bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gas‐phase basicity of methionine
Authors: Desaphy Sylvain , Malosse Christian , Bouchoux Guy 
Published: August 2007

AbstractProton affinity and protonation entropy of methionine (Met) were determined by the extended kinetic method from ESI‐Q‐TOF tandem mass spectrometry experiments. The values, PA(Met) = 937.5 ± 2.9 kJ mol−1 and ΔpS°(Met) = − 22 ± 5 J mol−1 K−1, lead to gas‐phase basicity GB(Met) = 898.2 ± 3.2 kJ.mol−1. Quantum chemical calculations using density functional theory confirm that the proton affinity of Met is indeed in the 940 kJ mol−1 range and that a significant entropy loss, of at least − 25 J mol−1 K−1, occurs upon protonation. This last point is evidenced here for the first time and suggests revision of the tabulated protonation thermochemistry of Met. A comparison with previous experimental data allows us to propose the following evaluated thermochemical values: PA(Met) = 943 ± 4 kJ mol−1 and ΔpS°(Met) = − 35 ± 15 J mol−1 K−1 and GB(Met) = 900 ± 2 kJ mol−1. Copyright © 2007 John Wiley & Sons, Ltd.
The relationships of the North Atlantic Oscillation to water temperature along the southern Baltic Sea coast
Authors: Girjatowicz Józef Piotr 
Published: August 2007

AbstractThe present paper focuses on the relationships between the North Atlantic oscillation (NAO) index and surface water temperature along the southern Baltic Sea coast. Monthly water temperature values from the period of 1951–2000 were measured in Świnoujście, Miȩdzyzdroje, Kołobrzeg, Mielno, Ustka, Władysławowo, Hel and Gdynia: sites which are located along the Polish coast. Correlation and regression methods were applied to calculate and analyse the relationships between the NAO index and water temperature.A statistically significant positive correlation between NAO index and the water temperature occurred in winter from December to March with the strongest relationships observed in January followed by February and March. The relationships between the NAO index and water temperature are usually statistically insignificant in the remaining part of the year (April–November).Various kinds of relationships were tested in this study. Our research revealed that asynchronous relationships are rather weak, although in winter they are also statistically significant. They are strongest for the January value of the NAO index combined with February water temperature. However, after three to four months they become statistically insignificant. They regain statistical significance only in late Autumn.It has also been shown that during the cold season, local factors, especially solar ones, weaken the NAO index relationships with the water temperature. This is clearly visible especially towards the turn of winter when insolation increases. During very mild winters the influence of the local factors may be significant beginning from mid‐winter. Copyright © 2007 Royal Meteorological Society
Vibrational spectra and quantum chemical calculations of uracilyl–pyridinium mesomeric betaine
Authors: Schmidt A. , Lindner A. S. , Casado J. , Ramírez F. J. 
Published: August 2007

AbstractModified nucleobases (MNs) are promising molecules with potential application in non‐linear optic (NLO) and drug design against a wide number of diseases. In the present paper we report studies on a cross‐conjugated mesomeric betaine, which can act as a MN, formed by the covalent union of a 4‐dimethylamino pyridinium and a uracilyl groups. The molecule thus formed must be presented by a dipolar canonical formulae in which positive and negative charges are delocalized within separated moieties. Quantum chemistry density functional theory (DFT) calculations, at the B3PW91/6‐31G** level, and Fourier transform (FT) infrared and Raman spectra of this molecule and its N‐deuterated derivative were performed. The calculated structural properties over the ground state optimized structure evidenced a strong separation between the two conjugated systems. Comparison with previous results obtained for the cationic species indicated that N‐protonation clearly affects the degree of conjugation. Assignments of the FT‐IR and FT‐Raman spectra were supported by the DFT wavenumbers, intensities and normal modes, which also evidenced the separation of the two conjugated systems. Significant deviations were found for the stretching force constants of the inter‐ring and the uracilyl skeletal bonds when comparing this molecule with its N‐protonated species. Copyright © 2007 John Wiley & Sons, Ltd.
Overcoming adverse effects of hailnets on fruit quality and microclimate in an apple orchard
Authors: Solomakhin Alexej A , Blanke Michael M 
Published: August 2007

