bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and activity of the NAD(P)+‐dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium
Authors: Zheng Hongyan , Beliavsky Alina , Tchigvintsev Anatoli , Brunzelle Joseph S. , Brown Greg , Flick Robert , Evdokimova Elena , Wawrzak Zdzislaw , Mahadevan Radhakrishnan , Anderson Wayne F. , Savchenko Alexei , Yakunin Alexander F. 
Published: February 2013

AbstractAldehyde dehydrogenases are found in all organisms and play an important role in the metabolic conversion and detoxification of endogenous and exogenous aldehydes. Genomes of many organisms including Escherichia coli and Salmonella typhimurium encode two succinate semialdehyde dehydrogenases with low sequence similarity and different cofactor preference (YneI and GabD). Here, we present the crystal structure and biochemical characterization of the NAD(P)+‐dependent succinate semialdehyde dehydrogenase YneI from S. typhimurium. This enzyme shows high activity and affinity toward succinate semialdehyde and exhibits substrate inhibition at concentrations of SSA higher than 0.1 mM. YneI can use both NAD+ and NADP+ as cofactors, although affinity to NAD+ is 10 times higher. High resolution crystal structures of YneI were solved in a free state (1.85 Å) and in complex with NAD+ (1.90 Å) revealing a two domain protein with the active site located in the interdomain interface. The NAD+ molecule is bound in the long channel with its nicotinamide ring positioned close to the side chain of the catalytic Cys268. Site‐directed mutagenesis demonstrated that this residue, as well as the conserved Trp136, Glu365, and Asp426 are important for activity of YneI, and that the conserved Lys160 contributes to the enzyme preference to NAD+. Our work has provided further insight into the molecular mechanisms of substrate selectivity and activity of succinate semialdehyde dehydrogenases. © 2012 Wiley Periodicals, Inc.
Erratum: Characterisation of multiple carrier transport in indium nitride grown by molecular beam epitaxy [Phys. Status Solidi C 4, 2423–2427 (2007)]
Authors: Fehlberg Tamara B. , Umana‐Membreno Gilberto A. , Gallinat Chad S. , Koblmüller Gregor , Bernardis Sarah , Nener Brett D. , Parish Giacinta , Speck James S. 
Published: February 2013

AbstractThis paper erroneously neglected to reference an earlier paper, an oversight which the authors wish to correct to improve the overall contribution of both papers. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Microstructural corrosion of aluminium alloys: a predictive finite element model based on corrosion–mimicking experiments
Authors: Sorriano Claire , Oltra Roland , Zimmer Alexandre , Vuillemin Bruno , Vuillemin Bruno , Borkowski Celine 
Published: February 2013

ABSTRACTThe purpose of this study is to implement the basis of a finite element model (FEM) based on the resolution of the Nernst–Planck equation in order to progress in the predictive simulation of microstructural corrosion on aluminium alloys. Certain constituent intermetallic particles at the surface of aluminium alloys are considered as preferential sites for the initiation of structural corrosion resulting in localised trenching around the particles and the surrounding Al matrix. In this work, a modified scanning electrochemical microscope (SECM) experiment was used to induce such phenomena via a local alkalinization on 200 nm thick aluminium coatings, promoting their local dissolution in an aerated 0.1 M NaCl electrolyte. Using a 2D finite element modelling to simulate the SECM experiments, the role of the local alkalinization was validated and the calculated Al dissolution rate was found in agreement with the experimental evaluation. The same FEM model was then successfully applied to simulate the damage formed around a micrometric copper particle embedded in pure aluminium. Copyright © 2013 John Wiley & Sons, Ltd.
Theoretical models of DNA flexibility
Authors: Dršata Tomáš , Lankaš Filip 
Published: February 2013

AbstractDNA sequence‐dependent three‐dimensional structure and mechanical deformability play a large role in biological processes such as protein–DNA interactions, nucleosome positioning, promoter identification, and drug–DNA recognition. On the important scale of 10–100 base pairs, models where DNA bases are represented by interacting rigid bodies have proved useful. We focus on a recently proposed rigid base model with nonlocal, harmonic interaction energy. We discuss the choice of internal coordinates and a method to obtain model parameters from coordinate fluctuations. Parameter transformation upon change of reference strand, coordinate constraints, and models with reduced number of degrees of freedom are described. Relation to traditional local harmonic models is clarified. We outline recent attempts to include anharmonic effects. A rigid base model of a DNA oligomer containing A‐tract is presented as an example. Perspectives of model development and application are discussed.This article is categorized under:

