bluuebunny/crossref_metadata_2025_split huggingface dataset:
ChemInform Abstract: Superconductivity and Magnetism in Quaternary F (F: Y or f Elements) Transition Metal Borocarbides and Magnetic Properties of LnNi4B (R: Y or Rare Earth)
Authors: NAGARAJAN R. , GUPTA L. C. , MAZUMDAR C. , HOSSAIN Z. , DHAR S. K. , GODART C. , PADALIA B. D. , VIJAYARAGHAVAN R. 
Published: September 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Synthesis of Sphingosines. Part 12. Sphingosines ‐ an Oxa‐Cope Rearrangement Route for Their Synthesis
Authors: SCHMIDT R. R. , BAER T. , WILD R. 
Published: September 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Design, Synthesis and Evaluation of D,D‐Peptidase and beta‐Lactamase Inhibitors: Azapeptides, Oxapeptides and Related Heterocycles
Authors: MARCHAND‐BRYNAERT J. , MOUGENOT P. , COMBRET Y. , BELOTTI D. , GUILLOT N. , GHOSEZ L. 
Published: September 2010

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Atypical molecular profile for joint development in the avian costal joint
Authors: Winslow B.B. , Burke A.C. 
Published: September 2010

AbstractDevelopment of synovial joints involves generation of cartilaginous anlagen, formation of interzones between cartilage anlagen, and cavitation of interzones to produce fluid filled cavities. Interzone development is not fully understood, but interzones are thought to develop from skeletogenic cells that are inhibited from further chondrogenic development by a cascade of gene expression including Wnt and Bmp family members. We examined the development of the rarely studied avian costal joint to better understand mechanisms of joint development. The costal joint is found within ribs, is morphologically similar to the metatarsophalangeal joint, and undergoes cavitation in a similar manner. In contrast to other interzones, Wnt14/9a, Gdf5, Chordin, Barx1, and Bapx1 are absent from the costal joint interzone, consistent with the absence of active β‐catenin and phosphorylated Smad 1/5/8. However Autotaxin and Noggin are expressed. The molecular profile of the costal joint suggests there are alternative mechanisms of interzone development. Developmental Dynamics 239:2547–2557, 2010. © 2010 Wiley‐Liss, Inc.
Diversity and organizational innovation: The role of employee involvement
Authors: Yang Yang , Konrad Alison M. 
Published: September 2010

AbstractThis study examined the interactive effects of workplace diversity and employee involvement on organizational innovation. Using a sample of 182 large Canadian organizations, we found a three‐way interaction between level of employee involvement, variation in involvement, and racioethnic diversity on innovation. In organizations with high levels of employee involvement, high variation in involvement was associated with higher involvement levels among racioethnic minorities, resulting in a stronger association between diversity and innovation. Furthermore, the association between White employee involvement and innovation was significantly more positive under the condition of high involvement among racioethnic minority group members. Thus, ensuring high levels of involvement among members of historically marginalized racioethnic groups enhances the innovation effects of employee empowerment systems. Copyright © 2010 John Wiley & Sons, Ltd.
Wavelength‐dependent amplitude of Teflon Raman lines
Authors: Manka C. K. , Nikitin S. , Lunsford R. , Kunapareddy P. , Grun J. 
Published: September 2010

AbstractRaman and other spectroscopy systems operating in the deep ultraviolet (DUV) spectral region below 250 nm lack scattering standards. Such standards are particularly important for experiments that use multiwavelength excitation and/or when results are compared across different experiment platforms. Teflon has been used as an external standard in the visible and near‐IR spectral regions and has been suggested for use in the ultraviolet (UV). Comparison of the relative amplitudes of prominent Teflon Raman lines indicates a significant effect on line ratios when the excitation wavelength is below 250 nm. This dependence on excitation wavelength has been commented on previously and attributed to pre‐resonance effects, but no detailed examination had been undertaken to date. We present the results of a study of Teflon Raman line ratios obtained from closely spaced excitation wavelengths in the DUV from 210 to 320 nm. The 731 cm−1 line is identified as well suited for a standard. Electronic transition energies associated with resonance of principal Teflon Raman lines are obtained. Copyright © 2010 John Wiley & Sons, Ltd.
Non‐Ionic Homo‐ and Copolymers with H‐Donor and H‐Acceptor Units with an UCST in Water
Authors: Seuring Jan , Agarwal Seema 
Published: September 2010

