bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of mouse sperm proteins correlated with epididymal maturation
Authors: Ijiri Takashi W. , Merdiushev Tanya , Cao Wenlei , Gerton George L. 
Published: August 2011

AbstractSperm need to mature in the epididymis to become capable of fertilization. To understand the molecular mechanisms of mouse sperm maturation, we conducted a proteomic analysis using saturation dye labeling to identify proteins of caput and cauda epididymal sperm that exhibited differences in amounts or positions on two‐dimensional gels. Of eight caput epididymal sperm‐differential proteins, three were molecular chaperones and three were structural proteins. Of nine cauda epididymal sperm‐differential proteins, six were enzymes of energy metabolism. To validate these proteins as markers of epididymal maturation, immunoblotting and immunofluorescence analyses were performed. During epididymal transit, heat shock protein 2 was eliminated with the cytoplasmic droplet and smooth muscle γ‐actin exhibited reduced fluorescence from the anterior acrosome while the signal intensity of aldolase A increased, especially in the principal piece. Besides these changes, we observed protein spots, such as glutathione S‐transferase mu 5 and the E2 component of pyruvate dehydrogenase complex, shifting to more basic isoelectric points, suggesting post‐translational changes such dephosphorylation occur during epididymal maturation. We conclude that most caput epididymal sperm‐differential proteins contribute to the functional modification of sperm structures and that many cauda epididymal sperm‐differential proteins are involved in ATP production that promotes sperm functions such as motility.
Protein 8‐class secondary structure prediction using conditional neural fields
Authors: Wang Zhiyong , Zhao Feng , Peng Jian , Xu Jinbo 
Published: August 2011

AbstractCompared with the protein 3‐class secondary structure (SS) prediction, the 8‐class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8‐class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non‐evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA.
An assessment of the ultrasonic probe‐based enhancement of protein cleavage with immobilized trypsin
Authors: Vale Gonçalo , Santos Hugo M. , Carreira Ricardo J. , Fonseca Luis , Miró Manuel , Cerdà Víctor , Reboiro‐Jato Miguel , Capelo José L. 
Published: August 2011

AbstractThe use of ultrasonic probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by the ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins – bovine serum albumin, α‐lactalbumin, carbonic anhydrase and ovalbumin – were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18‐O quantification. The digestion yields found were 90–117% for the ultrasonic and 5–21% for the vortex when those methods were compared with the classical overnight digestion.
Identification and removal of proteins that co‐purify with infectious prion protein improves the analysis of its secondary structure
Authors: Moore Roger A. , Timmes Andrew G. , Wilmarth Phillip A. , Safronetz David , Priola Suzette A. 
Published: August 2011

AbstractPrion diseases are neurodegenerative disorders associated with the accumulation of an abnormal isoform of the mammalian prion protein (PrP). Fourier transform infrared spectroscopy (FTIR) has previously been used to show that the conformation of aggregated, infectious PrP (PrPSc) varies between prion strains and these unique conformations may determine strain‐specific disease phenotypes. However, the relative amounts of α‐helix, β‐sheet and other secondary structures have not always been consistent between studies, suggesting that other proteins might be confounding the analysis of PrPSc secondary structure. We have used FTIR and LC‐MS/MS to analyze enriched PrPSc from mouse and hamster prion strains both before and after the removal of protein contaminants that commonly co‐purify with PrPSc. Our data show that non‐PrP proteins do contribute to absorbances that have been associated with α‐helical, loop, turn and β‐sheet structures attributed to PrPSc. The major contaminant, the α‐helical protein ferritin, absorbs strongly at 1652 cm−1 in the FTIR spectrum associated with PrPSc. However, even the removal of more than 99% of the ferritin from PrPSc did not completely abolish absorbance at 1652 cm−1. Our results show that contaminating proteins alter the FTIR spectrum attributed to PrPSc and suggest that the α‐helical, loop/turn and β‐sheet secondary structure that remains following their removal are derived from PrPSc itself.
Dermaseptin 01 as antimicrobial peptide with rich biotechnological potential: study of peptide interaction with membranes containing Leishmania amazonensis lipid‐rich extract and membrane models
Authors: Salay Luiz C. , Nobre Thatyane M. , Colhone Marcelle C. , Zaniquelli Maria E. D. , Ciancaglini Pietro , Stabeli Rodrigo G. , Leite José Roberto S. A. , Zucolotto Valtencir 
Published: August 2011

