bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extent of N‐terminal modifications in cytosolic proteins from eukaryotes
Authors: Martinez Aude , Traverso José A. , Valot Benoît , Ferro Myriam , Espagne Christelle , Ephritikhine Geneviève , Zivy Michel , Giglione Carmela , Meinnel Thierry 
Published: July 2008

AbstractMost proteins in all organisms undergo crucial N‐terminal modifications involving N‐terminal methionine excision, N‐α‐acetylation or N‐myristoylation (N‐Myr), or S‐palmitoylation. We investigated the occurrence of these poorly annotated but essential modifications in proteomes, focusing on eukaryotes. Experimental data for the N‐terminal sequences of animal, fungi, and archaeal proteins, were used to build dedicated predictive modules in a new software. In vitro N‐Myr experiments were performed with both plant and animal N‐myristoyltransferases, for accurate prediction of the modification. N‐terminal modifications from the fully sequenced genome of Arabidopsis thaliana were determined by MS. We identified 105 new modified protein N‐termini, which were used to check the accuracy of predictive data. An accuracy of more than 95% was achieved, demonstrating (i) overall conservation of the specificity of the modification machinery in higher eukaryotes and (ii) robustness of the prediction tool. Predictions were made for various proteomes. Proteins that had undergone both N‐terminal methionine (Met) cleavage and N‐acetylation were found to be strongly overrepresented among the most abundant proteins, in contrast to those retaining their genuine unblocked Met. Here we propose that the nature of the second residue of an ORF is a key marker of the abundance of the mature protein in eukaryotes.
Two‐dimensional immune profiles improve antigen microarray‐based characterization of humoral immunity
Authors: Papp Krisztián , Szekeres Zsuzsanna , Erdei Anna , Prechl József 
Published: July 2008

AbstractAntigen arrays are becoming widely used tools for the characterization of the complexity of humoral immune responses. Current antibody profiling techniques provide modest and indirect information about the effector functions of the antibodies that bind to particular antigens. Here we introduce an antigen array‐based approach for obtaining immune profiles reflecting antibody functionality. This technology relies on the parallel measurement of antibody binding and complement activation by features of the array. By comparing sera from animals immunized against the same antigen under different conditions, we show that identifying the position of an antigen in a 2‐D space, derived from antibody binding and complement deposition, permits distinction between immune profiles characterized by diverse antibody isotype distributions. Additionally, the technology provides a biologically interpretable graphical representation of the relationship between antigen and host. Our data suggest that 2‐D immune profiling could enrich the data obtained from proteomic scale serum profiling studies.
Bioengineering a humanized acne microenvironment model: Proteomics analysis of host responses to Propionibacterium acnes infection in vivo
Authors: Nakatsuji Teruaki , Shi Yang , Zhu Wenhong , Huang Cheng‐Po , Chen Yun‐Ru , Lee Dong‐Youn , Smith Jeffery W. , Zouboulis Christos C. , Gallo Richard L. , Huang Chun‐Ming 
Published: July 2008

AbstractAcne is a human disease of the sebaceous hair follicle. Unlike humans, most animals produce little or no triglycerides in hair follicles to harbor Propionibacterium acnes a fact that has encumbered the development of novel treatments for acne lesions. Although genetic mutant mice with acne‐like skins have been used for screening anti‐acne drugs, the mice generally have deficits in immune system that turns out to be inappropriate to generate antibodies for developing acne vaccines. Here, we employed a bioengineering approach using a tissue chamber integrated with a dermis‐based cell‐trapped system (DBCTS) to mimic the in vivo microenvironment of acne lesions. Human sebocyte cell lines were grown in DBCTS as a scaffold and inserted into a perforated tissue chamber. After implantation of a tissue chamber bearing human sebocytes into ICR mice, P. acnes or PBS was injected into a tissue chamber to induce host immune response. Infiltrated cells such as neutrophils and macrophages were detectable in tissue chamber fluids. In addition, a proinflammatory cytokine macrophage‐inflammatory protein‐2 (MIP‐2) was elevated after P. acnes injection. In tissue chamber fluids, 13 proteins including secreted proteins and cell matrix derived from mouse, human cells or P. acnes were identified by proteomics using isotope‐coded protein label (ICPL) coupled to nano‐LC‐MS analysis. After P. acnes infection, four proteins including fibrinogen, α polypeptide, fibrinogen β chain, S100A9, and serine protease inhibitor A3K showed altered concentrations in the mimicked acne microenvironment. The bioengineered acne model thus provides an in vivo microenvironment to study the interaction of host with P. acnes and offers a unique set‐up for screening novel anti‐acne drugs and vaccines.
Profiling the proteome dynamics during the cell cycle of human hepatoma cells
Authors: Hsieh Sen‐Yung , Zhuang Feng‐Hui , Wu Yi‐Ting , Chen Jen‐Kun , Lee Yun‐Lin 
Published: July 2008

