bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane–water partition coefficients
Authors: Jakobtorweihen Sven , Ingram Thomas , Smirnova Irina 
Published: February 2013

AbstractThe importance of membrane‐water partition coefficients led to the recent extension of the conductor‐like screening model for realistic solvation (COSMO‐RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO‐RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.
Musculoskeletal determinants of pelvic sucker function in hawaiian stream gobiid fishes: Interspecific comparisons and allometric scaling
Authors: Maie Takashi , Schoenfuss, Heiko L. , Blob Richard W. 
Published: February 2013

AbstractGobiid fishes possess a distinctive ventral sucker, formed from fusion of the pelvic fins. This sucker is used to adhere to a wide range of substrates including, in some species, the vertical cliffs of waterfalls that are climbed during upstream migrations. Previous studies of waterfall‐climbing goby species have found that pressure differentials and adhesive forces generated by the sucker increase with positive allometry as fish grow in size, despite isometry or negative allometry of sucker area. To produce such scaling patterns for pressure differential and adhesive force, waterfall‐climbing gobies might exhibit allometry for other muscular or skeletal components of the pelvic sucker that contribute to its adhesive function. In this study, we used anatomical dissections and modeling to evaluate the potential for allometric growth in the cross‐sectional area, effective mechanical advantage (EMA), and force generating capacity of major protractor and retractor muscles of the pelvic sucker (m. protractor ischii and m. retractor ischii) that help to expand the sealed volume of the sucker to produce pressure differentials and adhesive force. We compared patterns for three Hawaiian gobiid species: a nonclimber (Stenogobius hawaiiensis), an ontogenetically limited climber (Awaous guamensis), and a proficient climber (Sicyopterus stimpsoni). Scaling patterns were relatively similar for all three species, typically exhibiting isometric or negatively allometric scaling for the muscles and lever systems examined. Although these scaling patterns do not help to explain the positive allometry of pressure differentials and adhesive force as climbing gobies grow, the best climber among the species we compared, S. stimpsoni, does exhibit the highest calculated estimates of EMA, muscular input force, and output force for pelvic sucker retraction at any body size, potentially facilitating its adhesive ability. J. Morphol. 2013. © 2013 Wiley Periodicals, Inc.
Developing millennial tree ring chronologies in the fire‐prone North American boreal forest
Authors: ARSENEAULT DOMINIQUE , DY BENJAMIN , GENNARETTI FABIO , AUTIN JULIA , BÉGIN YVES 
Published: February 2013

AbstractA denser global network of millennial tree ring chronologies is needed to verify whether the warming of the last century is anomalously rapid or of large amplitude in the context of the last millennium. The North American boreal forest in particular has been poorly represented in long climatic reconstructions based on tree rings, because of short tree longevity, as well as frequent and severe wildfires. In this study, we exhaustively sampled tree remains in the littoral zone of two lakes and partially sampled seven additional lakes in the northern boreal forest of eastern Canada to verify if highly replicated millennial tree ring chronologies could be developed. In total, 989 black spruce [Picea mariana (Mill.) BSP.] tree remains were sampled, of which 529 could be crossdated, providing a master chronology spanning the AD 676–1991 time period. Radiocarbon dating of a floating chronology indicates that maximum residence time of tree remains outside of sediments is at least 1500 years. Past fires halted or reduced wood inputs at least once at all but one site and thus influenced the replication of local chronologies. However, fire effects can be minimized using appropriate site selection criteria (old‐growth forest on the leeward shore, sharp deepening of the littoral zone, burial of tree remains by fine sediments), such that it would be possible to develop a network of several highly and evenly replicated multi‐century local chronologies. These tree ring chronologies would have desirable properties for extracting low‐frequency tree growth trends and for reconstructing forest disturbance histories. Copyright © 2013 John Wiley & Sons, Ltd.
LeMAPK4 participated in cold‐induced ethylene production in tomato fruit
Authors: Zhao Ruirui , Xie Handing , Lv Shengnan , Zheng Yang , Yu Mengmeng , Shen Lin , Sheng Jiping 
Published: February 2013