AbstractA well‐studied example of a thermoresponsive polymer is PNiPAAm, which exhibits a sharp coil‐to‐globule transition in water at its LCST. A study relating to the missing counterpart of LCST polymers is presented: N‐acryloylglycinamide (NAGA) homopolymer and copolymers from NAGA and N‐acetylacrylamide (NAcAAm) that show a sharp UCST (where the sharpness depends on the composition). The polymers were synthesized by free‐radical copolymerization and the copolymerization parameters were determined by the method of Kelen‐Tüdös. The UCST was investigated by turbidimetry, regarding the influence of the copolymer composition, the polymer concentration and the addition of electrolytes.
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Hydrogen‐Bonded Shape‐Persistent Aryl Hydrazide Polymers: Side‐Chain‐Tuned Formation of Vesicles and Organogels
Authors: Zhou Cen , Cai Wei , Wang Gui‐Tao , Zhao Xin , Li Zhan‐Ting 
Published: September 2010

AbstractA new class of aromatic, hydrazide‐based, zigzag polymer has been synthesized using the Yamazaki polymerization conditions. Hydrophobic, hydrophilic or amphiphilic side chains are introduced to the backbones to tune their solubility in organic solvents of different polarities. The side chains form successive, intramolecular, six‐membered RO···HN hydrogen bonds, which increase the planarity of the backbones. The new shape‐persistent polymers are revealed to self‐assemble into vesicles or fibers to gelate organic solvents of different polarities. The polymeric backbones may be regarded as a conceptual extension of the emerging foldamers, which are usually constructed from oligomeric backbones.
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Controlled RAFT Cyclopolymerization of Oriented Styrenic Difunctional Monomers
Authors: Sharma Arvind K. , Cornaggia Claudio , Pasini Dario 
Published: September 2010

AbstractWe describe the first example of controlled free radical cyclopolymerization of difunctional styrenic monomers. The newly designed monomers are obtained from the introduction of two 4‐vinylbenzyl moieties as malonate or dialkylated malonate esters. The more sterically hindered monomer is particularly efficient in the cyclization and propagation processes, giving cyclopolymers, in diluted solvent conditions, with good yields and degrees of polymerization. In the presence of a suitable RAFT mediator, and, upon careful optimization of the solvent, temperature and monomer concentration, a linear increase in the number average molecular weight with conversion and low polydispersity indexes can be achieved.
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Radiation‐Grafted Fluoropolymers Soaked with Imidazolium‐Based Ionic Liquids for High‐Performance Ionic Polymer–Metal Composite Actuators
Authors: Lee Jang Yeol , Wang Hyuck Sik , Yoon Bye Ri , Han Man Jae , Jho Jae Young 
Published: September 2010

AbstractOn purpose to develop a polymer actuator with high stability in air‐operation as well as large bending displacement, a series of ionic polymer–metal composites (IPMC) was constructed with poly(styrene sulfonate)‐grafted fluoropolymers as ionomeric matrix and immidazolium‐based ionic liquids (IL) as inner solvent. The prepared IPMC actuators exhibited greatly enhanced bending displacement compared to Nafion‐based actuators. The actuators were stable in air‐operation, maintaining initial displacement for up to 104 cycles or 24 h. Investigating the material parameters and morphology of the IPMCs, high ion exchange capacity of the ionomers resulted in high ion conductivity and robust electrode of IPMC, which synergistically contributed to the high bending performance.magnified image
Nanofibers Self‐assembled from Structural Complementary Borono‐decapeptides
Authors: Chen Chang‐Sheng , Ji Tian‐Jiao , Xu Xiao‐Ding , Zhang Xian‐Zheng , Zhuo Ren‐Xi 
Published: September 2010

AbstractA series of structural complementary decapeptides with phenyl boronic acid tails or borono‐decapeptides (BPs) were designed and synthesized for supramolecular self‐assembly. After dissolving these borono‐decapeptides in deionized (DI) water, well‐defined nanofibers were formed in BP1 (B(OH)2VEKELVKEKL‐OH) and BP3 (B(OH)2AELELARARL‐OH). It was found that the self‐assembled borono‐decapeptide BP1 and BP3 have a parallel β‐sheet conformation in the formed nanofibers. The strategy demonstrated here shows a great prospect in preparation of well‐ordered nanofibers via rationally designing the molecular structures of peptides.magnified image
Synthesis and comparative properties of two amide‐generating resin linkers for use in solid phase peptide synthesis
Authors: Deng Fang‐Kun , Mandal Kalyaneswar , Luisier Sam , Kent Stephen B. H. 
Published: September 2010

AbstractWell‐characterized resins of high purity are critical for effective solid phase peptide synthesis (SPPS). The quality of commercial (4‐methyl)benzhydrylamine‐resin (MBHA‐resin), used for the synthesis of peptide amides, is not consistent and residual ketone functionalities are frequently present. Such ketone or aldehyde impurities lead to the formation of acylation‐resistant deletion peptides in SPPS. To avoid these undesirable side reactions, we have optimized the preparation of two amide‐generating linkers, which, in combination with aminomethyl‐resin prepared directly from polystyrene resin, serve as alternatives to MBHA‐resin for peptide amide synthesis. Then we have explored their comparative properties in SPPS. Use of sonication in reductive amination facilitated the synthesis of both benzhydrylamine (BHA) and MBHA linkers. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.
Pathophysiology of fatty acid oxidation disorders
Authors: Bennett M. J. 
Published: September 2010

