structural biology, are critically reviewed at in-person and virtual meetings regularly and frequently. Comprehensive documentation of the procedures, formats, and related data dictionaries used in data annotation are available at the wwPDB...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3379/version/1
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Annotation-based meta-analysis of microarray experiments Nature Precedings
Jie Zheng; Junmin Liu; Elisabetta Manduchi; Christian J. Stoeckert, Jr..
We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3569/version/1
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