bluuebunny/crossref_metadata_2025 huggingface dataset:
TSDW: Two‐stage word sense disambiguation using Wikipedia
Authors: Li Chenliang , Sun Aixin , Datta Anwitaman
Published: April 2013

The semantic knowledge of Wikipedia has proved to be useful for many tasks, for example, named entity disambiguation. Among these applications, the task of identifying the word sense based on Wikipedia is a crucial component because the output of this component is often used in subsequent tasks. In this article, we present a two‐stage framework (called TSDW) for word sense disambiguation using knowledge latent in Wikipedia. The disambiguation of a given phrase is applied through a two‐stage disambiguation process: (a) The first‐stage disambiguation explores the contextual semantic information, where the noisy information is pruned for better effectiveness and efficiency; and (b) the second‐stage disambiguation explores the disambiguated phrases of high confidence from the first stage to achieve better redisambiguation decisions for the phrases that are difficult to disambiguate in the first stage. Moreover, existing studies have addressed the disambiguation problem for English text only. Considering the popular usage of Wikipedia in different languages, we study the performance of TSDW and the existing state‐of‐the‐art approaches over both English and Traditional Chinese articles. The experimental results show that TSDW generalizes well to different semantic relatedness measures and text in different languages. More important, TSDW significantly outperforms the state‐of‐the‐art approaches with both better effectiveness and efficiency.
Improvement of Arterial Stiffness in the Transition From Acute Decompensated Heart Failure to Chronic Compensated Heart Failure
Authors: Kim Dong‐Bin , Baek Sang Hong , Jang Sung Won , Her Sung‐Ho , Shin Dong‐Il , Park Chan Seok , Park Hoon Joon , Kim Pum Joon , Jung Hae Ok , Seung Ki Bae
Published: April 2013

Background

Pulse wave velocity (PWV) is a well‐established marker for aortic stiffness and may be a prognostic factor in heart failure (HF). This study investigates whether PWV changes as patients transition from acute decompensated heart failure (ADHF) to chronic compensated heart failure (CCHF).

Hypothesis

Arterial stiffness is related with the development of HF.

Methods

Regional PWV was prospectively measured using noninvasive applanation tonometry in consecutive ADHF patients (n = 55). PWV measurements of 45 patients were taken at admission and 3‐month follow‐up (F/U).

Results

Central and upper‐extremity PWV, but not lower‐extremity PWVs, were found to have improved after 3 months compared with the admission PWV (central: 8.73 ± 1.17 vs 8.39 ± 0.99 m/s, P = 0.018; upper extremity: 8.59 ± 0.84 vs 8.33 ± 0.82 m/s, P = 0.028). Multivariate logistic regression analyses revealed that low‐density lipoprotein cholesterol was significantly associated with the change of PWV in HF (odds ratio: 1.037, 95% confidence interval: 1.003‐1.071, P = 0.030). In preserved left ventricular ejection fraction patients (n = 26) and ischemic patients (n = 31), central and upper‐extremity PWVs improved over the admission PWV at 3‐month F/U.

Conclusions

The present results indicate that central and upper‐extremity PWVs, but not lower‐extremity PWV, are increased in ADHF and improve as patients transition from ADHF to CCHF.
Tubulin‐β‐III overexpression by uterine serous carcinomas is a marker for poor overall survival after platinum/taxane chemotherapy and sensitivity to epothilones
Authors: Roque Dana M. , Bellone Stefania , English Diana P. , Buza Natalia , Cocco Emiliano , Gasparrini Sara , Bortolomai Ileana , Ratner Elena , Silasi Dan‐Arin , Azodi Masoud , Rutherford Thomas J. , Schwartz Peter E. , Santin Alessandro D.
Published: April 2013

BACKGROUND

Uterine serous carcinoma (USC) is a subtype of endometrial cancer associated with chemoresistance and poor outcome. Overexpression of tubulin‐β‐III and p‐glycoprotein has been linked to paclitaxel resistance in many cancers but has been undercharacterized among USCs. Epothilones have demonstrated activity in certain paclitaxel‐resistant malignancies. In this study, relationships are clarified, in USCs relative to ovarian serous carcinomas (OSCs), between tubulin‐β‐III and p‐glycoprotein expression, clinical outcome, and in vitro chemoresponsiveness to epothilone B, ixabepilone, and paclitaxel.

METHODS

Tubulin‐β‐III and p‐glycoprotein were quantified by real‐time polymerase chain reaction in 48 fresh‐frozen tissue samples and 13 cell lines. Copy number was correlated with immunohistochemistry and overall survival. Median inhibitory concentration (IC50) was determined using viability and metabolic assays. Impact of tubulin‐β‐III knockdown on IC50 was assessed with small interfering RNAs.

