bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Factor Mohawk and the Pathogenesis of Human Anterior Cruciate Ligament Degradation
Authors: Nakahara Hiroyuki , Hasegawa Akihiko , Otabe Koji , Ayabe Fumiaki , Matsukawa Tetsuya , Onizuka Naoko , Ito Yoshiaki , Ozaki Toshifumi , Lotz Martin K. , Asahara Hiroshi 
Published: May 2013

ObjectiveTo investigate the expression and function of Mohawk (MKX) in human adult anterior cruciate ligament (ACL) tissue and ligament cells from normal and osteoarthritis (OA)–affected knees.MethodsKnee joints were obtained at autopsy (within 24–48 hours postmortem) from 13 donors with normal knees (mean ± SD age 36.9 ± 11.0 years), 16 donors with knee OA (age 79.7 ± 11.4 years), and 8 aging donors without knee OA (age 76.9 ± 12.9 years). All cartilage surfaces were graded macroscopically. MKX expression was analyzed by immunohistochemistry and quantitative polymerase chain reaction. ACL‐derived cells were used to study regulation of MKX expression by interleukin‐1β (IL‐1β). MKX was knocked down with small interfering RNA (siRNA) to analyze the function of MKX in extracellular matrix (ECM) production and differentiation in ACL‐derived cells.ResultsThe expression of MKX was significantly decreased in ACL‐derived cells from OA knees compared with normal knees. Consistent with this finding, immunohistochemistry analysis showed that MKX‐positive cells were significantly reduced in ACL tissue from OA donors, in particular in cells located in disorientated fibers. In ACL‐derived cells, IL‐1β strongly suppressed MKX expression and reduced expression of the ligament ECM genes COL1A1 and TNXB. In contrast, SOX9, a chondrocyte master transcription factor, was up‐regulated by IL‐1β treatment. Importantly, knockdown of MKX expression with siRNA up‐regulated SOX9 expression in ACL‐derived cells, whereas the expression of COL1A1 and TNXB was reduced.ConclusionReduced expression of MKX is a feature of degenerated ACL in OA‐affected joints, and this may be mediated in part by IL‐1β. MKX appears necessary to maintain the tissue‐specific cellular differentiation status and ECM production in adult human tendons and ligaments.
An event attribution of the 2010 drought in the South Amazon region using the MIROC5 model
Authors: Shiogama Hideo , Watanabe Masahiro , Imada Yukiko , Mori Masato , Ishii Masayoshi , Kimoto Masahide 
Published: May 2013

AbstractWe produced 100‐member event attribution ensembles during 2009–2012 under all forcing conditions and in two different counterfactual worlds without anthropogenic forcing (mainly greenhouse gases and aerosols) and without aerosol emission changes using the MIROC5 atmospheric general circulation model. It seemed that both human influences and the sea surface temperature (SST) natural variability increased probabilities of the 2010 severe drought in the South Amazon region, and that changes in aerosols emissions had little effect on the drought. It should be noted that our assessments were sensitive to bias corrections according to the relationships between the SST natural variability and precipitation.
Changes in the tropopause height induced by landing typhoons in China during the last 50 years
Authors: Wu Jian , Yang Qidong , Yang Xiong , Zhao Deming 
Published: May 2013

AbstractTrends in the thermal tropopause height observed using radiosondes near landing typhoon tracks in China from 1951 to 2008 were analyzed. The main findings were that the majority of tropopause rises induced by typhoons are in the range of 200–500 m, and the maximum tropopause height is observed between 12 and 24 h after the typhoon had passed at each station. Tropopause height increase induced by a super typhoon is more rapid and prominent than that of a typhoon, although the absolute increases are similar. The magnitude of the increase in the tropopause height induced by typhoons has increased over the last 40 years.
The Sequences of the Eleven‐Residue Peptaibiotics: Suzukacillins‐B
Authors: Röhrich Christian René , Vilcinskas Andreas , Brückner Hans , Degenkolb Thomas 
Published: May 2013

