bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scheduling two chains of unit jobs on one machine: A polyhedral study
Authors: Arbib Claudio , Labbé Martine , Servilio Mara 
Published: August 2011

AbstractWe investigate polyhedral properties of the following scheduling problem: given two sets of unit, indivisible jobs and revenue functions of the jobs completion times, find a one‐machine schedule maximizing the total revenue under the constraint that the schedule of each job set respects a prescribed chain‐like precedence relation. A solution to this problem is an order preserving assignment of the jobs to a set of time‐slots. We study the convex hull of the feasible assignments and provide families of facet‐defining inequalities in two cases: (i) each job must be assigned to a time‐slot and (ii) a job does not need to be assigned to any time‐slot. © 2011 Wiley Periodicals, Inc. NETWORKS, 2011
Online traveling salesman problems with service flexibility
Authors: Jaillet Patrick , Lu Xin 
Published: August 2011

AbstractThe traveling salesman problem is a well‐known combinatorial optimization problem. We are concerned here with online versions of this problem defined on metric spaces. One novel aspect in this article is the introduction of a sound theoretical model to incorporate “yes‐no” decisions on which requests to serve, together with an online strategy to visit the accepted requests. To do so, we assume that there is a penalty for not serving a request. Requests for visit of points in the metric space are revealed over time to a server, initially at a given origin, who must decide in an online fashion which requests to serve to minimize the time to serve all accepted requests plus the sum of the penalties associated with the rejected requests. We first look at the special case of the non‐negative real line. After providing a polynomial time algorithm for the offline version of the problem, we propose and prove the optimality of a 2‐competitive polynomial time online algorithm based on reoptimization approaches. We also consider the impact of advanced information (lookahead) on this optimal competitive ratio. We then consider the generalizations of these results to the case of the real line. We show that the previous algorithm can be extended to an optimal 2‐competitive online algorithm. Finally we consider the case of a general metric space and propose an original c ‐competitive online algorithm, where
\documentclass{article}\usepackage{mathrsfs, amsmath, amsfonts, amssymb}\pagestyle{empty}\begin{document} $c = \sqrt{({17+5})}/{4} \approx 2.28$ \end{document}. We also give a polynomial‐time (1.5ρ + 1) ‐competitive online algorithm which uses a polynomial‐time ρ ‐approximation for the offline problem. © 2011 Wiley Periodicals, Inc. NETWORKS, 2011
Collection and storage of human blood and adipose for genomic analysis of clinical samples
Authors: Cashion Ann K. , Umberger Reba A. , Goodwin Shirlean B. , Sutter Thomas R. 
Published: August 2011

AbstractIn this methods article, we describe collection and storage of clinically acquired blood and adipose samples for transcript analysis in an ongoing study exploring obesity in renal transplant recipients. Total ribonucleic acid (RNA) was isolated from whole blood using the LeukoLOCK™ Total RNA Isolation System (n = 4), and comparisons between fresh and frozen samples were made. Abdominal subcutaneous adipose samples (n = 4) were obtained during kidney transplantation, flash frozen, and stored at −80°C. Adipose RNA was extracted using either the STAT‐60 method modified for lipids or Trizol plus RNeasy extraction. Affymetrix HG‐U133 plus 2.0 arrays and Affymetrix Human Gene 1.0 ST arrays were used for both blood and adipose transcriptome analysis. Purity, quality, and quantity of RNA were high with comparable results using both array platforms. © 2011 Wiley Periodicals, Inc. Res Nurs Health 34:408–418, 2011
HPLC Analysis of Oxindole Alkaloids in Uncaria Tomentosa: Sample Preparation and Analysis Optimisation by Factorial Design
Authors: Bertol Gustavo , Franco Luzia , de Oliveira Brás Heleno 
Published: August 2011