RESULTS

USC overexpressed tubulin‐β‐III but not p‐glycoprotein relative to OSC in both fresh‐frozen tissues (552.9 ± 106.7 versus 202.0 ± 43.99, P = .01) and cell lines (1701.0 ± 376.4 versus 645.1 ± 157.9, P = .02). Tubulin‐β‐III immunohistochemistry reflected quantitative real‐time polymerase chain reaction copy number and overexpression stratified patients by overall survival (copy number ≤ 400: 615 days; copy number > 400: 165 days, P = .049); p‐glycoprotein did not predict clinical outcome. USCs remained exquisitely sensitive to patupilone in vitro despite tubulin‐β‐III overexpression (IC50,USC 0.245 ± 0.11 nM versus IC50,OSC 1.01 ± 0.13 nM, P = .006).

CONCLUSIONS

Tubulin‐β‐III overexpression in USCs discriminates poor prognosis, serves as a marker for sensitivity to epothilones, and may contribute to paclitaxel resistance. Immunohistochemistry reliably identifies tumors with overexpression of tubulin‐β‐III, and a subset of individuals likely to respond to patupilone and ixabepilone. Epothilones warrant clinical investigation for treatment of USCs. Cancer 2013;119:2582–2592. © 2013 American Cancer Society.
Construction of a Multisoliton Blowup Solution to the Semilinear Wave Equation in One Space Dimension
Authors: Côte Raphaël , Zaag Hatem
Published: April 2013

We consider the semilinear wave equation with power nonlinearity in one space dimension. Given a blowup solution with a characteristic point, we refine the blowup behavior first derived by Merle and Zaag. We also refine the geometry of the blowup set near a characteristic point and show that, except for perhaps one exceptional situation, it is never symmetric with respect to the characteristic point. Then, we show that all blowup modalities predicted by those authors do occur. More precisely, given any integer k ≥ 2 and
$\zeta _0 \in {\cal R}$, we construct a blowup solution with a characteristic point a such that the asymptotic behavior of the solution near (a,T(a)) shows a decoupled sum of k solitons with alternate signs whose centers (in the hyperbolic geometry) have ζ0 as a center of mass for all times. © 2013 Wiley Periodicals, Inc.
Kinetic Evidence for a Non‐Langmuir‐Hinshelwood Surface Reaction: H/D Exchange over Pd Nanoparticles and Pd(111)
Authors: Savara Aditya , Ludwig Wiebke , Schauermann Swetlana
Published: April 2013

The mechanism of hydrogen recombination on a Pd(111) single crystal and well‐defined Pd nanoparticles is studied using pulsed multi‐molecular beam techniques and the H2/D2 isotope exchange reaction. The focus of this study is to obtain a microscopic understanding of the role of subsurface hydrogen in enhancing the associative desorption of molecular hydrogen. HD production from H2 and D2 over Pd is investigated using pulsed molecular beams, and the temperature dependence and reaction orders are obtained for the rate of HD production under various reaction conditions designed to modulate the amount of subsurface hydrogen present. The experimental data are compared to the results of kinetic modeling based on different mechanisms for hydrogen recombination. We found that under conditions where virtually no subsurface hydrogen species are present, the HD formation rate can be described exceptionally well by a classic Langmuir–Hinshelwood model. However, this model completely fails to reproduce the experimentally observed high HD formation rates and the reaction orders under reaction conditions where subsurface hydrogen is present. To analyze this phenomenon, we develop two kinetic models that account for the role of subsurface hydrogen. First, we investigate the possibility of a change in the reaction mechanism, where recombination of one subsurface and one surface hydrogen species (known as a breakthrough mechanism) becomes dominant when subsurface hydrogen is present. Second, we investigate the possibility of the modified Langmuir–Hinshelwood mechanism with subsurface hydrogen lowering the activation energy for recombination of two hydrogen species adsorbed on the surface. We show that the experimental reaction kinetics can be well described by both kinetic models based on non‐Langmuir–Hinshelwood‐type mechanisms.
The power‐of‐pull of economic sectors: A complex network analysis
Authors: Luo Jianxi
Published: April 2013

To compare the relative power of individual sectors to pull the entire economy, i.e., the power‐of‐pull, this article utilizes a complex system perspective to model the economy as a network of economic sectors connected by trade flows. A sector's power‐of‐pull is defined and calculated as a function of the powers‐of‐pull of those sectors that it pulls through network linkages, and their powers‐of‐pull are, in turn, functions of those sectors that they further pull ad infinitum throughout the network. Theoretically, boosting activities in sectors with a higher power‐of‐pull will generate greater network effects while stimulating the entire economy, especially during recessions. This method is applied to the United States in the years before and after the 2008 financial crisis. The results provide a fresh look at the U.S. government's economic revival policies and reveal fundamental changes in the economic structure of the U.S. This work advocates a network‐based analysis of the economy as a complex system. © 2013 Wiley Periodicals, Inc. Complexity 18: 37–47, 2013
Preparation of alkyl 11‐anilino‐10‐hydroxy undecanoates and evaluation of their antioxidant activity
Authors: Geethanjali Gorla , Padmaja Korlipara V. , Sreedhar Bojja , Prasad Rachapudi Badari N.
Published: April 2013