AbstractBACKGROUND: With the increase of hailstorms as a possible result of global warming, fruit crops are increasingly grown under hailnets. This results in lesser fruit quality in terms of colouration, fruit mass, firmness, starch and taste, i.e. sugar and acid, and vitamin content under hailnet due to altered microclimate and light deprivation. Reflective mulches (Extenday and Daybright) were spread in autumn 2006 to improve fruit quality and light utilisation under hailnet at Klein‐Altendorf Research Station near Bonn, Germany. A monophosphate (Seniphos) was applied twice for the same purpose; untreated apple cv. ‘Elstar’ trees served as control.RESULTS: Under the translucent, ‘white’ hailnet, humidity was increased by ca. 6%, air temperature reduced by ca. 1.6 °C, soil temperature increased by ca. 0.5 °C and light reduced by 11–15% resulting in lesser fruit quality of 2.5% less sugar and less taste. The two reflective mulches increased light reflection at 45° and 90° angles by 2.5‐ to 6.3‐fold. No differences in fruit ripening and firmness were observed, but fruit from trees under hailnet with reflective mulch contained up to 2.4% (from 13.3 to 15.7%) more sugar than those of the control (uncovered grass alleys). A less negative normalised differential vegetation index (NDVI) of − 0.3 on the red compared with − 0.5 on the green fruit side indicated more chlorophyll in the outer, sun‐exposed, red side of the apples relative to the shaded side. Monophosphate‐treated fruits maintained the peel chlorophyll with a greener ground colour of 92–97° hue and a NDVI of − 0.3 as in the grassed control. Fruit in the lower canopy with reflective mulch were darker red (a value 30; 22° hue) relative to the grassed control with a = 25 and 43° hue (light red), expressed in a 4‐fold increase in normalised anthocyanin index (NAI), but showed enhanced chlorophyll breakdown (NDVI from − 0.2 to − 0.5); similarly, the monophosphate increased the NAI by up to 2.5‐fold.CONCLUSIONS: The effect of both reflective mulch cloths was most pronounced on apple fruit in the lower canopy under hailnet, which developed large vitamin C contents and a dark red top colour relative to the grassed control with enhanced chlorophyll breakdown. Both reflective mulch cloths increased the percentage of class I fruit with > 25% colouration by 12% (from 82 to 94%) without and under hailnet by 23% (from 69 to 89%) relative to the grassed control resulting in financial net gains of up to 1300 € ha−1 Copyright © 2007 Society of Chemical Industry
Sentinel lymph node biopsy for gastrointestinal cancers
Authors: Bembenek A. , Gretschel S. , Schlag P.M. 
Published: August 2007

AbstractSentinel lymph node biopsy (SLNB) in gastrointestinal‐(GI)‐tract cancer is not yet of clinical relevance. Nevertheless, the results in the upper GI‐tract promise to be helpful to individualize the indication for surgical therapy. SLNB in colon cancer still fails to show high validity to predict the nodal status, but may be helpful to clarify the prognostic role of micrometastases/isolated tumor cells. In anal cancer SLNB is able to guide the indication for groin irradiation. J. Surg. Oncol. 2007;96:342–352. © 2007 Wiley‐Liss, Inc.
Effect of the Structure of Photosensitive Groups Contained in Novel PU‐Type Polymeric Benzophenone Photoinitiators on Photopolymerization
Authors: Wei Jun , Jiang Xue Song , Wang Hong Yu 
Published: August 2007

AbstractThree polymeric photoinitiators, PUSBA‐s, PUSBA‐o and PUSBA‐c, were synthesized through polycondensation of TDI, different photosensitive diamines, and BDEA. UV/Vis spectra indicate that the maximum absorption depends mainly on the structure of the photosensitive groups. ESR spectra show that PUSBA‐s can efficiently generate free radicals. The photopolymerization of TMPTA and a PU prepolymer, initiated by these polymeric photoinitiators, was studied by photo‐DSC. The results indicate that the structure of the photosensitive groups has an important effect on photopolymerization: PUSBA‐s is the most efficient and PUSBA‐c is the least efficient of the three polymeric photoinitiators.magnified image
Natural and Synthetic Polyampholytes, 1
Authors: Ciferri A. , Kudaibergenov S. 
Published: August 2007