AbstractBACKGROUND: Mitogen‐activated protein kinase (MAPK, EC 2.7.11.24) cascade from several plant species has been shown to be activated during response to abiotic stress. Ethylene plays an important role in fruit tolerance to environmental stress. However, the mechanisms by which MAPK regulates defence systems in fruit and the relationship between MAPK and ethylene remain to be determined.RESULTS: MAPK inhibitor significantly decreased the chilling tolerance of tomato (Lycopersicon esculentum cv. Lichun) fruit during cold storage. Moreover, decreases in ethylene content, LeACS2 expression and activities of 1‐aminocyclopropane‐1‐carboxylic acid (ACC) synthase (ACS, EC 4.4.1.14) and ACC oxidase (ACO, EC 1.14.17.4) due to MAPK inhibitor occurred within 24 h after cold treatment. Upon treatment with cold and ethephon, the ethylene content, activities of ACS and ACO and expression of LeACS2, LeACO1 and LeMAPK4 increased.CONCLUSION: The results showed the regulation of MAPK in ethylene biosynthesis to protect tomato fruit from cold stress. In addition, the participation of LeMAPK4 in cold‐induced ethylene biosynthesis in tomato fruit was indicated. © 2013 Society of Chemical Industry
Does antidepressant medication use affect persistence with diabetes medicines?
Authors: Caughey Gillian E. , Preiss Adrian K. , Vitry Agnes I. , Gilbert Andrew L. , Ryan Philip , Shakib Sepehr , Esterman Adrian , McDermott Robyn A. , Roughead Elizabeth E. 
Published: February 2013

ABSTRACTPurposeThis study aimed to examine the effect of antidepressant use on persistence with newly initiated oral antidiabetic medicines in older people.MethodsA retrospective study of administrative claims data from the Australian Government Department of Veterans' Affairs, from 1 July 2000 to 30 June 2008 of new users of oral antidiabetic medicines (metformin or sulfonylurea). Antidepressant medicine use was determined in the 6 months preceding the index date of the first dispensing of an oral antidiabetic medicine. The outcome was time to discontinuation of diabetes therapy in those with antidepressant use compared with those without. Competing risks regression analyses were conducted with adjustment for covariates.ResultsA total of 29 710 new users of metformin or sulfonylurea were identified, with 7171 (24.2%) dispensed an antidepressant. Median duration of oral antidiabetic medicines was 1.81 years (95% CI 1.72–1.94) for those who received an antidepressant at the time of diabetes medicine initiation, by comparison to 3.23 years (95% CI 3.10–3.40) for those who did not receive an antidepressant. Competing risk analyses showed a 42% increased likelihood of discontinuation of diabetes medications in persons who received an antidepressant (subdistribution hazard ratio 1.42, 95% CI 1.37–1.47, p < 0.001).ConclusionsThe results of this large population‐based study demonstrate that depression may be contributing to non‐compliance with medicines for diabetes and highlight the need to provide additional services to support appropriate medicine use in those initiating diabetes medicines with co‐morbid depression. Copyright © 2013 John Wiley & Sons, Ltd.
Synthesis, Structure, and Properties ofN,N′‐Dinitrourea
Authors: Il'yasov Sergey G. , Sakovich Gennady V. , Lobanova Antonina A. 
Published: February 2013

AbstractInformation on synthesis methods and properties ofN,N′‐dinitrourea and its salts, which were reported virtually simultaneously by different authors in different publications, is summarized and systematized. Merits and drawbacks of various approaches for the synthesis of the target products are discussed. The reactivity ofN,N′‐dinitrourea and its salts in the reactions of nucleophilic substitution and condensation is discussed.
Initial effects of woody biomass removal and intercropping of switchgrass (Panicum virgatum) on herpetofauna in eastern north Carolina
Authors: Homyack Jessica A. , Aardweg Zachary , Gorman Thomas A. , Chalcraft David R. 
Published: February 2013

AbstractForests are potential sources for a wide range of alternative fuels, which could reduce dependency on fossil fuels and carbon emissions, but sustainability of producing biofuels from forests has not been well‐studied. Therefore, we investigated effects of woody biomass harvest, intercropping perennial grasses, and combinations of these treatments on herpetofauna in loblolly pine (Pinus taeda) plantations in a randomized and replicated field experiment in eastern North Carolina, USA. We sampled amphibians and small reptiles with drift fence arrays from April to July during 1 and 2 years after treatment establishment. We had 425 captures of 15 species of herpetofauna across the 2 sampling seasons, but did not observe large general effects of biomass removal or planting of switchgrass (Panicum virgatum) in pine plantations on detection, diversity, or relative abundance. However, planned contrasts indicated Simpson's index of diversity was greater in plots managed for switchgrass only compared with pine plantations during year 2, and that captures of southern toads (Anaxyrus terrestris) were less common in switchgrass plots than in pine plantations intercropped with switchgrass. Neither intercropping switchgrass with pine nor removal of harvest residuals caused herpetofauna diversity or abundance of common species to differ from traditional plantation management during the first 2 years following treatment establishment. With the exception of switchgrass‐only plots, which had lower herpetofauna species evenness, the potential practices we considered for biofuels production are unlikely to have short‐term effects on herpetofauna relative to traditional pine management. Future research should monitor herpetofauna through succession and consider landscape‐scale effects and other potential feedstock sources. © 2013 The Wildlife Society.
GABA shunt mediates thermotolerance in Saccharomyces cerevisiae by reducing reactive oxygen production
Authors: Cao Juxiang , Barbosa Jose M. , Singh Narendra K. , Locy Robert D. 
Published: February 2013