AbstractThe filamentous fungus designated ‘Trichoderma viride’ strain 63 C‐1 simultaneously produces suzukacillins (SZs), two microheterogeneous groups of peptaibols, under submerged culture conditions. Both groups are readily distinguishable by TLC: the major group is designated SZ‐A, whereas the minor group with a higher Rf value is named SZ‐B. The peptide mixture was obtained from a MeOH extract of the mycelium. SZ‐B was separated from SZ‐A by Sephadex LH‐20 column chromatography. Although it provided one single spot on silica‐gel TLC plates, 15 individual peptides could be separated by C8 reversed‐phase (RP) HPLC, and their sequences were determined by HPLC/QqTOF‐ESI‐HRMS. Fourteen peptides exhibit the C‐terminal sequence Pro6‐Lxx‐Lxx‐Aib‐Pro‐Vxxol/Lxxol11, which is common for eleven‐residue peptaibols. The remaining peptide is tentatively assigned as a ten‐residue sequence, in which the C‐terminal 1,2‐amino alcohol is deleted, thus terminating in free proline. Nine of the peptides carry an Ac‐Aib residue at the N‐terminus, very frequently found in eleven‐residue peptaibols. Four peptides comprise the rare Ac‐Ala N‐terminus, and for two peptides, N‐terminal Ac‐D‐Iva residues were identified. One peptide contains a C‐terminal residue of yet undetermined structure. Comparison with previously reported eleven‐residue peptaibol sequences reveals that eight of the peptides represent new sequence analogs.
Spin‐Echo Electron Paramagnetic Resonance (EPR) Spectroscopy of a Pore‐Forming (Lipo)Peptaibol in Model and Bacterial Membranes
Authors: Dzuba Sergei A. , Raap Jan 
Published: May 2013

AbstractThis review compiles the unusual structural and dynamic peculiarities of trichogin GA IV and its analogs in lipid bilayers. Different electron spin echo (ESE) spectroscopic techniques were employed to study a set of spin‐labeled analogs of trichogin GA IV in model and natural membranes. Pulsed electron‐electron double resonance (PELDOR) method enabled the elucidation of the peptide conformation, while the ESE envelope modulation (ESEEM) technique was applied to study the insertion of the site‐specifically spin‐labeled peptide into the core of the membrane. The latter technique was also used to examine the water accessibility for peptide‐attached spin labels at different levels of membrane depth. Finally, it will be shown that measurement of the ESE decays at different temperatures reveals molecular information on the mobility of the transmembrane lipopeptide aggregate. The experimental results are discussed in terms of the antibiotic and toxic activities of trichogin GA IV.
3D Structure, Dynamics, and Activity of Synthetic Analog of the Peptaibiotic Trichodecenin I
Authors: Gatto Emanuela , Bocchinfuso Gianfranco , Palleschi Antonio , Oncea Simona , De Zotti Marta , Formaggio Fernando , Toniolo Claudio , Venanzi Mariano 
Published: May 2013

AbstractIn this contribution, we report on the conformational preferences of synthetic analogs of the antimicrobial peptide trichodecenin I in solution. This 6‐amino acid residue long peptide is characterized by a single, strongly helicogenic Aib residue in the central part of the sequence and is rich in the conformationally mobile Gly residues. It has been reported that, in CHCl3 solution and in the crystal state, this peptaibiotic adopts a non‐helical, multiple β‐turn conformation, whereas a 310/α‐helical structure was obtained from an X‐ray diffraction study on a trichodecenin I analog (TDT4W6) containing the fluorescent Trp residue in position 6 (replacing Ile) and an equally helicogenic TOAC residue in position 4 (replacing Aib). In this work, we applied spectroscopic techniques and molecular‐dynamics calculations, in particular, on the fluorescent TDT4W6 trichodecenin I analog with the aim at investigating its 3D‐structural and dynamical features in solution. Our results revealed that TDT4W6 can be described by an ensemble of conformers quickly interconverting in the nanosecond time scale. The most populated cluster has a conformation similar to the NMR structure of native trichodecenin I in CHCl3. However, also helical‐like conformers are present, even if poorly populated and less stable under the analytical conditions.
The Comprehensive Peptaibiotics Database
Authors: Stoppacher Norbert , Neumann Nora K. N. , Burgstaller Lukas , Zeilinger Susanne , Degenkolb Thomas , Brückner Hans , Schuhmacher Rainer 
Published: May 2013