A novel class of 10‐undecenoic acid‐based alkyl 11‐anilino‐10‐hydroxy undecanoates were prepared by reacting n‐alkyl (C1 and C4) and iso alkyl (C3, C4, and C8) epoxy undecanoates with aniline under catalyst‐free reaction conditions. The synthesized products were characterized by 1H NMR, IR, GC, and GC‐MS and evaluated for their antioxidant activity using rancimat and differential scanning calorimetry (DSC) methods. The effect of antioxidants was studied at 0.25 and 0. 5% concentrations using rancimat method and at 0.5% in DSC analysis by adding in a lubricant base stock, namely epoxy karanja fatty acid 2‐ethylhexyl esters. All the products exhibited good antioxidant properties at 0.25% concentration and enhanced antioxidant activity with the increased antioxidant concentration at 0.5%. The results obtained from isothermal DSC correlated well with those based on the rancimat method. n‐Butyl 11‐anilino‐10‐hydroxy undecanoate (4c) exhibited the best stabilizing effect on lubricant base stock with longest induction time compared to butylated hydroxytoluene (BHT) and other products. The data indicate that the synthesized products are potential antioxidants for lubricant formulations.
SAMI3 simulation of plasmasphere refilling
Authors: Krall J. , Huba J. D.
Published: April 2013

The Naval Research Laboratory three‐dimensional, first‐principles simulation code SAMI3 (Sami3 is Also a Model of the Ionosphere) is used to model plasmasphere refilling. A time‐dependent Volland‐Stern‐Maynard‐Chen potential is used to model an idealized magnetic storm that erodes the plasmasphere to L<3. The potential is then relaxed to the prestorm state, and refilling is simulated for a range of L shells 3≤L≤5 over a period of 7 days. Refilling rates compare well to observed refilling rates. The model plasmasphere during this quiet period displays a day‐to‐day repetition in its morphology that has not been previously observed.
Reduced products and sheaves of metric structures
Authors: Lopes Vinicius Cifú
Published: April 2013

We introduce reduced products in continuous logic, and provide ways to establish satisfaction in the reduced product based on the satisfaction in its fibers, and conversely, on the lines that Horn and Chang did for reduced products in classical logic. We also consider a definition of a sheaf of metric structures, endow its stalks with a metric prestructure, and determine what filters can be used so that a collection of reduced products of arbitrary structures forms a sheaf on a given index space.
Optimal edge‐coloring with edge rate constraints
Authors: Dereniowski Dariusz , Kubiak Wieslaw , Ries Bernard , Zwols Yori
Published: April 2013

We consider the problem of covering the edges of a graph by a sequence of matchings subject to the constraint that each edge e appears in at least a given fraction r(e) of the matchings. Although it can be determined in polynomial time whether such a sequence of matchings exists or not [Grötschel et al., Combinatorica (1981), 169–197], we show that several questions about the length of the sequence are computationally intractable. Therefore, as is commonly done [Golumbic, Algorithmic graph theory and perfect graphs, 2004], we restrict our investigation to a special class of graphs. In recent work [Birand et al., INFOCOM 2010 Proceedings, 2010], two of the authors dealt with so‐called OLoP (Overall Local Pooling) graphs, a class of graphs for which similar matching‐related problems are tractable (namely, in an online distributed wireless network scheduling setting). We therefore focus on these graphs and generalize the results to a larger class of graphs which we call GOLoP graphs. In particular, we show that deciding whether a given GOLoP graph has a matching sequence of length at most k can be done in linear time. In case the answer is affirmative, we show how to construct, in quadratic time, the matching sequence of length at most k. Finally, we prove that, for GOLoP graphs, the length of a shortest sequence does not exceed a constant times the least common denominator of the fractions r(e), leading to a pseudopolynomial‐time algorithm for minimizing the length of the sequence. We show that the constant equals 1 for OLoP graphs and, following Seymour [Seymour, Proc. London Math. Soc., 1979], conjecture that the constant is as small as 2 for general graphs. We then show that this conjecture holds for all graphs with at most 10 vertices. © 2013 Wiley Periodicals, Inc. NETWORKS, Vol 62(3), 165–182 2013
Nonequilibrium Plasma‐Activated Antimicrobial Solutions are Broad‐Spectrum and Retain their Efficacies for Extended Period of Time
Authors: Ercan Utku K. , Wang Hong , Ji Haifeng , Fridman Gregory , Brooks Ari D. , Joshi Suresh G.
Published: April 2013

By applying dielectric‐barrier discharge nonthermal plasma technique, we have treated fluids and generated antimicrobial solutions, tested for properties such as changes in pH, temperature, delay time, holding time, fluid‐aging, and detection and comparison of acid and hydrogen peroxide. All plasma‐treated solutions showed strong biocidal activity, and among them, NAC solution was the most powerful, inactivated biofilms of tested microorganisms in 15 min of holding time. During accelerated aging experiments, plasma‐treated NAC solution exhibited the equivalent of two years of shelf. These results indicate that it retained its antimicrobial properties for an extended period against a wide range of multidrug‐resistant pathogens, making it an excellent candidate for further testing in vivo.

