bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fatty acids composition of some freshwater fish
Authors: Ugoala Chukwuemeka , Ndukwe George , Audu Tokunbo 
Published: May 2009

AbstractThe aims of this paper were to investigate the component fatty acids of some freshwater fish species by comparing the levels of essential fatty acids present. The FAME were determined by GC-MS and were identified using retention time locked methods and retention time databases. The fatty acids profiles include minor amounts of odd-number, branched-chain, and even-number fatty acids as well as saturated components, the MUFA and PUFA. The major SFA were C14:0 and C16:0. The C18:1 was the prominent MUFA. The dominant PUFA are of the omega-6 series and are found chiefly in C18:2 fatty acids. The essential fatty acids compositions showed prominence in C18:3n-3 and C18:2n-6. The branched chain fatty acids identified C15:0, C16:0, C17:0, C18:2 and C20:0. The overall significance of this study is the revelation that freshwater fishes have irregular pattern of FA which are good sources of omega-6 EFA. The high percent of branched and saturated FA in freshwater fish gives them an advantage in curing processing.
The carbohydrate-binding domain on galectin-1 is more extensive for a complex glycan than for simple saccharides: implications for galectin–glycan interactions at the cell surface
Authors: Miller Michelle C. , Nesmelova Irina V. , Platt David , Klyosov Anatole , Mayo Kevin H. 
Published: May 2009

gal-1 (galectin-1) mediates cell–cell and cell–extracellular matrix adhesion, essentially by interacting with β-galactoside-containing glycans of cell-surface glycoconjugates. Although most structural studies with gal-1 have investigated its binding to simple carbohydrates, in particular lactose and N-acetyl-lactosamine, this view is limited, because gal-1 functions at the cell surface by interacting with more complex glycans that are heterogeneous in size and composition. In the present study we used NMR spectroscopy to investigate the interaction of human gal-1 with a large (120 kDa) complex glycan, GRG (galactorhamnogalacturonate glycan), that contains non-randomly distributed mostly terminal β(1→4)-linked galactose side chains. We used 15N–1H-HSQC (heteronuclear single quantum coherence) NMR experiments with 15N-enriched gal-1 to identify the GRG-binding region on gal-1 and found that this region covers a large surface area on gal-1 that includes the quintessential lactose-binding site and runs from that site through a broad valley or cleft towards the dimer interface. HSQC and pulsed-field-gradient NMR diffusion experiments also show that gal-1 binds GRG with a gal-1:GRG stoichiometry of about 5:1 (or 6:1) and with average macroscopic and microscopic equilibrium dissociation constants (Kd) of 8×10−6 M and 40×10−6 M (or 48×10−6 M) respectively, indicating stronger binding than to lactose (Kd=520×10−6 M). Although gal-1 may bind GRG in various ways, the glycan can be competed for by lactose, suggesting that there is one major mode of interaction. Furthermore, even though terminal motifs on GRG are Gal-β(1→4)-Gal rather than the traditional Gal-β(1→4)-Glc/GlcNAc (where GlcNAc is N-acetylglucosamine), we show that the disaccharide Gal-β(1→4)-Gal can bind gal-1 at the lactose-binding domain. In addition, gal-1 binding to GRG disrupts inter-glycan interactions and decreases glycan-mediated solution viscosity, a glycan decongestion effect that may help explain why gal-1 promotes membrane fluidity and lateral diffusion of glycoconjugates within cell membranes. Overall, our results provide an insight into the function of galectin in situ and have potential significant biological consequences.
Non-esterified fatty acids increase arterial pressure via central sympathetic activation in humans
Authors: Florian John P. , Pawelczyk James A. 
Published: May 2009