AbstractPeptaibiotics are nonribosomally biosynthesized peptides, which – according to definition – contain the marker amino acid α‐aminoisobutyric acid (Aib) and possess antibiotic properties. Being known since 1958, a constantly increasing number of peptaibiotics have been described and investigated with a particular emphasis on hypocrealean fungi. Starting from the existing online ‘Peptaibol Database’, first published in 1997, an exhaustive literature survey of all known peptaibiotics was carried out and resulted in a list of 1043 peptaibiotics. The gathered information was compiled and used to create the new ‘The Comprehensive Peptaibiotics Database’, which is presented here. The database was devised as a software tool based on Microsoft (MS) Access. It is freely available from the internet at http://peptaibiotics‐database.boku.ac.at and can easily be installed and operated on any computer offering a Windows XP/7 environment. It provides useful information on characteristic properties of the peptaibiotics included such as peptide category, group name of the microheterogeneous mixture to which the peptide belongs, amino acid sequence, sequence length, producing fungus, peptide subfamily, molecular formula, and monoisotopic mass. All these characteristics can be used and combined for automated search within the database, which makes The Comprehensive Peptaibiotics Database a versatile tool for the retrieval of valuable information about peptaibiotics. Sequence data have been considered as to December 14, 2012.
Conformational Properties of Secondary Amino Acids: Replacement of Pipecolic Acid by N‐Methyl‐L‐alanine in Efrapeptin C
Authors: Dutt Konar Anita , Vass Elemér , Hollósi Miklós , Majer Zsuzsanna , Grüber Gerhard , Frese Katrin , Sewald Norbert 
Published: May 2013

AbstractThe efrapeptins, a family of naturally occurring peptides with inhibitory activities against ATPases, contain several α,α‐disubstituted α‐amino acids such as α‐aminoisobutyric acid (Aib) or isovaline (Iva) besides pipecolic acid (Pip), β‐Ala, Leu, Gly, and a C‐terminal heterocyclic residue. Secondary α‐amino acids such as proline are known to stabilize discrete conformations in peptides. A similar influence is ascribed to N‐alkyl α‐amino acids. We synthesized two efrapeptin C analogs with replacement of Pip by N‐methyl‐L‐alanine (MeAla) using a combination of solid‐ and solution‐phase techniques in a fragment‐condensation strategy to compare the conformational bias of both secondary amino acids. The solution conformation was investigated by vibrational circular dichroism (VCD) to probe whether the analogs adopt a 310‐helical conformation. The MeAla‐containing analogs [MeAla1,3]efrapeptin C and [MeAla1,3,11]efrapeptin C inhibit ATP hydrolysis by the A3B3 complex of A1A0‐ATP synthase from Methanosarcina mazei Gö1.
Impact of Organic Ligands on the Structure and Hydrogenation Performance of Colloidally Prepared Bimetallic PtSn Nanoparticles
Authors: Altmann Lena , Wang Xiaodong , Stöver Jörg , Klink Miriam , Zielasek Volkmar , Thiel Karsten , Kolny‐Olesiak Joanna , Al‐Shamery Katharina , Borchert Holger , Parisi Jürgen , Bäumer Marcus 
Published: May 2013

AbstractThe catalytic performance of ligand‐capped monometallic Pt and bimetallic PtSn nanoparticles supported on SiO2 toward the selective hydrogenation of acetylene to ethylene in ethylene‐rich streams was investigated. To evaluate the effect of organic ligands on the hydrogenation performance, dodecylamine (DDA)‐capped monometallic and bimetallic nanoparticles were compared with ligand‐free nanoparticles. Both ligands and Sn promote the selectivity of the catalysts. The most selective catalyst was found to be the DDA‐capped PtSn catalyst, with a nominal metal atom ratio of 1:1. An increase in Pt content resulted in a decrease in the selectivity, whereas an increase in Sn content caused a decrease in the activity.
Application of a Slurry Bubble Column Reactor for the Production of Substitute Natural Gas
Authors: Götz Manuel , Bajohr Siegfried , Graf Frank , Reimert Rainer , Kolb Thomas 
Published: May 2013

AbstractBei der Methanisierung ist eine effektive Abfuhr der Reaktionswärme eine zentrale Herausforderung. Die Dreiphasen‐Methanisierung ist unter diesem Aspekt durch einfach zu gestaltende Energieabfuhr und Temperaturregelung vorteilhaft und erlaubt eine isotherme Fahrweise. Durch die hohe Wärmekapazität der Suspensionsflüssigkeit kühlt der Reaktor langsam aus und bietet sich daher für die Power‐to‐Gas (PtG) Prozesskette mit ihrer schwankenden Eduktgas‐Bereitstellung an. Verschiedene Flüssigkeiten und Betriebsbedingungen wurden bezüglich ihrer Eignung für die Dreiphasen‐Methanisierung untersucht.
Toward Improved Closure Relations for the Turbulent Kinetic Energy Equation in Bubble‐Driven Flows
Authors: Wörner Martin , Erdogan Sercan 
Published: May 2013