AbstractThis article addresses the interactions of the synthetic antimicrobial peptide dermaseptin 01 (GLWSTIKQKGKEAAIAAA‐ KAAGQAALGAL‐NH2, DS 01) with phospholipid (PL) monolayers comprising (i) a lipid‐rich extract of Leishmania amazonensis (LRE‐La), (ii) zwitterionic PL (dipalmitoylphosphatidylcholine, DPPC), and (iii) negatively charged PL (dipalmitoylphosphatidylglycerol, DPPG). The degree of interaction of DS 01 with the different biomembrane models was quantified from equilibrium and dynamic liquid‐air interface parameters. At low peptide concentrations, interactions between DS 01 and zwitterionic PL, as well as with the LRE‐La monolayers were very weak, whereas with negatively charged PLs the interactions were stronger. For peptide concentrations above 1 µg/ml, a considerable expansion of negatively charged monolayers occurred. In the case of DPPC, it was possible to return to the original lipid area in the condensed phase, suggesting that the peptide was expelled from the monolayer. However, in the case of DPPG, the average area per lipid molecule in the presence of DS 01 was higher than pure PLs even at high surface pressures, suggesting that at least part of DS 01 remained incorporated in the monolayer. For the LRE‐La monolayers, DS 01 also remained in the monolayer. This is the first report on the antiparasitic activity of AMPs using Langmuir monolayers of a natural lipid extract from L. amazonensis. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Conventional and microwave‐assisted SPPS approach: a comparative synthesis of PTHrP(1–34)NH2
Authors: Rizzolo Fabio , Testa Chiara , Lambardi Duccio , Chorev Michael , Chelli Mario , Rovero Paolo , Papini Anna Maria 
Published: August 2011

AbstractAttracted by the possibility to optimize time and yield of the synthesis of difficult peptide sequences by MW irradiation, we compared Fmoc/tBu MW‐assisted SPPS of 1–34 N‐terminal fragment of parathyroid hormone‐related peptide (PTHrP) with its conventional SPPS carried out at RT. MWs were applied in both coupling and deprotection steps of SPPS protocol. During the stepwise elongation of the resin‐bound peptide, monitoring was conducted by performing MW‐assisted mini‐cleavages and analyzing them by UPLC‐ESI‐MS. Identification of some deletion sequences was helpful to recognize critical couplings and as such helped to guide the introduction of MW irradiations to these stages. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Performance measurement with advanced diagnostic tools of all‐sky microwave imager radiances in 4D‐Var
Authors: Cardinali Carla , Prates Fernando 
Published: August 2011

AbstractIn this paper, a comprehensive assessment of the impact of all‐sky radiance observations in the operational European Centre for Medium‐Range Weather Forecasts' assimilation and forecast system is presented using advanced diagnostic tools. In particular, the observation influence in the assimilation process and the related contribution to the short‐range forecast error of radiance observations from microwave sensors is evaluated with recently developed diagnostic tools based on the adjoint version of the model. Recent operational changes to the assimilation of these observations result in a more beneficial impact on the initial condition and the short‐range forecast. The largest information content is obtained for observations that are located in clear‐sky regions as indicated by the model short‐range forecast and the observations themselves. However, the largest decrease in the forecast error is provided by observations detected in cloudy regions. It is shown that the use of Special Sensor Microwave/Imager data helps to reduce model systematic errors in the central eastern equatorial Pacific, where the intertropical convergence zone is located, and the Arabian Sea, where the monsoon season occurs. Copyright © 2011 Royal Meteorological Society
Tangent linear approximation based observation data impact estimation in 4D‐Var
Authors: Ishibashi Toshiyuki 
Published: August 2011