AbstractThis critical review analyzes the behavior of natural and synthetic polyampholytes and current theoretical descriptions based on Coulomb interactions between complementary charges. Sequences of bonds and groups that occur between fixed charges display interactions with other groups along the chain, or with solvent components, which may antagonize the behavior expected from intramolecular Coulomb attraction. The relevant thermodynamic description of charge‐independent interaction is also reviewed. The relationship between the various interactions hinges on the problem of the intra and intersupramolecular stabilization of biomacromolecules. Two results of the analysis of polyampholytes are, however, enlightening the complex problem. One is the verification that the basic predictions of current polyampholyte theory conform to selected aspects of the experimental behavior. The other is the astonishing variety of supramolecular structures and transformation exhibited by polyampholytes when hydrophobic and other non‐charge dependent interactions are operative.magnified image
Conducting Block Copolymers of Regioregular Poly(3‐hexylthiophene) and Poly(methacrylates): Electronic Materials with Variable Conductivities and Degrees of Interfibrillar Order
Authors: Iovu Mihaela C. , Zhang Rui , Cooper Jessica R. , Smilgies Detlef M. , Javier Anna E. , Sheina Elena E. , Kowalewski Tomasz , McCullough Richard D. 
Published: August 2007

AbstractIntegration of regioregular poly(3‐hexylthiophene) in diblock copolymers with various poly(methacrylates) yielded electronic materials with variable conductivities and different types of nanoscale order. Solid state analysis of poly(3‐hexylthiophene)‐block‐poly(methyl methacrylate) and poly(3‐hexylthiophene)‐block‐poly(t‐butyl methacrylate) diblock copolymers revealed the presence of densely packed, locally parallel nanofibrils. By contrast, poly(3‐hexylthiophene)‐block‐poly(isobornyl methacrylate) copolymers containing bulkier isobornyl functional groups exhibited nanofibrillar morphology with isolated fibrils and no interfibrillar order.magnified image
A new computational approach to contact mechanics using variable‐node finite elements
Authors: Kim Jong Hoon , Lim Jae Hyuk , Lee Jun Ho , Im Seyoung 
Published: August 2007

AbstractIn this paper, a new computational strategy for two‐dimensional contact problems is developed with the aid of variable‐node finite elements within the range of infinitesimal deformations. The variable‐node elements, which are among MLS (moving least square)‐based finite elements, enable us to transform node‐to‐surface contact problems into node‐to‐node contact problems. This contact formulation with variable‐node elements leads to an accurate and effective solution procedure, needless to mention that the contact patch test is passed without any additional treatment. Through several numerical examples, we demonstrate its simplicity and the effectiveness of the
proposed scheme. Copyright © 2007 John Wiley & Sons, Ltd.
Solving linear and non‐linear space–time fractional reaction–diffusion equations by the Adomian decomposition method
Authors: Yu Q. , Liu F. , Anh V. , Turner I. 
Published: August 2007

AbstractIn this paper, we consider linear and non‐linear space–time fractional reaction–diffusion equations (STFRDE) on a finite domain. The equations are obtained from standard reaction–diffusion equations by replacing a second‐order space derivative by a fractional derivative of order β∈(1, 2], and a first‐order time derivative by a fractional derivative of order α∈(0, 1]. We use the Adomian decomposition method to construct explicit solutions of the linear and non‐linear STFRDE. Finally, some examples are given. Copyright © 2007 John Wiley & Sons, Ltd.
Fourier series and integral equation method for the exterior Stokes problem
Authors: Lubuma Jean M.‐S. 
Published: August 2007

AbstractThe exterior Stokes problem between two parallel planes that are separated by a prismatic cylinder is extended to the interior of the prism by requiring the continuity of the velocity across the lateral faces. The well‐posedness of the exterior–interior problem is proved in suitable weighted Sobolev spaces. The solution is represented by Fourier series in the z‐variable. The Fourier coefficients, solutions of auxiliary two‐dimensional exterior–interior problems, are analyzed by viewing them as boundary integral equations of potential theory and global regularity of the densities, is established in weighted Sobolev spaces of traces. A boundary element method, with suitably refined mesh size, is implemented for the numerical treatment of the Fourier coefficients. This provides optimal convergent semi‐ and fully‐discrete spectral methods of Fourier–Galerkin type. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
Transcriptional silencing of hedgehog‐interacting protein by CpG hypermethylation and chromatic structure in human gastrointestinal cancer
Authors: Taniguchi H , Yamamoto H , Akutsu N , Nosho K , Adachi Y , Imai K , Shinomura Y 
Published: August 2007