AbstractThere is a considerable interest within both academia and industry to develop improved computational fluid dynamic methods for gas‐liquid flows in bubble columns in order to support their scale‐up and optimal design. One main model limitation in current Eulerian two‐fluid and multi‐fluid models concerns adequate closure relations for turbulence in bubble‐driven flows. This article highlights some special features of bubble‐induced turbulence, discusses shortcomings of common concepts for closure of the liquid phase turbulence kinetic energy equation and presents an approach for development and validation of improved models. Some problematic issues related to the direct numerical simulation of bubble swarms in narrow bubble columns are also discussed.
A general metric and parallel framework for adaptive image fusion in clusters
Authors: Wei Jingbo , Liu Dingsheng , Wang Lizhe 
Published: May 2013

SUMMARYThis article is dedicated to techniques and theories of image fusion in automatic ways and addresses two issues—the parameter setting and quality assessment. Optimal parameters are in demand for specific applications or comparison between fusion methods because, as basic evidence, different parameters bring different fusion effects varying over a large range. In this paper, we propose a general framework of online parameter training to search optimal values that best suit input images. Furthermore, we optimized the compute‐intensive training process using parallelization and genetic algorithm, as well as patches extraction. We also propose a metric—spatial and spectral distortion—as the learning target. The spatial and spectral distortion is a fuzzy combination of mean potential energy measuring spatial distortion and Q4 measuring spectral distortion. Optimization validation on weighted Gram–Schmidt fusion indicated linear or superlinear acceleration ability, which proved that the proposed learning framework can speed up the learning process of image fusion to an acceptable time, and can thus be applied to high‐performance platforms to process large volumes of data. Copyright © 2013 John Wiley & Sons, Ltd.
Parallel spherical harmonic transforms on heterogeneous architectures (graphics processing units/multi‐core CPUs)
Authors: Szydlarski Mikolaj , Esterie Pierre , Falcou Joel , Grigori Laura , Stompor Radek 
Published: May 2013

SUMMARYSpherical harmonic transforms (SHT) are at the heart of many scientific and practical applications ranging from climate modelling to cosmological observations. In many of these areas, new cutting‐edge science goals have been recently proposed requiring simulations and analyses of experimental or observational data at very high resolutions and of unprecedented volumes. Both these aspects pose formidable challenge for the currently existing implementations of the transforms. This paper describes parallel algorithms for computing SHT with two variants of intra‐node parallelism appropriate for novel supercomputer architectures, multi‐core processors and Graphic Processing Units (GPU). It also discusses their performance, alone and embedded within a top‐level, Message Passing Interface‐based parallelisation layer ported from the S2HAT library, in terms of their accuracy, overall efficiency and scalability. We show that our inverse SHT run on GeForce 400 Series GPUs equipped with latest Compute Unified Device Architecture architecture (Fermi) outperforms the state of the art implementation for a multi‐core processor executed on a current Intel Core i7‐2600K. Furthermore, we show that an Message Passing Interface/Compute Unified Device Architecture version of the inverse transform run on a cluster of 128 Nvidia Tesla S1070 is as much as 3 times faster than the hybrid Message Passing Interface/OpenMP version executed on the same number of quad‐core processors Intel Nehalem for problem sizes motivated by our target applications. Performance of the direct transforms is however found to be at the best comparable in these cases. We discuss in detail the algorithmic solutions devised for the major steps involved in the transforms calculation, emphasising those with a major impact on their overall performance and elucidates the sources of the dichotomy between the direct and the inverse operations.Copyright © 2013 John Wiley & Sons, Ltd.
PGAS‐FMM: Implementing a distributed fast multipole method using the X10 programming language
Authors: Milthorpe Josh , Rendell Alistair P. , Huber Thomas 
Published: May 2013

