bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural insights into a low‐spin myoglobin variant with bis‐histidine coordination from molecular modeling
Authors: Lin Ying‐Wu 
Published: November 2010

AbstractRational design of functional enzymes is a powerful strategy to gain deep insights into more complex native enzymes, such as nitric oxide reductase (NOR). Recently, we engineered a functional model of NOR by creating a two His and one Glu (2‐His‐1‐Glu) non‐heme iron center in sperm whale myoglobin (swMb L29E, F43H, H64, called FeBMb(‐His)). It was found that FeBMb(‐His) adopts a low‐spin state with bis‐His coordination in the absence of metal ions binding to the designed metal center. However, no structural information was available for the variant in this special spin state. We herein performed molecular modeling of FeBMb(‐His) and compared with the X‐ray structure of its copper bound derivative, Cu(II)‐CN−‐FeBMb(‐His), resolved recently at a high resolution (1.65 Å) (PDB entry 3MN0). The simulated structure shows that mutation of Leu to Glu at position 29 in the hydrophobic heme pocket alters the folding behavior of Mb. The hydrogen bond between Glu29 and His64 further plays a role in stabilizing the bis‐His (His64/His93) coordination structure. This study offers an excellent example of using molecular modeling to gain insights in rational design of both structural and functional proteins. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Characterization of ZnO crystals grown by the vertical Bridgman method
Authors: Eisermann Sebastian , Laufer Andreas , Graubner Swen , Pinnisch Melanie , Stehr Jan , Lautenschläger Stefan , Hofmann Detlev M. , Meyer Bruno K. , Klimm Detlev , Schulz Detlev 
Published: November 2010

AbstractZnO crystals grown by the vertical Bridgman technique were comprehensively characterized in view of the impurities and intrinsic defects in the material. It is shown that residual Al is the cause of the residual n‐type conductivity and intrinsic defects play only a minor role in the samples. Annealing the samples at 1100 °C for 1 h in oxygen atmosphere improves the surface properties of the samples without having negative effects on their optical and electrical properties.
Mechanism of excitation energy transfer between ring‐shaped aggregates of pigments
Authors: Nakatani Masatoshi , Tei Go , Ishihara Hajime 
Published: November 2010

AbstractWe theoretically study the mechanism of excitation energy transfer (EET) between two ring‐shaped aggregates of pigments. Dynamics of the pigment system and the light field are described by a Markovian quantum master equation and the Maxwell's equations, respectively. Self‐consistently solving these equations, we investigate the interplay between light and aggregates of pigments. From our calculation, it is revealed that the isotropic property gives two coupling constants, which prevents the deterioration of the EET rate between anisotropic dipoles. The distance dependence of the coupling strengths is also calculated for all excited states of the aggregate, which shows that each excited state has a different distance dependence of the coupling strength.
Upregulation of bradykinin receptors is implicated in the pain associated with caerulein‐induced acute pancreatitis
Authors: Takemura Yoshinori , Furuta Sadayoshi , Hirayama Shigeto , Miyashita Kazuhiko , Imai Satoshi , Narita Michiko , Kuzumaki Naoko , Tsukiyama Yoshi , Yamazaki Mitsuaki , Suzuki Tsutomu , Narita Minoru 
Published: November 2010

