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| Registros recuperados: 3.453 | |
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| Jesualdo Tomas Fernandez-Breis; Mikel Egaña Aranguren; Robert Stevens. |
| Over the past few years the number of bio-ontologies has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies' Cell Type Ontology, is included as an illustration. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3478/version/1 |
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| Jesualdo Tomas Fernandez-Breis; Mikel Egaña Aranguren; Robert Stevens. |
| Over the past few years the number of bio-ontologies has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies' Cell Type Ontology, is included as an illustration. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3479/version/1 |
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| Robert M. Sinclair. |
| Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate splicing in environments harboring... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5770/version/1 |
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| Gang Zhang; Anurag Tandon. |
| Lentiviral vectors (LVs) were a powerful tool for transgene expression in vivo and in vitro. However, the construction of LVs is of low efficiency, due to the large sizes and lack of proper clone sites. Therefore, it is critical to develop efficient strategies for cloning LVs. Here, we reported a combinatorial strategy to efficiently construct LVs using EGFP, hPlk2 wild type (WT) and mutant genes as inserts. Firstly, site-directed mutagenesis (SDM) was performed to create BamH I site for the inserts; secondly, pWPI LV was dephosphorylated after BamH I digestion; finally, the amounts and ratios of the insert and vector DNA were optimized to increase monomeric ligation. Our results showed that the total percentage of positive clones was approximately... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6876/version/1 |
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| Sk. Sarif Hassan; Pabitra Pal Choudhury; Aritra Bose. |
| A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model, a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6967/version/2 |
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| Sk. Sarif Hassan; Pabitra Pal Choudhury; Aritra Bose. |
| A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6967/version/1 |
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| Louise Linsell; Lindsay J. L. Forbes; Marcia Kapari; Caroline Burgess; Lynne Omar; Lorraine Tucker; Amanda J. Ramirez. |
| There is virtually no evidence for the effectiveness of interventions to promote early presentation in breast cancer. We tested the efficacy of an intervention to equip older women with the knowledge, skills, confidence and motivation to detect symptoms and seek help promptly, with the aim of promoting early presentation with breast cancer symptoms. We randomised 867 women aged 67 to 70 attending for their final routine appointment on the UK NHS Breast Screening Programme to receive: a scripted ten-minute interaction with a radiographer plus a booklet; a booklet alone; or usual care. The primary outcome was whether or not a woman was breast cancer aware based on knowledge of breast cancer symptoms and age-related risk; and reported breast checking. At one... |
| Tipo: Manuscript |
Palavras-chave: Cancer. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3816/version/1 |
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| Rodrick Wallace. |
| A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the 'energy' picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual 'developmental' perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or... |
| Tipo: Manuscript |
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4280/version/2 |
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| Ilie Fishtik. |
| Background: Flux balance and network-based pathway analyses are theoretical tools aimed to find optimal steady state flux distributions in a metabolic network subject to additional constraints on the rates of the reaction steps. Although these methods are mathematically accurate, there are several physicochemical and computational aspects that are questionable and misleading. In particular, it is well known that the flux balance analysis may result in multiple flux distributions for the same objective function. 

Results: The flux balance and network-based pathway analyses are reformulated in terms of reaction routes (RRs), a theoretical framework that has been developed by Horiuti over 50 years ago. Not only does the... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Chemistry; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2788/version/1 |
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| Sosale Chandrasekhar. |
| It is argued that the Carnot cycle is a highly inaccurate representation of a steam engine, and that the net work obtained in its operation would be zero. This conclusion is also supported by an elementary mathematical approach, which re-examines the work done in the four individual steps of the cycle. An important consequence of this is that the concept of entropy, originally proposed on the basis of the Carnot theorem, may not be a fundamentally valid thermodynamic quantity. Also, the experimental approach generally adopted in the determination of entropy is questionable, and the importance of increasing randomness in natural processes not universally valid. In fact, a more viable basis, at least vis-à-vis chemical reactions, appears to be the... |
| Tipo: Manuscript |
Palavras-chave: Chemistry. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1852/version/1 |
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| Xiaoqing Su. |
| Mosquito causes problems in both disease transmission and disturbance to people's daily life. The controlling methods used now are mainly application of chemical pesticides which result in serious harm to environment. Biological control of the pest is one of the ideal ways. But, lack of suitable agent makes it difficult to extend this technique in wider scope. _Pythium guiyangense_ Su is a newly found fungal pathogen of mosquitoes and is promising for practical use. Here we summarize a list of mosquitoes that can be infected by the fungus so far, which shows the potential significance of the application of the fungus in the future. |
| Tipo: Manuscript |
Palavras-chave: Microbiology; Earth & Environment. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1875/version/1 |
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| Heather A. Piwowar; Wendy W. Chapman. |
| *Background:* Sharing data is a tenet of science, yet commonplace in only a few subdisciplines. Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers. The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing. 

*Methods:* We investigated these relationships with respect to gene expression microarray data in the... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1700/version/1 |
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| Edwin Wang. |
| What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed. |
| Tipo: Manuscript |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4322/version/1 |
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| Edwin Wang. |
| What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed. |
| Tipo: Manuscript |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4322/version/2 |
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| Vicenta Salvador-Recatala; Robert M. Greenberg. |
| The beta subunit of high voltage-activated Ca (Cav) channels targets the pore forming [alpha]~1~ subunit to the plasma membrane and defines the biophysical phenotype of the Cav channel complex. Cav channel inactivation following activation and opening is tightly regulated and is an essential property that not only prevents excessive entry of Ca^2+^ into the cell but may also have functions in signal transduction. The [beta] subunit modulates Ca^2+^-dependent and voltage-dependent components of Cav channel inactivation via its interaction with the I-II linker of the [alpha]~1~ subunit. Here, using Cav2.3 and whole-cell patch-clamp, we show that a [beta] subunit from the human parasite _Schistosoma mansoni_ ([beta]~Sm~) accelerates inactivation via a unique,... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Neuroscience. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4230/version/1 |
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| Adeilton Brandao. |
| With the thousands of scientific papers being produced every month, picking an authors name, associate it to a research field and right evaluate his or her performance is in most of times a cumbersome task. I am proposing here that science indexes as h-index, g-index, total citations and published papers could be added to biomedical bibliographic citation in order to create a unique identifier for a given researcher. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/794/version/1 |
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| Tomohisa Asai; Eriko Sugimori; Yoshihiko Tanno. |
| Presenting a suggestion of heaviness to a person in a hypnotic trance (e.g., "your arm is getting heavier and heavier") tends to result in a corresponding change in the person's body position (e.g., the arm lowers). This phenomenon may be a result of activation of the mirror neuron system, which leads the subject to anticipate actual weight on the arm. The mirror system underlies people's ability to sense, in the absence of actual sensory input, experiences of other people. Perhaps this system allows the same anticipatory experience regarding non-human objects. In this study, we showed participants a picture of a rubber hand holding what appeared to be a lightweight rubber ball. In reality, the ball was weighted with... |
| Tipo: Manuscript |
Palavras-chave: Neuroscience. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2276/version/1 |
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| Registros recuperados: 3.453 | |
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