SUMMARYThe fast multipole method (FMM) is a complex, multi‐stage algorithm over a distributed tree data structure, with multiple levels of parallelism and inherent data locality. X10 is a modern partitioned global address space language with support for asynchronous activities. The parallel tasks comprising FMM may be expressed in X10 by using a scalable pattern of activities. This paper demonstrates the use of X10 to implement FMM for simulation of electrostatic interactions between ions in a cyclotron resonance mass spectrometer. X10's task‐parallel model is used to express parallelism by using a pattern of activities mapping directly onto the tree. X10's work stealing runtime handles load balancing fine‐grained parallel activities, avoiding the need for explicit work sharing. The use of global references and active messages to create and synchronize parallel activities over a distributed tree structure is also demonstrated. In contrast to previous simulations of ion trajectories in cyclotron resonance mass spectrometers, our code enables both simulation of realistic particle numbers and guaranteed error bounds. Single‐node performance is comparable with the fastest published FMM implementations, and critical expansion operators are faster for high accuracy calculations. A comparison of parallel and sequential codes shows the overhead of activity management and work stealing in this application is low. Scalability is evaluated for 8k cores on a Blue Gene/Q system and 512 cores on a Nehalem/InfiniBand cluster. Copyright © 2013 John Wiley & Sons, Ltd.
A Versatile Approach towards the Compaction, Decompaction, and Immobilization of DNA at Interfaces by Using Cyclodextrins
Authors: González‐Pérez Alfredo , Ruso Juan M. 
Published: May 2013

AbstractWe investigate the temperature dependence of interactions of β‐cyclodextrin (CD)/hexadecyltrimethylammonium bromide (CTAB) self‐assemblies with DNA during the decompaction of DNA/CTAB complexes. By combining direct imaging techniques with density and sound‐velocity measurements, we can explain the decompaction process and suggest a suitable model. The DNA‐decompaction process by using CDs is accompanied by interactions with surfaces, such as glass or mica. The mechanism of β‐CD/CTAB self‐assembly is elucidated and the immobilization of DNA onto negatively charged surfaces is explained. Differences between the fractal dimensions of DNA that is adsorbed onto the surfaces are related to strong and weak binding, which permit the partial relaxation of DNA on the surfaces. The β‐CD/CTAB self‐assembled monolayers are demonstrated to be a facile and efficient route for surface functionalization, which allows for the immobilization of biomacromolecules in close proximity without any intermediate binding or deprotection steps. Moreover, this route is expected to show several advantages that might contribute to improving the performance of future biosensors as gentle immobilization‐limiting alteration of the protein structure, oriented immobilization, thereby allowing homogeneous accessibility, reversible immobilization, thereby allowing reutilizations, and high compatibility with various types of biomacromolecules.
Facile Synthesis of Phosphate‐Functionalized MWCNT–TiO2 Nanocomposites as Efficient Photocatalysts and Insights into the Roles of Nanostructured Carbon
Authors: Li Zhijun , He Lumei , Jing Liqiang , Lin Jingsheng , Luan Yunbo 
Published: May 2013

AbstractEffectively contacted multiwalled carbon nanotube (MWCNT)–titanium dioxide nanocomposites and phosphate‐functionalized MWCNT–TiO2 composites have been successfully synthesized by simple one‐pot phase‐separated hydrolysis–solvothermal processes. The key to this synthetic strategy is to disperse MWCNTs uniformly in Ti(OBu)4 in advance and then to put them into the toluene organic phase. The as‐prepared nanocomposites between TiO2 and the correct amount of MWCNT exhibits higher activity in the photocatalytic degradation of rhodamine B than that with the resulting TiO2, although the activity in the photocatalytic degradation of gas‐phase aldehyde and liquid‐phase phenol is lower. Interestingly, the functionalization of MWCNTs with an appropriate amount of phosphoric acids prior to the synthesis could greatly improve the activity of the MWCNT–TiO2 nanocomposites for the degradation of aldehyde and phenol, even superior to that of commercial P25 TiO2. Based on the measurements of atmosphere‐controlled surface photovoltage spectra and O2 temperature‐programmed desorption, it is suggested that MWCNTs are favorable to increase rhodamine B adsorption on the composite to promote the photosensitization oxidation reactions, whereas it is unfavorable for the adsorption of O2 and responsible for the low photocatalytic activity for the degradation of colorless pollutants. Phosphate functionalization greatly enhances the amount of O2 adsorbed on the MWCNT, which leads to significant charge separation, and thus, to significant photoactivity for the degradation of colored and colorless pollutants of the nanocomposites.