AbstractThe GABA shunt pathway involves three enzymes, glutamate decarboxylase (GAD), GABA aminotransferase (GAT) and succinate semialdehyde dehydrogenase (SSADH). These enzymes act in concert to convert glutamate (α‐ketoglutarate) to succinate. Deletion mutations in each of these genes in Saccharomyces cerevisiae resulted in growth defects at 45°C. Double and triple mutation constructs were compared for thermotolerance with the wild‐type and single mutant strains. Although wild‐type and all mutant strains were highly susceptible to brief heat stress at 50°C, a non‐lethal 30 min at 40°C temperature pretreatment induced tolerance of the wild‐type and all of the mutants to 50°C. The mutant strains collectively exhibited similar susceptibility at 45°C to the induced 50°C treatments. Intracellular reactive oxygen intermediate (ROI) accumulation was measured in wild‐type and each of the mutant strains. ROI accumulation in each of the mutants and in various stress conditions was correlated to heat susceptibility of the mutant strains. The addition of ROI scavenger N‐tert‐butyl‐α‐phenylnitrone (PBN) enhanced survival of the mutants and strongly inhibited the accumulation of ROI, but did not have significant effect on the wild‐type. Measurement of intracellular GABA, glutamate and α‐ketoglutarate during lethal heat exposure at 45°C showed higher levels of accumulation of GABA and α‐ketoglutarate in the uga1 and uga2 mutants, while glutamate accumulated at higher level in the gad1 mutant. These results suggest that the GABA shunt pathway plays a crucial role in protecting yeast cells from heat damage by restricting ROI production involving the flux of carbon from α‐ketoglutarate to succinate during heat stress. Copyright © 2013 John Wiley & Sons, Ltd.
Fluorinated Weakly Coordinating Anions [M(hfip)6]– (M = Nb, Ta): Syntheses, Structural Characterizations and ­Computations
Authors: Preiss Ulrich P. , Steinfeld Gunther , Scherer Harald , Erle Anna M. T. , Benkmil Boumahdi , Kraft Anne , Krossing Ingo 
Published: February 2013

AbstractThe synthesis, spectroscopic and structural characterisation of a series of [M(hfip)6]– (M = Nb, Ta; hfip = O–C(H)(CF3)2) salts that are the typical starting materials to introduce these weakly coordinating anions by metathesis reactions into a given system is described. The salts Li[Nb(hfip)6] and Li[Ta(hfip)6] formed in 65 to 77 % yield from freshly sublimed MCl5 and Li[hfip]. By contrast, several attempts to synthesize Li[Sb(hfip)6] on the similar route (replace NbCl5 by SbCl5) failed to yield a pure product. Upon metathesis of the Li‐niobate with AgF in CH2Cl2, the pure Ag[Nb(hfip)6] formed. Mixing Li[Nb(hfip)6] with an equimolar amount of Cl–CPh3 in CH2Cl2 gave the yellow [CPh3][Nb(hfip)6]. Several of the compounds were characterized by X‐ray analysis. Thus, the crystal structures of the Li+‐ and Ag+‐solvates 1, 2‐C6H4F2{LiNb(hfip)6}2, [Li(H2O)][Ta(hfip)6], and [Ag(C6H5F)][Nb(hfip)6] as well as that of [CPh3][Nb(hfip)6] were solved and are described in this work.
The relationship between substance use and delinquency among high‐school students in Cape Town, South Africa
Authors: Carney Tara , Myers Bronwyn J. , Louw Johann , Lombard Carl , Flisher Alan J. 
Published: February 2013

