bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catechols in caffeic acid phenethyl ester are essential for inhibition of TNF‐mediated IP‐10 expression through NF‐κB‐dependent but HO‐1‐ and p38‐independent mechanisms in mouse intestinal epithelial cells
Authors: Mapesa Job O. , Waldschmitt Nadine , Schmoeller Ingrid , Blume Carolin , Hofmann Thomas , Mahungu Symon , Clavel Thomas , Haller Dirk 
Published: October 2011

AbstractScope: Caffeic acid phenethyl ester (CAPE) is an active constituent of honeybee propolis inhibiting nuclear factor (NF)‐κB. The aims of our study were to provide new data on the functional relevance and mechanisms underlying the role of CAPE in regulating inflammatory processes at the epithelial interface in the gut and to determine the structure/activity relationship of CAPE.Methods and results: CAPE significantly inhibited TNF‐induced IP‐10 expression in intestinal epithelial cells. Using various analogues, we demonstrated that substitution of catechol hydroxyl groups and addition of one extra hydroxyl group on ring B reversed the functional activity of CAPE to inhibit IP‐10 production. The anti‐inflammatory potential of CAPE was confirmed in ileal tissue explants and embryonic fibroblasts derived from TNFΔARE/+ mice. Interestingly, CAPE inhibited both TNF‐ and LPS‐induced IP‐10 production in a dose‐dependent manner, independently of p38 MAPK, HO‐1 and Nrf2 signaling pathways. We found that CAPE did not inhibit TNF‐induced IκB phosphorylation/degradation or nuclear translocation of RelA/p65, but targeted downstream signaling events at the level of transcription factor recruitment to the gene promoter.Conclusion: This study reveals the structure–activity effects and anti‐inflammatory potential of CAPE in the intestinal epithelium.
The vehicle routing problem with time windows and temporal dependencies
Authors: Dohn Anders , Rasmussen Matias Sevel , Larsen Jesper 
Published: October 2011

AbstractIn this article, we formulate the vehicle routing problem with time windows and temporal dependencies. The problem is an extension of the well studied vehicle routing problem with time windows. In addition to the usual constraints, a scheduled time of one visit may restrain the scheduling options of other visits. Special cases of temporal dependencies are synchronization and precedence constraints. Two compact formulations of the problem are introduced and the Dantzig–Wolfe decompositions of these formulations are presented to allow for a column generation‐based solution approach. Temporal dependencies are modeled by generalized precedence constraints. Four different master problem formulations are proposed and it is shown that the formulations can be ranked according to the tightness with which they describe the solution space. A tailored time window branching is used to enforce feasibility on the relaxed master problems. Finally, a computational study is performed to quantitatively reveal strengths and weaknesses of the proposed formulations. It is concluded that, depending on the problem at hand, the best performance is achieved either by relaxing the generalized precedence constraints in the master problem, or by using a time‐indexed model, where generalized precedence constraints are added as cuts when they become severely violated. © 2011 Wiley Periodicals, Inc. NETWORKS, Vol. 58(4), 273–289 2011
Improved exact method for the double TSP with multiple stacks
Authors: Lusby Richard M. , Larsen Jesper 
Published: October 2011

AbstractThe Double TSP with Multiple Stacks is a logistics problem where one must, using a container, transport a given number of orders from a set of pickup customers to a set of delivery customers at minimum cost. Each order corresponds to the movement of one pallet, all pickups must be completed before the first delivery, and the container cannot be repacked once packed. In this paper we improve the previously proposed exact method of Lusby et al. (Int Trans Oper Res 17 (2010), 637–652) through an additional preprocessing technique that uses the longest common subsequence between the respective pickup and delivery problems. The results suggest an impressive improvement, and we report, for the first time, optimal solutions to several unsolved instances from the literature containing 18 customers. Instances with 28 customers are also shown to be solvable within a few percent of optimality. © 2011 Wiley Periodicals, Inc. NETWORKS, Vol. 58(4), 290–300 2011
Worldwide first fully up‐scaled fabrication of 60 × 100 cm2 dye solar module prototypes
Authors: Hinsch Andreas , Veurman Welmoed , Brandt Henning , Loayza Aguirre Ramiro , Bialecka Katarzyna , Flarup Jensen Katrine 
Published: October 2011