AbstractAlthough the way for pain management associated with acute pancreatitis has been searched for, there are not enough medications available for it. The aim of the present study was to investigate the role of bradykinin (BK) in pain related to acute pancreatitis. After repeated injections of caerulein (50 μg/kg and 6 times), mice showed edema in the pancreas, and blood concentrations of pancreatic enzymes (amylase and lipase) were clearly elevated. A histopathological study demonstrated that caerulein caused tissue damage characterized by edema, acinar cell necrosis, interstitial hemorrhage, and inflammatory cell infiltrates. Furthermore, the mRNA levels of interleukin‐1β and monocyte chemotactic protein (MCP)‐1 were significantly increased in the pancreas of caerulein‐treated mice. The sensitivity of abdominal organs as measured by abdominal balloon distension was enhanced in caerulein‐injected mice, suggesting that caerulein caused pancreatic hyperalgesia. Moreover, repeated treatment with caerulein resulted in cutaneous tactile allodynia of the upper abdominal region as demonstrated by the use of von Frey filaments, indicating that caerulein‐treated mice exhibited referred pain. Under this condition, the mRNA levels of bradykinin B1 receptor (BKB1R) and bradykinin B2 receptor (BKB2R) were significantly increased in the dorsal root ganglion (DRG). Finally, we found that des‐Arg9‐(Leu8)‐bradykinin (BKB1R antagonist) and HOE‐140 (BKB2R antagonist) attenuated the acute pancreatitis pain‐like state in caerulein‐treated mice. These findings suggest that the upregulation of BK receptors in the DRG may, at least in part, contribute to the development of the acute pancreatitis pain‐like state in mice. Synapse, 2011. © 2010 Wiley‐Liss, Inc.
Rapid Quantitative Analysis of Lipids Using a Colorimetric Method in a Microplate Format
Authors: Cheng Yu‐Shen , Zheng Yi , VanderGheynst Jean S. 
Published: November 2010

AbstractA colorimetric sulfo‐phospho‐vanillin (SPV) method was developed for high throughput analysis of total lipids. The developed method uses a reaction mixture that is maintained in a 96‐well microplate throughout the entire assay. The new assay provides the following advantages over other methods of lipid measurement: (1) background absorbance can be easily corrected for each well, (2) there is less risk of handling and transferring sulfuric acid contained in reaction mixtures, (3) color develops more consistently providing more accurate measurement of absorbance, and (4) the assay can be used for quantitative measurement of lipids extracted from a wide variety of sources. Unlike other spectrophotometric approaches that use fluorescent dyes, the optimal spectra and reaction conditions for the developed assay do not vary with the sample source. The developed method was used to measure lipids in extracts from four strains of microalgae. No significant difference was found in lipid determination when lipid content was measured using the new method and compared to results obtained using a macro‐gravimetric method.
Evidence for a quiet revolution: seasonal variation in colonies of the specialist tansy aphid,Macrosiphoniella tanacetaria(Kaltenbach) (Hemiptera: Aphididae) studied using microsatellite markers
Authors: Loxdale H.D. , Massonnet B. , Schöfl G. , Weisser W.W. 
Published: November 2010

AbstractIn cyclical parthenogens, clonal diversity is expected to decrease due to selection and drift during the asexual phase per number of asexual generations. The decrease in diversity may be counteracted by immigration of new genotypes. We analysed temporal variation in clonal diversity in colonies of the monophagous tansy aphid,Macrosiphoniella tanacetaria(Kaltenbach), sampled four times over the course of a growing season. In a related field study, we recorded aphid colony sizes and the occurrence of winged dispersers throughout the season. The number of colonies increased from April, when asexual stem mothers hatched from the sexually produced eggs, to the end of June. The proportion of colonies with winged individuals also increased over this period. After a severe reduction in colony sizes in late summer, a second expansion phase occurred in October when sexuals were produced. At the season's end, the only winged forms were males. A linked genetic study showed that the number of microsatellite multilocus genotypes and genetic variability assessed at three polymorphic loci per colony decreased from June to October. Overall, the relatedness of wingless to winged individuals within colonies was lower than average relatedness among wingless individuals, suggesting that winged forms mainly originated in different colonies. The results demonstrate that patterns of genetic diversity within colonies can be explained by the antagonistic forces of clonal selection, migration and genetic drift (largely due to midsummer population bottlenecks). We further suggest that the males emigrate over comparatively longer distances than winged asexual females.
The Term Structure of Bond Market Liquidity and Its Implications for Expected Bond Returns
Authors: Goyenko Ruslan , Subrahmanyam Avanidhar , Ukhov Andrey 
Published: November 2010