AbstractMitochondrial fatty acid oxidation represents an important pathway for energy generation during periods of increased energy demand such as fasting, febrile illness and muscular exertion. In liver, the primary end products of the pathway are ketone bodies, which are released into the circulation and provide energy to tissues that are not able to oxidize fatty acids such as brain. Other tissues, such as cardiac and skeletal muscle are capable of direct utilization of the fatty acids as sources of energy. This article provides an overview of the pathogenesis of fatty acid oxidation disorders. It describes the different tissue involvement with the disease processes and correlates disease phenotype with the nature of the genetic defect for the known disorders of the pathway.
Efficient generation of multi-gigawatt power by a klystron-like relativistic backward wave oscillator
Authors: Xiao R.Z. , Zhang X.W. , Zhang L.J. , Li X.Z. , Zhang L.G. , Song W. , Hu Y.M. , Sun J. , Huo S.F. , Chen C.H. , Zhang Q.Y. , Liu G.Z. 
Published: September 2010

AbstractEfficient generation regime with a high power output has been experimentally realized in a klystron-like relativistic backward wave oscillator, in which a modulation cavity is inserted between the slow wave structure to decrease the energy spread of modulated beam electrons, and an extraction cavity is employed at the end of the slow wave structure to further recover energy from the electron beam. At a guiding magnetic field of 2.2 T, a microwave pulse with power of 6.5 GW, frequency of 4.26 GHz, pulse duration of 38 ns, and efficiency of 36% was generated when the diode voltage was 1.1 MV, and diode current was 16.4 kA. When the diode voltage was 820 kV, efficiency up to 47% with microwave power 4.4 GW was also realized experimentally.
Extensification — implications for animal performance, health and welfare
Authors: Waterhouse A. 
Published: September 2010

AbstractPressures to reduce stocking densities (extensify) are arising for a number of reasons. There are two main options once the decision to reduce stocking occurs: (1) to maintain management and physical inputs pro rata to remaining livestock which may or may not have full access to the same land area; (2) to reduce management and/or physical inputs to remaining stock because of real or perceived increases in availability of grazed resources to remaining livestock. These two options have widely different implications for the health, welfare and performance of the extensified systems. A third option open to producers is merely to reduce inputs, de-intensify, without reducing stock numbers. All the options raise major questions in relation to their benefit or otherwise to ecological or landscape values which tend to be underpinning these initiatives. However, significant uncertainty arises as to how producers will respond. Economic factors will play a part in justifying changes and levels of compensation deemed adequate. Levels of animal performance are crucial in terms of economic viability and as an indicator of animal welfare. Three programmes of research work are in hand in the UK which address these concerns and the associated impact on the environment. At ADAS's Redesdale and Pwllpeiran Farms the experimental protocol has been to reduce stocking rate with no change in inputs per ewe. At SAC's Kirkton and Auchtertyre unit a different farm scale strategy has been adopted. Here stock numbers have been reduced, but alongside these physical (food) and management inputs (labour) have also been reduced. Preliminary data on animal performance from all experiments suggests no improvement in animal performance as a result of reduced stocking density. In the latter study, where inputs per ewe have also been reduced, reduced output per ewe has been found, partly as a result of increased lamb mortality.
Classification of ncRNAs using position and size information in deep sequencing data
Authors: Erhard Florian , Zimmer Ralf 
Published: September 2010

Abstract
Motivation: Small non-coding RNAs (ncRNAs) play important roles in various cellular functions in all clades of life. With next-generation sequencing techniques, it has become possible to study ncRNAs in a high-throughput manner and by using specialized algorithms ncRNA classes such as miRNAs can be detected in deep sequencing data. Typically, such methods are targeted to a certain class of ncRNA. Many methods rely on RNA secondary structure prediction, which is not always accurate and not all ncRNA classes are characterized by a common secondary structure. Unbiased classification methods for ncRNAs could be important to improve accuracy and to detect new ncRNA classes in sequencing data.
Results: Here, we present a scoring system called ALPS (alignment of pattern matrices score) that only uses primary information from a deep sequencing experiment, i.e. the relative positions and lengths of reads, to classify ncRNAs. ALPS makes no further assumptions, e.g. about common structural properties in the ncRNA class and is nevertheless able to identify ncRNA classes with high accuracy. Since ALPS is not designed to recognize a certain class of ncRNA, it can be used to detect novel ncRNA classes, as long as these unknown ncRNAs have a characteristic pattern of deep sequencing read lengths and positions. We evaluate our scoring system on publicly available deep sequencing data and show that it is able to classify known ncRNAs with high sensitivity and specificity.
Availability: Calculated pattern matrices of the datasets hESC and EB are available at the project web site http://www.bio.ifi.lmu.de/ALPS. An implementation of the described method is available upon request from the authors.
Contact: florian.erhard@bio.ifi.lmu.de
Vorescore—fold recognition improved by rescoring of protein structure models
Authors: Csaba Gergely , Zimmer Ralf 
Published: September 2010