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A multi‐faceted analysis of RutD reveals a novel family of α/β hydrolases
Authors: Knapik Aleksandra A. , Petkowski Janusz J. , Otwinowski Zbyszek , Cymborowski Marcin T. , Cooper David R. , Majorek Karolina A. , Chruszcz Maksymilian , Krajewska Wanda M. , Minor Wladek
Published: April 2013

The rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the α/β hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the α/β hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys, or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the α/β hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3‐oxoadipate‐enol‐lactonase with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Structural insights into catalysis by βC‐S lyase from Streptococcus anginosus
Authors: Kezuka Yuichiro , Yoshida Yasuo , Nonaka Takamasa
Published: April 2013

Hydrogen sulfide (H2S) is a causative agent of oral malodor and may play an important role in the pathogenicity of oral bacteria such as Streptococcus anginosus. In this microorganism, H2S production is associated with βC‐S lyase (Lcd) encoded by lcd gene, which is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the α,β‐elimination of sulfur‐containing amino acids. When Lcd acts on L‐cysteine, H2S is produced along with pyruvate and ammonia. To understand the H2S‐producing mechanism of Lcd in detail, we determined the crystal structures of substrate‐free Lcd (internal aldimine form) and two reaction intermediate complexes (external aldimine and α‐aminoacrylate forms). The formation of intermediates induced little changes in the overall structure of the enzyme and in the active site residues, with the exception of Lys234, a PLP‐binding residue. Structural and mutational analyses highlighted the importance of the active site residues Tyr60, Tyr119, and Arg365. In particular, Tyr119 forms a hydrogen bond with the side chain oxygen atom of L‐serine, a substrate analog, in the external aldimine form suggesting its role in the recognition of the sulfur atom of the true substrate (L‐cysteine). Tyr119 also plays a role in fixing the PLP cofactor at the proper position during catalysis through binding with its side chain. Finally, we partly modified the catalytic mechanism known for cystalysin, a βC‐S lyase from Treponema denticola, and proposed an improved mechanism, which seems to be common to the βC‐S lyases from oral bacteria. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Motion of transfer RNA from the A/T state into the A‐site using docking and simulations
Authors: Caulfield Thomas , Devkota Batsal
Published: April 2013

The ribosome catalyzes peptidyl transfer reactions at the growing nascent polypeptide chain. Here, we present a structural mechanism for selecting cognate over near‐cognate A/T transfer RNA (tRNA). In part, the structural basis for the fidelity of translation relies on accommodation to filter cognate from near‐cognate tRNAs. To examine the assembly of tRNAs within the ribonucleic–riboprotein complex, we conducted a series of all‐atom molecular dynamics (MD) simulations of the entire solvated 70S Escherichia coli ribosome, along with its associated cofactors, proteins, and messenger RNA (mRNA). We measured the motion of the A/T state of tRNA between initial binding and full accommodation. The mechanism of rejection was investigated. Using novel in‐house algorithms, we determined trajectory pathways. Despite the large intersubunit cavity, the available space is limited by the presence of the tRNA, which is equally large. This article describes a “structural gate,” formed between helices 71 and 92 on the ribosomal large subunit, which restricts tRNA motion. The gate and the interacting protein, L14, of the 50S ribosome act as steric filters in two consecutive substeps during accommodation, each requiring: (1) sufficient energy contained in the hybrid tRNA kink and (2) sufficient energy in the Watson–Crick base pairing of the codon–anticodon. We show that these barriers act to filter out near‐cognate tRNA and promote proofreading of the codon–anticodon. Since proofreading is essential for understanding the fidelity of translation, our model for the dynamics of this process has substantial biomedical implications. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model
Authors: Salsbury Freddie R. , Poole Leslie B. , Fetrow Jacquelyn S.
Published: April 2013

One of the most popular and simple models for the calculation of pKas from a protein structure is the semi‐macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Dead‐end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility
Authors: Hallen Mark A. , Keedy Daniel A. , Donald Bruce R.
Published: April 2013