AbstractPrevious studies of Treasury market illiquidity span short time periods and focus on particular maturities. In contrast, we study the time series of illiquidity for different maturities over an extended period of time. We also compare time-series determinants of on-the-run and off-the-run illiquidity. Illiquidity increases and the difference between spreads of long- and short-term bonds significantly widens during recessions, suggesting a “flight to liquidity,” wherein investors shift into the more liquid short-term bonds during economic contractions. Macroeconomic variables such as inflation and federal funds rates forecast off-the-run illiquidity significantly but have only modest forecasting ability for on-the-run illiquidity. Bond returns across maturities are forecastable by off-the-run but not on-the-run bond illiquidity. Thus, off-the-run illiquidity, by reflecting macro shocks first, is the primary source of the liquidity premium in the Treasury market.
Ligulaintestinalis infection is associated with alterations of both brain and gonad aromatase expression in roach (Rutilusrutilus)
Authors: Boulange-Lecomte C. , Geraudie P. , Forget-Leray J. , Gerbron M. , Minier C. 
Published: November 2010

AbstractThe tapeworm Ligulaintestinalis commonly infests roach (Rutilusrutilus) and is responsible for the inhibition of gonad development. In order to better understand the effect of the plerocercoid on fish physiology, and to discriminate parasitization effects from those of endocrine-disrupting compounds (EDC), Cyp19b and Cyp19a aromatase expression was investigated by real-time quantitative polymerase chain reaction (PCR) in brain and gonads of ligulosed roach, caught from a reference site. Data were compared to reproductive and endocrine endpoints previously reported in a larger cohort study (including the sampled population of the present one), such as gonadosomatic index, Fulton index, gonadal histology, plasma sex steroid levels and brain aromatase activity. A decrease in Cyp19b expression in the brain of infected fish was demonstrated, in agreement with the reduction of aromatase activity previously described. In contrast, Cyp19a expression in the gonads appeared to be enhanced in ligulosed fish, in accordance with the presence of immature but differentiated sexual tissues. Together these results show that: (1) L. intestinalis infestation results in an alteration of aromatase expression which, in particular, may have profound effects on the fish brain; and (2) L. intestinalis infection must be considered as a major confounding factor in ecotoxicological studies using aromatase expression as an EDC biomarker. Moreover, the concordance between activity and expression – investigated for the first time in the same population – gives a functional relevance to the transcript aromatase dosage in the brain. Finally, quantitative PCR was confirmed as a sensitive approach, enabling aromatase status to be defined in the poorly developed gonads of ligulosed individuals.
Spatial Variability in Soil Microbial Communities in a Nitrogen-Saturated Hardwood Forest Watershed
Authors: Gilliam Frank 
Published: November 2010

AbstractThe long-term reference watershed (WS4), at Fernow Experimental Forest, West Virginia, displays symptoms of N saturation despite considerable spatial heterogeneity in soil properties, such as texture, N pools, and cycling rates. We identified a weathering gradient of three sites within WS4 by assessing differences in clay content across a common geologic substrate. Across these sites (LN, MN, and HN), NO3 production rates vary significantly (low, medium, and high nitrification, respectively) and are negatively related to clay content. It is unknown whether microbial communities vary across these sites and contribute to variability in NO3 production. This study characterized soil microbial communities along this gradient and assessed factors potentially important in explaining microbial composition. We sampled mineral soil from each of the sites, analyzing for moisture, pH, organic matter, extractable N, and microbial biomass and community composition via phospholipid fatty acid (PLFA) analysis. Analysis of variance and canonical correspondence analysis indicated that microbial community composition varied among sites, with a predominance of fungal markers (18:2n6 and 18:1n9c) at the most weathered LN site and Gram negative bacteria (18:1n7c) at the less weathered MN and HN sites. Accordingly, the fungi/bacteria ratio increased in the direction of LN plots in ordination space. Correlations between measured environmental parameters and PLFA data suggest that acidic conditions and low NO3 abundance at the LN site have selected for fungal dominance, although other important factors known to exert an influence on soil microbial communities, such as differences in plant community and clay and organic matter content, may also be playing a role in determining the observed patterns.
Seasonal priority effects: Implications for invasion and restoration in California coastal sage scrub
Authors: Wainwright Claire , Cleland Elsa 
Published: November 2010

