bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?
Authors: Strand Tanja M. , Segelbacher Gernot , Quintela María , Xiao Lingyun , Axelsson Tomas , Höglund Jacob 
Published: January 2012

AbstractThe ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here, we use both neutral and major histocompatibility complex (MHC) markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled 11 different populations; five continuous, three isolated, and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs) which both were found to be neutral, and two functional MHC genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented.
Predicting climate change impact on nutrient pollution in waterways: a case study in the upper catchment of the Latrobe River, Australia
Authors: Alam Md Jahangir , Dutta Dushmanta 
Published: January 2012

ABSTRACTClimate change, together with the increasing influence of anthropogenic activities in the atmosphere, has impacted ecosystems enormously, escalating much concern for pollution control and management. Proper assessment of the effect of temperature rise due to global warming and the subsequent changes in hydrology on catchment biogeochemical processes is essential for accurate prediction of pollution level. Not many studies have been carried out on the aspect of climate change‐driven nutrient pollution assessment, and inability of many existing modelling tools persists. With these research needs in focus, this study has made an assessment of climate change impact on nutrient pollution by applying a distributed hydrological modelling tool with newly developed nutrient modules that incorporate climate‐based description of catchment and in‐stream processes. The model has been applied to the Latrobe River basin in Australia and calibrated and validated prior to simulation of climate change scenarios. The scenarios have been developed on the basis of the Intergovernmental Panel on Climate Change projections of higher‐emission scenario A1F1 for this region. The model has predicted the impact of temperature rise on the nutrient‐transformation processes and the subsequent releases into waterways for projected high‐flow and low‐flow situations. The results show that climate change is likely to contribute to increase in nutrient pollution in the waterways. The results have been used to assess future stream water quality condition in the study area. Copyright © 2012 John Wiley & Sons, Ltd.
Punishing and compensating others at your own expense: The role of empathic concern on reactions to distributive injustice
Authors: Leliveld Marijke C. , van Dijk Eric , van Beest Ilja 
Published: January 2012

AbstractWhen confronted with violations of justice, people may be motivated not only to punish the violator, but also to compensate the victim. Whereas prior research has primarily concentrated on the question of when people are willing to punish, we provide a more comprehensive picture by also studying the willingness to compensate and by assessing the moderating role of empathic concern. Study 1 introduces the altruistic compensation game and shows that especially high empathic (compared to low empathic) people are willing to give up parts of their own resources to financially compensate the victims of distributive injustice. Study 2 completes the picture by directly comparing altruistic compensation with altruistic punishment. The study showed that high empathic people decided to compensate the victim, but low empathic people decided to punish the offender. Copyright © 2012 John Wiley & Sons, Ltd.
Modeling and simulation of nanoparticle separation through a solid‐state nanopore
Authors: Jubery Talukder Z. , Prabhu Anmiv S. , Kim Min J. , Dutta Prashanta 
Published: January 2012

AbstractRecent experimental studies show that electrokinetic phenomena such as electroosmosis and electrophoresis can be used to separate nanoparticles on the basis of their size and charge using nanopore‐based devices. However, the efficient separation through a nanopore depends on a number of factors such as externally applied voltage, size and charge density of particle, size and charge density of membrane pore, and the concentration of bulk electrolyte. To design an efficient nanopore‐based separation platform, a continuum‐based mathematical model is used for fluid. The model is based on Poisson–Nernst–Planck equations along with Navier–Stokes equations for fluid flow and on the Langevin equation for particle translocation. Our numerical study reveals that membrane pore surface charge density is a vital parameter in the separation through a nanopore. In this study, we have simulated high‐density lipoprotein (HDL) and low‐density lipoprotein (LDL) as the sample nanoparticles to demonstrate the capability of such a platform. Numerical results suggest that efficient separation of HDL from LDL in a 0.2 M KCL solution (resembling blood buffer) through a 150 nm pore is possible if the pore surface charge density is ∼ −4.0 mC/m2. Moreover, we observe that pore length and diameter are relatively less important in the nanoparticle separation process considered here.
Electrophoretically driven SDS removal and protein fractionation in the shotgun analysis of membrane proteomes
Authors: Liu Yi , Lin Yong , Yan Yizhong , Li Jianjun , He Quanze , Chen Ping , Wang Xianchun , Liang Songping 
Published: January 2012

