bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA capping machinery as an anti‐infective target
Authors: Issur Moheshwarnath , Picard‐Jean Frédéric , Bisaillon Martin 
Published: October 2010

AbstractA number of different human pathogens code for their own enzymes involved in the synthesis of the RNA cap structure. Although the RNA cap structures originating from human and microbial enzymes are often identical, the subunit composition, structure and catalytic mechanisms of the microbial‐encoded enzymes involved in the synthesis of the RNA cap structure are often significantly different from those of host cells. As a consequence, these pathogenic cap‐forming enzymes are potential targets for antimicrobial drugs. During the past few years, experimental studies have started to demonstrate that inhibition of the RNA capping activity is a reasonable approach for the development of antimicrobial agents. The combination of structural, biochemical, and molecular modeling studies are starting to reveal novel molecules that can serve as starting blocks for the design of more potent and specific antimicrobial agents. Here, we examine various strategies that have been developed to inhibit microbial enzymes involved in the synthesis of the RNA cap structure, emphasizing the challenges remaining to design potent and selective drugs.WIREs RNA2011 2 184–192 DOI: 10.1002/wrna.43This article is categorized under:RNA Processing > Capping and 5' End Modifications
Critical Micelle Concentration and HLB of the Sodium Oleate–Hexadecyltrimethylammonium Bromide Mixed System
Authors: Miraglia Daniela B. , Rodríguez José L. , Minardi Rossana M. , Schulz Pablo C. 
Published: October 2010

AbstractThe critical micelle concentration of sodium oleate—hexadecyltrimethylammonium bromide mixtures was determined as a function of the mixture composition and analyzed with Rubingh's theory, showing a strong nonideality. The hydrophile–lipophile balance (HLB) of the mixtures was also measured and the validity of the additivity rule for the HLB of surfactants mixtures was tested. Results were compared with the aggregation behavior of that mixture. Both the HLB and the critical micelle concentration dependencies on the mixture composition exhibit a negative deviation when compared with ideal behavior, which is explained on the basis of the interactions between components and surfactant partitioning between the bulk and the interface.
Biological first principles for design competence
Authors: Dong Andy 
Published: October 2010

AbstractThis paper interprets the concept of biologically inspired design as understanding design based on the biological evidence. Borrowing its concept of design competence from Chomsky's definition of linguistic competence, the paper reviews biological evidence from fields including evolution, genetics, and animal behavior from the perspective of design research to propose that design competence is the product of an evolutionary history during which five key developments in cognitive evolution came together: conception unbounded by sensory perception, symbolic manipulation at a level of metarepresentation, theory of mind, curiosity, and mental time travel. These cognitive capabilities were derived from the biological evidence based upon the criteria that they are presumed to be unique to humans (Homo sapiens), they may be lost because of neurodegenerative diseases or they may fail to develop because of neurodevelopmental disorders, and they are not immediately present upon birth and develop as a child's brain matures. Based on these five capabilities, the paper concludes by discussing how computation may provide a useful way to understand the origins and evolution of design competence.
A content account of creative analogies in biologically inspired design
Authors: Vattam Swaroop S. , Helms Michael E. , Goel Ashok K. 
Published: October 2010

AbstractThe growing movement of biologically inspired design is driven in part by the need for sustainable development and in part by the recognition that nature could be a source of innovation. Biologically inspired design by definition entails cross-domain analogies from biological systems to problems in engineering and other design domains. However, the practice of biologically inspired design at present typically isad hoc, with little systemization of either biological knowledge for the purposes of engineering design or the processes of transferring knowledge of biological designs to engineering problems. In this paper we present an intricate episode of biologically inspired engineering design that unfolded over an extended period of time. We then analyze our observations in terms ofwhy,what,how, andwhenquestions of analogy. This analysis contributes toward a content theory of creative analogies in the context of biologically inspired design.
A methodology for supporting “transfer” in biomimetic design
Authors: Sartori Julian , Pal Ujjwal , Chakrabarti Amaresh 
Published: October 2010