Computational protein and drug design generally require accurate modeling of protein conformations. This modeling typically starts with an experimentally determined protein structure and considers possible conformational changes due to mutations or new ligands. The DEE/A* algorithm provably finds the global minimum‐energy conformation (GMEC) of a protein assuming that the backbone does not move and the sidechains take on conformations from a set of discrete, experimentally observed conformations called rotamers. DEE/A* can efficiently find the overall GMEC for exponentially many mutant sequences. Previous improvements to DEE/A* include modeling ensembles of sidechain conformations and either continuous sidechain or backbone flexibility. We present a new algorithm, DEEPer (Dead‐End Elimination with Perturbations), that combines these advantages and can also handle much more extensive backbone flexibility and backbone ensembles. DEEPer provably finds the GMEC or, if desired by the user, all conformations and sequences within a specified energy window of the GMEC. It includes the new abilities to handle arbitrarily large backbone perturbations and to generate ensembles of backbone conformations. It also incorporates the shear, an experimentally observed local backbone motion never before used in design. Additionally, we derive a new method to accelerate DEE/A*‐based calculations, indirect pruning, that is particularly useful for DEEPer. In 67 benchmark tests on 64 proteins, DEEPer consistently identified lower‐energy conformations than previous methods did, indicating more accurate modeling. Additional tests demonstrated its ability to incorporate larger, experimentally observed backbone conformational changes and to model realistic conformational ensembles. These capabilities provide significant advantages for modeling protein mutations and protein–ligand interactions. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Folding of multidomain proteins: Biophysical consequences of tethering even in apparently independent folding
Authors: Arviv Oshrit , Levy Yaakov
Published: April 2013

Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering‐induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse‐grained and atomistic molecular dynamics simulations of two two‐domain constructs from the immunoglobulin‐like β‐sandwich fold. Each of these was experimentally shown to behave as the “sum of its parts,” that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two‐domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Principal component analysis of chemical shift perturbation data of a multiple‐ligand‐binding system for elucidation of respective binding mechanism
Authors: Konuma Tsuyoshi , Lee Young‐Ho , Goto Yuji , Sakurai Kazumasa
Published: April 2013

Chemical shift perturbations (CSPs) in NMR spectra provide useful information about the interaction of a protein with its ligands. However, in a multiple‐ligand‐binding system, determining quantitative parameters such as a dissociation constant (Kd) is difficult. Here, we used a method we named CS‐PCA, a principal component analysis (PCA) of chemical shift (CS) data, to analyze the interaction between bovine β‐lactoglobulin (βLG) and 1‐anilinonaphthalene‐8‐sulfonate (ANS), which is a multiple‐ligand‐binding system. The CSP on the binding of ANS involved contributions from two distinct binding sites. PCA of the titration data successfully separated the CSP pattern into contributions from each site. Docking simulations based on the separated CSP patterns provided the structures of βLG–ANS complexes for each binding site. In addition, we determined the Kd values as 3.42 × 10−4M2 and 2.51 × 10−3M for Sites 1 and 2, respectively. In contrast, it was difficult to obtain reliable Kd values for respective sites from the isothermal titration calorimetry experiments. Two ANS molecules were found to bind at Site 1 simultaneously, suggesting that the binding occurs cooperatively with a partial unfolding of the βLG structure. On the other hand, the binding of ANS to Site 2 was a simple attachment without a significant conformational change. From the present results, CS‐PCA was confirmed to provide not only the positions and the Kd values of binding sites but also information about the binding mechanism. Thus, it is anticipated to be a general method to investigate protein–ligand interactions. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Swfoldrate: Predicting protein folding rates from amino acid sequence with sliding window method
Authors: Cheng Xiang , Xiao Xuan , Wu Zhi‐cheng , Wang Pu , Lin Wei‐zhong
Published: April 2013

Protein folding is the process by which a protein processes from its denatured state to its specific biologically active conformation. Understanding the relationship between sequences and the folding rates of proteins remains an important challenge. Most previous methods of predicting protein folding rate require the tertiary structure of a protein as an input. In this study, the long‐range and short‐range contact in protein were used to derive extended version of the pseudo amino acid composition based on sliding window method. This method is capable of predicting the protein folding rates just from the amino acid sequence without the aid of any structural class information. We systematically studied the contributions of individual features to folding rate prediction. The optimal feature selection procedures are adopted by means of combining the forward feature selection and sequential backward selection method. Using the jackknife cross validation test, the method was demonstrated on the large dataset. The predictor was achieved on the basis of multitudinous physicochemical features and statistical features from protein using nonlinear support vector machine (SVM) regression model, the method obtained an excellent agreement between predicted and experimentally observed folding rates of proteins. The correlation coefficient is 0.9313 and the standard error is 2.2692. The prediction server is freely available at http://www.jci‐bioinfo.cn/swfrate/input.jsp. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Separability between overall and internal motion: A protein folding problem
Authors: Johnson Eric
Published: April 2013

The separability between overall and internal motions is evaluated over multiple folding trajectories of the villin headpiece subdomain. The analysis, which relies on the Prompers‐Brüschweiler separability index, offers a potentially useful perspective on protein folding. The protein is considered folded in this study, not when it reaches some static target, but rather when it tumbles as a dynamically constrained object. The analysis also demonstrates how the separability index, when applied to protein folding simulations, can facilitate the analysis of NMR relaxation data. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Crystal structure of the Campylobacter jejuni Cj0090 protein reveals a novel variant of the immunoglobulin fold among bacterial lipoproteins
Authors: Paek Seonghee , Kawai Fumihiro , Choi Kyoung‐Jae , Yeo Hye‐Jeong
Published: April 2013

