bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization of selected dermatophytes and their identification by electrophoretic mutation scanning
Authors: Cafarchia Claudia , Otranto Domenico , Weigl Stefania , Campbell Bronwyn E. , Parisi Antonio , Cantacessi Cinzia , Mancianti Francesca , Danesi Patrizia , Gasser Robin B. 
Published: October 2009

AbstractDermatophytes are fungi that can be contagious and cause infections in the keratinized skin of mammals, including humans. The etiological diagnosis of dermatophytosis relies on a combination ofin vitro‐culture and microscopic methods. Effective molecular tools could overcome the limitations of conventional methods of identification. In the present study, following phenetic identification asM. canis, M. fulvum, M. gypseum, T. mentagrophytesandT. terrestre, we genetically characterized key dermatophytes, employing the sequences of the first and second internal transcribed spacers of nuclear ribosomal DNA as well as part of the chitin synthase‐1 gene, and assessed the utility of these DNA regions (based on levels of nucleotide variation within and among species/taxa) as markers for the classification of species and genotypes. Employing partial chitin synthase‐1 gene as the marker, we also established a PCR‐coupled SSCP approach as a diagnostic/analytical mutation‐scanning tool. This tool should facilitate fundamental investigations of the ecology, epidemiology and population genetics of dermatophytes and, importantly, should assist in allowing a more rapid diagnosis of dermatophytoses in humans and other animals, thus overcoming the significant delays in targeted chemotherapy following diagnosis using conventional methods. (Nucleotide sequence data reported in this paper are available in the EMBL, GenBank and DDJB datadases under accession numbers FJ897707–FJ897713 (ITS‐1), FJ897714–FJ897720 (ITS‐2) and FJ897700–FJ897706 (pchs‐1)).
Steady‐state electrophoresis of RNA against a gradient of cationic charges in a polyacrylamide matrix
Authors: Zilberstein Gleb , Shlar Ilya , Baskin Emmanuil , Korol Leonid , Righetti Pier Giorgio , Bukshpan Shmuel 
Published: October 2009

AbstractA novel method for separation of RNA fragments is reported here, based on migrating the polyanionic RNA fragments in a polycationic polyacrylamide gel, made by incorporating positively charged monomers (the Immobilines used for creating immobilized pH gradients) into the neutral polyacrylamide backbone. Separations are typically performed in a 0–10 mM, pK 10.3 Immobiline gradient under denaturing conditions (6 M urea). In the 100–1000 bp length, it is shown that separations of RNA are optimal and very sharp bands can be obtained, in comparison with conventional electrophoresis, due to the “focusing” effect originated by the charge balancing between the positively charged gel matrix and the negatively charged RNA species. Excellent separations are also obtained from micro‐RNAs, single‐stranded RNA molecules of 21–23 nucleotides in length, which appear to regulate gene expression in animal and plant tissues. As a third example, 2‐D runs in control and polycationic gels are shown. Under native conditions, RNAs are not aligned in a diagonal, suggesting that molecular shape has a strong influence on the interaction between RNA and the charged gel matrix. Thus, 2‐D runs in cationic matrices might be exploited for structural studies of RNA molecules.
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
Authors: Bertsch Andreas , Leinenbach Andreas , Pervukhin Anton , Lubeck Markus , Hartmer Ralf , Baessmann Carsten , Elnakady Yasser Abbas , Müller Rolf , Böcker Sebastian , Huber Christian G. , Kohlbacher Oliver 
Published: October 2009

AbstractDe novo sequencing of peptides using tandem MS is difficult due to missing fragment ions in the spectra commonly obtained after CID of peptide precursor ions. Complementing CID spectra with spectra obtained in an ion‐trap mass spectrometer upon electron transfer dissociation (ETD) significantly increases the sequence coverage with diagnostic ions. In the de novo sequencing algorithm CompNovo presented here, a divide‐and‐conquer approach was combined with an efficient mass decomposition algorithm to exploit the complementary information contained in CID and ETD spectra. After optimizing the parameters for the algorithm on a well‐defined training data set obtained for peptides from nine known proteins, the CompNovo algorithm was applied to the de novo sequencing of peptides derived from a whole protein extract of Sorangium cellulosum bacteria. To 2406 pairs of CID and ETD spectra contained in this data set, 675 fully correct sequences were assigned, which represent a success rate of 28.1%. It is shown that the CompNovo algorithm yields significantly improved sequencing accuracy as compared with published approaches using only CID spectra or combined CID and ETD spectra.
Three‐dimensional photogrammetry for surgical planning of tissue expansion in hemifacial microsomia
Authors: Jayaratne Yasas S. N. , Lo John , Zwahlen Roger A. , Cheung Lim K. 
Published: October 2009