AbstractDeregulation of cell cycle leads to cell transformation and cancer development. Here we present profiling the proteome dynamics using 2‐DE and constructing the associated functional networks during the cell cycle of human hepatoma cells, Mahlavu. The protein dynamics was validated by hierarchical clustering analysis on the proteome, and by Northern blot assays on the selected 14‐3‐3 proteins. Of the 2665 protein spots, 201 with variation coefficient of expression dynamics >20% throughout the cell cycle were subjected to analysis. Degree of the global protein dynamics was phase dependent with the greatest in transitional phases of S/G2, G2/M, and G1/S. Concurrence of pathways coordinating cell‐cycle progression versus arrest, and/or pathways regulating apoptosis versus antiapoptosis was always identified during the cell cycle, suggesting the existence of counteracting mechanisms for intracellular homeostasis. Data mining of the results suggested that the key transcription factors in G0/G1, G1/S, S, and G2/M were p53 and SP1, c‐Myc, c‐Myc and p53, and YY1 and c‐Jun, respectively. Our findings for the first time provide insights into the regulation of mammalian cell‐cycle progression at the proteome level, and grant a model to study disease mechanisms and to discover therapeutic targets for anticancer therapy.
Interfacial friction of thin PDMS network films
Authors: Landherr Lucas J. T. , Zhang Qing , Cohen Claude , Archer Lynden A. 
Published: July 2008

AbstractThis study focuses on developing dry, surface‐tethered polymeric lubricant coatings capable of significantly decreasing friction and wear of nano‐ and micrometer scale machines. Vinyl‐terminated polydimethylsiloxane chains are spin‐coated with a crosslinking agent and platinum catalyst onto silicon wafers functionalized with a self‐assembling monolayer containing reactive vinyl groups. Lateral force microscopy (LFM) measurements employing a bead probe are used to quantify the coefficient of friction (COF) and adhesion characteristics of the PDMS‐SAM surface tethered networks. The combined polymer network and SAM layer manifest extremely low friction coefficients, μ = 4 × 10−3, which is nearly one order of magnitude lower than the friction coefficient of the bare silicon substrate. The lowest friction forces are measured using silicon substrates covered with nanometer thick, peroxide crosslinked PDMS networks; though poorly crosslinked, these networks display COFs as much as ten‐times lower than a solitary SAM coating layer. Micrometer thick end‐linked optimal networks also manifest attractive interfacial friction properties, with COFs approximately three times larger than the thinner, imperfect networks. These observations are discussed in terms of the structure of the polymer networks and the role of adhesion forces on interfacial friction. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1773–1787, 2008
Understanding the causes of depression among prostate cancer patients: development of the effects of prostate cancer on lifestyle questionnaire
Authors: Sharpley Christopher F. , Bitsika Vicki , Christie David R. H. 
Published: July 2008

AbstractObjective: Depression among prostate cancer patients remains a major source of distress for them and their families, has been linked with suicide, and has been shown to contribute to poorer longterm treatment outcomes. Most psychological assessment strategies focus upon the presence of depressive symptomatology without identifying the specific causal antecedents that lead to depression among this patient group, although this underlies effective individually‐oriented treatment planning and delivery.Method: 150 prostate cancer patients completed self reports on anxiety, depression and lifestyle changes that they had experienced as a result of receiving a diagnosis of, and treatment for their cancer. The principal instrument being investigated was a measure of 50 lifestyle changes that had been developed from previous interviews with prostate cancer patients.Results: Data indicated significant relationships between depression scores and the frequency of unpleasant lifestyle changes and the ratings that participants gave to these changes, supporting a model of depression as an adaptive withdrawal from noxious stimuli and environments. Psychometric data provided a method of deleting several items so that a clinical analysis and a research scale of 36 items was developed for use with prostate cancer patients.Conclusion: Implications for treatment are discussed in terms of accurate identification of antecedents that lead to a further understanding of depression as an ‘adaptive’ response of active withdrawal from noxious environments. Copyright © 2008 John Wiley & Sons, Ltd.
Adding flavor on the Higgs branch
Authors: Areán D. 
Published: July 2008