ABSTRACTLarge‐scale (6000 cm2) dye solar cell modules were developed using a meander and integrated series connection design in combination with a glass frit‐sealing technique. The manufacturing process, as developed at Fraunhofer Institute for Solar Energy Systems (ISE) for glass frit‐sealed dye solar cell modules, is based entirely on screen printing and does not require the interconnection of sub‐modules. With the same technique and appropriate quality control, a good reproducibility on smaller‐scaled modules (10 × 10 cm²) is already achieved and a solar efficiency of 7.1% on the active area has been reached, resulting in 5.3% efficiency on total aperture area. The scope of the recent work is to prove that the manufacturing concept is up‐scalable to attractive areas for the building‐integrated photovoltaic market. For the size of 60 × 100 cm² to be reached, it was necessary to transfer each process step into an industrial environment. Additionally, a half‐automated station for coloring and electrolyte filling made out of standard parts was constructed, which forms the basis for the final processing steps. Additional functions (processes and quality control) to ensure the long‐term stability are integrated into the station. First operating module prototypes have been manufactured with this equipment. Different processing steps and the electrical characterization of these first 60 × 100 cm2 prototypes are presented along with an overview of the advantages of this module concept in terms of cost effective up‐scaling and transfer to industrial production. Copyright © 2011 John Wiley & Sons, Ltd.
Synthesis and thermal crosslinking of carbosiloxane and oligo(oxyethylene) polymers
Authors: Delgado Paula A. , Matloka Piotr , Zuluaga Fabio , Wagener Kenneth B. 
Published: October 2011

AbstractAcyclic diene metathesis (ADMET) polymerization has been used in the synthesis of telechelic materials using alkoxy‐functionalized carbosiloxane or oligo(oxyethylene)‐based polymers, varying from internal to terminal cured materials or the combination of them. Previous investigations demonstrated that introduction of chain‐end crosslinking improves the stress–strain behavior of such materials. A series of saturated and unsaturated carbosiloxane and oligo(oxyethylene)‐based polymers were synthesized by ADMET polymerization using silacyclobutane as chain‐end, thermally induced crosslinker. The carbosiloxane derivatives presented pure amorphous behavior, whereas the oligo(oxyethylene) polymers were semicrystalline. The thermal curing process was monitored by differential scanning calorimetry via the exotherm between 160 and 210 °C. Mechanical properties on thermoset polymers were measured, where cured polymers showed moduli from 0.6 to 9.3 MPa, tensile strengths from 0.3 to 1.0 MPa, and elongations from 12 to 76%. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
PDB‐scale analysis of known and putative ligand‐binding sites with structural sketches
Authors: Ito Jun‐Ichi , Tabei Yasuo , Shimizu Kana , Tomii Kentaro , Tsuda Koji 
Published: October 2011

AbstractComputational investigation of protein functions is one of the most urgent and demanding tasks in the field of structural bioinformatics. Exhaustive pairwise comparison of known and putative ligand‐binding sites, across protein families and folds, is essential in elucidating the biological functions and evolutionary relationships of proteins. Given the vast amounts of data available now, existing 3D structural comparison methods are not adequate due to their computation time complexity. In this article, we propose a new bit string representation of binding sites called structural sketches, which is obtained by random projections of triplet descriptors. It allows us to use ultra‐fast all‐pair similarity search methods for strings with strictly controlled error rates. Exhaustive comparison of 1.2 million known and putative binding sites finished in ∼30 h on a single core to yield 88 million similar binding site pairs. Careful investigation of 3.5 million pairs verified by TM‐align revealed several notable analogous sites across distinct protein families or folds. In particular, we succeeded in finding highly plausible functions of several pockets via strong structural analogies. These results indicate that our method is a promising tool for functional annotation of binding sites derived from structural genomics projects. Proteins 2011. © 2012 Wiley Periodicals, Inc.
Novel high‐affinity binders of human interferon gamma derived from albumin‐binding domain of protein G
Authors: Ahmad Jawid N. , Li Jingjing , Biedermannová Lada , Kuchař Milan , Šípová Hana , Semerádtová Alena , Černý Jiří , Petroková Hana , Mikulecký Pavel , Polínek Jiří , Staněk Ondřej , Vondrášek Jiří , Homola Jiří , Malý Jan , Osička Radim , Šebo Peter , Malý Petr 
Published: October 2011