Previous studies have shown that acute increases in plasma NEFAs (non-esterified fatty acids) raise SVR (systemic vascular resistance) and BP (blood pressure). However, these studies have failed to distinguish between CNS (central nervous system) mechanisms that raise sympathetic activity and paracrine mechanisms that increase SVR directly, independent of CNS involvement. The aim of the present study was to directly determine whether the sympathetic nervous system contributes to the pressor response to NEFAs. On 2 days separated by at least 2 weeks, 17 lean healthy volunteers (ten male/seven female; age, 22±1 years; body mass index, 23±1 kg/m2; values are means±S.E.M.) received a 4-h intravenous infusion of 20% Intralipid® or placebo (in a single-blind randomized balanced order). MSNA (muscle sympathetic nerve activity), HR (heart rate), BP (oscillometric brachial measurement) and (cardiac output; acetylene rebreathing) were measured before and throughout infusion. The change in HR (+8.2±1.0 and +2.4±1.2 beats/min), systolic BP (+14.0±1.6 and +3.2±2.5 mmHg) and diastolic BP (+8.2±1.0 and −0.1±1.7 mmHg) were significantly greater after the 4-h infusion of Intralipid® compared with placebo (P&lt;0.001). The change in BP with Intralipid® resulted from an increase in SVR (/mean arterial pressure; P&lt;0.001) compared with baseline, without a change in . MSNA burst frequency increased during Intralipid® infusion compared with baseline (+4.9±1.3 bursts/min; P&lt;0.05), and total MSNA (frequency×amplitude) was augmented 65% (P&lt;0.001), with no change during placebo infusion. Lipid infusion increased insulin, aldosterone and F2-isoprostane, but not leptin, concentrations. On the basis of the concomitant increase in BP, MSNA and SVR, we conclude that central sympathetic activation contributes to the pressor response to NEFAs.
Beyond Surface Similarities: Telecommunications Industry Structure Evolution in Finland and New Zealand
Authors: Howell Bronwyn , Sangekar Manisha 
Published: May 2009

Abstract
Finland and New Zealand share many geographic, demographic and economic similarities. Their telecommunications markets also demonstrate many similarities; but behind these superficial similarities lie important structural differences that influence market performance. By tracing the evolutionary path of each market from the nineteenth century, this paper identifies how ownership and control structures in the very early stages of market development have influenced the shape of each market today. The paper concludes that an appreciation of the different economic histories and cultures in each country’s telecommunications market is helpful for understanding subsequent industry responses to changes in regulatory processes and government policies.
E‐commerce and SMEs—The Need for Caution
Authors: Hashim Noor 
                      Azuan 
Published: May 2009

Abstract
Much has been written about e‐commerce. Many authors seem certain that e‐commerce conveys undisputed benefits. Yet, e‐commerce is not being adopted readily by SMEs. The disinclination of SMEs to adopt and use e‐commerce deserves serious attention, given the role that SMEs play in all economies. This paper looks critically at the issue. It highlights findings from a large‐scale survey of SMEs and interviews with SME managers across Malaysia. Results show online payment and online buying are not common. Websites are used for little more than providing contact details of the company and information about the company’s goods and services. While there may be good, logical reasons for SME managers having websites, many are clearly just boys with toys.
Reverse Salients at the Meta‐System Level: The Case of Containerization
Authors: Sawhney Harmeet , Wang Xiaofei 
Published: May 2009

Abstract
The power of Hughes’ concept of reverse salients is evident in its widespread adoption and use in areas as diverse as water distribution, metals production, and mobile music businesses. In all these studies the reverse salient concept has been mainly applied to internal problems in the development of a large‐scale system. We focus not only on reverse salients within a system but also at the meta‐system level, wherein different systems come together to create a system of systems. We draw on the experience with containerization, which is a particularly interesting case study because it developed in response to the reverse salients at the meta‐system level—the bottlenecks at the interfaces between motor carriers, railroads, and water carriers, the three systems that together form the overall surface transportation system. We examine the processes both within each system and also at the meta‐system level and expand our understanding of reverse salients as a system development phenomenon.
Robust synthetic biology design: stochastic game theory approach
Authors: Chen Bor-Sen , Chang Chia-Hung , Lee Hsiao-Ching 
Published: May 2009