AbstractIn variational data assimilation systems (variational DASs), the effect of each assimilated observation dataset on an analysis field is one of the main factors in determining analysis and succeeding forecast accuracy. We call the effects ‘observation impacts’. However, the estimation of the observation impacts is difficult because variational DASs do not construct the Kalman gain that fully determines them. Therefore, all known methods for the estimation have some shortcomings. We construct a new method for the observation impact estimation. The method estimates the observation impacts as a partial analysis increment vector (PIV) that is generated by each observation dataset. For real calculation of the PIVs, we introduce partial departure vectors. The method enables us to see how the Kalman gain transforms information of observations into analysis increments. The method can also estimate the observation impacts on a forecast field while the tangent linear approximation of a forecast model is valid. Comparisons of formulations of three types of the known methods with the new method clarify the origins of nonlinear interactions between observation impacts in the known methods. We perform a preliminary experiment of one analysis cycle on the global variational DAS of the Japan Meteorological Agency to demonstrate the validity and performance of the method. Observation data are divided into satellite radiance and other conventional data, and the latter are further divided into rawinsondes, satellite winds, and the others. The experimental results are as follows: (i) the method can identify the observation impacts of each observation dataset on an analysis and a forecast field in the operational variational DAS, (ii) there are negative correlations between an integrated background error vector and dominant PIVs, and (iii) the nonlinear interactions between observation impacts in the known methods can be estimated quantitatively. The method is useful for observational data impact estimation in variational DASs. Copyright © 2011 Royal Meteorological Society
Masked illumination scheme for a galvanometer scanning high‐speed confocal fluorescence microscope
Authors: Kim Dong Uk , Moon Sucbei , Song Hoseong , Kwon Hyuk‐Sang , Kim Dug Young 
Published: August 2011

AbstractHigh‐speed beam scanning and data acquisition in a laser scanning confocal microscope system are normally implemented with a resonant galvanometer scanner and a frame grabber. However, the nonlinear scanning speed of a resonant galvanometer can generate nonuniform photobleaching in a fluorescence sample as well as image distortion near the edges of a galvanometer scanned fluorescence image. Besides, incompatibility of signal format between a frame grabber and a point detector can lead to digitization error during data acquisition. In this article, we introduce a masked illumination scheme which can effectively decrease drawbacks in fluorescence images taken by a laser scanning confocal microscope with a resonant galvanometer and a frame grabber. We have demonstrated that the difference of photobleaching between the center and the edge of a fluorescence image can be reduced from 26 to 5% in our confocal laser scanning microscope with a square illumination mask. Another advantage of our masked illumination scheme is that the zero level or the lowest input level of an analog signal in a frame grabber can be accurately set by the dark area of a mask in our masked illumination scheme. We have experimentally demonstrated the advantages of our masked illumination method in detail. SCANNING 33:455–462, 2011. © 2011 Wiley Periodicals, Inc.
The informational relevance of corporate social responsibility: evidence from DS400 index reconstitutions
Authors: Ramchander Sanjay , Schwebach Robert G. , Staking KIM 
Published: August 2011

AbstractThis study examines the relationship between corporate social responsibility and financial performance by analyzing the intra‐industry wealth impact of additions and deletions to the Domini Social 400 index. Results from the event study analysis indicate that additions to the index generate a positive share price response for the announcement firm and a negative response by rival firms. The opposite reaction is observed for index deletions. Additionally, the share price response is more pronounced for informationally opaque industries. Our study highlights the importance of external monitoring agencies in providing meaningful information that helps resolve investor uncertainty regarding the quality of a firm's relationships with its primary stakeholders. Copyright © 2011 John Wiley & Sons, Ltd.
Amylose content, molecular structure, physicochemical properties and in vitro digestibility of starches from different mung bean (Vigna radiata L.) cultivars
Authors: Kaur Maninder , Sandhu Kawaljit Singh , Singh Narpinder , Lim Seung‐Taik 
Published: August 2011