AbstractRecombinant ligands derived from small protein scaffolds show promise as robust research and diagnostic reagents and next generation protein therapeutics. Here, we derived high‐affinity binders of human interferon gamma (hIFNγ) from the three helix bundle scaffold of the albumin‐binding domain (ABD) of protein G from Streptococcus G148. Computational interaction energy mapping, solvent accessibility assessment, and in silico alanine scanning identified 11 residues from the albumin‐binding surface of ABD as suitable for randomization. A corresponding combinatorial ABD scaffold library was synthesized and screened for hIFNγ binders using in vitro ribosome display selection, to yield recombinant ligands that exhibited Kd values for hIFNγ from 0.2 to 10 nM. Molecular modeling, computational docking onto hIFNγ, and in vitro competition for hIFNγ binding revealed that four of the best ABD‐derived ligands shared a common binding surface on hIFNγ, which differed from the site of human IFNγ receptor 1 binding. Thus, these hIFNγ ligands provide a proof of concept for design of novel recombinant binding proteins derived from the ABD scaffold. Proteins 2011. © 2012 Wiley Periodicals, Inc.
Structural studies of a signal peptide in complex with signal peptidase I cytoplasmic domain: The stabilizing effect of membrane‐mimetics on the acquired fold
Authors: De Bona Paolo , Deshmukh Lalit , Gorbatyuk Vitaliy , Vinogradova Olga , Kendall Debra A. 
Published: October 2011

AbstractA protein destined for export from the cell cytoplasm is synthesized as a preprotein with an amino‐terminal signal peptide. In Escherichia coli, typically signal peptides that guide preproteins into the SecYEG protein conduction channel are subsequently removed by signal peptidase I. To understand the mechanism of this critical step, we have assessed the conformation of the signal peptide when bound to signal peptidase by solution nuclear magnetic resonance. We employed a soluble form of signal peptidase, which laks the two transmembrane domains (SPase I Δ2‐75), and the E. coli alkaline phosphatase signal peptide. Using a transferred NOE approach, we found clear evidence of a weak peptide‐enzyme complex formation. The peptide adopts a U‐turn shape originating from the proline residues within the primary sequence that is stabilized by its interaction with the peptidase and leaves key residues of the cleavage region exposed for proteolysis. In dodecylphosphocholine (DPC) micelles the signal peptide also adopts a U‐turn shape comparable with that observed in association with the enzyme. In both environments this conformation is stabilized by the signal peptide phenylalanine side chain‐interaction with enzyme or lipid mimetic. Moreover, in the presence of DPC, the N‐terminal core region residues of the peptide adopt a helical motif and based on PRE (paramagnetic relaxation enhancement) experiments are shown to be buried within the membrane. Taken together, this is consistent with proteolysis of the preprotein occurring while the signal peptide remains in the bilayer and the enzyme active site functioning at the membrane surface. Proteins 2011. © 2012 Wiley Periodicals, Inc.
Case‐to‐case variability of predictability of deep convection in a mesoscale model
Authors: Done J. M. , Craig G. C. , Gray S. L. , Clark P. A. 
Published: October 2011

AbstractSuccessful quantitative precipitation forecasts under convectively unstable conditions depend on the ability of the model to capture the location, timing and intensity of convection. Ensemble forecasts of two mesoscale convective outbreaks over the UK are examined with a view to understanding the nature and extent of their predictability. In addition to a control forecast, twelve ensemble members are run for each case with the same boundary conditions but with perturbations added to the boundary layer. The intention is to introduce perturbations of appropriate magnitude and scale so that the large‐scale behaviour of the simulations is not changed. In one case, convection is in statistical equilibrium with the large‐scale flow. This places a constraint on the total precipitation, but the location and intensity of individual storms varied. In contrast, the other case was characterised by a large‐scale capping inversion. As a result, the location of individual storms was fixed, but their intensities and the total precipitation varied strongly. The ensemble shows case‐to‐case variability in the nature of predictability of convection in a mesoscale model, and provides additional useful information for quantitative precipitation forecasting. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office
Influence of Side Chain Length on Fluorescence Intensity of ROMP‐Based Polymeric Nanoparticles and Their Tumor Specificity in In‐Vivo Tumor Imaging
Authors: Miki Koji , Oride Kazuaki , Kimura Akinori , Kuramochi Yoshiaki , Matsuoka Hideki , Harada Hiroshi , Hiraoka Masahiro , Ohe Kouichi 
Published: October 2011