Abstract
Motivation: Synthetic biology is to engineer artificial biological systems to investigate natural biological phenomena and for a variety of applications. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to uncertain initial conditions and disturbances of extra-cellular environments on the host cell. At present, how to design a robust synthetic gene network to work properly under these uncertain factors is the most important topic of synthetic biology.
Results: A robust regulation design is proposed for a stochastic synthetic gene network to achieve the prescribed steady states under these uncertain factors from the minimax regulation perspective. This minimax regulation design problem can be transformed to an equivalent stochastic game problem. Since it is not easy to solve the robust regulation design problem of synthetic gene networks by non-linear stochastic game method directly, the Takagi–Sugeno (T–S) fuzzy model is proposed to approximate the non-linear synthetic gene network via the linear matrix inequality (LMI) technique through the Robust Control Toolbox in Matlab. Finally, an in silico example is given to illustrate the design procedure and to confirm the efficiency and efficacy of the proposed robust gene design method.
Availability: http://www.ee.nthu.edu.tw/bschen/SyntheticBioDesign_supplement.pdf
Contact: bschen@ee.nthu.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
Complex discovery from weighted PPI networks
Authors: Liu Guimei , Wong Limsoon , Chua Hon Nian 
Published: May 2009

Abstract
Motivation: Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, which makes it possible to predict protein complexes from protein–protein interaction (PPI) networks. However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately.
Results: We use an iterative scoring method to assign weight to protein pairs, and the weight of a protein pair indicates the reliability of the interaction between the two proteins. We develop an algorithm called CMC (clustering-based on maximal cliques) to discover complexes from the weighted PPI network. CMC first generates all the maximal cliques from the PPI networks, and then removes or merges highly overlapped clusters based on their interconnectivity. We studied the performance of CMC and the impact of our iterative scoring method on CMC. Our results show that: (i) the iterative scoring method can improve the performance of CMC considerably; (ii) the iterative scoring method can effectively reduce the impact of random noise on the performance of CMC; (iii) the iterative scoring method can also improve the performance of other protein complex prediction methods and reduce the impact of random noise on their performance; and (iv) CMC is an effective approach to protein complex prediction from protein interaction network.
Contact: liugm@comp.nus.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
TheNGATHADistal Organ Development Genes Are Essential for Style Specification inArabidopsis
Authors: Alvarez John Paul , Goldshmidt Alexander , Efroni Idan , Bowman John L. , Eshed Yuval 
Published: May 2009

AbstractFloral organ identities are specified by a few transcription factors that act as master regulators. Subsequently, specification of organ axes programs the distribution of distinct tissue types within the organs that themselves develop unique identities. The C-class, AGAMOUS-clade MADS box genes are primary promoters of the gynoecium, which is divided into a distal style and a subtending ovary along the apical-basal axis. We show that members of a clade of B3 domain transcription factors, NGATHA1 (NGA1) to NGA4, are expressed distally in all lateral organs, and all four have a redundant and essential role in style development. Loss of all four genes results in gynoecia where style is replaced by valve-like projections and a reduction in style-specific SHATTERPROOF1 (SHP1) expression. In agreement, floral misexpression of NGA1 promotes ectopic style and SHP1 expression. STYLISH1, an auxin biosynthesis inducer, conditionally activated NGA genes, which in turn promoted distal expression of other STY genes in a putative positive feedback loop. Inhibited auxin transport or lack of YABBY1 gene activities resulted in a basally expanded style domain and broader expression of NGA genes. We speculate that early gynoecium factors delimit NGA gene response to an auxin-based signal, elicited by STY gene activity, to restrict the activation of style program to a late and distal carpel domain.
Expression and regulation of the NALP3 inflammasome complex in periodontal diseases
Authors: Bostanci N , Emingil G , Saygan B , Turkoglu O , Atilla G , Curtis M A , Belibasakis G N 
Published: May 2009