AbstractWe study the holographic dual of the Higgs branch of 𝒩 = 4 SYM in four dimensions coupled to quenched fundamental matter. The fundamentals are added via flavor D7‐branes and the Higgs phase is obtained when the color D3‐branes and the flavor D7‐branes recombine with each other. The holographic dual consists of D7‐brane probes in the background generated by the color D3‐branes. In this supergravity dual the Higgs phase is realized by switching on a selfdual field strength on the worldvolume of the D7‐branes. A complementary microscopic description in terms of dielectric D3‐branes is also possible. This microscopic approach permits a better matching with the dual field theory analysis. Finally, the meson mass spectrum is computed by studying the fluctuations of the flavor D7‐branes.
Geometric massive higher spins and current exchanges
Authors: Francia D. 
Published: July 2008

AbstractGeneralised Fierz‐Pauli mass terms allow to describe massive higher‐spin fields on flat background by means of simple quadratic deformations of the corresponding geometric, massless Lagrangians. In this framework there is no need for auxiliary fields. We briefly review the construction in the bosonic case, and study the interaction of these massive fields with external sources, computing the corresponding propagators. In the same fashion as for the massive graviton, but differently from theories where auxiliary fields are present, the structure of the current exchange is completely determined by the form of the mass term itself.
Constraints from F and D supersymmetry breaking in general supergravity theories
Authors: Gomez‐Reino M. , Scrucca C.A. 
Published: July 2008

AbstractWe study the conditions under which a generic supergravity model involving chiral and vector multiplets can admit vacua with spontaneously broken supersymmetry and realistic cosmological constant. We find that the existence of such viable vacua implies some constraints involving the curvature tensor of the scalar geometry and the charge and mass matrices of the vector fields, and also that the vector of F and D auxiliary fields defining the Goldstino direction is constrained to lie within a certain domain. We illustrate the relevance of these results through some examples and also discuss the implications of our general results on the dynamics of moduli fields in string models. This contribution is based on [1–3].
Thermal and quantum superstring cosmologies
Authors: Catelin‐Jullien T. , Kounnas C. , Partouche H. , Toumbas N. 
Published: July 2008

AbstractWe consider four dimensional heterotic string backgrounds for which supersymmetry is spontaneously broken via the Scherk‐Schwarz mechanism on an internal spatial cycle and by finite temperature effects. We concentrate on initially flat backgrounds with N = 4 and N = 2 amount of supersymmetry. Thermal and quantum corrections give rise to a non‐trivial cosmological evolution. We show that these corrections are under control and calculable due to the underlying no‐scale structure of the effective supergravity theory. The effective Friedmann‐Hubble equation involves a radiation term ∼1/a4 and a curvature term ∼1/a2 , whose coefficients are functions of ratio of the gravitino mass scale to the temperature.
The landscape of string theory (orientifolds and their statistics, D‐brane instantons, AdS4 domain walls and black holes)
Authors: Lüst D. 
Published: July 2008

AbstractIn this talk we discuss various aspects of the string landscape: D‐brane model building and their statistics, the generation of non‐perturbative superpotentials from D‐brane instantons, moduli stabilization by fluxes and non‐perturbative effects, the relation between flux vacua and BPS black holes, the construction of AdS4 vacua and related domain wall solutions, transitions between flux vacua and also some constraints on the string landscape from black hole considerations.
On cancellations of ultraviolet divergences in supergravity amplitudes
Authors: Bjerrum‐Bohr N.E.J. , Vanhove P. 
Published: July 2008