AbstractPhysicochemical and in vitro digestibility characteristics of starches isolated from six cultivars of mung bean (Vigna radiata L.) were studied. Significant differences (p < 0.05) were observed between the cultivars with respect to amylose content (29.9–33.6%), relative crystallinity (29.0 to 31.7%), particle diameter (16.2–17.1 µm) and molecular weight of amylopectin (260–289 × 106 g/mol). The scanning electron micrographs revealed the presence of large oval to small round shape granules with average particle diameter of 16.2–17.1 µm. The X‐ray diffraction pattern was of the C‐type. The enthalpies of gelatinization and retrogradation were 8.9–10.3 and 4.6–6.3 J/g, respectively. The amounts of slowly digesting and resistant starch of mung bean followed the order: PBM‐1 > SML‐32 > ML‐613 > SML‐134 > ML‐267 > ML‐5 and ML‐5 > ML‐267 > SML‐134 > ML‐613 > SML‐32 > PBM‐1, respectively. The six starches exhibited significant (p < 0.05) differences in their pasting parameters. Correlation analysis showed that amylose content, granule diameter and relative crystallinity values were important in determining thermal, pasting and in vitro digestibility of starches.
Tumor necrosis factor inhibits mesenchymal stem cell differentiation into osteoblasts via the ubiquitin E3 ligase Wwp1
Authors: Zhao Lan , Huang Jian , Zhang Hengwei , Wang Yi , Matesic Lydia E. , Takahata Masahiko , Awad Hani , Chen Di , Xing Lianping 
Published: August 2011

AbstractPatients with chronic inflammatory disorders, such as rheumatoid arthritis, often have osteoporosis due to a combination of Tumor necrosis factor-induced increased bone resorption and reduced bone formation. To test if TNF inhibits bone formation by affecting the commitment and differentiation of mesenchymal stem cells (MSCs) into osteoblasts, we examined the osteogenic potential of MSCs from TNF transgenic (TNF-Tg) mice, a model of chronic inflammatory arthritis. MSC-enriched cells were isolated from bone marrow stromal cells using negative selection with anti-CD45 antibody coated magnetic beads. The expression profile of MSC surface markers the osteogenic, chondrogenic, and adipogenic properties of CD45− cells were confirmed by FACS and cell differentiation assays. MSC-enriched CD45− cells from TNF-Tg mice formed significantly decreased numbers of fibroblast and ALP+ colonies and had a decreased expression of osteoblast marker genes. As TNF may upregulate ubiquitin ligases, which negatively regulate osteoblast differentiation, we examined the expression levels of several ubiquitin ligases and found that Wwp1 expression was significantly increased in MSC-enriched CD45− cells of TNF-Tg mice. Wwp1 knockdown rescued impaired osteoblast differentiation of TNF-Tg CD45− cells. Wwp1 promotes ubiquitination and degradation of JunB, an AP-1 transcription factor that positively regulates osteoblast differentiation. Injection of TNF into wild-type mice resulted in decreased osteoblast differentiation of MSCs and increased JunB ubiquitination, which was completely blocked in Wwp1−/− mice. Thus, Wwp1 targets JunB for ubiquitination and degradation in MSCs after chronic exposure to TNF, and inhibition of Wwp1 in MSCs could be a new mechanism to limit inflammation-mediated osteoporosis by promoting their differentiation into osteoblasts.
Aerodynamic characteristics of wind turbine blades with a sinusoidal leading edge
Authors: Zhang Ri‐Kui , Wu Van Dam Jie‐Zhi 
Published: August 2011