Summary
Periodontitis is an infectious process characterized by inflammation affecting the supporting structures of the teeth. Porphyromonas gingivalis is a major oral bacterial species implicated in the pathogenesis of periodontitis. Processing of interleukin (IL)-1 family cytokines is regulated by an intracellular innate immune response system, known as the NALP3 [nacht domain-, leucine-rich repeat-, and pyrin domain (PYD)-containing protein 3] inflammasome complex. The aim of the present study was to investigate by quantitative real-time polymerase chain reaction (PCR) the mRNA expression of NALP3, its effector molecule apoptosis associated speck-like protein (ASC), its putative antagonist NLRP2 (NLR family, PYD-containing protein 2), IL-1β and IL-18 (i) in gingival tissues from patients with gingivitis (n = 10), chronic periodontitis (n = 18), generalized aggressive periodontitis (n = 20), as well as in healthy subjects (n = 20), (ii) in vitro in a human monocytic cell line (Mono-Mac-6), in response to P. gingivalis challenge for 6 h. The clinical data indicate that NALP3 and NLRP2, but not ASC, are expressed at significantly higher levels in the three forms of inflammatory periodontal disease compared to health. Furthermore, a positive correlation was revealed between NALP3 and IL-1β or IL-18 expression levels in these tissues. The in vitro data demonstrate that P. gingivalis deregulates the NALP3 inflammasome complex in Mono-Mac-6 cells by enhancing NALP3 and down-regulating NLRP2 and ASC expression. In conclusion, this study reveals a role for the NALP3 inflammasome complex in inflammatory periodontal disease, and provides a mechanistic insight to the host immune responses involved in the pathogenesis of the disease by demonstrating the modulation of this cytokine-signalling pathway by bacterial challenge.
Root responses along a subambient to elevated CO2gradient in a C3–C4grassland
Authors: ANDERSON LAUREL J. , DERNER JUSTIN D. , POLLEY H. WAYNE , GORDON WENDY S. , EISSENSTAT DAVID M. , JACKSON ROBERT B. 
Published: May 2009

AbstractAtmospheric CO2(Ca) concentration has increased significantly during the last 20 000 years, and is projected to double this century. Despite the importance of belowground processes in the global carbon cycle, community‐level and single species root responses to risingCaare not well understood. We measured net community root biomass over 3 years using ingrowth cores in a natural C3–C4grassland exposed to a gradient ofCafrom preglacial to future levels (230–550 μmol mol−1). Root windows and minirhizotron tubes were installed below naturally occurring stands of the C4perennial grassBothriochloa ischaemumand its roots were measured for respiration, carbohydrate concentration, specific root length (SRL), production, and lifespan over 2 years. Community root biomass increased significantly (P<0.05) withCaover initial conditions, with linear or curvilinear responses depending on sample date. In contrast,B. ischaemumproduced significantly more roots at subambient than elevatedCain minirhizotrons. The lifespan of roots with five or more neighboring roots in minirhizotron windows decreased significantly at highCa, suggesting that after dense root growth depletes soil resource patches, plants with carbon surpluses readily shed these roots. Root respiration inB. ischaemumshowed a curvilinear response toCaunder moist conditions in June 2000, with the lowest rates atCa<300 μmol mol−1and peak activity at 450 μmol mol−1in a quadratic model.B. ischaemumroots at subambientCahad higher SRLs and slightly higher carbohydrate concentrations than those at higherCa, which may be related to drier soils at lowCa. Our data emphasize that belowground responses of plant communities toCacan be quite different from those of the individual species, and suggest that complex interactions between and among roots and their immediate soil environment influence the responses of root physiology and lifespan to changingCa.
Marshland conversion to cropland in northeast China from 1950 to 2000 reduced the greenhouse effect
Authors: HUANG YAO , SUN WENJUAN , ZHANG WEN , YU YONGQIANG , SU YANHUA , SONG CHANGCHUN 
Published: May 2009