AbstractBiomimetics involves transfer from one or more biological examples to a technical system. This study addresses four questions. What are the essential steps in a biomimetic process? What is transferred? How can the transferred knowledge be structured in a way useful for biologists and engineers? Which guidelines can be given to support transfer in biomimetic design processes? In order to identify the essential steps involved in carrying out biomimetics, several procedures found in the literature were summarized, and four essential steps that are common across these procedures were identified. For identification of mechanisms for transfer, 20 biomimetic examples were collected and modeled according to a model of causality called the SAPPhIRE model. These examples were then analyzed for identifying the underlying similarity between each biological and corresponding analogue technical system. Based on the SAPPhIRE model, four levels of abstraction at which transfer takes place were identified. Taking into account similarity, the biomimetic examples were assigned to the appropriate levels of abstraction of transfer. Based on the essential steps and the levels of transfer, guidelines for supporting transfer in biomimetic design were proposed and evaluated using design experiments. The 20 biological and analogue technical systems that were analyzed were similar in the physical effects used and at the most abstract levels of description of their functionality, but they were the least similar at the lowest levels of abstraction: the parts involved. Transfer most often was carried out at the physical effect level of abstraction. Compared to a generic set of guidelines based on the literature, the proposed guidelines improved design performance by about 60%. Further, the SAPPhIRE model turned out to be a useful representation for modeling complex biological systems and their functionality. Databases of biological systems, which are structured using the SAPPhIRE model, have the potential to aid biomimetic concept generation.
A natural-language approach to biomimetic design
Authors: Shu L.H. 
Published: October 2010

AbstractThis paper summarizes various aspects of identifying and applying biological analogies in engineering design using a natural-language approach. To avoid the immense as well as potentially biased task of creating a biological database specifically for engineering design, the chosen approach searches biological knowledge in natural-language format, such as books and papers, for instances of keywords describing the engineering problem. Strategies developed to facilitate this search are identified, and how text descriptions of biological phenomena are used in problem solving is summarized. Several application case studies are reported to illustrate the approach. The value of the natural-language approach is demonstrated by its ability to identify relevant biological analogies that are not limited to those entered into a database specifically for engineering design.
Function-based, biologically inspired concept generation
Authors: Nagel Jacquelyn K.S. , Nagel Robert L. , Stone Robert B. , McAdams Daniel A. 
Published: October 2010

AbstractThe natural world provides numerous cases for inspiration in engineering design. Biological organisms, phenomena, and strategies, which we refer to as biological systems, provide a rich set of analogies. These systems provide insight into sustainable and adaptable design and offer engineers billions of years of valuable experience, which can be used to inspire engineering innovation. This research presents a general method for functionally representing biological systems through systematic design techniques, leading to the conceptualization of biologically inspired engineering designs. Functional representation and abstraction techniques are used to translate biological systems into an engineering context. The goal is to make the biological information accessible to engineering designers who possess varying levels of biological knowledge but have a common understanding of engineering design. Creative or novel engineering designs may then be discovered through connections made between biology and engineering. To assist with making connections between the two domains concept generation techniques that use biological information, engineering knowledge, and automatic concept generation software are employed. Two concept generation approaches are presented that use a biological model to discover corresponding engineering components that mimic the biological system and use a repository of engineering and biological information to discover which biological components inspire functional solutions to fulfill engineering requirements. Discussion includes general guidelines for modeling biological systems at varying levels of fidelity, advantages, limitations, and applications of this research. The modeling methodology and the first approach for concept generation are illustrated by a continuous example of lichen.
ACBD: Database for Ascidian Chemical Genomics
Authors: Hotta Kohji , Hira Yuichiro , Terai Jun , Nakamura Mitsuru , Tashiro Etsu , Imoto Masaya , Oka Kotaro 
Published: October 2010

AbstractChemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database).First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted from more than 900 articles in PubMed database since 1964. ACBD is free and open to the public on the web. ACBD consists of two main parts. One part consists of information about already-used chemicals to ascidians. This part is based on the record of already-published articles. In this part, we realized that more than 351 kinds of chemicals were applied for ascidian and that more than 399 kinds of chemicals were isolated from120 kinds of tunicates.The other part consists of "not-yet-used chemicals" information. Although the total number of Ciona protein model (KH model, Satou et al., 2008) is said to be 24,025, only 199 kinds of KH models have ever targeted by chemical compounds. To know the number of potentially modifiable target proteins by currently available chemicals, we searched KH model against amino acid sequences of drug targets recorded in DrugBank (Wishart DS et al., 2008). As a result, we found that 1,862 KH Ciona models might be modifiable by using commercially available chemicals. Thus, we can say that 7.8% of Ciona models have a potential to be modified their functions by chemicals. These information in ACBD are useful for researchers interested in drug screening as well as chemical genomics. In near future, we are planning to integrate ACBD into FABA, CIPRO and ANISEED databases.
Epitopes in ChEBI - A Collaboration with the IEDB
Authors: Josephs Zara , Ennis Marcus , Turner Steve , Owen Gareth , Peters Bjoern , Vita Randi , Steinbeck Christoph 
Published: October 2010