ABSTRACTThe aerodynamic characteristics of a kind of bionic wind turbine blades with a sinusoidal leading edge have been investigated in this paper based on a three‐dimensional Reynolds‐averaged Navier–Stokes simulation. The calculated results show that compared with a straight leading‐edge blade, the new‐type blade has a great improvement in shaft torque at high wind speeds. The localized vortices shedding from the leading‐edge tubercles, which can generate a much greater peak of the leading‐edge suction pressure than that from the straight leading‐edge case, are the physical essentials to enhance the wavy blade's aerodynamic performances as the blade goes into stall. In particular, the outboard segment from the 60%R station to the blade tip is the key region for wavy leading‐edge blades to improve the aerodynamic characteristics at high‐speed inflows. In this key region, a wavy blade can obtain a greater power output as the wavelength l and the waveheight δ increase.The present numerical results also show that the wavy leading‐edge shape is unfavorable for a wind turbine blade under the design conditions (e.g., at the rated wind speed). At these conditions, an early boundary‐layer separation as a result of the geometric disturbances of the leading‐edge tubercles will inevitably result in a visible shaft‐torque reduction in the wavy‐blade cases. Anyway, the wavy blades still tend to generate a more robust power output as a whole from 10 to 20 m s −1 than the original NREL phase‐VI blade. Copyright © 2011 John Wiley & Sons, Ltd.
Assessing atmospheric stability and its impacts on rotor‐disk wind characteristics at an onshore wind farm
Authors: Wharton Sonia , Lundquist Julie K. 
Published: August 2011

ABSTRACTAs the average hub height and blade diameter of new wind turbine installations continue to increase, turbines typically encounter higher wind speeds, which enable them to extract large amounts of energy, but they also face challenges due to the complex nature of wind flow and turbulence in the planetary boundary layer (PBL). Wind speed and turbulence can vary greatly across a turbine's rotor disk; this variability is partially due to whether the PBL is stable, neutral or convective. To assess the influence of stability on these wind characteristics, we utilize a unique data set including observations from two meteorological towers, a surface flux tower and high‐resolution remote‐sensing sound detection and ranging (SODAR) instrument. We compare several approaches to defining atmospheric stability to the Obukhov length (L). Typical wind farm observations only allow for the calculation of a wind shear exponent (α) or horizontal turbulence intensity (IU) from cup anemometers, whereas SODAR gives measurements at multiple heights in the rotor disk of turbulence intensity (I) in the latitudinal (Iu), longitudinal (Iv) and vertical (Iw) directions and turbulence kinetic energy (TKE). Two methods for calculating horizontal Ifrom SODAR data are discussed. SODAR stability parameters are in high agreement with the more physically robust L,with TKE exhibiting the best agreement, and show promise for accurate characterizations of stability. Vertical profiles of wind speed and turbulence, which likely affect turbine power performance, are highly correlated with stability regime. At this wind farm, disregarding stability leads to over‐assessments of the wind resource during convective conditions and under‐assessments during stable conditions. Copyright © 2011 John Wiley & Sons, Ltd.
Food additives such as sodium sulphite, sodium benzoate and curcumin inhibit leptin release in lipopolysaccharide-treated murine adipocytes in vitro
Authors: Ciardi Christian , Jenny Marcel , Tschoner Alexander , Ueberall Florian , Patsch Josef , Pedrini Michael , Ebenbichler Christoph , Fuchs Dietmar 
Published: August 2011

Obesity leads to the activation of pro-inflammatory pathways, resulting in a state of low-grade inflammation. Recently, several studies have shown that the exposure to lipopolysaccharide (LPS) could initiate and maintain a chronic state of low-grade inflammation in obese people. As the daily intake of food additives has increased substantially, the aim of the present study was to investigate a potential influence of food additives on the release of leptin, IL-6 and nitrite in the presence of LPS in murine adipocytes. Leptin, IL-6 and nitrite concentrations were analysed in the supernatants of murine 3T3-L1 adipocytes after co-incubation with LPS and the food preservatives, sodium sulphite (SS), sodium benzoate (SB) and the spice and colourant, curcumin, for 24 h. In addition, the kinetics of leptin secretion was analysed. A significant and dose-dependent decrease in leptin was observed after incubating the cells with SB and curcumin for 12 and 24 h, whereas SS decreased leptin concentrations after 24 h of treatment. Moreover, SS increased, while curcumin decreased LPS-stimulated secretion of IL-6, whereas SB had no such effect. None of the compounds that were investigated influenced nitrite production. The food additives SS, SB and curcumin affect the leptin release after co-incubation with LPS from cultured adipocytes in a dose- and time-dependent manner. Decreased leptin release during the consumption of nutrition-derived food additives could decrease the amount of circulating leptin to which the central nervous system is exposed and may therefore contribute to an obesogenic environment.