AbstractIt has been well recognized that converting wetlands to cropland results in loss of soil organic carbon (SOC), while less attention was paid to concomitant changes in methane (CH4) and nitrous oxide (N2O) emissions. Using datasets from the literature and field measurements, we investigated loss of SOC and emissions of CH4 and N2O due to marshland conversion in northeast China. Analysis of the documented crop cultivation area indicated that 2.91 Mha of marshland were converted to cropland over the period 1950–2000. Marshland conversion resulted in SOC loss of ∼240 Tg and introduced ∼1.4 Tg CH4 and ∼138 Gg N2O emissions in the cropland, while CH4 emissions reduced greatly in the marshland, cumulatively ∼28 Tg over the 50 years. Taking into account the loss of SOC and emissions of CH4 and N2O, the global warming potential (GWP) at a 20‐year time horizon was estimated to be ∼180 Tg CO2_eq. yr−1 in the 1950s and ∼120 Tg CO2_eq. yr−1 in the 1990s, with a ∼33% reduction. When calculated at 100‐year time horizon, the GWP was ∼73 Tg CO2 _eq. yr−1 in the 1950s and ∼58 Tg CO2_eq. yr−1 in the 1990s, with a ∼21% reduction. It was concluded that marshland conversion to cropland in northeast China reduced the greenhouse effect as far as GWP is concerned. This reduction was attributed to a substantial decrease in CH4 emissions from the marshland. An extended inference is that the declining growth rate of atmospheric CH4 since the 1980s might be related to global loss of wetlands, but this connection needs to be confirmed.
Reproductive interference determines persistence and exclusion in species interactions
Authors: Kishi Shigeki , Nishida Takayoshi , Tsubaki Yoshitaka 
Published: May 2009

Summary 1. Reproductive interference is a negative interspecific sexual interaction that adversely affects the fitness of males and females during reproductive process. Theoretical studies suggest that because reproductive interference is characterized by positive frequency dependence it is far more likely to cause species exclusion than the density dependence of resource competition. However, the respective contributions of resource competition and reproductive interference to species exclusion, which have been frequently observed in many competition studies, remain unclear. 2. We show that reproductive interference is a far more critical cause of species exclusion than resource competition in the competition between Callosobruchus bean weevil species. In competition experiments over several generations, we manipulated the initial relative abundance of the adzuki bean beetle, Callosobruchus chinensis, and the southern cowpea beetle, Callosobruchus maculatus. When the initial adult ratio of C. chinensis : C. maculatus were 6 : 2 and 4 : 4, C. chinensis excluded C. maculatus. However, when C. maculatus was four times more abundant than C. chinensis at the start, we observed the opposite outcome. 3. A behavioural experiment using adults of the two species revealed asymmetric reproductive interference. The fecundity and longevity of C. maculatus females, but not those of C. chinensis females, decreased when the females were kept with heterospecific males. Fecundities of females of both species decreased as the number of heterospecific males increased. In contrast, resource competition at the larval stage resulted in higher survival of C. maculatus than of C. chinensis. 4. These results suggest that the positive frequency‐dependent effect of reproductive interference resulted in species exclusion, depending on the initial population ratio of the two species, and the asymmetry of the interference resulted in C. chinensis being dominant in this study, as in previous studies. Classical competition studies should be reviewed in light of this evidence for reproductive interference.
Quantifying the genetic component of phenotypic variation in unpedigreed wild plants: tailoring genomic scan for within‐population use
Authors: HERRERA C. M. , BAZAGA P. 
Published: May 2009

AbstractThe study of adaptive genetic variation in natural populations is central to evolutionary biology. Quantitative genetics methods, however, are hardly applicable to long‐lived organisms, and current knowledge on adaptive genetic variation in wild plants mostly refers to annuals and short‐lived perennials. Studies on long‐lived species are essential to explore possible life‐history correlates of genetic variation, selection, and trait heritability. In this paper, we propose a method based on molecular markers to quantify the genetic basis of individual phenotypic differences in wild plants under natural conditions. Rather than focusing on inferring individual relatedness to estimate the heritability of phenotypic traits, we directly estimate the proportion of observed phenotypic variance that is statistically accounted for by genotypic differences between individuals. This is achieved by (i) identifying loci that are correlated across individuals with the phenotypic trait of interest by means of an amplified fragment length polymorphism (AFLP)‐based explorative genomic scan, and (ii) fitting multiple regression and linear random effect models to estimate the effects of genotype, environment and genotype × environment on phenotypes. We apply this method to estimate genotypic and environmental effects on cumulative maternal fecundity in a wild population of the long‐livedViola cazorlensismonitored for 20 years. Results show that between 56–63% (depending on estimation method) of phenotypic variance in fecundity is accounted for by genotypic differences in 11 AFLP loci that are significantly related to fecundity. Genotype × environment effects accounted for 38% of fecundity variance, which may help to explain the unexpectedly high levels of genetic variance for fecundity found.