bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
Authors: Peña Arantxa , Teeling Hanno , Huerta-Cepas Jaime , Santos Fernando , Yarza Pablo , Brito-Echeverría Jocelyn , Lucio Marianna , Schmitt-Kopplin Philippe , Meseguer Inmaculada , Schenowitz Chantal , Dossat Carole , Barbe Valerie , Dopazo Joaquín , Rosselló-Mora Ramon , Schüler Margarete , Glöckner Frank Oliver , Amann Rudolf , Gabaldón Toni , Antón Josefa 
Published: February 2010

Abstract
Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere
Authors: Knief Claudia , Ramette Alban , Frances Lisa , Alonso-Blanco Carlos , Vorholt Julia A 
Published: February 2010

Abstract
The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium–plant association is not highly host plant species specific.
A Bacterial Enzyme Catalyzing Double Reduction of a β,δ-Diketo Ester with Unprecedented Stereoselectivity
Authors: Wu Xuri , Liu Nan , He Yunmian , Chen Yijun 
Published: February 2010

AbstractVarious ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in Escherichia coli and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A reductases. However, recombinant diketoreductase does not reduce HMG-CoA, showing that the inference of function of enzymes like the diketoreductase based on sequence homology may be in error. The enzyme directly converts a β,δ-diketo ester to the corresponding dihydroxy ester. More remarkably, our results demonstrate that the recombinant enzyme possesses unprecedented stereoselectivity with both diastereomeric and enantiomeric excesses of greater than 99%. This new enzyme is of immediate value in developing a practical biocatalytic route to the side chains of statin drugs, such as Lipitor®.
Transglutaminase-2: a new endostatin partner in the extracellular matrix of endothelial cells
Authors: Faye Clément , Inforzato Antonio , Bignon Marine , Hartmann Daniel J. , Muller Laurent , Ballut Lionel , Olsen Bjorn R. , Day Anthony J. , Ricard-Blum Sylvie 
Published: February 2010

Endostatin, a C-terminal fragment of collagen XVIII, binds to TG-2 (transglutaminase-2) in a cation-dependent manner. Recombinant human endostatin binds to TG-2 with an affinity in the nanomolar range (Kd=6.8 nM). Enzymatic assays indicated that, in contrast with other extracellular matrix proteins, endostatin is not a glutaminyl substrate of TG-2 and is not cross-linked to itself by the enzyme. Two arginine residues of endostatin, Arg27 and Arg139, are crucial for its binding to TG-2. They are also involved in the binding to heparin [Sasaki, Larsson, Kreuger, Salmivirta, Claesson-Welsh, Lindahl, Hohenester and Timpl (1999) EMBO J. 18, 6240–6248], and to α5β1 and αvβ3 integrins [Faye, Moreau, Chautard, Jetne, Fukai, Ruggiero, Humphries, Olsen and Ricard-Blum (2009) J. Biol. Chem. 284, 22029–22040], suggesting that endostatin is not able to interact simultaneously with TG-2 and heparan sulfate, or with TG-2 and integrins. Inhibition experiments support the hypothesis that the GTP-binding site of TG-2 is a potential binding site for endostatin. Endostatin and TG-2 are co-localized in the extracellular matrix secreted by endothelial cells under hypoxia, which stimulates angiogenesis. This interaction, occurring in a cellular context, might participate in the concerted regulation of angiogenesis and tumorigenesis by the two proteins.
Isolation and characterization of selective and potent human Fab inhibitors directed to the active-site region of the two-component NS2B–NS3 proteinase of West Nile virus
Authors: Shiryaev Sergey A. , Radichev Ilian A. , Ratnikov Boris I. , Aleshin Alexander E. , Gawlik Katarzyna , Stec Boguslaw , Frisch Christian , Knappik Achim , Strongin Alex Y. 
Published: February 2010