AbstractHedgehog‐interacting protein (HHIP) was identified as a putative antagonist of the Hh pathway and as a target of Hh signalling. Our aim was to clarify the expression profiles and epigenetic alterations of the HHIP gene in gastrointestinal cancer. The expression and promoter epigenetic status of HHIP in cancer cell lines and freshly resected gastrointestinal cancer tissues were examined using RT‐PCR, tissue microarray analysis, methylation‐specific PCR, and chromatin immunoprecipitation assay. Cells were treated with the demethylating agent 5‐aza‐2′‐deoxycytidine and/or histone deacetylase inhibitor trichostatin A. WST‐8 assays and in vitro invasion assays after treatment with HHIP‐specific siRNA were performed. HHIP expression levels were reduced in most of the gastrointestinal cancer cell lines and in a certain subset of cancer tissues, and these were correlated with promoter hypermethylation. A heterochromatic structure characterized by neither acetylated H3 nor acetylated H4, and histone H3 lysine 9 hypermethylation and histone H3 lysine 4 hypomethylation was observed in cancer cells in which the HHIP gene was aberrantly silenced. On the other hand, overexpression of the HHIP gene was also found in some cancer tissues and there were significant correlations between protein expression levels of HHIP and those of Sonic hedgehog (Shh), Indian hedgehog, Patched, and glioma‐associated oncogene homologue‐1. An association was found between lymph node metastasis and HHIP silencing in colorectal cancer tissues with strong Shh expression and between advanced TNM stage and HHIP silencing in diffuse‐type gastric cancer tissues with strong Shh expression. Down‐regulation of HHIP expression by siRNA resulted in a significant increase in colon cancer cell growth and invasion in vitro. Silencing of the HHIP gene due to hypermethylation and chromatin remodelling appears to be frequently involved in gastrointestinal tumourigenesis. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Impairment of the ubiquitin–proteasome system associated with extracellular transthyretin aggregates in familial amyloidotic polyneuropathy
Authors: Santos SD , Cardoso I , Magalhães J , Saraiva MJ 
Published: August 2007

AbstractThe ubiquitin–proteasome system (UPS) has been associated with neurodegenerative disorders of intracellular protein aggregation. We have studied the UPS in familial amyloidotic polyneuropathy (FAP), a neurodegenerative disorder caused by extracellular deposition of mutant transthyretin (TTR). The studies were conducted in TTR‐synthesizing and non‐synthesizing tissues from affected individuals, in transgenic mouse models for FAP, and in neuronal or Schwannoma cell lines cultured with TTR aggregates. In human FAP tissues presenting extracellular TTR aggregates, ubiquitin–protein conjugates were up‐regulated, the proteasome levels were decreased and parkin and α‐synuclein expression were both decreased. A similar response was detected in mouse models for TTR V30M or L55P. On the other hand, the liver, which normally synthesizes variant TTR V30M, did not show this response. Furthermore, transgenic mice immunized to decrease TTR deposition showed a significant reduction in ubiquitin levels and an increase in parkin and α‐synuclein levels in comparison to control mice. Studies performed in cell lines with aggregates in the medium resulted in increased ubiquitin and decreased parkin levels. The overall results are indicative of TTR deposition as an external stimulus to an intracellular UPS response in FAP. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Host‐extract induced changes in the secretome of the plant pathogenic bacterium Pectobacterium atrosepticum
Authors: Mattinen Laura , Nissinen Riitta , Riipi Tero , Kalkkinen Nisse , Pirhonen Minna 
Published: August 2007