AbstractSDS is mostly used to enhance the solubilization and extraction of membrane proteins due to its strong detergency and low cost. Nevertheless, SDS interferes with the subsequent procedures and needs to be removed from the samples. In this work, a special gradient gel electrophoresis (GGE) system was developed to remove SDS from the SDS‐solubilized protein samples. As a proof‐of‐principle experiment, the GGE system was designed to be composed of an agarose loading layer, six polyacrylamide fractionation layers with different concentrations and a high‐concentration polyacrylamide sealing layer. The advantages of the GGE system are that it not only can electrophoretically remove SDS efficiently so that the protein loss resulted from the repeated gel washing after electrophoresis was avoided, but also can reduce the complexity of the sample, prevent the precipitation of proteins after loading and avoid the loss of proteins with low molecular weight during the electrophoresis. Using GGE system, about 85% of SDS in the sample and gel was electrophoretically removed and the proteins were fractionated. Compared with the two representative gel‐based sample cleanup methods reported in literature, GGE‐based strategy significantly improved the identification efficiency of proteins in terms of the number and coverage of the identified proteins.
Poly(ethylene glycol)‐coated microfluidic devices for chip electrophoresis
Authors: Schulze Marcel , Belder Detlev 
Published: January 2012

AbstractHerein, we report on a strategy for durable modification of the channel surface in microfluidic glass chips with the neutral hydrophilic‐coating material poly(ethylene glycol) PEG‐1M‐100. Applied in microchip electrophoresis such PEG‐coated devices exhibit a suppressed electroosmotic flow and reduced analyte adsorption. The PEG‐coated chips were successfully applied in chip electrophoresis of FITC‐labelled amines and amino acids and native proteins as well as in chiral separations. The performance of the coated chips was found to be superior compared with uncoated microchips. The coated chips exhibited high stability and the relative standard deviation of migration times in PEG‐coated devices was less than 2%.
On the efficiency of viscous dampers in reducing various seismic responses of wall structures
Authors: Lavan Oren 
Published: January 2012

SUMMARYThis paper rigorously assesses the efficiency of viscous dampers connecting two walls to result in “viscously coupled shear walls”. This assessment also holds for viscous dampers in wall structures as they are mounted on frames parallel to the walls leading to “wall‐viscous frame” systems. A continuum approach is adopted to model the structure so as to enable non‐dimensional formulation of the governing equations. Those equations reveal that, under the approximations considered, the system damping ratio (defined here by 0.5 sqrt(c^2/(m*EI))) is a convenient compact single parameter controlling the response reduction w.r.t. the response of the corresponding undamped system. In contrast to coupled shear walls, this controlling parameter does not depend on the height of the building; therefore, the viscously damped system is efficient for low‐rise buildings as well. The continuum approach also allows a semi‐analytical solution of the eigenproblem in the complex domain followed by a complex modal spectral analysis. Those solutions reveal the efficiency of the added damping in reducing not only the displacements, inter‐story drifts, and wall moments but also the absolute accelerations, wall shear, total shear, and total overturning moments. The results of the analyses and the non‐dimensional tables and graphs developed for important response parameters lead to a simple method that could easily be implemented in practice for the purpose of initial design. Copyright © 2012 John Wiley & Sons, Ltd.
Synthesis and characterization of magnetic beads containing aminated fibrous surfaces for removal of Reactive Green 19 dye: kinetics and thermodynamic parameters
Authors: Bayramoglu Gulay , Altintas Begum , Arica Mehmet Yakup 
Published: January 2012

AbstractBACKGROUND: Poly(HEMA‐co‐MMA) beads were prepared from 2‐hydroxyethyl‐methacrylate (HEMA) and methylmethacrylate (MMA) in the presence of FeCl3. Thermal co‐precipitation of Fe(III) ions containing beads with Fe(II) ions was carried out under alkaline conditions. The magnetic beads were grafted with poly(glycidylmethacrylate; p(GMA)), and the epoxy groups of the grafted p(GMA) brushes were converted into amino groups by reaction with ammonia.RESULTS: The magnetic beads were characterized by surface area measurement, electron spin resonance (ESR), Mössbauer spectroscopy and scanning electron microscopy (SEM). The maximum adsorption of Reactive Green‐19 (RG‐19) dye on the p(GMA) grafted and amine modified magnetic beads was around pH 3.0. The adsorption capacity of magnetic beads was 84.6 mg dye g−1. The effects of adsorbent dosage, ionic strength and temperature have also been reported. Batch kinetic sorption experiments showed that a pseudo‐second‐order rate kinetic model was applicable.CONCLUSION: The p(GMA) grafted and amine modified magnetic beads (adsorbent) were expected to have the advantage of mobility of the grafted chains in the removal of acidic dyes from aqueous solutions. The magnetic beads have potential as an adsorbent for removal of pollutants under various experimental conditions without significant reduction in their initial adsorption capacity. Copyright © 2011 Society of Chemical Industry
ASM3 extended for two‐step nitrification–denitrification: a model reduction for sequencing batch reactors
Authors: Cruz Bournazou M. N. , Arellano‐Garcia H. , Wozny G. , Lyberatos G. , Kravaris C. 
Published: January 2012