AbstractBackground.We aim to illustrate the applications of 3‐dimensional (3‐D) photogrammetry for surgical planning and longitudinal assessment of the volumetric changes in hemifacial microsomia.Methods.A 3‐D photogrammetric system was employed for planning soft tissue expansion and transplantation of a vascularized scapular flap for a patient with hemifacial microsomia. The facial deficiency was calculated by superimposing a mirror of the normal side on the preoperative image. Postsurgical volumetric changes were monitored by serial superimposition of 3‐D images.Results.A total of 31 cm3 of tissue expansion was achieved within a period of 4 weeks. A scapular free flap measuring 8 cm × 5 cm was transplanted to augment the facial deficiency. Postsurgical shrinkage of the flap was observed mainly in the first 3 months and it was minimal thereafter.Conclusion.3‐D photogrammetry can be used as a noninvasive objective tool for assessing facial deformity, planning, and postoperative follow‐up of surgical correction of facial asymmetry. © 2009 Wiley Periodicals, Inc. Head Neck, 2010
Time series and stochastic analyses to study the hydrodynamic characteristics of karstic aquifers
Authors: Gárfias‐Soliz J. , Llanos‐Acebo H. , Martel R. 
Published: October 2009

AbstractThe regional study of hydrodynamic characteristics of karstic aquifers is challenging because of the great variety of lithology and the structural complexity found in carbonate formations. In order to improve this situation, a combined approach of time series and stochastic analyses was adopted to assess the hydrodynamic behaviour of the karstic aquifers. To achieve this, daily flow rates of 20 springs were taken from the 11 most significant aquifer units of the Basque Country. The results demonstrate the presence of memory effects, which modulated the input rainfall for short‐, medium‐ and long‐term storage capacity, resulting in hydrodynamic properties such as system memory, response time and mean delay between input and output. They reflect the storage and the manner in which these are filled and emptied, thus indicating the karstification of the aquifer. Likewise, the hydrodynamic and hydraulic classification obtained from the stochastic analysis provides a complementary approach to characterize the hydraulic behaviour of the studied karstic aquifers. The discussed examples indicate that this approach provides an excellent method to research hydrological karst systems. It is also shown that the use of hydrologic time series, alone, does not lead to a satisfactory classification of the hydrodynamic characteristics. Therefore, the general approach to hydrological regionalization in karst areas should take into account the structural complexity, heterogeneity of the lithology and the degree of karstification. Only in this case will the regionalization be physically founded, leading to a regional understanding of the hydrodynamic characteristics and flow conditions in a karst aquifer. Copyright © 2009 John Wiley & Sons, Ltd.
Computational design of protein–ligand binding: Modifying the specificity of asparaginyl‐tRNA synthetase
Authors: Lopes Anne , Busch Marcel Schmidt Am , Simonson Thomas 
Published: October 2009

AbstractA method for computational design of protein–ligand interactions is implemented and tested on the asparaginyl‐ and aspartyl‐tRNA synthetase enzymes (AsnRS, AspRS). The substrate specificity of these enzymes is crucial for the accurate translation of the genetic code. The method relies on a molecular mechanics energy function and a simple, continuum electrostatic, implicit solvent model. As test calculations, we first compute AspRS‐substrate binding free energy changes due to nine point mutations, for which experimental data are available; we also perform large‐scale redesign of the entire active site of each enzyme (40 amino acids) and compare to experimental sequences. We then apply the method to engineer an increased binding of aspartyl‐adenylate (AspAMP) into AsnRS. Mutants are obtained using several directed evolution protocols, where four or five amino acid positions in the active site are randomized. Promising mutants are subjected to molecular dynamics simulations; Poisson‐Boltzmann calculations provide an estimate of the corresponding, AspAMP, binding free energy changes, relative to the native AsnRS. Several of the mutants are predicted to have an inverted binding specificity, preferring to bind AspAMP rather than the natural substrate, AsnAMP. The computed binding affinities are significantly weaker than the native, AsnRS:AsnAMP affinity, and in most cases, the active site structure is significantly changed, compared to the native complex. This almost certainly precludes catalytic activity. One of the designed sequences has a higher affinity and more native‐like structure and may represent a valid candidate for Asp activity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010
Fabrication and characterization of electrospun poly‐DL‐lactide (PDLLA) fibrous coatings on 45S5 Bioglass® substrates for bone tissue engineering applications
Authors: Yunos D. M. , Ahmad Z. , Boccaccini A. R. 
Published: October 2009