Electronic Structure Theory > Density Functional Theory
Effect of laminin 332 on motility and invasion in bladder cancer
Authors: Kang Sung‐Gu , Ha Young‐Ran , Ko Young‐Hwii , Kang Seok‐Ho , Joo Kwan‐Joong , Cho Hyun‐Yee , Park Hong‐Seok , Kim Chul‐Hwan , Kwon Soon‐Young , Kim Je‐Jong , Cheon Jun , Lee Jeong‐Gu 
Published: February 2013

AbstractWe examined the correlation between laminin 332 and malignancy in bladder cancer patients, and, using a strain of invasive bladder cancer cells, determined whether laminin 332 causes bladder cancer motility and invasion. To investigate the correlation between laminin 332 g2 distribution and patient outcome, we performed a semiquantitative immunohistochemical analysis of 35 paraffin‐embedded samples using the antibody D4B5, which is specific for the laminin 5 γ2 chain. To evaluate the role of laminin 332 in NBT‐II cell motility and invasion, we used a scratch assay and the Boyden chamber chemoinvasion system. Tumor stage and grade were significantly correlated with a loss of laminin 332 γ2 chain from the basement membrane (p = 0.001) and its retention in the cytoplasm (p = 0.001) (Kruskal–Wallis test). Kaplan–Meier survival curves revealed an association between the risk of progression and cytoplasmic retention of the laminin 332 γ2 chain. In addition, an in vitro scratch assay showed an increase in the migration of cells treated with laminin 332 from their cluster. The Boyden chamber assay showed that laminin 332 potentiated NBT‐II cell invasion. Immunohistochemistry results showed that bladder cancer patients with a higher malignancy expressed more laminin 332. The in vitro scratch and invasion assay showed that laminin 332 stimulated the motility and invasion of bladder cancer cells. The invasion assay explains the correlation between laminin 332 expression and bladder cancer malignancy.
Soil–landscape response to mid and late Quaternary climate fluctuations based on numerical simulations
Authors: Cohen Sagy , Willgoose Garry , Hancock Greg 
Published: February 2013

AbstractWe use a numerical dynamic soil–landscape model to study one aspect of the spatio-temporal soil–landscape evolution process, the effect of climatic fluctuations on soil grading distribution in space and time in response to the interplay between physical weathering and surface erosion (soil mineralogical fluxes). We simulate a synthetic soil–landscape system over the middle and late Quaternary (last 400 ka). The results show that (1) soil–landscape response to climate change is non-linear and highly spatially variable, even at hillslope scale; and (2) soil–landscape adjustment to climate change can lag tens of thousands of years and is both spatially and temporally variable. We propose that the legacy of past climatic condition (i.e. last glacial maximum) in modern soil–landscape systems vary considerably in space. This implies that the spatiotemporal uniformity in which soil is typically described in Earth system modeling and analysis (e.g. carbon cycle) grossly underestimates their actual complexity.
Inertial collapse of liquid rings
Authors: Darbois Texier Baptiste , Piroird Keyvan , Quéré David , Clanet Christophe 
Published: February 2013

AbstractLiquid rings can be generated in the Leidenfrost state using liquid oxygen of low boiling point ($- 183~\textdegree \mathrm{C} $) and high magnetic susceptibility, allowing one to ‘sculpt’ the liquid into a ring shape using an annular magnet. When the magnetic field is turned off, the ring shrinks back into a puddle with a constant acceleration. A potential flow approach accurately describes the dynamics of closure with an equation reminiscent of the Rayleigh–Plesset equation for the collapse of transient cavities.
Postauricular hypodermic injection to treat inner ear disorders: experimental feasibility study using magnetic resonance imaging and pharmacokinetic comparison
Authors: Li J , Yu L , Xia R , Gao F , Luo W , Jing Y 
Published: February 2013

AbstractBackground:To investigate the feasibility of postauricular hypodermic injection for treating inner ear disorders, we compared perilymph pharmacokinetics for postauricular versus intravenous injection, using magnetic resonance imaging, in an animal model.Methods:Twelve albino guinea pigs were divided randomly into two groups and administered gadopentetate dimeglumine via either a postauricular or an intravenous bolus injection. A 7.0 Tesla magnetic resonance imaging system was used to assess the signal intensities of gadolinium-enhanced images of the cochlea, as a biomarker for changes in gadopentetate dimeglumine concentration in the perilymph. Pharmacokinetic parameters were calculated based on these signal intensity values.Results:Guinea pigs receiving postauricular injection showed longer times to peak signal intensity, longer elimination half-life, longer mean residence time and a greater area under the signal–time curve (from pre-injection to the last time point) (p < 0.05).Conclusion:Postauricular injection shows potential as an efficient drug delivery route for the treatment of inner ear disorders.
Seasonal fruiting and seed dispersal by the brown lemur in a tropical dry forest, north-western Madagascar
Authors: Sato Hiroki 
Published: February 2013