Bacterial lipoproteins play an important role in bacterial pathogenesis and physiology. The genome of Campylobacter jejuni, a major foodborn pathogen, is predicted to contain over 20 lipoproteins. However, the functions of the majority of C. jejuni lipoproteins remain unknown. The Cj0090 protein is encoded by a lipoprotein operon composed of cj0089, cj0090, and cj0091. Here, we report the crystal structure of Cj0090 at 1.9 Å resolution, revealing a novel variant of the immunoglobulin fold with β‐sandwich architecture. The structure suggests that Cj0090 may be involved in protein‐protein interactions, consistent with a possible role for bacterial lipoproteins. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Enhanced herbicide metabolism induced by 2,4‐D in herbicide susceptible Lolium rigidum provides protection against diclofop‐methyl
Authors: Han Heping , Yu Qin , Cawthray Gregory R , Powles Stephen B
Published: April 2013

Background

The auxinic herbicide 2,4‐D amine is known, in vitro, as a cytochrome P450 inducer. The current study uses 2,4‐D pre‐treatment, at the whole plant level, to study mechanism(s) of non‐target site based herbicide resistance to the ACCase‐inhibiting herbicide diclofop‐methyl in Lolium rigidum.

Results

The 2,4‐D pre‐treatment caused up to 10‐fold shift in LD50 and GR50 in dose–response to subsequently applied diclofop‐methyl in a herbicide susceptible L. rigidum population. Foliar uptake and translocation of 14C‐diclofop‐methyl did not differ in 2,4‐D pre‐treated versus untreated plants. HPLC analysis revealed that de‐esterification of diclofop‐methyl to toxic diclofop acid was similar, but further metabolism of diclofop acid to non‐toxic metabolites was significantly (1.8‐fold) faster in 2,4‐D pre‐treated than untreated plants. HPLC profile of major polar metabolites was similar when L. rigidum and diclofop‐methyl tolerant wheat were compared, but wheat metabolised diclofop acid three‐fold faster than L. rigidum. In addition, 2,4‐D pre‐treatment also induced cross‐protection against the ALS‐inhibiting herbicide chlorsulfuron, and the known P450 inhibitor malathion can reverse this effect.

Conclusions

Protection against diclofop‐methyl provided by 2,4‐D pre‐treatment in susceptible L. rigidum is associated with higher rates of herbicide metabolism, mirroring that identified in field‐evolved, non‐target site‐based diclofop‐methyl resistant populations. 2,4‐D may induce higher level expression of herbicide‐metabolising genes hence providing protection, and therefore, this 2,4‐D induction system can be used, in combination with other genomic approaches, to assist isolating cytochrome P450 and other genes that are involved in herbicide metabolism and endow herbicide resistance in L. rigidum. © 2013 Society of Chemical Industry
Decursin Exerts Anti‐cancer Activity in MDA‐MB‐231 Breast Cancer Cells Via Inhibition of the Pin1 Activity and Enhancement of the Pin1/p53 Association
Authors: Kim Ji‐Hyun , Jung Ji Hoon , Kim Sung‐Hoon , Jeong Soo‐Jin
Published: April 2013

The peptidyl‐prolyl cis/trans isomerase Pin1 is overexpressed in a wide variety of cancer cells and thus considered as an important target molecule for cancer therapy. This study demonstrates that decursin, a bioactive compound from Angelica gigas, exert the anti‐cancer effect against breast cancer cells via regulation of Pin1 and its related signaling molecules. We observed that decursin induced G1 arrest with decrease in cyclin D1 level in Pin1‐expressing breast cancer cells MDA‐MB‐231, but not Pin1‐non‐expressing breast cancer cells MDA‐MB‐157. In addition, decursin significantly reduced protein expression and enzymatic activity of Pin1 in MDA‐MB‐231 cells. Further, we found that decursin treatment enhanced the p53 expression level and failed to down‐regulate Pin1 in the cells transfected with p53 siRNA, indicating the importance of p53 in the decursin‐mediated Pin1 inhibition in MDA‐MB‐231 cells. Decursin stimulated association between Pin1 to p53. Moreover, decursin facilitated p53 transcription in MDA‐MB‐231 cells. Overall, our current study suggests the potential of decursin as an attractive cancer therapeutic agent for breast cancer by targeting Pin1 protein. Copyright © 2013 John Wiley & Sons, Ltd.
H ∞  preview tracking control of retarded state‐multiplicative stochastic systems
Authors: Gershon E. , Shaked U.
Published: April 2013