ABSTRACTIntroductionUncaria tomentosa (“cat's claw”) is widely used for the treatment of some infectious and inflammatory diseases. Oxindole alkaloids are regarded as the most important components responsible for the biological activities attributed to the plant. Their analysis require efficient sample preparation and suitable reference standards but few are commercially available.ObjectiveTo develop and validate a HPLC analytical method for oxindole alkaloids in Uncaria tomentosa with emphasis on sample preparation.MethodFactorial experimental designs were used for the optimisation of both sample preparation and chromatographic separation. The optimised sample preparation involved extraction with aqueous ethanol, and the granulometry of the powdered plant material significantly influenced extraction yields. Mitraphylline was used as a calibration reference for the determination of total alkaloids.ResultsThe method was fully validated and showed good selectivity, linearity (r2 ≥ 0.9996), accuracy (≥ 96%) and precision (RSD < 2.4%). Detection and quantification limits for mitraphylline were 0.8 and 2.4 ppm, respectively.ConclusionThe optimised chromatographic method, using organic buffer in the mobile phase, provided baseline separation of tetracyclic and pentacyclic alkaloids in the samples. Calibration using mitraphylline provided more accurate estimates of total alkaloid content when compared to other available reference alkaloids. Copyright © 2011 John Wiley & Sons, Ltd.
A high intake of industrial or ruminant trans fatty acids does not affect the plasma proteome in healthy men
Authors: de Roos Baukje , Wanders Anne J. , Wood Sharon , Horgan Graham , Rucklige Garry , Reid Martin , Siebelink Els , Brouwer Ingeborg A. 
Published: August 2011

AbstractConsumption of industrial trans fat raises the risk of cardiovascular disease, but it is unclear whether cis9,trans11‐conjugated linoleic acid (CLA) – a trans fatty acid in dairy products – modulates disease development. We investigated the effects of complete diets providing 7% of energy as industrial trans fat or cis9, trans11 CLA, compared with oleic acid, on regulation of plasma proteins in 12 healthy men. Diets were provided for 3 wk each, in random order. Plasma was collected at the end of each 3 wk intervention period, depleted of its 12 most abundant proteins and analyzed by 2‐DE. Principal component analysis of protein spot intensity values revealed that the nature of the dietary intervention did not significantly affect the plasma proteome. The intervention provided in the 1st period produced a significant treatment effect compared with the interventions provided in the other two periods, and there was a significant subject effect. In conclusion, the nature of an extreme dietary intervention, i.e. 7% of energy provided by industrial trans fat or cis9,trans11 CLA, did not markedly affect the plasma proteome. Thus plasma proteomics using 2‐DE appears, by and large, an unsuitable approach to detect regulation of plasma proteins due to changes in the diet.
Clinimetric properties of breath‐stacking technique for assessment of inspiratory capacity
Authors: de Sá Feitosa Larissa Andrade , Barbosa Paula Antas , Pessoa Maíra Floretino , Rodrigues‐Machado Maria da Glória , de Andrade Armèle Dornelas 
Published: August 2011

AbstractBackground and PurposeBreath stacking (BS) is used as an alternative method for lung expansion therapy and the assessment of inspiratory capacity in uncooperative patients. The aims of the present study were to identify the reproducibility of the BS technique in healthy volunteers and to compare BS with conventional spirometry with regard to inspiratory capacity.MethodsA cross‐sectional study was carried out. Eighty‐five healthy volunteers (21.78 ± 2.79 years; 41 men, 44 women) underwent spirometry and BS. Lung function, anthropometric and cardiopulmonary parameters were evaluated prior to the intervention. BS was performed with a unidirectional inspiratory valve by two different examiners. The order of each examiner was randomized. Spirometric tests were performed three times, and the BS manoeuvre was evaluated three times by each examiner. Respiratory rate, heart rate and peripheral arterial oxygen saturation were determined before, during and following the manoeuvre.ResultsThere were no statistically significant differences in the intra‐examiner and inter‐examiner analyses for the volume mobilized during BS, respiratory rate, duration of BS manoeuvre or perceived effort index (p > 0.05). The intra‐class correlation coefficient was greater than 0.7 for all variables analysed. Maximal volumes achieved using the BS technique were significantly higher than those achieved with conventional spirometry (p < 0.0001).ConclusionData from both the intra‐examiner and inter‐examiner analyses suggest that the BS technique is reproducible. This technique mobilizes greater lung volumes than conventional spirometry. Copyright © 2011 John Wiley & Sons, Ltd.
The X‐ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: Comparison of paralogous functions in B. thetaiotaomicron
Authors: Lu Zhibing , Dunaway‐Mariano Debra , Allen Karen N. 
Published: August 2011