AbstractCompetition from exotic annual grasses (EAGs) threatens native plant communities in California. Coastal sage scrub communities have substantially diminished in area over the last century, in some instances by greater than 90%, while EAGs continue to proliferate. Several mechanisms may explain the success of EAGs, including the suppression of native seedlings by accumulated litter, exhaustion of soil moisture, and low seed production or dispersal of natives.The timing and magnitude of rainfall plays a significant role in determining the survival and reproduction of plant species in Mediterranean ecosystems. Populations of annuals fluctuate greatly from year to year, corresponding with variability in autumn precipitation. EAGs in California germinate quickly following small threshold rain events, whereas native species have more complex germination cues, such that exotic annual grasses become active earlier in the growing season. In this way, EAGs may exhibit a priority effect over native plant species with respect to establishment; however, they may have reduced success if their germination is induced at a time followed by a substantial drought (for instance, in the summer) so that they will not persist.The goal of this investigation is 1) to evaluate whether seasonal priority effects contribute to community-level patterns of abundance, and 2) whether late summer watering could be a feasible restoration technique for suppression of exotic annual grasses and weeds in Mediterranean ecosystems.
Accelerating reaction–diffusion simulations with general-purpose graphics processing units
Authors: Vigelius Matthias , Lane Aidan , Meyer Bernd 
Published: November 2010

Abstract
Summary We present a massively parallel stochastic simulation algorithm (SSA) for reaction-diffusion systems implemented on Graphics Processing Units (GPUs). These are designated chips optimized to process a high number of floating point operations in parallel, rendering them well-suited for a range of scientific high-performance computations. Newer GPU generations provide a high-level programming interface which turns them into General-Purpose Graphics Processing Units (GPGPUs). Our SSA exploits GPGPU architecture to achieve a performance gain of two orders of magnitude over the fastest existing implementations on conventional hardware.
Availability: The software is freely available at http://www.csse.monash.edu.au/~berndm/inchman/.
Contact: matthias.vigelius@monash.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
IgE, IgGa, IgGb and IgG(T) serum antibody levels in offspring of two sires affected with equine recurrent airway obstruction
Authors: Scharrenberg A. , Gerber V. , Swinburne J. E. , Wilson A. D. , Klukowska‐Rötzler J. , Laumen E. , Marti E. 
Published: November 2010

SummaryEquine recurrent airway obstruction (RAO) is a chronic lower airway disease of the horse caused by hypersensitivity reactions to inhaled stable dust, including mould spores such asAspergillus fumigatus. The goals of this study were to investigate whether total serum IgE levels and allergen‐specific IgE and IgG subclasses are influenced by genetic factors and/or RAO and whether quantitative trait loci (QTL) could be identified for these parameters. The offspring of two RAO‐affected sires (S1:n = 56 and S2:n = 65) were grouped by stallion and disease status, and total serum IgE levels and specific IgE, IgGa, IgGb and IgG(T) levels against recombinantAspergillus fumigatus7 (rAspf7) were measured by ELISA. A panel of 315 microsatellite markers covering the 31 equine autosomes were used to genotype the stallions and their offspring. A whole‐genome scan using half‐sib regression interval mapping was performed for each of the IgG and IgE subclasses. There was no significant effect of disease status or sire on total IgE levels, but there was a significant effect of gender and age. rAspf7‐specific IgGa levels were significantly higher in RAO‐affected than in healthy horses. The offspring of S1 had significantly higher rAspf7‐specific IgGa and IgE levels than those of S2. Five QTLs were significant chromosome‐wide (P < 0.01). QTLs for rAspf7‐specific IgGa and IgE were identified on ECA 1, for rAspf7‐specific IgGa and IgGb on ECA 24 and for rAspf7 IgGa on ECA 26. These results provide evidence for effects of disease status and genetics on allergen‐specific IgGa and IgE.
De novo mutation of KIT discovered as a result of a non‐hereditary white coat colour pattern
Authors: Holl H. , Brooks S. , Bailey E. 
Published: November 2010

