bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of a compressible laminar boundary layer to free-stream vortical disturbances
Authors: RICCO PIERRE , WU XUESONG 
Published: August 2007

As a first step towards understanding the role of free-stream turbulence in laminar–turbulent transition, we calculate the fluctuations induced by free-stream vortical disturbances in a compressible laminar boundary layer. As with the incompressible case investigated by Leibet al. (J. Fluid Mech. vol. 380, 1999, p. 169), attention is focused on components with long streamwise wavelength. The boundary-layer response is governed by the linearized unsteady boundary-region equations in the typical streamwise region where the local boundary-layer thickness δ* iscomparable with the spanwise length scale Λ of the disturbances. The compressible boundary-region equations are solved numerically for a single Fourier component to obtain the boundary-layer signature. The root-mean-square of the velocity and mass-flux fluctuations induced by a continuous spectrum of free-stream disturbances are computed by an appropriate superposition of the individual Fourier components.Low-frequency vortical disturbances penetrate into the boundary layer to form slowly modulating streamwise-elongated velocity streaks. In the compressible regime, vortical disturbances are found to induce substantial temperature fluctuations so that ‘thermalstreaks’ also form. They may have a significant effect on the secondary instability. The calculations indicate that for a vortical disturbance with a relatively large Λ, the induced boundary-layer fluctuation ultimately evolves into an amplifying wave. This is due to a receptivity mechanism, in which a vortical disturbance first excites a decaying quasi-three-dimensional Lam–Rott eigensolution. The latter then undergoes wavelength shortening to generate a spanwise pressure gradient, which eventually converts the Lam–Rott mode into an exponentially growing mode. The latter is recognized to bea highly oblique Tollmien–Schlichting wave. A parametric study suggests that this receptivity mechanism could be significant when the free-stream Mach number is larger than 0.8.
Sound generated by instability wave/shock-cell interaction in supersonic jets
Authors: RAY PRASUN K. , LELE SANJIVA K. 
Published: August 2007

Broadband shock-associated noise is an important component of the overall noise generated by modern airplanes. In this study, sound generated by the weakly nonlinear interaction between linear instability waves and the shock-cell structure in supersonic jets is investigated numerically in order to gain insight into the broadband shock-noise problem. The model formulation decomposes the overall flow into a mean flow, linear instability waves, the shock-cell structure and shock-noise. The mean flow is obtained by solving RANSequations with a k-ε model. Locally parallel stability equations are solved for the shock structure, and linear parabolized stability equations are solved for the instability waves. Then, source terms representing the instability wave/shock-cell interaction are assembled and the inhomogeneous linearized Euler equations are solved for the shock-noise.Three cases are considered, a cold under-expanded Mj = 1.22 jet, a hot under-expanded Mj = 1.22 jet, and a cold over-expanded Mj = 1.36 jet.Shock-noise computations are used to identify and understand significant trends in peak sound amplitudes and radiation angles. The peak sound radiation angles are explained well with the Mach wave model of Tam & Tanna J. Sound Vib. Vol. 81, 1982, p. 337). The observed reduction of peak sound amplitudes with frequency correlates well with the corresponding reduction of instability wave growth with frequency. However, in order to account for variation of sound amplitude for different azimuthal modes, the radial structure of the instability waves must be considered in additionto streamwise growth. The effect of heating on the Mj = 1.22 jet is shown to enhance the sound radiated due to the axisymmetric instability waves while the other modesare relatively unaffected. Solutions to a Lilley–Goldstein equation show that soundgenerated by ‘thermodynamic’ source terms is small relative to sound from ‘momentum’ sources though heating does increase the relative importance of the thermodynamic source. Furthermore, heating preferentially amplifies sound associated with the axisymmetric modes owing to constructive interference between sound from the momentumand thermodynamic sources. However, higher modes show destructive interference between these two sources and are relatively unaffected by heating.
Molecular epidemiology with subtype analysis ofCryptosporidiumin calves in Belgium
Authors: GEURDEN T. , BERKVENS D. , MARTENS C. , CASAERT S. , VERCRUYSSE J. , CLAEREBOUT E. 
Published: August 2007