Abstract:Community-wide seasonal fruiting and seed dispersal by the common brown lemur (Eulemur fulvus fulvus) was investigated in a tropical dry forest, north-western Madagascar. The brown lemur is the sole disperser of large seeds > 10 mm in diameter. Considering the limited assemblage of dispersers, large-seeded plants should display distinctive fruiting patterns to acquire dispersers. To compare fruiting patterns and seed dispersal by the brown lemur between small-seeded and large-seeded plants, fruiting conditions for 432 trees on a transect, feeding activity over 1212 h of observation, and the composition of 1126 dung samples were recorded for 1 y. Seeds of a total of 52 species were identified through both observations and faecal analysis. As rainfall increased, larger numbers of species and individuals of small-seeded plants fruited. Among the 52 species, the brown lemur dispersed 29 and 13 species with small and large seeds, respectively, during the rainy season. High moisture levels probably favoured seed germination and seedling establishment in various species. During the dry season, although small-seeded species rarely fruited, a few large-seeded species, particularly Vitex beraviensis, formed a long-term fruiting peak and provided essential food resources for the brown lemur. Because seeds of these large-seeded plants were frequently dispersed by the brown lemur, dry-season fruiting seemed to be favourable to avoid competition for dispersers with other plant species.
Update on diversity and distribution of HIV-1 subtypes in Yunnan province
Authors: SU Y.-Z. , MA Y.-L. , JIA M.-H. , HE X. , YANG L. , CHENG C.-L. , CHEN M. , SHI Y.-H. , CHEN L. , CHEN H.-C. , YANG C.-J. , YU S.-Y. , LU L. 
Published: February 2013

SUMMARYThe aim of this study was to characterize updated HIV subtypes in Yunnan to determine their origins and distribution within the population. RT–PCR of both thegagandenvgenes were sequenced from Yunnan province inhabitants newly diagnosed with HIV-1. Sequence data from 290 samples were used for statistical analysis of subtype distribution and phylogenetic tree construction. Distribution data were adjusted to account for different geographical distributions of HIV-1 subtypes in the population. Phylogenetic analysis revealed six HIV-1 subtypes in Yunnan, including eight types of unique recombination forms (URFs). The most prevalent subtypes in this province, CRF07_BC (18·9%), CRF08_BC (39·1%), CRF01_AE (22·4%), and URFs (subtype C, 5·9% and subtype B, 4·5%), were all recombinants. We found significant differences in the distribution of these HIV-1 subtypes not only geographically, but also between various ethnic groups and with respect to transmission routes. Our findings indicate a complex population of HIV-1 subtypes, URFs, and recombinant subtypes in Yunnan province. This diversity could make the prevention and control of HIV infection in Yunnan more difficult due to the possibility of virus recombination or infection by multiple subtypes.
Stress Levels in EMS Personnel: A National Survey
Authors: Cydulka Rita K. , Emerman Charles L. , Shade Bruce , Kubincanek John 
Published: February 2013

AbstractObjective:The purpose of this study was to evaluate stress levels in emergency medical services personnel across the United States.Design:Confidential, 20-question survey tool, Medical Personnel Stress Survey-Abbreviated (MPSS-R). A total score of 50 indicates average stress levels. A score of 12.5 on the subset measurements of somatic distress, job dissatisfaction, organizational stress, and negative attitudes towards patients indicates average levels of stress. Data were analyzed using ANOVA and t-test.Interventions:None.Results:A total of 658 of 3,000 emergency medical technicians (EMTs) (22%) completed the survey. The mean value of 69.3±6.3 for the total stress scores was very high Mean values for the subset scores were: somatic distress = 19.6±3.3; organizational stress = 17.3±2.4; job dissatisfaction = 17.0±2.6; negative attitudes towards patients = 15.5±2.3. Characteristics predicting higher stress were EMT-basic (A) licensure, basic life support (BLS) only service provider, volunteer status, new employee working in a small EMS organization, and providing service to a small town.Conclusion:Stress levels in EMS personnel were very high, were manifested primarily as somatic distress, secondarily as organizational stress and job dissatisfaction, and lastly as negative patient attitudes. Stress levels and subset manifestations of occupational stress among EMS personnel varied depending on gender, marital status, age, level of training and function, on salaried or volunteer status, length of time as an EMT, and size of the organization, city, and population served. Care should be taken to address stresses peculiar to individual EMS system needs.
God Save This “Broken” Land: The Efficacy of Closed-Circuit Voter Targeting in a U.K. Election
Authors: Calfano Brian Robert , Djupe Paul A. , Wilson Angelia R. 
Published: February 2013