AbstractAnalysis of the haloalkanoate dehalogenase superfamily (HADSF) has uncovered homologues occurring within the same organism that are found to possess broad, overlapping substrate specificities, and low catalytic efficiencies. Here we compare the HADSF phosphatase BT1666 from Bacteroides thetaiotaomicron VPI‐5482 to a homologue with high sequence identity (40%) from the same organism BT4131, a known hexose‐phosphate phosphatase. The goal is to find whether these enzymes represent duplicated versus paralogous activities. The X‐ray crystal structure of BT1666 was determined to 1.82 Å resolution. Superposition of the BT1666 and BT4131 structures revealed a conserved fold and identical active sites suggestive of a common physiological substrate. The steady‐state kinetic constants for BT1666 were determined for a diverse panel of phosphorylated metabolites to define its substrate specificity profile and overall level of catalytic efficiency. Whereas BT1666 and BT4131 are both promiscuous, their substrate specificity profiles are distinct. The catalytic efficiency of BT1666 (kcat/Km = 4.4 × 102M−1 s−1 for the best substrate fructose 1,6‐(bis)phosphate) is an order of magnitude less than that of BT4131 (kcat/Km = 6.7 × 103M−1 s−1 for 2‐deoxyglucose 6‐phosphate). The seemingly identical active‐site structures point to sequence variation outside the active site causing differences in conformational dynamics or subtle catalytic positioning effects that drive the divergence in catalytic efficiency and selectivity. The overlapping substrate profiles may be understood in terms of differential regulation of expression of the two enzymes or a conferred advantage in metabolic housekeeping functions by having a larger range of possible metabolites as substrates. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
The structure, molecular dynamics, and energetics of centrin–melittin complex
Authors: Sosa Liliana del Valle , Alfaro Elisa , Santiago Jorge , Narváez Daniel , Rosado Marie Cely , Rodríguez Aslin , Gómez Ana María , Schreiter Eric R. , Pastrana‐Ríos Belinda 
Published: August 2011

AbstractCentrin is a calcium binding protein (CaBP) belonging to the EF‐hand superfamily. As with other proteins within this family, centrin is a calcium sensor with multiple biological target proteins. We chose to study Chlamydomonas reinhardtii centrin (Crcen) and its interaction with melittin (MLT) as a model for CaBP complexes due to its amphipathic properties. Our goal was to determine the molecular interactions that lead to centrin–MLT complex formation, their relative stability, and the conformational changes associated with the interaction, when compared to the single components. For this, we determined the thermodynamic parameters that define Crcen–MLT complex formation. Two‐dimensional infrared (2D IR) correlation spectroscopy were used to study the amide I′, I′*, and side chain bands for 13C‐Crcen, MLT, and the 13C‐Crcen–MLT complex. This approach resulted in the determination of MLT's increased helicity, while centrin was stabilized within the complex. Herein we provide the first complete molecular description of centrin–MLT complex formation and the dissociation process. Also, discussed is the first structure of a CaBP–MLT complex by X‐ray crystallography, which shows that MLT has a different binding orientation than previously characterized centrin‐bound peptides. Finally, all of the experimental results presented herein are consistent with centrin maintaining an extended conformation while interacting with MLT. The molecular implications of these results are: (1) the recognition of hydrophobic contacts as requirements for initial binding, (2) minimum electrostatic interactions within the C‐terminal end of the peptide, and (3) van der Waals interactions within MLTs N‐terminal end are required for complex formation. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Elastic network model‐based normal mode analysis reveals the conformational couplings in the tripartite AcrAB‐TolC multidrug efflux complex
Authors: Wang Beibei , Weng Jingwei , Fan Kangnian , Wang Wenning 
Published: August 2011