Abstract*ChEBI background:* Chemical Entities of Biological Interest (ChEBI) is a curated database of small chemical entities important in biosystems. As well as a description of entities, it provides a semantically rich knowledge base; and an internal hierarchy that organises the entities by their molecular structure types and potential rôles.*The ChEBI-IEDB collaboration:* The Immune Epitope and Analysis Resource (IEDB) is a project supported by contract from the National Institute of Allergy and Infectious Diseases (NIAID). Its goal is to make epitope-related data on infectious diseases and immune disorders freely available to researchers worldwide. In June 2009, ChEBI began working with the IEDB on a project aimed at incorporating into ChEBI, by manual curation, a pilot subset of immunologically important chemicals identified as immune epitopes.*The significance of the project:* Numerous reports attest to an increasing global prevalence of immune-related diseases, with a multiplicity of contributing factors. This situation underscores the need for cross-talk among the various scientific disciplines, and makes ChEBI involvement in this project particularly relevant.*Collaboration outcome:* That collaboration among curators working on different databases can be reciprocally beneficial has been amply demonstrated by the ChEBI-IEDB teamwork described: while the incorporated IEDB items have substantially enriched ChEBI, the latter’s multiplicity of synonyms, structure tree lay-out and expertise in describing non-peptidic epitopes have been equally useful to the IEDB in facilitating the search process.*Status quo and plans:* We continue to refine our task of assisting the identification, understanding and utilisation of biologically meaningful chemical entities by engaging in further joint projects.
Apply of Textmining Method to Study the Roles in Improving the Health by Lactoferrin, a Multi-Functional Milk Protein
Authors: Shimazaki Kei-ichi , Kushida Tatsuya , Yamauchi Koji , Takagi Toshihisa 
Published: October 2010

AbstractLactoferrin is a metal-binding glycoprotein found in milk, blood and other exocrine secretions. This is a multi-functional protein that exhibits many activities such as: anti-microbial, anti-viral, immunomodulatory, anti-inflammatory, anti-tumor, anti-metastatic, cell growth-promoting, and anti-oxidant activities, as well as regulation of granulopoiesis and iron absorption, etc. To date, a number of academic reports concerning the biological activities of lactoferrin have been published and are easily accessible through public databases. In order to overcome the information overload associated with lactoferrin information, we have applied the text mining method to the accumulated lactoferrin literature. To this end, we used the information extraction system GENPAC (provided by Nalapro Technologies Inc., Tokyo), which uses natural language processing and text mining technology. Using GENPAC, text extraction was carried out on literature containing the term “lactoferrin” and any of keywords concerning health conditions or diseases from PubMed. Subsequently, network mappings of the information obtained were produced using Cytoscape. We will exhibit that such textmining method and information visualization analysis is useful in studying novel relationships among a multitude of lactoferrin functions and mechanisms to improve our health.
Biophysical Effects Of Ion Concenteration On The Affinity Between Nanopore, OmpF Lumen and Passing Nucleotide
Authors: Hadi Saeid , Mobasheri Hamid 
Published: October 2010

AbstractOmpF an outer-membrane porin channel of E. Coli posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information However, due to the instrument limitation in monitoring ontime submolecular motions occurring during the translocation, theoretical studies attractive, modeling and simulation are inevitable. In this study we calculated the changes in the affinity of OmpF towards pyrimidin at molecular level within channel lumen by Delphi 4, and monitored by VMD 1.8.5. A non-linear Poisson-Boltzmann calculator with definite element integrator found to be appropriate choice to calculate the net energy of OmpF nucleotide interactions at different ion concentration. Our results indicate that upon increasing the ion concentration the OmpF affinity to pyrimidin decreases along the channel axis showing a minimum at the inner mouth of the channel. These observations shed lights to understand the selective molecular translocation means involved in the OmpF.
Octanol/water distribution coefficients of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates: Comparison of the IEFPCM-UFF, CPCM, and SMD solvation models
Authors: Rayne Sierra , Forest Kaya 
Published: October 2010