AbstractBACKGROUND: The ASM3 extended for two‐step nitrification–denitrification represents the most accurate model for the description of the activated sludge process with nitrate bypass nitrification–denitrification. This model includes 20 reaction rates, 15 state variables, and more than 35 parameters, which make its calculation costly and difficult to estimate. The lack of a fast and accurate model able to predict both concentration of nitrite and nitrate over time is the principal obstacle for efficient model‐based optimization and model‐based control.RESULTS: In this work, a fast and accurate model for the activated sludge process in a sequencing batch reactor is proposed. For this purpose, the ASM3 extended for two‐step nitrification–denitrification, a 15‐state variable model built for a general description of the ASP, is reduced to match the specific conditions of sequencing batch reactor systems with shortcut biological nitrogen removal to a nine‐state model and then further to a six‐state and five‐state model under appropriate assumptions. The proposed model maintains the two‐step nitrification–denitrification process feature of the original model and can thus describe the bypass of nitrate, showing increased tractability and lower computer costs. Different approaches for model reduction together with an exhaustive analysis of the extended ASM3 model as well as the process are discussed.CONCLUSIONS: The resulting model with only five differential equations reduces the calculation time by up to one order of magnitude, while maintaining a high description accuracy, demonstrating the advantages of model reduction. Copyright © 2012 Society of Chemical Industry
Optimization of biological synthesis of silver nanoparticles using Lactobacillus casei subsp. casei
Authors: Korbekandi Hassan , Iravani Siavash , Abbasi Sajjad 
Published: January 2012

AbstractBACKGROUND: The objectives of this study were optimization of silver nanoparticle synthesis using biotransformations by Lactobacillus casei subsp. casei, and studying the location of nanoparticles synthesis in this microorganism.RESULTS: The presence of AgNO3 (0.1 mmol L−1) in the culture as the enzyme inducer, and glucose (56 mmol L−1) as the electron donor in the reaction mixture had positive effects on nanoparticle production. By gradually increasing the concentration of AgNO3 (as the substrate) to 6 mmol L−1, nanoparticle production was increased. By increasing biomass, nanoparticles production was also increased. Biosynthesized silver nanoparticles were almost spherical, single (25–50 nm) or in aggregates (100 nm), attached to the surface of biomass or were inside and outside of the cells.CONCLUSION: The present study demonstrated the bioreductive synthesis of silver nanoparticles using L. casei subsp. casei at room temperature. In this research, and due to experience in optimization of biotransformation reactions, the reaction conditions were successfully optimized to increase the yield of nanoparticles production and productivity of this biosynthetic approach. Copyright © 2012 Society of Chemical Industry
Enhanced intracellular delivery and multi‐target gene silencing triggered by tripodal RNA structures
Authors: Chang Chan Il , Lee Tae Yeon , Kim Sera , Sun Xiangao , Hong Sun Woo , Yoo Jae Wook , Dua Pooja , Kang Hye Suk , Kim Soyoun , Li Chiang J. , Lee Dong‐Ki 
Published: January 2012

AbstractBackgroundThe development of gene interfering RNA (iRNA) molecules such as small interfering RNAs (siRNAs) and antagomirs provides promising therapeutic modalities for targeting specific mRNAs and microRNAs (miRNAs) involved in disease mechanisms. Therapeutic iRNA strategy against cancer or hypermutable viruses prefers targeting multiple genes simultaneously to achieve synergistic inhibition and to prevent resistance.MethodsIn the present study, we report chemically synthesized, multi‐target gene interfering RNA structures based upon branched, tripodal interfering RNAs (termed T‐tiRNAs).ResultsThe T‐tiRNAs could simultaneously inhibit up to three different mRNAs or miRNAs by harboring three siRNA or antagomir units. Moreover, when complexed with cationic delivery vehicles, T‐tiRNAs showed enhanced gene interfering activity over conventional siRNAs or antagomirs as a result of increased intracellular delivery.ConclusionsThe data obtained in the present study provide an example of synthetic multi‐functional RNA structures that enable multiple gene interference in mammalian cells, which could become powerful tools for an efficient combinatorial iRNA strategy. Copyright © 2012 John Wiley & Sons, Ltd.
Anthocyanin‐rich red cabbage (Brassica oleracea L.) extract attenuates cardiac and hepatic oxidative stress in rats fed an atherogenic diet
Authors: Sankhari Jayanta M , Thounaojam Menaka C , Jadeja Ravirajsinh N , Devkar Ranjitsinh V , Ramachandran A V 
Published: January 2012