AbstractRecent research in the United States has found candidates for elected office are able to use a rhetorical form of closed-circuit communication with evangelical Protestants — “God Talk” — that communicates valuable political information without alerting other constituencies. Close observation of the 2010 parliamentary elections in the United Kingdom (U.K.) uncovered what appeared to be a form of God Talk in use by David Cameron and the Conservative Party, especially the use of “broken” to describe the state of Britain. Thus, we assess whether God Talk is an efficacious communication strategy in the U.K. using an experiment that selectively exposes participants to God Talk statements. The mixed results suggest that some forms of God Talk are better than others in conveying to U.K. evangelicals that a candidate is conservative and religious without triggering the same associations by non-evangelical voters. We close with a discussion of the normative impact of such communication strategies.
Robust estimation of microbial diversity in theory and in practice
Authors: Haegeman Bart , Hamelin Jérôme , Moriarty John , Neal Peter , Dushoff Jonathan , Weitz Joshua S 
Published: February 2013

AbstractQuantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao’s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities’), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao’s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.
Changes in assembly processes in soil bacterial communities following a wildfire disturbance
Authors: Ferrenberg Scott , O’Neill Sean P , Knelman Joseph E , Todd Bryan , Duggan Sam , Bradley Daniel , Robinson Taylor , Schmidt Steven K , Townsend Alan R , Williams Mark W , Cleveland Cory C , Melbourne Brett A , Jiang Lin , Nemergut Diana R 
Published: February 2013

Abstract
Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.
Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades
Authors: Baker David M , Andras Jason P , Jordán-Garza Adán Guillermo , Fogel Marilyn L 
Published: February 2013

Abstract
Many reef-building corals form symbioses with dinoflagellates from the diverse genus Symbiodinium. There is increasing evidence of functional significance to Symbiodinium diversity, which affects the coral holobiont’s response to changing environmental conditions. For example, corals hosting Symbiodinium from the clade D taxon exhibit greater resistance to heat-induced coral bleaching than conspecifics hosting the more common clade C. Yet, the relatively low prevalence of clade D suggests that this trait is not advantageous in non-stressful environments. Thus, clade D may only be able to out-compete other Symbiodinium types within the host habitat when conditions are chronically stressful. Previous studies have observed enhanced photosynthesis and fitness by clade C holobionts at non-stressful temperatures, relative to clade D. Yet, carbon-centered metrics cannot account for enhanced growth rates and patterns of symbiont succession to other genetic types when nitrogen often limits reef productivity. To investigate the metabolic costs of hosting thermally tolerant symbionts, we examined the assimilation and translocation of inorganic 15N and 13C in the coral Acropora tenuis experimentally infected with either clade C (sub-type C1) or D Symbiodinium at 28 and 30 °C. We show that at 28 °C, C1 holobionts acquired 22% more 15N than clade D. However, at 30 °C, C1 symbionts acquired equivalent nitrogen and 16% less carbon than D. We hypothesize that C1 competitively excludes clade D in hospite via enhanced nitrogen acquisition and thus dominates coral populations despite warming oceans.
Haem oxygenase-1 induction reverses the actions of interleukin-1β on hypoxia-inducible transcription factors and human chondrocyte metabolism in hypoxia
Authors: Clérigues Victoria , Murphy Christopher L. , Guillén Maria Isabel , Alcaraz Maria José 
Published: February 2013

HO-1 (haem oxygenase-1) catalyses the degradation of haem and possesses anti-inflammatory and cytoprotective properties. The role of inflammatory mediators in the pathogenesis of OA (osteoarthritis) is becoming increasingly appreciated. In the present study, we investigated the effects of HO-1 induction in OA and healthy HACs (human articular chondrocytes) in response to inflammatory cytokine IL-1 β (interleukin-1β) under hypoxic conditions. Hypoxia was investigated as it is a more physiological condition of the avascular cartilage. Hypoxic signalling is mediated by HIFs (hypoxia-inducible factors), of which there are two main isoforms, HIF-1α and HIF-2α. Normal and OA chondrocytes were stimulated with IL-1β. This cytokine suppresses HO-1 expression and exerts both catabolic and anti-anabolic effects, while increasing HIF-1α and suppressing HIF-2α protein levels in OA chondrocytes in hypoxia. Induction of HO-1 by CoPP (cobalt protoporphyrin IX) reversed these IL-1β actions. The hypoxia-induced anabolic pathway involving HIF-2α, SOX9 [SRY (sex determining region Y)-box 9] and COL2A1 (collagen type II α1) was suppressed by IL-1β, but importantly, levels were restored by HO-1 induction, which down-regulated TNFα (tumour necrosis factor α), MMP (matrix metalloproteinase) activity and MMP-13 protein levels. Depletion of HO-1 using siRNA (small interfering RNA) abolished the CoPP effects, further demonstrating that these were due to HO-1. The results of the present study reveal the different mechanisms by which HO-1 exerts protective effects on chondrocytes in physiological levels of hypoxia.