AbstractBACKGROUND: This work focuses on combining electrospun biodegradable poly‐DL‐lactide (PDLLA) fibres and 45S5 Bioglass® for tissue engineering applications.RESULTS: A variety of fibrous structures were produced upon application of an electric field to a flowing solution of PDLLA (5 wt/v%) in di‐methyl carbonate (DMC). Electrospinning was achieved at an applied voltage of 8.5 kV for a fixed flow rate of 5 µL min−1. Scanning electron microscopy images of PDLLA fibres deposited on 45S5 Bioglass® sintered pellets revealed that the fibres had diameters in the range 100–200 nm, leading to increased surface roughness, as assessed by white light interferometry. Bioactivity studies on PDLLA fibre coated Bioglass® substrates were carried out in simulated body fluid (SBF) for 7, 14 and 28 days. It was found that mineralization of PDLLA fibres on 45S5 Bioglass® substrate (formation of hydroxyapatite) occurred after 7 days of immersion in SBF and full coverage of PDLLA fibres with HA nanocrystals was achieved after 14 days in SBF.CONCLUSION: The approach investigated represents a convenient method to develop a controlled mineralized fibrous topography on bioactive glass substrates for improved cell attachment, which can be exploited in bone tissue engineering applications. Copyright © 2009 Society of Chemical Industry
Sexual sadism, psychopathy, and recidivism in juvenile sexual murderers
Authors: Myers Wade C. , Chan Heng Choon (Oliver) , Vo Eleanor Justen , Lazarou Emily 
Published: October 2009

AbstractJuvenile sexual homicide is rare, occurring just 10–15 times a year in the United States. No study addressing how convicted juvenile sexual murderers adjust upon reentering the community exists. A safety concern, given this research gap, is the social movement afoot to abolish life sentences for juvenile offenders. If successful, then more of these offenders will be released back into society. This descriptive study examined: (1) the clinical findings and legal outcomes of 22 sexually homicidal juveniles following arrest; and (2) the relationship between post‐incarceration community adjustment and the variables of sexual sadism and psychopathy. All 22 offenders were tried in adult court—59% received one or more life sentences. Conduct disorder, personality disorders, sexual sadism, and psychopathic traits were prevalent. Mean intelligence quotient was 103. Follow‐up community recidivism data was available for 11 cases: five (45%) remained free of further convictions for an average of 8.9 years, whereas six (55%) recidivated 4.4 years later on average. Recidivators had higher Hare Psychopathy Checklist‐Revised scores. Three of the six recidivators survived an average of 5.3 years before committing additional sexually homicidal acts (all three had sexual sadism). Thus, 27% of the follow‐up group evolved into serial sexual murderers. The remaining three recidivators committed non‐sexual offences. These findings have relevance to criminal investigations, courtroom sentencing, and treatment strategies. Copyright © 2009 John Wiley & Sons, Ltd.
Vertebrae in compression: Mechanical behavior of arches and centra in the gray smooth‐hound shark (Mustelus californicus)
Authors: Porter Marianne E. , Long John H. 
Published: October 2009

AbstractIn swimming sharks, vertebrae are subjected, in part, to compressive loads as axial muscles contract. We currently have no information about which vertebral elements, centra, arch cartilages, or both, actually bear compressive loads in cartilaginous vertebrae. To address this issue, the goal of this experiment was to determine the load‐bearing ability of arch and centrum cartilages in compression, to determine the material properties of shark vertebrae, and to document fracture patterns in the centra with and without the arches. Intact vertebrae and vertebrae with the arch cartilages experimentally removed (centra alone) were subjected to compressive loading to failure at a single strain rate. The maximum compressive forces sustained by the vertebrae and the centra are statistically indistinguishable. Thus we conclude that under these testing conditions the arch does not bear appreciable loads. Independent evidence for this conclusion comes from the fact that vertebrae fail in compression at the centra, and not at the arches. Overall, the results of these mechanical tests suggest that the neural arches are not the primary load‐bearing structure during axial compression. J. Morphol. 2010. © 2009 Wiley‐Liss, Inc.
Pre‐fractionation of rat liver cytosol proteins prior to mass spectrometry‐based proteomic analysis using tandem biomimetic affinity chromatography
Authors: Tan Qingqiao , Dong Dexian , Ye Long , Huo Chenxi , Huang Feiyun , Li Rongxiu 
Published: October 2009