There is a need to develop inhibitors of mosquito-borne flaviviruses, including WNV (West Nile virus). In the present paper, we describe a novel and efficient recombinant-antibody technology that led us to the isolation of inhibitory high-affinity human antibodies to the active-site region of a viral proteinase. As a proof-of-principal, we have successfully used this technology and the synthetic naive human combinatorial antibody library HuCAL GOLD® to isolate selective and potent function-blocking active-site-targeting antibodies to the two-component WNV NS (non-structural protein) 2B–NS3 serine proteinase, the only proteinase encoded by the flaviviral genome. First, we used the wild-type enzyme in antibody screens. Next, the positive antibody clones were counter-screened using an NS2B–NS3 mutant with a single mutation of the catalytically essential active-site histidine residue. The specificity of the antibodies to the active site was confirmed by substrate-cleavage reactions and also by using proteinase mutants with additional single amino-acid substitutions in the active-site region. The selected WNV antibodies did not recognize the structurally similar viral proteinases from Dengue virus type 2 and hepatitis C virus, and human serine proteinases. Because of their high selectivity and affinity, the identified human antibodies are attractive reagents for both further mutagenesis and structure-based optimization and, in addition, for studies of NS2B–NS3 activity. Conceptually, it is likely that the generic technology reported in the present paper will be useful for the generation of active-site-specific antibody probes for multiple enzymes.
CandiSNPer: a web tool for the identification of candidate SNPs for causal variants
Authors: Schmitt Armin O. , Aßmus Jens , Bortfeldt Ralf H. , Brockmann Gudrun A. 
Published: February 2010

Abstract
Summary: Human single nucleotide polymorphism (SNP) chips which are used in genome-wide association studies (GWAS) permit the genotyping of up to 4 million SNPs simultaneously. To date, about 1000 human SNPs have been identified as statistically significantly associated with a disease or another trait of interest. The identified SNP is not necessarily the causal variant, but it is rather in linkage disequilibrium (LD) with it. CandiSNPer is a software tool that determines the LD region around a significant SNP from a GWAS. It provides a list with functional annotation and LD values for the SNPs found in the LD region. This list contains not only the SNPs for which genotyping data are available, but all SNPs with rs-IDs, thus increasing the likelihood to include the causal variant. Furthermore, plots showing the LD values are generated. CandiSNPer facilitates the preselection of candidate SNPs for causal variants.
Availability and Implementation: The CandiSNPer server is freely available at http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer. The source code is available to academic users ‘as is’ upon request. The web site is implemented in Perl and R and runs on an Apache server. The Ensembl database is queried for SNP data via Perl APIs.
Contact: armin.schmitt@agrar.hu-berlin.de
Energy and emission assessments of continuous descent approach
Authors: Turgut Enis T. , Usanmaz Oznur , Ozan Canarslanlar Ali , Sahin Ozlem 
Published: February 2010

PurposeContinuous descent approach (CDA) is a method, which allows the aircraft flying its individual optimal vertical profile down to runway threshold with engines operating at low‐thrust power. The main objective of this paper is to provide less‐fuel consumption, less noise and less emission with using CDA procedures instead of conventional procedures.Design/methodology/approachConventional and CDA procedures were modelled in the Istanbul terminal area (TMA), which has five entry points. The real speed and the real altitude limitations were maintained on these entry points. System for Assessing Aviation's Global Emissions research results were also used to determine the emission savings.FindingsWith CDA procedures, more than 40 kg fuel and 2 min time savings per flight are obtained; furthermore, regarding CO2and H2O, significant emission savings are also noted.Originality/valueSome of the benefits of CDA procedures are reported for Istanbul TMA by using true flight data.
Fruit and vegetable playing cards
Authors: Torkar Gregor , Pintarič Miša , Koch Verena 
Published: February 2010