AbstractThe AcrAB‐TolC drug efflux system, energized by proton movement down the transmembrane electrochemical gradient, is responsible for the resistance of the organism to a wide range of drugs. Experimental data suggest functional roles of each part of the assembly, but the detailed working mechanism of this machinery remains elusive. We used elastic network‐based normal mode analysis (NMA) to explore the conformational dynamics of the AcrAB‐TolC complex. The intrinsic flexibilities of the pore domain in AcrB monomer conform to the previously proposed three‐step functionally rotating mechanism for asymmetric AcrB trimer. Conformational couplings across monomers in the AcrB trimer were observed, and the coupling between the transmembrane domain and the other parts of AcrB are strengthened through trimeric assembly. In the tripartite AcrAB‐TolC assembly obtained through molecular docking, concerted motions were observed not only at the direct contact interfaces between various components but also between distant parts of the whole complex. The presence of AcrA was shown to significantly strengthen the motional couplings between AcrB and TolC. Overall, NMA revealed an allosteric network in the AcAB‐TolC efflux system, which provides hints to our understanding of its detailed working mechanism. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Phosphorylation alters backbone conformational preferences of serine and threonine peptides
Authors: Kim Su‐Yeon , Jung Youngae , Hwang Geum‐Sook , Han Hogyu , Cho Minhaeng 
Published: August 2011

AbstractDespite the notion that a control of protein function by phosphorylation works mainly by inducing its conformational changes, the phosphorylation effects on even small peptide conformation have not been fully understood yet. To study its possible effects on serine and threonine peptide conformations, we recently carried out pH‐ and temperature‐dependent circular dichroism (CD) as well as 1H NMR studies of the phosphorylated serine and threonine peptides and compared them with their unphosphorylated analogs. In the present article, by performing the self‐consistent singular value decomposition analysis of the temperature‐dependent CD spectra and by analyzing the 3J(HN,Hα) coupling constants extracted from the NMR spectra, the populations of the polyproline II (PPII) and β‐strand conformers of the phosphorylated Ser and Thr peptides are determined. As temperature is increased, the β‐strand populations of both phosphorylated serine and threonine peptides increase. However, the dependences of PPII/β‐strand population ratio on pH are different for these two cases. The phosphorylation of the serine peptide enhances the PPII propensity, whereas that of the threonine peptide has the opposite effect. This suggests that the serine and threonine phosphorylations can alter the backbone conformational propensity via direct but selective intramolecular hydrogen‐bonding interactions with the peptide NH groups. This clearly indicates that the phosphoryl group actively participates in modulating the peptide backbone conformations. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Effects of the Val211Gly substitution on molecular dynamics of the CMY‐2 cephalosporinase: Implications on hydrolysis of expanded‐spectrum cephalosporins
Authors: Kotsakis Stathis D. , Tzouvelekis Leonidas S. , Petinaki Efthymia , Tzelepi Eva , Miriagou Vivi 
Published: August 2011

AbstractCMY‐30, a naturally occurring class C β‐lactamase differing from the Citrobacter freundii‐derived CMY‐2 by a Val211Gly substitution in the Ω‐loop, exhibits increased hydrolytic efficiency against ceftazidime and cefotaxime. Kinetic constants of CMY‐2 and CMY‐30 against the latter substrates suggested that the improved efficiency of the Gly211 variant was due to an increase in kcat. The structural basis of the increased turn‐over rates of oxyimino‐cephalosporins caused by Val211Gly was studied using 5 ns molecular dynamics simulations of CMY‐2 and CMY‐30 in their free forms and in covalent complexes with ceftazidime (acyl‐enzyme) as well as a boronic acid analogue of ceftazidime (deacylation transition state). Analysis of thermal factors indicated that Val211Gly increased the flexibility of the Ω‐loop/H7‐helix and the Q120‐loop formed by amino acids 112–125, and also altered the vibrations of the H10‐helix/R2‐loop. Structural elements containing the catalytic residues remained relatively rigid except Tyr150 in acyl‐enzyme species. Regions exhibiting altered flexibility due to the substitution appear to move in a concerted manner in both enzymes. This movement was more intense in CMY‐30 and also at directions different to those observed for CMY‐2. Additionally, it appeared that the Val211Gly increased the available space for the accommodation of the R1 side chain of ceftazidime. These findings are likely associated with the significantly increased vibrations of the bound compounds observed in CMY‐30 complexes. Therefore, the extended spectrum properties of CMY‐30 seem to arise through a complex process implicating changes in protein movement and in the mode of substrate accommodation. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen‐fixing bacteria
Authors: Marassi Francesca M. 
Published: August 2011