The problem of infinite‐horizon H ∞  state‐feedback tracking control for linear continuous time‐invariant retarded systems with stochastic parameter uncertainties is investigated. Two tracking patterns are considered depending on the nature of the reference signal; that is, whether it is measured online or previewed in a fixed time‐interval ahead. The stochastic uncertainties appear in the dynamics matrices for both the retarded and the non‐retarded states of the system. The delayed system is transformed via the input–output approach, to an uncertain norm‐bounded system. A new method that efficiently yields a min–max strategy to the solution of each of the aforementioned two cases is suggested where, given a specific reference signal, the controller plays against nature, which chooses the maximizing energy‐bounded disturbance. The theoretical results are demonstrated by two examples that show the impact of the delay length and the preview length on the system performance. Copyright © 2013 John Wiley & Sons, Ltd.
Preparation of ordered mesoporous TiO2 thin film and its application in methanol catalytic combustion
Authors: Bian Yurong , Wang Xiaohong , Zeng Zhigang , Hu Zhiyu
Published: April 2013

Ordered mesoporous titania thin films were synthesized by evaporation induced self‐assembly process in the presence of Pluronic block copolymers P123 (EO20‐PO70‐EO20). The influence of several experimental parameters, including aging humidity, aging temperature, substrate properties and methods for organic templates removal, on the mesostructure of titania thin films was investigated in details. The mesoporous titania thin film supported Pt catalyst was prepared, and its methanol catalytic combustion performance was studied. The results showed that mesoporous titania thin film is an active support for catalyst. Mesoporous titania thin film supported platinum catalysts yields 70% methanol conversion at room temperature and 100% conversion at 100 °C. Copyright © 2013 John Wiley & Sons, Ltd.
The same-sign dilepton signature of RPV/MFV SUSY
Authors: Berger Joshua , Perelstein Maxim , Saelim Michael , Tanedo Philip
Published: April 2013

Abstract

The lack of observation of superpartners at the Large Hadron Collider so far has led to a renewed interest in supersymmetric models with R-parity violation (RPV). In particular, imposing the Minimal Flavor Violation (MFV) hypothesis on a general RPV model leads to a realistic and predictive framework. Naturalness suggests that stops and gluinos should appear at or below the TeV mass scale. We consider a simplified model with these two particles and MFV couplings. The model predicts a significant rate of events with same-sign dileptons and b-jets. We re-analyze a recent CMS search in this channel and show that the current lower bound on the gluino mass is about 800 GeV at 95% confidence level, with only a weak dependence on the stop mass as long as the gluino can decay to an on-shell top-stop pair. We also discuss how this search can be further optimized for the RPV/MFV scenario, using the fact that MFV stop decays often result in jets with large invariant mass. With the proposed improvements, we estimate that gluino masses of up to about 1.4 TeV can be probed at the 14 TeV LHC with a 100 fb−1 data set.
Measuring Collective Efficacy Among Children in Community‐based Afterschool Programs: Exploring Pathways toward Prevention and Positive Youth Development
Authors: Smith Emilie Phillips , Osgood D. Wayne , Caldwell Linda , Hynes Kathryn , Perkins Daniel F.
Published: April 2013

Collective efficacy refers to a perceived sense of connectedness and willingness to intervene among youth, and is a potential aspect of positive youth development (Larson in Am Psychol 55:170–183, 2000; Lerner et al. in Child Dev 71:11–20, 2000; Sampson et al. in Science 277:918–924, 1997). Theoretically, those who feel connected to a group that is empowered to positively influence the behavior of their peers may demonstrate fewer problem behaviors. Few studies, however, have measured the impact of youth perceptions of collective efficacy. As a relatively new child‐related research topic, there is much to be learned. One contribution to the foundation of this research agenda begins by evaluating the reliability and validity of a measure of collective efficacy with elementary children attending community‐based afterschool programs. This paper describes the internal consistency reliability and various indicators of construct and concurrent validity of the Collective Efficacy Among Children Scale. The measure was found to have high internal consistency reliability. Construct validity was tested using exploratory factor analyses of collective efficacy including the dimensions of willingness to intervene and cohesion found in previous research (Sampson et al. in Science 277:918–924, 1997). Concurrent validity assessed relations between the scale and other measures in theoretically congruent ways. Using Hierarchical Linear Models to account for children's nestedness in after‐school programs, connectedness was found to be more related to emotional adjustment, particularly children's prosocial attitudes (caring about others and sharing). Children's perception of the willingness of the group to intervene was found to be related to less problem behavior, (i.e. smoking tobacco, drinking alcohol, vandalism, and stealing). The implications suggest that future research should further explore children's collective efficacy, and ways to foster its development in youth‐serving afterschool settings.
Energy intake from human milk covers the requirement of 6-month-old Senegalese exclusively breast-fed infants
Authors: Agne-Djigo Anta , Kwadjode Komlan M. , Idohou-Dossou Nicole , Diouf Adama , Guiro Amadou T. , Wade Salimata
Published: April 2013