AbstractIn this study, amphiphilic brush‐like copolymers conjugated with short alkyl or long polymeric chains of various lengths are synthesized using ring‐opening metathesis polymerization (ROMP) of substituted norbornadiene monomers followed by chemical transformations. These amphiphilic copolymers form spherical self‐assemblies in aqueous media with diameters of 132–244 nm. The low critical aggregation concentration of these assemblies (2.5 × 10−3−1.4 × 10−5 g/L) indicates that they are quite stable in dilute conditions. An appropriate length of polymer side chain that conjugates the polymer backbone with a hydrophobic ICG (indocyanine green) moiety enhanced the fluorescence intensities of these self‐assemblies in aqueous solution as well as in tumor‐bearing mice. A longer side chain conjugated with tumor targeting agents could significantly affect the tumor specificity of self‐assemblies to a greater extent. The self‐assemblies bearing hydrophilic tumor targeting agents, such as a glucosamine molecule and a cyclic RGD (arginine–glycine–asparatic acid) peptide, accumulated in tumor tissues with high selectivity, while those having a hydrophobic targeting agent, such as folate moieties, accumulated in tumor sites with low selectivity. The results demonstrated here unambiguously indicate that the fluorescence intensity and tumor specificity of self‐assemblies are strongly affected by the length of side chains that conjugate with dyes and targeting agents.
Indices for monitoring changes in extremes based on daily temperature and precipitation data
Authors: Zhang Xuebin , Alexander Lisa , Hegerl Gabriele C. , Jones Philip , Tank Albert Klein , Peterson Thomas C. , Trewin Blair , Zwiers Francis W. 
Published: October 2011

AbstractIndices for climate variability and extremes have been used for a long time, often by assessing days with temperature or precipitation observations above or below specific physically‐based thresholds. While these indices provided insight into local conditions, few physically based thresholds have relevance in all parts of the world. Therefore, indices of extremes evolved over time and now often focus on relative thresholds that describe features in the tails of the distributions of meteorological variables. In order to help understand how extremes are changing globally, a subset of the wide range of possible indices is now being coordinated internationally which allows the results of studies from different parts of the world to fit together seamlessly. This paper reviews these as well as other indices of extremes and documents the obstacles to robustly calculating and analyzing indices and the methods developed to overcome these obstacles. Gridding indices are necessary in order to compare observations with climate model output. However, gridding indices from daily data are not always straightforward because averaging daily information from many stations tends to dampen gridded extremes. The paper describes recent progress in attribution of the changes in gridded indices of extremes that demonstrates human influence on the probability of extremes. The paper also describes model projections of the future and wraps up with a discussion of ongoing efforts to refine indices of extremes as they are being readied to contribute to the IPCC's Fifth Assessment Report. WIREs Clim Change 2011, 2:851–870. doi: 10.1002/wcc.147This article is categorized under:

Paleoclimates and Current Trends > Modern Climate Change
Accurate variational calculations for line lists to model the vibration–rotation spectra of hot astrophysical atmospheres
Authors: Tennyson Jonathan 
Published: October 2011

AbstractThe first principles calculation of the spectra of small molecules is making a significant impact on high‐resolution spectroscopy as well as astrophysics and atmospheric physics. Variational nuclear motion calculations, combined with high‐accuracy ab initio electronic structure computations, are being used to make spectral predictions of increasing accuracy with very few a priori assumptions. This work is important for spectral analysis and particularly for dipole transition intensities, which are often very difficult to measure reliably but are essential inputs for many applications such as modeling of radiative transport and remote sensing. Demands for very extended line lists covering many, many millions of transitions which are required to simulate spectra of hot sources are best met using high‐quality theoretical models. This aspect of the use of variational nuclear motion calculations is discussed with reference to both the benchmark water molecule and future data needs, in particular, for models of the atmospheres of extrasolar planets. © 2011 John Wiley & Sons, Ltd.This article is categorized under:

Theoretical and Physical Chemistry > Spectroscopy
Na5[CN2]2[CN], (Li, Na)5[CN2]2[CN], and K2[CN2]: Carbodiimides from High‐Pressure Synthesis
Authors: Zhang Shiyu , Zherebtsov Dmitry A. , DiSalvo Francis J. , Niewa Rainer 
Published: October 2011