AbstractThe Mycobacterium tuberculosis membrane protein Rv0899 confers adaptation of the bacterium to acidic environments. Due to strong sequence homology of its C‐terminus to bacterial OmpA‐like domains, Rv0899 has been proposed to constitute an outer membrane porin of M. tuberculosis. However, OmpA‐like domains are widespread in a wide variety of bacterial proteins with different functions. Furthermore, the three‐dimensional structure of Rv0899 does not contain a transmembrane β‐barrel, and recent evidence demonstrates that it does not have porin activity. Instead, the rv0899 gene is part of an operon (rv0899‐rv0901) that is required for fast ammonia secretion, pH neutralization, and growth of M. tuberculosis in acidic environments. The mechanism whereby these functions are accomplished is not known. To gain further functional insights, a targeted search of the genomic databases was performed for proteins with sequence similarity beyond the OmpA‐like C‐terminus. The results presented here, show that Rv0899‐like proteins are widespread in bacteria with functions in nitrogen metabolism, adaptation to nutrient poor environments, and/or establishing symbiosis with the host organism, and appear to form a protein family. These findings suggest that M. tuberculosis Rv0899 may also assist similar processes and lend further support to its role in ammonia secretion and M. tuberculosis adaptation to the host environment. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Inhibition of α‐synuclein aggregation by small heat shock proteins
Authors: Bruinsma Ilona B. , Bruggink Kim A. , Kinast Karsten , Versleijen Alexandra A. M. , Segers‐Nolten Ine M. J. , Subramaniam Vinod , Bea Kuiperij H. , Boelens Wilbert , de Waal Robert M. W. , Verbeek Marcel M. 
Published: August 2011

AbstractThe fibrillization of α‐synuclein (α‐syn) is a key event in the pathogenesis of α‐synucleinopathies. Mutant α‐syn (A53T, A30P, or E46K), each linked to familial Parkinson's disease, has altered aggregation properties, fibril morphologies, and fibrillization kinetics. Besides α‐syn, Lewy bodies also contain several associated proteins including small heat shock proteins (sHsps). Since α‐syn accumulates intracellularly, molecular chaperones like sHsps may regulate α‐syn folding and aggregation. Therefore, we investigated if the sHsps αB‐crystallin, Hsp27, Hsp20, HspB8, and HspB2B3 bind to α‐syn and affect α‐syn aggregation. We demonstrate that all sHsps bind to the various α‐syns, although the binding kinetics suggests a weak and transient interaction only. Despite this transient interaction, the various sHsps inhibited mature α‐syn fibril formation as shown by a Thioflavin T assay and atomic force microscopy. Interestingly, HspB8 was the most potent sHsp in inhibiting mature fibril formation of both wild‐type and mutant α‐syn. In conclusion, sHsps may regulate α‐syn aggregation and, therefore, optimization of the interaction between sHsps and α‐syn may be an interesting target for therapeutic intervention in the pathogenesis of α‐synucleinopathies. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Simulation of the β‐ to α‐sheet transition results in a twisted sheet for antiparallel and an α‐nanotube for parallel strands: Implications for amyloid formation
Authors: Hayward Steven , James Milner‐White E. 
Published: August 2011

Abstractα‐sheet has been proposed to be the main constituent of the toxic amyloid intermediate. Molecular dynamics simulations on proteins known to be involved in amyloid diseases have demonstrated that β‐sheet can, under certain conditions, spontaneously convert to α‐sheet via ββ→αRαL peptide‐plane flipping. Using torsion‐angle driving to simulate this flip the transition has been investigated for parallel and antiparallel sheets. Concerted and sequential flipping processes were simulated, the former allowing direct calculation of helical parameters. For antiparallel sheet, the strands tend to splay apart during the transition. This can be understood by consideration of the geometry of repeating dipeptide conformations. At the end of the transition antiparallel α‐sheet is slightly twisted, comprising gently curving strands. In parallel sheet, the strands maintain identical conformations and stay hydrogen bonded during the transition as they curl up to suggest a hitherto unseen structure, the multi‐helix α‐nanotube. Intriguingly, the α‐nanotube has some of the characteristics of the parallel β‐helix, a single‐helix structure also implicated in amyloid. Unlike the β‐helix, α‐nanotube formation could involve identical strands aligning with each other in register as in most amyloids. Proteins 2011;. © 2011 Wiley‐Liss, Inc.