AbstractEfficient and high resolution separation of the protein mixture prior to trypsin digestion and mass spectrometry (MS) analysis is generally used to reduce the complexity of samples, an approach that highly increases the probability of detecting low‐copy‐number proteins. Our laboratory has constructed an affinity ligand library composed of thousands of ligands with different protein absorbance effects. Structural differences between these ligands result in different non‐bonded protein–ligand interactions, thus each ligand exhibits a specific affinity to some protein groups. In this work, we first selected out several synthetic affinity ligands showing large band distribution differences in proteins absorbance profiles, and a tandem composition of these affinity ligands was used to distribute complex rat liver cytosol into simple subgroups. Ultimately, all the fractions collected from tandem affinity pre‐fractionation were digested and then analyzed by LC‐MS/MS, which resulted in high confidence identification of 665 unique rat protein groups, 1.8 times as many proteins as were detected in the un‐fractionated sample (371 protein groups). Of these, 375 new proteins were identified in tandem fractions, and most of the proteins identified in un‐fractionated sample (290, 80%) also emerged in tandem fractions. Most importantly, 430 unique proteins (64.7%) only characterized in specific fractions, indicating that the crude tissue extract was well distributed by tandem affinity fractionation. All detected proteins were bioinformatically annotated according to their physicochemical characteristics (such as MW, pI, GRAVY value, TM Helices). This approach highlighted the sensitivity of this method to a wide variety of protein classes. Combined usage of tandem affinity pre‐fractionation with MS‐based proteomic analysis is simple, low‐cost, and effective, providing the prospect of broad application in proteomics. Copyright © 2009 John Wiley & Sons, Ltd.
British Ice Sheet dynamics inferred from North Atlantic ice‐rafted debris records spanning the last 175 000 years
Authors: Hibbert Fiona D. , Austin William E. N. , Leng Melanie J. , Gatliff Robert W. 
Published: October 2009

AbstractSediment core MD04‐2822 from the Rockall Trough, northeast Atlantic, provides lithological evidence for the expansion of the British Ice Sheet (BIS) onto the Hebridean margin during both the penultimate (Marine Isotope Stage (MIS) 6/Wolstonian/Saalian) and last glaciation (Devensian/Weichselian). A composite chronology is constructed using: (i) the benthic foraminiferal oxygen isotope record, matched to an orbitally tuned stacked record of global ice volume (SPECMAP); (ii) the synchronisation of the planktonic foraminiferal (Neogloboquadrina pachyderma (sinistral)) and ITRAX XRF Ca records to the Greenland ice core (NGRIP) back to ca. 123 ka; and (iii) the synchronisation of the same N. pachyderma (sinistral)) and ITRAX XRF Ca records to the atmospheric methane record of the Antarctic ice core (EPICA Dome C) beyond 123 ka. The first offshore evidence for the expansion of the last BIS within MIS 4 is presented, suggesting extensive glaciation of northwestern Britain during the Devensian/Weichselian as early as 70 ka. The proximity of this long sediment core to the glaciated margin of northwestern Scotland makes it ideal to capture the ice‐rafted debris (IRD) signal of the BIS for the last 175 ka, via a continuous flux record of IRD. British Geological Survey © NERC 2009. All rights reserved.
Microwave‐Assisted Synthesis of Poly(L‐lactic acid) via Direct Melt Polycondensation Using Solid Super‐Acids
Authors: Cao Hai Lei , Wang Peng , Yuan Wei Bo 
Published: October 2009

AbstractA microwave‐assisted method of synthesizing high‐molecular‐weight PLA using SSA as green catalyst was developed. Yellowish PLA with $\overline M _{\rm v}$ above 2.0 × 104 g · mol−1 was obtained when the reaction was run at 260 °C within 60 min under microwave irradiation with 0.4 wt.‐% SSA. This method used only 10% of the energy consumption necessary for conventional heating, and the catalyst could be used five times without losing catalytic activity. The improvement in $\overline M _{\rm v}$ and the decrease in the energy consumption under microwave irradiation suggested that selective heating and hot spots effects played a crucial role. The method was shown to be a time‐saving, green and a promising way to lower the cost and spread the application of PLA.magnified image
Poly(allylamine)‐graft‐poly(N‐isopropylacrylamide)/Poly(styrene sulfonate) Sodium Salt Multilayers: Buildup, Wettability, and Mechanical Properties
Authors: Wang Feng , Li Linhui , Gao Changyou 
Published: October 2009