AbstractConcrete calculations have pointed out that amplitudes in perturbative gravity exhibit unanticipated cancellations taming their ultraviolet behaviour independently of supersymmetry. Similar ultraviolet behaviour of 𝒩 = 4 super‐Yang‐Mills and 𝒩 = 8 maximal supergravity has explicitly been observed until three loops. The cancellations can be connected to two manifest features of gravitational theories: firstly gauge invariance from diffeomorphism symmetries and secondly that amplitudes are colourless and exhibits crossing symmetry. We will discuss these two properties in turn as well as the rôle of supersymmetry and string theory dualities in the structure of multiloop amplitudes in supergravity.
Deconstructing the Little Hagedorn holography
Authors: Fuertes C.A. 
Published: July 2008

AbstractWe study aspects of the thermodynamics of Little String Theory, using its geometrical definition in critical ten‐dimensional string theory. We find that bulk radiation effects tend to screen the Hagedorn behaviour of the theory, in contrast to the behaviour in the AdS system background. The resulting density of states of the system, when stable, is described by a seven‐dimensional nonrelativistic gas. This requires modifications of the holographic Little Hagedorn picture. Using deconstructions we suggest such modifications. The model is embedded into a system which has an ultraviolet fixed point with an AdS description. Upon investigation the thermodynamical properties of these UV completed models, it is found that the Hagedorn regime survives in a finite band of superheated states that eventually decay into the plasma phase of the conformal field theory that serves as UV regulator. This is manifested in a first‐order phase transition that is driven by radiative corrections.
Kaluza‐Klein consistency and supersymmetric AdS solutions
Authors: Gauntlett J.P. , Colgáin E.Ó , Varela O. 
Published: July 2008

AbstractWe discuss the conjecture that for any supersymmetric solution of D = 10 or D = 11 supergravity consisting of a warped product of a d + 1‐dimensional anti‐de‐Sitter space with a Riemannian manifold M, there is a consistent Kaluza‐Klein truncation on M to a gauged supergravity theory in d + 1‐dimensions for which the fields are dual to those in the superconformal current multiplet of the d‐dimensional dual SCFT. This means that any solution of the gauged supergravity theory can be uplifted on M to obtain an exact solution of D = 10 or D = 11 supergravity. We verify this conjecture for the most general class of supersymmetric AdS5 solutions of D = 11 supergravity by constructing an explicit KK reduction ansatz to minimal gauged supergravity in D = 5, at the level of the bosonic fields.
An evaluation of PCR primer sets used for detection of Propionibacterium acnes in prostate tissue samples
Authors: Sfanos Karen S. , Isaacs William B. 
Published: July 2008

AbstractBACKGROUNDMultiple studies have now shown that Propionibacterium acnes can be cultured from post‐prostatectomy derived prostate tissue samples. In contrast, both universal eubacterial 16S rDNA PCR and P. acnes‐specific 16S rDNA PCR have failed to detect this organism at a frequency similar to that of bacterial culture. A potential explanation for this discrepancy, proposed by Cohen et al., involves mismatches in 16S rDNA primer sets used for bacterial detection.METHODSThe sensitivity of both a previously published P. acnes‐specific primer set containing a potential mismatch and a new primer set with no mismatches was determined. Both primer sets were used to interrogate two sets of DNA samples derived from post‐prostatectomy prostate tissues that differed in the level of sterile precautions maintained during tissue collection.RESULTSThe number of P. acnes positive samples was associated with the sterility of the sample collection process. In all instances, positive samples were determined to reflect low cell numbers (<10 CFU).CONCLUSIONSAlthough the results of previous studies have shown that P. acnes is not the only organism potentially present in the prostates of prostate cancer patients, mismatches in PCR primer sets may have also influenced the sensitivity of P. acnes detection. When using PCR in determining the presence of P. acnes in the human prostate, care should be taken to establish the potential influence of exogenous contamination and, due to the sensitivity of the assay, samples exposed to the urethra during the collection process (prostatic secretions, TURP specimens) should not be used. Prostate 68: 1492–1495, 2008. © 2008 Wiley‐Liss, Inc.
Influence of 16S rDNA primer sequence mismatches on the spectrum of bacterial genera detected in prostate tissue by universal eubacterial PCR
Authors: Shannon Beverley A. , Cohen Ronald J. , Garrett Kerryn L. 
Published: July 2008