SUMMARYThe prevalence ofCryptosporidiumin calves younger than 10 weeks was estimated in a cross-sectional epidemiological study on 100 dairy (n=499) and 50 beef (n=333) farms in East Flanders (Belgium), using a previously evaluated immunofluorescence assay (Merifluor®). The calf prevalence was 37% (95% Probability Interval (PI): 7–70%) in dairy calves and 12% (95% PI: 1–30%) in beef calves. To elucidate the genetic diversity, theCryptosporidium18S ribosomal DNA and the 70 kDa heat shock protein gene were targeted. In the majority of the samplesC. parvumwas present, althoughC. boviswas also identified, all but one in calves older than 1 month. The porcine-specificC. suiswas identified in 1 beef calf. Subtyping ofC. parvumpositive isolates by sequence analysis of the 60 kDa glycoprotein gene indicated the presence of 4 allele IIa subtypes, along with 1 subtype IIdA22G1. The subtype IIaA15G2R1 was most prevalent, next to subtype IIaA13G2R1 and IIaA16G2R1, and a new subtype IIaA14G2R1. The results of the present study indicate a high prevalence ofCryptosporidiuminfections in calves in Belgium and confirm that these calves should be considered as a potential zoonotic reservoir for human infections.
Genetic fingerprinting and identification of differentially expressed genes in isolates ofLeishmania donovanifrom Indian patients of post-kala-azar dermal leishmaniasis
Authors: SUBBA RAJU B. V. , SINGH R. , SREENIVAS G. , SINGH S. , SALOTRA P. 
Published: August 2007

SUMMARYPost-kala-azar dermal leishmaniasis (PKDL) is an unusual dermatosis that develops as a sequel in 5–15% of cured cases of kala-azar (KA) after months or years of treatment in India. Molecular differences are reported to exist between the KA and PKDL isolates which may underlie the diversity in clinical manifestations of the disease. Here, arbitrary primed-PCR (AP-PCR) has been used for genetic fingerprinting of parasite isolates from dermal lesions of PKDL patients (n=14) and compared with bone-marrow derived parasites from KA patients (n=3). All isolates showed an identical AP-PCR pattern with 4 arbitrary primers. Further, AP-PCR was exploited to identify the stage regulated genes of the parasite. Six polymorphic fragments were identified in PKDL in comparison with KA isolates, and were subjected to Northern blot analysis. Five polymorphic fragments represented transcribed sequences; 4 out of 5 drew differential expression in pro- and amastigote stages, although the expression was comparable between PKDL and KA isolates. The study led to the identification of genes, which exhibit stage-regulated expression inLeishmania donovaniderived from PKDL or KA patients, including a putative phosphodiesterase, DEAD box RNA helicase, iron superoxide dismutase b (fesodb) and a hypothetical protein. Demonstration of transcripts of DEAD box RNA helicase in PKDL and KA diseased tissues implicates its role in disease pathogenesis.
Conductance and amantadine binding of a pore formed by a lysine‐flanked transmembrane domain of SARS coronavirus envelope protein
Authors: Torres Jaume , Maheswari Uma , Parthasarathy Krupakar , Ng Lifang , Liu Ding Xiang , Gong Xiandi 
Published: August 2007