PurposeThe purpose of this paper is to measure the effectiveness of fruit and vegetable playing cards for teaching schoolchildren about fruits and vegetables, health, and nutrition.Design/methodology/approachThe participants come from two primary schools in Slovenia: 53 boys and 57 girls. Their average age is 10 (8, 11). The pre‐intervention questioning is completed two or three days before and post‐intervention questioning is completed a week after playing the card game. The participating children answer ten multiple‐choice questions and one open‐ended question. Each participant plays the game for two 45‐min lessons. The main goal of the research is to measure changes in their knowledge about fruits and vegetables, health, and nutrition.FindingsAfter the intervention more children understand why the human body needs dietary fiber, water, and vitamins. The majority of those questioned also understand why fruits and vegetables are important in nutrition. The children learn which fruits and vegetables contain the most vitamin A, vitamin C, vitamin E, dietary fiber, and water.Originality/valueThe evaluation of the fruit and vegetable playing cards demonstrates that this game helps teach children about the nutrients in fruits and vegetables and importance of fruits and vegetables in a healthy diet.
Effect of filler morphology on tribological performances of polyimide composites
Authors: Yanjiang Song , Peng Zhu , Xiaodong Wang , Pei Huang 
Published: February 2010

PurposeThe purpose of this paper is to provide some useful information on the tribological performance of thermoplastic polyimide (TPI) reinforced with rigid glass fillers of different shapes and sizes under dry, water, and oil lubrication conditions.Design/methodology/approachRigid glass fillers of different shapes and sizes are chosen to modify TPI and its mechanical properties are measured. The stress‐strain behaviors of the composites are simulated by the finite element method and the effect of filler morphology is also considered. Furthermore, the tribological performance of the composites is investigated in different environmental media, including air, water, and oil.FindingsIt is demonstrated that the toughness of the materials decreases on filling them with rigid glass, and that stress concentration causes cracks around the spherical glass beads, which reduces the material impact strength. Owing to heat moulding technology, glass fiber has certain orientation and absorbs the impact energy effectively. A better wear‐resistant material is obtained by choosing a bigger filler due to its higher bond strength with the matrix. Under water and oil lubrication, the fatigue failure is the main reason for material wear, and fiber‐reinforced TPI has favorable wear‐resistance due to its shape. Meanwhile, glass beads could roll on the contact surface, which polishes the surface and reduces the friction coefficient, and its effect is reduced on oil lubrication for its high viscosity.Originality/valueThis paper analyzes the effect of rigid glass fillers of different shapes and sizes on the mechanical properties and tribological performance of polyimide composites.
Application of shape memory materials in fluid sealing technology
Authors: Ochoński Włodzimierz 
Published: February 2010

PurposeThe purpose of this paper is to present short characteristics of shape memory alloys (SMA) and shape memory polymers (SMP) and some examples of application of these materials in industrial sealing technology.Design/methodology/approachIn this paper, short characteristic of shape memory materials and design examples of applying them in industrial sealing technology such as: tube coupling in hydraulic systems, flanged pipe connections, lip radial seal, mechanical face seal, soft gland packing, magnetic fluid seal, and in bearing seal system for drill bit, are given.FindingsThe paper provides information about innovative fluid seal designs based on particular properties of the shape memory materials, applied in stationary joints, and rotary equipments. These new solutions provide often to simplify seal design, their miniaturization, increase of tightness, and reduction of operating costs.Originality/valueThis paper offers some new fluid seal designs based on the shape memory materials and their practical application in industrial sealing technology.
Size effects of SiO2 nanoparticles as oil additives on tribology of lubricant
Authors: Peng De‐Xing , Chen Cheng‐Hsien , Kang Yuan , Chang Yeon‐Pun , Chang Shi‐Yan 
Published: February 2010

PurposeThe purpose of this paper is to investigate the tribological properties of liquid paraffin with SiO2 nanoparticles additive made by a sol‐gel method.Design/methodology/approachThe tribological properties of the SiO2 nanoparticles as an additive in liquid paraffin are measured using a ball‐on‐ring wear tester to determine the optimal additive concentration. The mechanism that wear and friction are reduced is studied using scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), and atomic force microscope (AFM).FindingsExperimental results indicate that the sizes of the synthesized SiO2 nanoparticles are distributed uniformly and that the optimal concentrations of SiO2 nanoparticles in liquid paraffin is associated with better tribological properties than pure paraffin oil, and an anti‐wear (AW) ability that depends on the particle size.Originality/valueIt is shown in the paper that by reducing friction and AW, the lubricant prepared by the methods described can prolong operating hours of machinery.
An analytic hierarchy approach for intellectual capital
Authors: Asonitis Stefanos , Kostagiolas Petros A. 
Published: February 2010