AbstractBACKGROUNDPropionibacterium sp. and Staphylococcus spp. are the most frequent bacteria cultured from prostatectomy specimens but are seldom detected by universal eubacterial PCR.MATERIALS AND METHODSWe obtained from GenBank representative 16S rRNA gene sequences from Propionibacterium sp., Staphylococcus spp. and from 34 bacterial genera that were recently detected in prostate tissues using universal eubacterial PCR. We compared these 16S rDNA sequences with the universal eubacterial 16S PCR primer sets chosen for detection of bacterial DNA in prostate tissues.RESULTSWe show that failure to detect DNA from Propionibacterium sp. and Staphylococcus spp. in prostate tissues is strongly associated with the presence of mismatches near the 3′ termini of the16S rDNA primer sets used.CONCLUSIONSThe choice of 16S PCR primers may play an important role in determining the spectrum of bacterial genera detected in prostate tissue by universal eubacterial PCR. Prostate 68: 1487–1491, 2008. © 2008 Wiley‐Liss, Inc.
Professional outcomes of internal migration by couples: evidence from France
Authors: Pailhé Ariane , Solaz Anne 
Published: July 2008

AbstractThis article examines the impact of internal migration on the labour‐market participation and earnings of couples in France. The analysis is based on longitudinal data from the French version of the European Community Household Panel. Controlling for self‐selection of migrants, the results show that household income falls after migration, as does women's likelihood of being employed. Controlling for labour‐market participation, migration has a positive impact on women's income, but not on men's. In France, mobility is quite scarce, especially for couples. One explanation is that migration is generally not profitable in terms of professional outcomes. The rigidity of the French labour market, associated with high unemployment, may explain both the difficulty and the limited benefits of moving as a couple, especially for the women who are often the ‘tied movers’. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation and characterization of TiO2 thin films grown by RF magnetron sputtering
Authors: Selmi M. , Chaabouni F. , Abaab M. , Rezig B. 
Published: July 2008

AbstractTitanium dioxide (TiO2) thin films were obtained by RF sputtering technique. The samples were deposited on glass and p‐ silicon substrates at an argon flow rate of 4.9 sccm and at room temperature during 4 h. In this work, the influences of RF power density and annealing temperature on properties of obtained thin films were investigated. The morphological, structural and optical properties were studied by Atomic Force Microscope (AFM), X‐ray Diffractometer and UV–VIS–NIR spectrophotometer respectively. A high transmission (about 80%) in the visible region, crystalline structure and a direct band gap (between 3.4 and 3.5 eV) were ob‐ served by the measurements. Thin films were annealed at different temperatures (from 300 to 500 °C) during 30 minutes in order to investigate the annealing effect on properties of TiO2 thin films. The refractive index and the roughness increase with increasing annealing temperature. The results of this work suggest that the properties of TiO2 thin films are sensitive to sputtering parameters. It is possible to obtain sputter‐deposited TiO2 films at room temperature, without using reactive oxygen, with a good predominance of anatase (101) structure after the annealing at 400°C. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lithographically patterned nanowire electrodeposition
Authors: Xiang Chengxiang , Thompson Michael A. , Yang Fan , Menke Erik J. , Yang Li‐Mei C. , Penner Reginald M. 
Published: July 2008

AbstractLithographically Patterned Nanowire Electrodeposition (LPNE) is a new nanofabrication technique in which photolithography is used to define the position of electrodeposited nanowires on the surface of a dielectric such as glass or oxidized silicon. In LPNE, a resist‐covered nickel film with a thickness of beween 6 and 100 nm is photopatterned. After development of the resist, the exposed nickel is dissolved in nitric acid under conditions that produce an “undercut” at the resist edges. This undercut functions as a horizontal trench into which metals (e.g., Au, Pt, Pd) can be electrodeposited using the exposed nickel edge present within this trench. As this trench is filled during electrodeposition, a nanowire with a precisely defined height and width is formed along the entire perimeter of the photoresist. LPNE nanowires can have minimum dimensions of 6 nm (h) x 20 nm (w) and lengths of more than 1 cm. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)