AbstractThe coronavirus responsible for the severe acute respiratory syndrome (SARS‐CoV) contains a small envelope protein, E, with putative involvement in host cell apoptosis and virus morphogenesis. It has been suggested that E protein can form a membrane destabilizing transmembrane (TM) hairpin, or homooligomerize to form a regular TM α‐helical bundle. We have shown previously that the topology of the α‐helical putative TM domain of E protein (ETM), flanked by two lysine residues at C and N termini to improve solubility, is consistent with a regular TM α‐helix, with orientational parameters in lipid bilayers that are consistent with a homopentameric model. Herein, we show that this peptide, reconstituted in lipid bilayers, shows sodium conductance. Channel activity is inhibited by the anti‐influenza drug amantadine, which was found to bind our preparation with moderate affinity. Results obtained from single or double mutants indicate that the organization of the transmembrane pore is consistent with our previously reported pentameric α‐helical bundle model.
Modeling mutations in protein structures
Authors: Feyfant Eric , Sali Andrej , Fiser András 
Published: August 2007

AbstractWe describe an automated method for the modeling of point mutations in protein structures. The protein is represented by all non‐hydrogen atoms. The scoring function consists of several types of physical potential energy terms and homology‐derived restraints. The optimization method implements a combination of conjugate gradient minimization and molecular dynamics with simulated annealing. The testing set consists of 717 pairs of known protein structures differing by a single mutation. Twelve variations of the scoring function were tested in three different environments of the mutated residue. The best‐performing protocol optimizes all the atoms of the mutated residue, with respect to a scoring function that includes molecular mechanics energy terms for bond distances, angles, dihedral angles, peptide bond planarity, and non‐bonded atomic contacts represented by Lennard‐Jones potential, dihedral angle restraints derived from the aligned homologous structure, and a statistical potential for non‐bonded atomic interactions extracted from a large set of known protein structures. The current method compares favorably with other tested approaches, especially when predicting long and flexible side‐chains. In addition to the thoroughness of the conformational search, sampled degrees of freedom, and the scoring function type, the accuracy of the method was also evaluated as a function of the flexibility of the mutated side‐chain, the relative volume change of the mutated residue, and its residue type. The results suggest that further improvement is likely to be achieved by concentrating on the improvement of the scoring function, in addition to or instead of increasing the variety of sampled conformations.
Solution structure of recombinant somatomedin B domain from vitronectin produced in Pichia pastoris
Authors: Kjaergaard Magnus , Gårdsvoll Henrik , Hirschberg Daniel , Nielbo Steen , Mayasundari Anand , Peterson Cynthia B. , Jansson Anna , Jørgensen Thomas J.D. , Poulsen Flemming M. , Ploug Michael 
Published: August 2007

AbstractThe cysteine‐rich somatomedin B domain (SMB) of the matrix protein vitronectin is involved in several important biological processes. First, it stabilizes the active conformation of the plasminogen activator inhibitor (PAI‐1); second, it provides the recognition motif for cell adhesion via the cognate integrins (αvβ3, αvβ5, and αIIbβ3); and third, it binds the complex between urokinase‐type plasminogen activator (uPA) and its glycolipid‐anchored receptor (uPAR). Previous structural studies on SMB have used recombinant protein expressed in Escherichia coli or SMB released from plasma‐derived vitronectin by CNBr cleavage. However, different disulfide patterns and three‐dimensional structures for SMB were reported. In the present study, we have expressed recombinant human SMB by two different eukaryotic expression systems, Pichia pastoris and Drosophila melanogaster S2‐cells, both yielding structurally and functionally homogeneous protein preparations. Importantly, the entire population of our purified, recombinant SMB has a solvent exposure, both as a free domain and in complex with PAI‐1, which is indistinguishable from that of plasma‐derived SMB as assessed by amide hydrogen (1H/2H) exchange. This solvent exposure was only reproduced by one of three synthetic SMB products with predefined disulfide connectivities corresponding to those published previously. Furthermore, this connectivity was also the only one to yield a folded and functional domain. The NMR structure was determined for free SMB produced by Pichia and is largely consistent with that solved by X‐ray crystallography for SMB in complex with PAI‐1.
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme‐inhibitor complexes? Implications for enzyme design
Authors: DeChancie Jason , Clemente Fernando R. , Smith Adam J.T. , Gunaydin Hakan , Zhao Yi‐Lei , Zhang Xiyun , Houk K.N. 
Published: August 2007

AbstractQuantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate‐determining transition state plus the catalytic groups modeled by side‐chain mimics was optimized using B3LYP/6–31G(d) or, in one case, HF/3–21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X‐ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate–active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 Å from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 Å. The implications for computational enzyme design are discussed.
Structure–activity study of the antibacterial peptide fallaxin
Authors: Nielsen Sandra L. , Frimodt‐Møller Niels , Kragelund Birthe B. , Hansen Paul R. 
Published: August 2007

AbstractFallaxin is a 25‐mer antibacterial peptide amide, which was recently isolated from the West Indian mountain chicken frog Leptodactylus fallax. Fallaxin has been shown to inhibit the growth of several Gram‐negative bacteria including Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Here, we report a structure–activity study of fallaxin based on 65 analogs, including a complete alanine scan and a full set of N‐ and C‐terminal truncated analogs. The fallaxin analogs were tested for hemolytic activity and antibacterial activity against methicillin‐resistant Staphylococcus aureus (MRSA), vancomycin‐intermediate resistant S. aureus, (VISA), methicillin‐susceptible S. aureus (MSSA), E. coli, K. pneumoniae, and P. aeruginosa. We identified several analogs, which showed improved antibacterial activity compared to fallaxin. Our best candidate was FA12, which displayed MIC values of 3.12, 25, 25, and 50 μM against E. coli, K. pneumoniae, MSSA, and VISA, respectively. Furthermore, we correlated the antibacterial activity with various structural parameters such as charge, hydrophobicity 〈H〉, mean hydrophobic moment 〈μH〉, and α‐helicity. We were able to group the active and inactive analogs according to mean hydrophobicity 〈H〉 and mean hydrophobic moment 〈μH〉. Far‐UV CD‐spectroscopy experiments on fallaxin and several analogs in buffer, in TFE, and in membrane mimetic environments (small unilamellar vesicles) indicated that a coiled‐coil conformation could be an important structural trait for antibacterial activity. This study provides data that support fallaxin analogs as promising lead structures in the development of new antibacterial agents.
The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector‐binding mode
Authors: Gao Yong‐Gui , Yao Min , Itou Hiroshi , Zhou Yong , Tanaka Isao 
Published: August 2007

AbstractAmong the transcription factors, the helix‐turn‐helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N‐terminal DNA‐binding domain and a C‐terminal effector‐binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120–130 residues with about 50 residues located in the C‐terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C‐terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA‐binding domain containing a winged HTH motif in the N terminus and two helices (α4 and α5) with a fishhook‐shaped arrangement in the C terminus. Helices α4 and α5 of two monomers intertwine together to form a novel homodimer assembly. The effector‐accommodating pocket with 2‐methyl‐2,4‐pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD‐free and ‐bound in the proposed effector‐binding pocket) were solved. The structural variations have implications regarding how the effector‐induced conformational change modulates DNA affinity for YtrA family members.
A metacommunity‐scale comparison of species‐abundance distribution models for plant communities of eastern Australia
Authors: Forster Michael A. , Warton David I. 
Published: August 2007