PurposeThis paper aims to present a methodological framework for the identification of a hierarchy among the three categories of intellectual capital, i.e. human, organizational/structural and relational capital, with respect to their contribution to the objective of improving a library's performance. It also seeks to provide a case study of Greek central public libraries.Design/methodology/approachThe framework is based on an analytic hierarchy process (AHP) application including utilization of a Delphi method and ISO 11620 international standards. Finally, empirical evidence is produced for the Greek central public libraries.FindingsThe proposed framework may be employed for prioritizing intangible assets in libraries. For the Greek central public libraries it has been indicated that human capital contributes more than the organizational/structural capital and this in turn more than the relational capital.Research limitations/implicationsAlthough the proposed methodological framework is intended to be widely applicable, the case study results cannot be directly generalized due to the uniqueness of the Greek public libraries environment.Practical implicationsA hierarchy may be an invaluable tool for the library's management in order to better utilize the intangible resources and effectively allocate investments to human, organizational and relation capital assets in order to improve the library's performanceOriginality/valueThe paper shows that the framework for building a hierarchy of intellectual capital in libraries is based on a rather challenging research approach for prioritizing intangible assets with respect to predefined management objectives.
A study on application of multi‐sensor information fusion in pulsed GTAW
Authors: Chen Bo , Wang Jifeng , Chen Shanben 
Published: February 2010

PurposeWelding sensor technology is the key technology in welding process, but a single sensor cannot acquire adequate information to describe welding status. This paper addresses arc sensor and sound sensor to acquire the voltage and sound information of pulsed gas tungsten arc welding (GTAW) simultaneously, and uses multi‐sensor information fusion technology to fuse the information acquired by the two sensors. The purpose of this paper is to explore the feasibility and effectiveness of multi‐sensor information fusion in pulsed GTAW.Design/methodology/approachThe weld voltage and weld sound information are first acquired by arc sensor and sound sensor, then the features of the two signals are extracted, and the features are fused by weighted mean method to predict the changes of arc length. The weights of each feature are determined by optional distribution method.FindingsThe research findings show that multi‐sensor information fusion technology can effectively utilize the information of different sensors and get better result than single sensor.Originality/valueThe arc sensor and sound sensor are first used at the same time to get information about pulsed GTAW and the fusion result shows its advantages over single sensor; this reveals that multi‐sensor fusion technology is a valuable research area in welding process.
A model of environmental control and effective work
Authors: O'Neill Michael J. 
Published: February 2010

PurposeThe purpose of this paper is to present a model of “environmental control”. Environmental control can be provided through: furnishings and work tools that can be modified or manipulated, choice of time and location of work, organizational policies for flexible work programs, training, and computing and communications technologies that extend control. This paper seeks to propose that enhanced environmental control is related to improved individual, group and organizational performance.Design/methodology/approachA conceptual model is presented of environmental control coupled with a review and analysis of relevant literature that support the model and identify areas that require further development and research.FindingsThe literature review and analysis show support for the model of environmental control. The research reviewed reveals a consistent relationship between workplace capabilities that provide control, and positive behavioral and business performance outcomes for individuals, teams and business units. The review identifies gaps in the empirical support for the model and provides directions for future research.Practical implicationsUltimately, environmental control is proposed as a means for providing choice about where, when and how to work, which can be used to improve the performance of people and organizations. Thus, environmental control is a crucial capability in which organizations should invest, by optimizing choice through workspace, policies, and technology. By leveraging control as a central component of workplace strategy, organizations may enhance their competitive advantage.Originality/valueMuch of the research described in the paper, and methods employed, are appropriate for exploratory research and theory‐building.