AbstractPoly(allylamine)‐graft‐poly(N‐isopropylacrylamide) (PAH‐g‐PNIPAAm)/poly(styrene sulfonate) sodium salt (PSS) multilayer films are prepared using electrostatic layer‐by‐layer assembly. Buildup of the PAH/PSS and PAH‐g‐PNIPAAm/PSS multilayers under different salt concentrations and different temperatures is compared by using ellipsometry and scanning force microscopy. All the film thicknesses increase linearly with the increase of layer number regardless of their assembly conditions. However, the average layer thickness of the PAH‐g‐PNIPAAm/PSS multilayers is larger than that of the PAH/PSS multilayers under the same assembling conditions. Their surfaces also become rougher and show higher water contact angles. In contrast to the apparent loss transition in the friction force curve of the PAH/PSS multilayers, the PAH‐g‐PNIPAAm/PSS multilayers with PAH‐g‐PNIPAAm as the outmost layer do not undergo a pressure‐induced glass transition in water. Nanoindentation tests show that the elastic modulus of the PAH‐g‐PNIPAAm/PSS multilayers is only 75% of that of the PAH/PSS multilayers.magnified image
Advances in Dielectric Elastomers for Actuators and Artificial Muscles
Authors: Brochu Paul , Pei Qibing 
Published: October 2009

AbstractA number of materials have been explored for their use as artificial muscles. Among these, dielectric elastomers (DEs) appear to provide the best combination of properties for true muscle‐like actuation. DEs behave as compliant capacitors, expanding in area and shrinking in thickness when a voltage is applied. Materials combining very high energy densities, strains, and efficiencies have been known for some time. To date, however, the widespread adoption of DEs has been hindered by premature breakdown and the requirement for high voltages and bulky support frames. Recent advances seem poised to remove these restrictions and allow for the production of highly reliable, high‐performance transducers for artificial muscle applications.magnified image
Self‐association promoted conformational transition of (3R,4S,8R,9R)‐9‐[(3,5‐bis(trifluoromethyl)phenyl))‐thiourea](9‐deoxy)‐epi‐cinchonine
Authors: Király Péter , Soós Tibor , Varga Szilárd , Vakulya Benedek , Tárkányi Gábor 
Published: October 2009

AbstractThe conformational diversity of the (3R,4S,8R,9R)‐9‐[(3,5‐bis(trifluoromethyl)phenyl))‐thiourea](9‐deoxy)‐epi‐cinchonine organocatalyst is discussed. Low‐temperature NMR experiments confirmed a self‐association process, which promotes the quinoline rotation between two intramolecularly hydrogen‐bonded monomeric conformers of the catalyst. The balanced population of the coexisting monomeric and dimeric species allowed us to conduct a structural study of a rather complex conformational dynamics of the pure catalyst. The study is extended by a comparison with other members of the bifunctional amine‐thiourea organocatalyst family. Changes in the molecular structure of the catalysts influence the interplay between intra‐ and intermolecular hydrogen bonding, and yield different extent of catalyst self‐association. By assessing the conformation of the individual states, we established the thermodynamic model of a self‐association promoted conformational transition. Copyright © 2009 John Wiley & Sons, Ltd.
A Simplified Comprehensive Kinetic Scheme for Modeling of Ethylene/1‐butene Copolymerization Using Ziegler‐Natta Catalysts
Authors: Ahmadi Mostafa , Nekoomanesh Mehdi , Arabi Hassan 
Published: October 2009

AbstractA simplified kinetic scheme of eythylene/α‐olefin copolymerization has been developed by adding reactions responsible for the unusual kinetic behavior to a general mechanism. The estimation of rate constants has been simplified by making physically meaningful initial guesses. Rate constants affecting yield, MWD and comonomer content have been estimated separately. Experiments were designed to investigate the effects of each rate constant independently. The obtained rate constants show that the sites which are responsible for formation of short chains with higher 1‐butene content are more active at the beginning of polymerization, while the sites which are responsible for formation of longer chains with lower 1‐butene units are more active at the final stages of polymerization.magnified image