AbstractThe first alkali metal carbodiimide cyanides Na5[CN2]2[CN] and (Li, Na)5[CN2]2[CN] were obtained from reaction of carbon with nitrogen gas pressure of 7 MPa in sodium melts without orwith admixture of Li3N, respectively. The crystal structures wererefined from single‐crystal X‐ray diffraction (Na5[CN2]2[CN]:a = 7.201(2) Å, c = 6.605(4) Å, I4/mmm, R1 = 0.028, wR2 = 0.079; (Li1.40Na3.60(3))5[CN2]2[CN]: a = 7.0034(3) Å, Im$\bar{3}$m, R1 = 0.038,wR2 = 0.084). Whereas in Na5[CN2]2[CN] a fully ordered arrangement of the anions is realized, in (Li, Na)5[CN2]2[CN] both the alkali metal cations and the anions are disordered, with some site preference of lithium and sodium, leading to an increase of space group symmetry from I4/mmm for the pure sodium compound to Im$\bar{3}$m for the mixed Li/Na phase. Ammonothermal synthesis at 90 MPa leads to crystal growth of carbodiimide K2[CN2] (a = 5.762(1) Å, b = 5.669(1) Å,c = 5.756(1) Å, β = 108.78(3)°, C2/m) crystals in the cold zone of an autoclave. The crystal structure was analyzed and compared to the carbodiimide cyanides.
Identification of C18 Intermediates Formed During Stearidonic Acid Biohydrogenation by Rumen Microorganisms In Vitro
Authors: Alves S. P. , Maia M. R. G. , Bessa R. J. B. , Fonseca A. J. M. , Cabrita A. R. J. 
Published: October 2011

AbstractIn vitro batch incubations were used to study the rumen biohydrogenation of unsaturated fatty acids. An earlier study using increasing supplementation levels of stearidonic acid (18:4n‐3), revealed that the rumen microbial population extensively biohydrogenates 18:4n‐3 after 72 h of in vitro incubation, though several intermediates formed were not completely characterized. Therefore, in the present study, samples were reanalyzed in order to identify the 18:2, 18:3 and 18:4 biohydrogenation intermediates of 18:4n‐3. Gas–liquid chromatography coupled to mass spectrometry was used to characterize these intermediates. The acetonitrile chemical ionization mass spectrometry of the fatty acid methyl esters derivatives enabled the discrimination of fatty acids as non‐conjugated or conjugated biohydrogenation intermediates. In addition, the acetonitrile covalent adduct chemical ionization tandem mass spectrometry yielded prominent ions indicative of the double bond position of the major 18:3 isomers, i.e. Δ5,11,15 18:3. Furthermore, the 4,4‐dimethyloxazoline derivatives prepared from the fatty acid methyl esters enabled the structure of novel 18:2, 18:3 and 18:4 biohydrogenation intermediates to be elucidated. The intermediates accumulated in the fermentation media after 72 h of incubation of 18:4n‐3 suggest that similar to the biohydrogenation pathways of linoleic (18:2n‐6) and α‐linolenic (18:3n‐3) acids, the pathway of the 18:4n‐3 also proceeds with the formation of conjugated fatty acids followed by hydrogenation, although no conjugated dienes were found. The formation of the novel biohydrogenation intermediates of 18:4n‐3 seems to follow an uncommon isomerization pattern with distinct double bond migrations.
Niemann‐Pick C2 Protein Expression Regulates Lithogenic Diet‐Induced Gallstone Formation and Dietary Cholesterol Metabolism in Mice
Authors: Balboa Elisa , Morales Gabriela , Aylwin Paula , Carrasco Gonzalo , Amigo Ludwig , Castro Juan , Rigotti Attilio , Zanlungo Silvana 
Published: October 2011

AbstractNiemann‐Pick C2 protein (NPC2) is a lysosomal soluble protein that is highly expressed in the liver; it binds to cholesterol and is involved in intracellular cholesterol trafficking, allowing the exit of lysosomal cholesterol obtained via the lipoprotein endocytic pathway. Thus, this protein may play an important role in controlling hepatic cholesterol transport and metabolism. The aim of this work was to study the relevance of NPC2 protein expression in hepatic cholesterol metabolism, biliary lipid secretion and gallstone formation by comparing NPC2 hypomorph [NPC2 (h/h)] and wild‐type mice fed control, 2% cholesterol, and lithogenic diets. NPC2 (h/h) mice exhibited resistance to a diet‐induced increase in plasma cholesterol levels. When consuming the chow diet, we observed increased biliary cholesterol and phospholipid secretions in NPC2 (h/h) mice. When fed the 2% cholesterol diet, NPC2 (h/h) mice exhibited low and high gallbladder bile cholesterol and phospholipid concentrations, respectively. NPC2 (h/h) mice fed with the lithogenic diet showed reduced biliary cholesterol secretion, gallbladder bile cholesterol saturation, and cholesterol crystal and gallstone formation. This work indicates that hepatic NPC2 expression is an important factor in the regulation of diet‐derived cholesterol metabolism and disposal as well as in diet‐induced cholesterol gallstone formation in mice.