AbstractThe octanol/water distribution coefficients (log D~ow~) of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates (PFSAs) were calculated using the M062X/6-311++G(d,p) and MP2/6-311++G(d,p)//M062X/6-311++G(d,p) levels of theory and the IEFPCM-UFF, CPCM, and SMD solvation models. At both levels of theory with all solvation models, absolute log D~ow~ calculated for the straight chain C~1~ through C~7~ PFSAs display a substantial negative bias against available experimental data and expected trends by several log units. However, the SMD solvation model achieves accurate relative log D~ow~ accuracy, yielding fragmental contributions of a -CF~2~- group towards the log D~ow~ of 0.51+/-0.02 to 0.54+/-0.01 units (-3.0+/-0.1 to -3.1+/-0.1 kJ/mol), in good agreement with the experimental value of 0.61 units (-3.4+/-0.1 kJ/mol). In contrast, the IEFPCM-UFF and CPCM solvation models exhibit either invariant log D~ow~ with increasing perfluoro-n-alkyl chain length (CPCM) or a modestly decreasing trend (IEFPCM-UFF).
neXtProt, a new knowledgebase on human proteins
Authors: Lane Lydie 
Published: October 2010

AbstractIn September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from ~20'300 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our bodies! Therefore, in the framework of CALIPHO, a new interdisciplinary group from the University of Geneva and the SIB, we are developing neXtProt, a human-centric protein knowledge resource.We aim to help researchers answer pertinent questions relevant to human proteins. This requires answering three different challenges: 1) Add to the corpus of data on human proteins that is already in Swiss-Prot, a lot of additional information. We will import in neXtProt data originating from a variety of highthroughput approaches such as proteomics, microarray, antibodies, siRNAs, interactomics, etc. All of these data sets must be carefully selected so as to only provide high-quality data as we want to avoid creating a noisy and dirty compendium.2) Organize the data in such a way that it is possible to make powerful queries in the most user-friendly environment. Here also, it is necessary to be able to capture the complexity and the heterogeneity of the data that will be available in neXtProt, yet make it easy for the user to forget this complexity!3) Build a software platform that will allows tools ranging from sequence analysis to text and data mining to be integrated in various research environments so as to answer specific needs of academic and industrial users.Finally, we also aim in enabling researchers to collaborate and share data and ideas through the use of the neXtProt platform. neXtProt is a common development of the SIB and of GeneBio SA. We hope you will enjoy working with it and will help us making it evolve by telling us of your specific needs.
Functional annotation of bacterial sugars
Authors: Lisacek Frederique 
Published: October 2010

AbstractGlyco-bioinformatics means different things to different people. It ranges, for example, from the mining of the genome for glycosylation pathway enzymes, through to analysis of microarray expression of glycosyltransferases, to glycoprotein identification data, to the development of tools that facilitate the interpretation of mass spectra and to the construction of structural glycan databases. Lastly, these data need to be mined so that the function of the glycan structures attached to the range of glycoconjugates in nature can be determined. The quality of the data in these databases needs to be maintained for this work to be meaningful.For easier analysis, glycan structures are often characterised independent of the protein on which these sugars were originally attached. GlycosuiteDB ("http://glycosuitedb.expasy.org/glycosuite/glycodb":http://glycosuitedb.expasy.org/glycosuite/glycodb) is a freely accessible resource that has annotated this glycan structural data with protein and tissue information that sets the basis of functional interpretation. Information on cellular interactions associated with changes in glycosylation structures is essential for the understanding of the functional role of sugars and needs to be collected in order to exploit the knowledge of these posttranslational additions to proteins. One such database is SugarBind ("http://sugarbind.expasy.org/sugarbind":http://sugarbind.expasy.org/sugarbind), which collates the known glycan binding sites of human pathogens. These structural glycan epitopes occur on both proteins and lipids and will add to the knowledgebase of glycosylation function and expand the structural data contained in GlycoSuiteDB. In this presentation, the knowledge obtained on the function of glycosylation by linking the information between two databases will be highlighted as an example of the value to be gained from manual curation of literature-extracted knowledge.