Abstract
Summary: The identification of good protein structure models and their appropriate ranking is a crucial problem in structure prediction and fold recognition. For many alignment methods, rescoring of alignment-induced models using structural information can improve the separation of useful and less useful models as compared with the alignment score. Vorescore, a template-based protein structure model rescoring system is introduced. The method scores the model structure against the template used for the modeling using Vorolign. The method works on models from different alignment methods and incorporates both knowledge from the prediction method and the rescoring.
Results: The performance of Vorescore is evaluated in a large-scale and difficult protein structure prediction context. We use different threading methods to create models for 410 targets, in three scenarios: (i) family members are contained in the template set; (ii) superfamily members (but no family members); and (iii) only fold members (but no family or superfamily members). In all cases Vorescore improves significantly (e.g. 40% on both Gotoh and HHalign at the fold level) on the model quality, and clearly outperforms the state-of-the-art physics-based model scoring system Rosetta. Moreover, Vorescore improves on other successful rescoring approaches such as Pcons and ProQ. In an additional experiment we add high-quality models based on structural alignments to the set, which allows Vorescore to improve the fold recognition rate by another 50%.
Availability: All models of the test set (about 2 million, 44 GB gzipped) are available upon request.
Contact: csaba@bio.ifi.lmu.de; ralf.zimmer@ifi.lmu.de
Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources
Authors: Mizianty Marcin J. , Stach Wojciech , Chen Ke , Kedarisetti Kanaka Durga , Disfani Fatemeh Miri , Kurgan Lukasz 
Published: September 2010

Abstract
Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed.
Results: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with ≤25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions.
Availability: http://biomine.ece.ualberta.ca/MFDp.html
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: lkurgan@ece.ualberta.ca
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes
Authors: Naamati Guy , Askenazi Manor , Linial Michal 
Published: September 2010

Abstract
Motivation: Animal toxins operate by binding to receptors and ion channels. These proteins are short and vary in sequence, structure and function. Sporadic discoveries have also revealed endogenous toxin-like proteins in non-venomous organisms. Viral proteins are the largest group of quickly evolving proteomes. We tested the hypothesis that toxin-like proteins exist in viruses and that they act to modulate functions of their hosts.
Results: We updated and improved a classifier for compact proteins resembling short animal toxins that is based on a machine-learning method. We applied it in a large-scale setting to identify toxin-like proteins among short viral proteins. Among the ∼26 000 representatives of such short proteins, 510 sequences were positively identified. We focused on the 19 highest scoring proteins. Among them, we identified conotoxin-like proteins, growth factors receptor-like proteins and anti-bacterial peptides. Our predictor was shown to enhance annotation inference for many ‘uncharacterized’ proteins. We conclude that our protocol can expose toxin-like proteins in unexplored niches including metagenomics data and enhance the systematic discovery of novel cell modulators for drug development.
Availability: ClanTox is available at http://www.clantox.cs.huji.ac.il
Contact: michall@cc.huji.ac.il
Discriminative and informative features for biomolecular text mining with ensemble feature selection
Authors: Van Landeghem Sofie , Abeel Thomas , Saeys Yvan , Van de Peer Yves 
Published: September 2010

Abstract
Motivation: In the field of biomolecular text mining, black box behavior of machine learning systems currently limits understanding of the true nature of the predictions. However, feature selection (FS) is capable of identifying the most relevant features in any supervised learning setting, providing insight into the specific properties of the classification algorithm. This allows us to build more accurate classifiers while at the same time bridging the gap between the black box behavior and the end-user who has to interpret the results.
Results: We show that our FS methodology successfully discards a large fraction of machine-generated features, improving classification performance of state-of-the-art text mining algorithms. Furthermore, we illustrate how FS can be applied to gain understanding in the predictions of a framework for biomolecular event extraction from text. We include numerous examples of highly discriminative features that model either biological reality or common linguistic constructs. Finally, we discuss a number of insights from our FS analyses that will provide the opportunity to considerably improve upon current text mining tools.
Availability: The FS algorithms and classifiers are available in Java-ML (http://java-ml.sf.net). The datasets are publicly available from the BioNLP'09 Shared Task web site (http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/).
Contact: yves.vandepeer@psb.ugent.be