Exclusive breast-feeding until 6 months is advised by the WHO as the best practice to feed infants. Yet, some studies have suggested a gap between energy requirements and the energy provided by human milk for many infants at 6 months. In order to assess the adequacy of WHO recommendations in 6-month-old Senegalese lactating infants, a comprehensive study was designed to measure human milk intake by the dose-to-the mother2H2O turnover method. Infants' energy intakes were calculated using daily breast milk intake and the energy content of milk was estimated on the basis of creamatocrit. Of the fifty-nine mother–infant pairs enrolled, fifteen infants were exclusively breast-fed (Ex) while forty-four were partially breast-fed (Part). Infants' breast milk intake was significantly higher in the Ex group (993 (sd135) g/d,n15) compared with the Part group (828 (sd222) g/d,n44,P= 0·009). Breast milk energy content as well as infants' growth was comparable in both groups. However, infants' energy intake from human milk was significantly higher (364 (sd50) kJ/kg per d (2586 (sd448) kJ/d)) in the Ex group than in the Part group (289 (sd66) kJ/kg per d (2150 (sd552) kJ/d),P< 0·01). Compared with WHO recommendations, the results demonstrate that energy intake from breast milk was low in partially breast-fed infants while exclusively breast-fed 6-month-old Senegalese infants received adequate energy from human milk alone, the most complete food for infants. Therefore, advocacy of exclusive breast-feeding until 6 months should be strengthened.
AnIchthyosaurus brevicepscollected by Mary Anning: new information on the species
Authors: MASSARE JUDY A. , LOMAX DEAN R.
Published: April 2013

An ichthyosaur in the collections of the Sedgwick Museum, Cambridge (CAMSMX.50187) was collected in the nineteenth century by the renowned fossil collector Mary Anning, but has never been adequately described in the literature. As an Anning specimen, it is certainly from the Lower Jurassic of Lyme Regis, west Dorset. The near complete presacral skeleton is lying on its left side and includes a complete skull, one complete and one partial forefin, pectoral bones, all six elements of the pelvic girdle, and both hindfins. The centra in the anterior caudal region, however, are from another individual and may have replaced the original ones. The specimen is identified asIchthyosaurusbased on the morphology of the humerus and forefin. It is assigned toI. brevicepson the basis of the relatively short snout, large eye, and tall neural spines. This is the only known specimen ofI. brevicepsto preserve a complete pelvis. Notably, the ilium is longer than the pubis and ischium, and the pubis is longer than the ischium. This individual is the largestI. brevicepsreported in the literature, with jaw length of 33.5 cm and estimated length from snout to tail bend of 1.6 m.
The differences in cellulolytic activity of the Arctic soils of Calypsostranda, Spitsbergen
Authors: Świtoniak Marcin , Melke Jerzy , Bartmiński Piotr
Published: April 2013

The aim of this study was to determine the differences in cellulolytic activity of soils around the coastal lowlands of the southwestern part of Wedel Jarlsberg Land (west Spitsbergen). Two positions (Calypso and Skilvika) representing typical soil types in this area were chosen for investigation. Within the area of Calypso, arctic brown soils formed from loamy sands with a significant addition of coarser gravel and pebble fractions occur. The Skilvika position represents the arctic gley soils of a loamy texture, with significant content of silt, associated with the occurrence of cell grounds created under the strong influence of cryogenic processes. Cellulolytic activity of the soils was determined by a gravimetric method involving estimation of a weight loss of cellulosic material buried in the surface soil horizons. The investigation showed significant differences in the cellulose decomposition rate between the two research locations. The cellulolytic activity of arctic brown soils –0,412–0,656 g*g−1*year−1 during the vegetation season (Olson's k = 0,231–0,563), was twice higher than the activity in the case of Skilvika gley soils –0,185–0,310g*g−1*year−1 during vegetation season (k = 0,089–0,131). This should be attributed, among other factors, to the grain size distribution, thereby determining more favourable water-air conditions of soils within the area of Calypso.
Eye evolution and its functional basis
Authors: NILSSON DAN-E.
Published: April 2013

Eye evolution is driven by the evolution of visually guided behavior. Accumulation of gradually more demanding behaviors have continuously increased the performance requirements on the photoreceptor organs. Starting with nondirectional photoreception, I argue for an evolutionary sequence continuing with directional photoreception, low-resolution vision, and finally, high-resolution vision. Calculations of the physical requirements for these four sensory tasks show that they correlate with major innovations in eye evolution and thus work as a relevant classification for a functional analysis of eye evolution. Together with existing molecular and morphological data, the functional analysis suggests that urbilateria had a simple set of rhabdomeric and ciliary receptors used for directional photoreception, and that organ duplications, positional shifts and functional shifts account for the diverse patterns of eyes and photoreceptors seen in extant animals. The analysis also suggests that directional photoreception evolved independently at least twice before the last common ancestor of bilateria and proceeded several times independently to true vision in different bilaterian and cnidarian groups. This scenario is compatible withPax-gene expression in eye development in the different animal groups. The whole process from the first opsin to high-resolution vision took about 170 million years and was largely completed by the onset of the Cambrian, about 530 million years ago. Evolution from shadow detectors to multiple directional photoreceptors has further led to secondary cases of eye evolution in bivalves, fan worms, and chitons.