Various models of the species‐abundance distribution (SAD) have been proposed to fit empirically derived data however there is no general consensus as to which model provides the best fit. Further, the zero‐sum multinomial SAD model (ZSM) was proposed as a metacommunity model, yet it has not previously been fitted at the metacommunity scale. We note that SAD models based on compound lognormal distributions (such as the Poisson‐lognormal, PLN, and the negative binomial‐lognormal models, NBLN) can also be thought of as metacommunity models, and we compare these with the ZSM when fitted as metacommunity models to SADs of related communities.We collected five datasets in the Sydney Basin, eastern Australia, representing five different types of subtropical/temperate plant communities ranging from closed warm‐temperate rainforest to open wet sclerophyll forest to dry sclerophyll woodland. For each type of plant community, five local communities were identified across the Sydney Basin, and SAD data collected in five randomly placed 0.2‐ha quadrats at each local community. Analysis was performed at two levels: all abundance data from each local community were pooled across each metacommunity and analysed as a single pooled community; and a metacommunity model was fitted to all five local communities of a community type, simultaneously. For the pooled data, we considered the negative‐binomial (NB) and the log‐series (LS) models in addition to ZSM, PLN and NBLN. All five models performed similarly, however the LS had a better fit to three pooled communities and the ZSM and PLN to the remaining two communities. By contrast, the ZSM performed statistically better against the PLN and NBLN when considered as a metacommunity model. We conclude that the ZSM generally provides a more reliable null model for metacommunity abundance data than the lognormal model.
Prospective cohort study of body mass index in adolescence and death from stomach cancer in Japan
Authors: Tanaka Tagayasu , Nagata Chisato , Oba Shino , Takatsuka Naoyoshi , Shimizu Hiroyuki 
Published: August 2007

We investigated the association between body mass index (BMI) values and the risk of death from stomach cancer later in life. From 1992 to 2000, 28 443 participants (13 211 men and 15 232 women) were followed, and 129 deaths from stomach cancer (86 men and 43 women) occurred. BMI (BMI at the baseline) and BMI20y(BMI at age 20 years) were obtained by questionnaire at the beginning of the study. Men in the middle and highest tertiles of BMI20yhad a higher risk of death from stomach cancer than those in the lowest tertile (after controlling for covariates, hazard ratio [HR] = 2.73 with 95% confidence interval [CI] 1.26–5.89 for the middle tertile; HR = 2.15 with 95% CI 0.97–4.73 for the highest tertile), although there was no significant trend (P = 0.30). Likewise, women in the middle and highest tertiles of BMI20yhad an increased risk of death from stomach cancer (HR = 5.17 with 95% CI 1.50–17.87 for the middle tertile; HR = 4.22 with 95% CI 1.18–15.05 for the highest tertile;Pfor trend = 0.05). The analysis of BMI at the baseline did not show a significant relationship with the risk of death from stomach cancer. These results suggest that a high BMI20yis associated with an increased risk of death from stomach cancer. (Cancer Sci2007; 98: 1785–1789)
Induction of MHC class I molecule cell surface expression and epigenetic activation of antigen‐processing machinery components in a murine model for human papilloma virus 16‐associated tumours
Authors: Manning Jasper , Indrova Marie , Lubyova Barbora , Pribylova Hana , Bieblova Jana , Hejnar Jiri , Simova Jana , Jandlova Tana , Bubenik Jan , Reinis Milan 
Published: August 2007

SummaryEpigenetic events play an important role in tumour progression and also contribute to escape of the tumour from immune surveillance. In this study, we investigated the up‐regulation of major histocompatibility complex (MHC) class I surface expression on tumour cells by epigenetic mechanisms using a murine tumour cell line expressing human E6 and E7 human papilloma virus 16 (HPV16) oncogenes and deficient in MHC class I expression, as a result of impaired antigen‐presenting machinery (APM). Treatment of the cells with the histone deacetylase inhibitor Trichostatin A, either alone or in combination with the DNA demethylating agent 5‐azacytidine, induced surface re‐expression of MHC class I molecules. Consequently, the treated cells became susceptible to lysis by specific cytotoxic T lymphocytes. Further analysis revealed that epigenetic induction of MHC class I surface expression was associated with the up‐regulation of APM genes [transporter associated with antigen processing 1 (TAP‐1), TAP‐2, low‐molecular‐mass protein 2 (LMP‐2) and LMP‐7]. The results demonstrate that expression of the genes involved in APM are modulated by epigenetic mechanisms and suggest that agents modifying DNA methylation and/or histone acetylation have the potential to change the effectiveness of antitumour immune responses and therapeutically may have an impact on immunological output.