AbstractBACKGROUND: Oxidative stress induced by reactive oxygen species plays an important role in the aetiology of several diseases including atherosclerosis and coronary heart disease. Anthocyanin‐rich extracts have been shown to possess a variety of therapeutic roles, including antioxidant, cardioprotective and hepatoprotective properties. The present inventory was undertaken to evaluate the protective role of anthocyanin‐rich red cabbage extract (ARCE) on an atherogenic (ATH) diet‐induced hypercholesterolaemia and related cardiac and, hepatic oxidative stress in rats.RESULTS: ARCE (100 mg kg−1 body weight) treatment of rats fed the ATH diet significantly prevented elevation in serum and tissue lipids, circulating levels of cardiac and hepatic damage markers, and resulted in excretion of lipids through faeces. Also, the ARCE extract significantly attenuated alterations in the cardiac and hepatic antioxidants and lipid peroxidation, and histopathological changes in cardiac and hepatic tissue.CONCLUSION: Thus, the present study provides the first scientific evidence for a protective role of ARCE against ATH diet‐induced hypercholesterolaemia and cardiac and hepatic oxidative stress. Copyright © 2012 Society of Chemical Industry
Land reclamation and short‐term cultivation change soil microbial communities and bacterial metabolic profiles
Authors: He Xun‐yang , Su Yi‐rong , Liang Yue‐ming , Chen Xiang‐bi , Zhu Han‐hua , Wang Ke‐lin 
Published: January 2012

AbstractBACKGROUND: Soil microbes play an important role in many critical ecosystem processes, but little is known about the effects of land reclamation and short‐term cultivation on microbial communities in red soil. In this study, soil microbial communities under five land use patterns—artificial pine forest (Fp), tussock and shrub (TS), shrubbery (Sh), sugarcane (Su) and maize and cassava rotation (Ma)—were characterised by DNA fingerprinting and metabolic profiling to reveal how land reclamation and cultivation affect the underlying diversity and function of soil microbial communities in southwestern China.RESULTS: Eight years of reclamation and cultivation significantly affected population size, composition and structure, bacterial metabolic profiles and diversity values (Shannon–Wiener index) of soil microbial communities. Soil organic carbon and pH were the most important factors shaping the underlying microbial communities; however, with significant correlations between soil carbon/nitrogen ratio and bacterial taxonomic and metabolic diversities, soil total nitrogen was a potentially important factor for soil microbial composition and function, as well as soil moisture, cation exchange capacity and physical structure to a lesser extent. In addition, the lowest pH, lower nutrient availability and the most compact soil in pine forest resulted in the lowest microbial taxonomic and metabolic diversities among the five land use patterns studied.CONCLUSION: Soil organic carbon, nitrogen and pH appeared to be the most important factors influencing microbial biomass, composition and function in red soil of southwestern China. The study suggests that measures to lessen the impact of changes in this edaphic environment should be taken to avoid an imbalance of microbial function and improve ecological sustainability in southwestern China. Copyright © 2012 Society of Chemical Industry
The effect of rice straw incorporation into paddy soil on carbon sequestration and emissions in the double cropping rice system
Authors: Xionghui Ji , Jiamei Wu , Hua Peng , Lihong Shi , Zhenhua Zhang , Zhaobing Liu , Faxiang Tian , Liangjie Huo , Jian Zhu 
Published: January 2012

AbstractBACKGROUND: Soil organic carbon (SOC) sequestration, methane emission, and the net carbon sink represented by rice straw incorporated into soil (RIS) were studied using long‐term experimentation with rice straw incorporated into soil (LRIS) and short‐term experimentation with different patterns of rice straw incorporated into soil (SPRIS).RESULTS: Soil organic carbon could be improved by RIS combined with soil ploughing. The increased rate of SOC deposition per cultivated layer was 0.10 t C ha−1 for 2.625 t ha−1 straw incorporated each season in LRIS and 0.36 t C ha−1 for 4.5 t straw ha−1 season−1 incorporated in SPRIS; the apparent SOC conversion by rice straw (stubble) was reduced as the amount of incorporated straw increased. However, RIS methane emission from paddy fields also significantly exacerbated the CH4 emission flux observed during the early and late rice growing seasons, which was increased by 75.0% (P < 0.01) and 251.5% (P < 0.01), respectively, compared with combined application of nitrogen, phosphorus and potassium fertiliser (NPK). The apparent methane conversion of straw was almost uniform with a similar rice yield and soil cultivating mode. Among the patterns of RIS, methane emission was significantly reduced under straw covering untilled land, and this property led to the lowest apparent methane conversion.CONCLUSION: RIS with ploughing and tilling resulted in negative carbon sequestration because of increased methane emissions. A combined NPK application with only rice stubble incorporation may be sustainable for a higher rice yield, but this approach has a reduced rate of negative carbon sequestration in the paddy field. Straw covering with no tillage was the best measure to realise high yield and low carbon emission for RIS. Copyright © 2012 Society of Chemical Industry