SummaryA new dominant white allele was suspected when two Thoroughbred horses with minimal white marking on the coat produced a colt with a large amount of coat depigmentation. Because of its association with similar patterns in other horses, the KIT gene was selected as a candidate gene, and all 21 exons were sequenced in the colt. A novel 5‐bp deletion was discovered in exon 3 and was confirmed with allele‐specific PCR. The mutation introduced a pre‐mature stop codon, resulting in truncation of the protein. The deletion was not present in either parent and is suspected to be responsible for the extensive white coat colour in the colt. Additionally, a previously described missense mutation was detected in exon 14 of both the colt and sire but is not believe to be causative. Parentage testing was conducted as required by The Jockey Club for Thoroughbred registration, and the foal qualified for the stated parentage. This novel deletion in exon 3 is the 12th discovered dominant white allele in the horse.
An open-label study assessing the safety and efficacy of alitretinoin in patients with severe chronic hand eczema unresponsive to topical corticosteroids
Authors: Dirschka T. , Reich K. , Bissonnette R. , Maares J. , Brown T. , Diepgen T. L. 
Published: November 2010

SummaryBackground. Blinded, controlled studies have found that oral alitretinoin is well tolerated and effective in the treatment of severe chronic hand eczema (CHE).Aim. To assess the safety and efficacy of oral alitretinoin in patients with severe CHE in an open-label study using flexible dosing and a new measurement of patient-relevant benefits.Methods. In total, 249 patients aged 18–75 years with severe CHE unresponsive to treatment with topical corticosteroids received alitretinoin 30 mg once daily for up to 24 weeks. Safety assessments included adverse events (AEs) and laboratory tests. Efficacy assessments included Physician’s Global Assessment (PGA), the Modified Total Lesion Symptom Score, Patient’s Global Assessment and extent of disease, as well as intensity of pain and pruritus as determined by visual analogue scale (VAS) and a categorical scale for pruritus.Results. Alitretinoin was well tolerated when given for up to 24 weeks. Dose reduction occurred in 16.5% of patients. Dose interruption was required for 15.7% of patients, most commonly for headache. AEs and laboratory changes comprised effects typical of the retinoid class. A PGA response of ‘clear’ or ‘almost clear’ hands was reported for 46.6% of patients, similar to the response rate seen in blinded trials. Results of VAS and categorical assessments of pruritus provided supporting evidence of efficacy, and treatment was assessed as providing meaningful benefits to patients.Conclusions. Oral alitretinoin 30 mg was well tolerated and effective, and provided distinct therapeutic benefits in severe CHE, as assessed by patients.
Plasma membrane Ca2+ transporters mediate virus‐induced acquired resistance to oxidative stress
Authors: SHABALA SERGEY , BÆKGAARD LONE , SHABALA LANA , FUGLSANG ANJA , BABOURINA OLGA , PALMGREN MICHAEL G. , CUIN TRACEY A. , RENGEL ZED , NEMCHINOV LEV G. 
Published: November 2010

ABSTRACTThis paper reports the phenomenon of acquired cross‐tolerance to oxidative stress in plants and investigates the activity of specific Ca2+ transport systems mediating this phenomenon. Nicotiana benthamiana plants were infected with Potato virus X (PVX) and exposed to oxidative [either ultraviolet (UV‐C) or H2O2] stress. Plant adaptive responses were assessed by the combined application of a range of electrophysiological (non‐invasive microelectrode ion flux measurements), biochemical (Ca2+‐ and H+‐ATPase activity), imaging (fluorescence lifetime imaging measurements of changes in intracellular Ca2+ concentrations), pharmacological and cytological transmission electrone microscopy techniques. Virus‐infected plants had a better ability to control UV‐induced elevations in cytosolic‐free Ca2+ and prevent structural and functional damage of chloroplasts. Taken together, our results suggest a high degree of crosstalk between UV and pathogen‐induced oxidative stresses, and highlight the crucial role of Ca2+ efflux systems in acquired resistance to oxidative stress in plants.