AbstractPectobacterium atrosepticum is a Gram‐negative plant pathogenic bacterium that causes rotting in potato stems and tubers. The secreted proteins of this pathogen were analyzed with proteomics from culture supernatant of cells grown in minimal medium supplemented with host extracts. More than 40 proteins were identified, among them known virulence determinants, such as pectic enzymes, metalloprotease, and virulence protein Svx, along with flagella proteins, GroEL and cyclophilin‐type chaperones and several hypothetical proteins or proteins with unknown function. Some of the identified proteins may be involved in utilization of nutrients or transport of minerals. Northern and real‐time RT‐PCR analyses suggested that most of the proteins upregulated by plant extract were transcriptionally regulated. Among the identified proteins were VgrG and four homologs of hemolysin‐coregulated proteins (Hcps). A mutant strain lacking one of the hcp genes was not affected in virulence, while a bacterial strain overexpressing the same gene was shown to have increased virulence, which suggests that these proteins may be new virulence determinants of P. atrosepticum. Comparison of the secretomes of wild type cells and hrcC mutant defective in Type III secretion suggested that the production of the identified proteins was independent of functional Type III secretion system.
SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling
Authors: Mueller Lukas N. , Rinner Oliver , Schmidt Alexander , Letarte Simon , Bodenmiller Bernd , Brusniak Mi‐Youn , Vitek Olga , Aebersold Ruedi , Müller Markus 
Published: August 2007

AbstractLabel‐free quantification of high mass resolution LC‐MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC‐MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn, that comprises a set of modules to process LC‐MS data acquired on a high resolution mass spectrometer. The program includes newly developed functionalities to analyze LC‐MS data such as feature extraction and quantification, LC‐MS similarity analysis, LC‐MS alignment of multiple datasets, and intensity normalization. These program routines extract profiles of measured features and comprise tools for clustering and classification analysis of the profiles. SuperHirn was applied in an MS1‐based profiling approach to a benchmark LC‐MS dataset of complex protein mixtures with defined concentration changes. We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.
Quantitative proteomics using uniform 15N‐labeling, MASCOT, and the trans‐proteomic pipeline
Authors: Palmblad Magnus , Bindschedler Laurence V. , Cramer Rainer 
Published: August 2007

AbstractStable isotope labeling combined with MS is a powerful method for measuring relative protein abundances, for instance, by differential metabolic labeling of some or all amino acids with 14N and 15N in cell culture or hydroponic media. These and most other types of quantitative proteomics experiments using high‐throughput technologies, such as LC‐MS/MS, generate large amounts of raw MS data. This data needs to be processed efficiently and automatically, from the mass spectrometer to statistically evaluated protein identifications and abundance ratios. This paper describes in detail an approach to the automated analysis of uniformly 14N/15N‐labeled proteins using MASCOT peptide identification in conjunction with the trans‐proteomic pipeline (TPP) and a few scripts to integrate the analysis workflow. Two large proteomic datasets from uniformly labeled Arabidopsis thaliana were used to illustrate the analysis pipeline. The pipeline can be fully automated and uses only common or freely available software.
Optimized temperature and deadspace correction improve analysis of multiple breath washout measurements by ultrasonic flowmeter in infants
Authors: Latzin P. , Sauteur L. , Thamrin C. , Schibler A. , Baldwin D. , Hutten G.J. , Kyburz M. , Kraemer R. , Riedel T. , Frey U. 
Published: August 2007

AbstractBackground:Assessment of lung volume (FRC) and ventilation inhomogeneities with ultrasonic flowmeter and multiple breath washout (MBW) has been used to provide important information about lung disease in infants. Sub‐optimal adjustment of the mainstream molar mass (MM) signal for temperature and external deadspace may lead to analysis errors in infants with critically small tidal volume changes during breathing.Methods:We measured expiratory temperature in human infants at 5 weeks of age and examined the influence of temperature and deadspace changes on FRC results with computer simulation modeling. A new analysis method with optimized temperature and deadspace settings was then derived, tested for robustness to analysis errors and compared with the previously used analysis methods.Results:Temperature in the facemask was higher and variations of deadspace volumes larger than previously assumed. Both showed considerable impact upon FRC and LCI results with high variability when obtained with the previously used analysis model. Using the measured temperature we optimized model parameters and tested a newly derived analysis method, which was found to be more robust to variations in deadspace. Comparison between both analysis methods showed systematic differences and a wide scatter.Conclusion:Corrected deadspace and more realistic temperature assumptions improved the stability of the analysis of MM measurements obtained by ultrasonic flowmeter in infants. This new analysis method using the only currently available commercial ultrasonic flowmeter in infants may help to improve stability of the analysis and further facilitate assessment of lung volume and ventilation inhomogeneities in infants. Pediatr Pulmonol. 2007; 42:888–897. © 2007 Wiley‐Liss, Inc.