ABSTRACTResearch has shown a positive relationship between substance use and delinquent‐type behaviours among adolescents. The aim of this study is to explore the temporal relationships between these outcomes through secondary data analysis of a longitudinal study of high‐school students' risk behaviours. Two regression models were compared and gender, socioeconomic status and repeating a grade were found to be consistent predictors of delinquent‐type behaviour. Alcohol (OR: 1.26, CI: 1.02–1.55, p = 0.03) and drug use (OR: 1.10, CI: 1.03–1.16, p = 0.002) in the ordinal regression models were significantly associated with delinquent‐type behaviours at Time 2 only. A transition model use was then used to measure delinquent‐type behaviours as predicted by the previous time period, and results indicated that gender and delinquency were predictive of delinquency. Smoking also significantly interacted with delinquent‐type behaviour to increase future risk of this behaviour. The findings point to the need for intervening early with adolescents who show delinquent‐type behaviour.
An epidemiological survey of Mycoplasma hominis and Ureaplasma urealyticum in gynaecological outpatients, Rome, Italy
Authors: VERTERAMO R. , PATELLA A. , CALZOLARI E. , RECINE N. , MARCONE V. , OSBORN J. , CHIARINI F. , DEGENER A. M. 
Published: February 2013

SUMMARYThe objective of this study was to assess the prevalence of Ureaplasma urealyticum and Mycoplasma hominis infections and to investigate associations between their presence in the lower female genital tract and lifestyle characteristics. The study was performed on a population of 3115 women, comparing the demographic and behavioural characteristics of 872 women with U. urealyticum infection and 142 women with M. hominis with uninfected women, using univariate and multiple logistic regression analysis. The prevalence of infection with U. urealyticum was 28% and M. hominis was 4·6%. In multivariate logistic regression analysis, intrauterine device, number of sexual partners and age (<35 years) were significantly associated with U. urealyticum while previous induced abortion, condom use and young age at first intercourse (<16 years) were associated with M. hominis infection. U. urealyticum infection presents the same demographic and behavioural characteristics of a sexually transmitted disease. The unprotective role of condom use suggests a non-sexual mode of transmission of M. hominis infection.
A bio-economic model for the ecosystem-based management of the coastal fishery in French Guiana
Authors: Cissé A.A. , Gourguet S. , Doyen L. , Blanchard F. , Péreau J.-C. 
Published: February 2013

AbstractThis paper offers a theoretical and empirical model of ecosystem-based fishery management. A multi-species and multi-fleet model integrating Lotka–Volterra trophic dynamics as well as production and profit assessments is developed and applied to the coastal fishery of French Guiana. This small-scale fishery constitutes a challenging example with high fish biodiversity, several non-selective fleets and a potentially increasing local food demand due to demographic growth. The dynamic model is calibrated with 13 species and four fleets using monthly catch and effort data from 2006 to 2009. Several contrasted fishing scenarios including status quo, total closure, economic and viable strategies are then simulated. They are compared from the viewpoints of both biodiversity preservation and socioeconomic performance, assuming fixed landing prices and fixed costs. We show that fishing outputs, including food supply and fleet profitability, can be sustained on average but a loss of species cannot be avoided.
Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses
Authors: Jon McIlroy Simon , Kristiansen Rikke , Albertsen Mads , Michael Karst Søren , Rossetti Simona , Lund Nielsen Jeppe , Tandoi Valter , James Seviour Robert , Nielsen Per Halkjær 
Published: February 2013

Abstract
‘Candidatus Microthrix parvicella’ is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community ‘Ca. M. parvicella’ strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium.
G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy
Authors: Ding Xiaoyan , Zhao Xin , Watts Anthony 
Published: February 2013

GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.
How Sox2 maintains neural stem cell identity
Authors: Thiel Gerald 
Published: February 2013

The transcription factor Sox2 [SRY (sex-determining region Y)-box 2] is expressed at the earliest developmental stages in the nervous system and functions as a marker protein for neural development. Sox2 is found in embryonic neural stem cells as well as in virtually all adult neural stem cells of the subventricular region and the subgranular zone of the hippocampus. Gain-of-function and loss-of-function experiments in transgenic animals revealed a key role for Sox2 in the maintenance of neural stem cell properties, including proliferation/survival, self-renewal and neurogenesis. A limited set of Sox2-responsive target genes have been identified, including the genes encoding the neural stem cell marker nestin and the signalling molecule sonic hedgehog. In this issue of the Biochemical Journal, Feng et al. identified the survivin gene as a target for Sox2 in neural stem cells. Survivin protects cells from programmed cell death and functions as a regulator of cell division. The regulation of survivin expression by Sox2 explains why the reduction of the Sox2 concentration in neural stem cells is accompanied by a reduced proliferation of the cells and an induction of apoptosis. It would be of interest to know whether the Sox2–survivin connection is a common scheme to maintain the ‘stemness’ identity of other stem/progenitor cells.