bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mining quorum sensing regulated proteins – Role of bacterial cell‐to‐cell communication in global gene regulation as assessed by proteomics
Authors: Eberl Leo , Riedel Katharina 
Published: March 2011

AbstractMany bacteria utilize cell‐to‐cell communication systems that rely on small diffusible signal molecules to monitor the size of their population in a process known as quorum sensing (QS). QS plays a central role in coordinating genes that are generally mediating prokaryotic interactions with its eukaryotic host. In pathogens, this form of gene regulation is, for instance, believed to ensure that the cells remain invisible to the immune system until the pathogen has reached a critical population density sufficient to overwhelm host defenses and to establish an infection. This review summarizes proteome analyses to identify QS‐regulated proteins focussing on Gram‐negative bacteria interacting with their eukaryotic hosts either as symbionts or as pathogens. In most studies, the power of comparative 2‐D PAGE coupled to MS analysis has been employed to recognize and identify QS‐controlled proteins. The high number of QS‐regulated proteins in the majority of the investigated species strongly supports the importance of QS as global regulatory system and suggests that it also operates via post‐transcriptional mechanisms. As QS has been proven to be a central regulator for the expression of pathogenic traits and biofilm formation in various opportunistic pathogens, it represents a highly attractive target for the development of novel antibacterial drugs. Proteomics has also been exploited to validate the target specificity of natural and synthetic QS inhibitors that have a great potential as alternative therapeutics for the treatment of bacterial infections.
Polymer thermal and acoustic properties using heterodyne detected transient grating technique
Authors: Amirkhani Masoud , Taschin Andrea , Cucini Riccardo , Bartolini Paolo , Leporini Dino , Torre Renato 
Published: March 2011

AbstractWe investigated the acoustic and thermal features of a polymeric system by a heterodyne detected transient grating technique. We studied two polymers characterized by different molecular weights. Transient grating experiments could reveal a reliable series of information on sound velocity, acoustic damping time, and thermal diffusion of the polymers. The temperature and molecular weight dependence of the polymer acoustic and thermal properties are reported. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Surface Modification of COC Microfluidic Devices: A Comparative Study of Nitrogen Plasma Treatment and its Advantages Over Argon and Oxygen Plasma Treatments
Authors: Roy Sunanda , Yue Chee Yoon 
Published: March 2011

AbstractControl of surface properties is very important in high performance microfluidic devices because appropriate functionalization of the surface of the microchannel helps to minimize adsorption of certain analytes thus improving its performance. In this regard, both the argon and oxygen plasma techniques have been used to improve the adaption of polymer surfaces to biological environments. However, the less common nitrogen plasma technique has not been used for surface modification of cyclic olefin copolymer (COC) in microfluidic applications. This paper presents a comparative study between the argon, oxygen, and nitrogen plasma treatments with the aim to identify the most suitable process for the development of a smart, disposable chip for the Bio‐MEMS application. The chemical and morphological changes of the plasma modified COC surfaces were characterized using X‐ray photoelectron spectroscopy, atomic force microscopy, and water contact angle measurements. The effect of plasma treatment on the strength of thermally bonded lap‐shear specimens was studied. The influence of plasma treatment on the integrity of thermally sealed microdevices was assessed using burst pressure tests. The plasma treatments had a significant impact on the electroosmosis flow mobility in the microchannels. The hemocompatibility of the various plasma‐modified COC surfaces was determined using the static platelets adhesion experiment. It was shown that the nitrogen plasma treatment was more effective than the argon and oxygen treatments for the modification of COC based microfluidic devices.
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Diagnosis of subclinical and clinical acute T‐cell‐mediated rejection in renal transplant patients by urinary proteome analysis
Authors: Metzger Jochen , Chatzikyrkou Christos , Broecker Verena , Schiffer Eric , Jaensch Lothar , Iphoefer Alexander , Mengel Michael , Mullen William , Mischak Harald , Haller Hermann , Gwinner Wilfried 
Published: March 2011

AbstractPurpose: Noninvasive diagnosis of acute renal allograft rejection may be advantageous compared with the allograft biopsy.Experimental design: In this study, a multi‐marker classification model for rejection was defined on a training set of 39 allograft patients by statistical comparison of capillary electrophoresis mass spectrometry (CE‐MS) peptide spectra in urine samples from 16 cases with subclinical acute T‐cell‐mediated tubulointerstitial rejection and 23 nonrejection controls.Results: Application of the rejection model to a blinded validation set (n=64) resulted in an AUC value of 0.91 (95% CI: 0.82–0.97, p=0.0001). In total, 16 out of 18 subclinical and 10 out of 10 clinical rejections (BANFF grades Ia/Ib), and 28 out of 36 controls without rejection were correctly classified. Acute tubular injury in the biopsies or concomitant urinary tract infection did not interfere with CE‐MS‐based diagnosis. Sequence information of identified altered collagen α(I) and α (III) chain fragments in rejection samples suggested an involvement of matrix metalloproteinase‐8 (MMP‐8). Biopsy stainings revealed matrix metalloproteinase‐8 exclusively in neutrophils located within peritubular capillaries and sparsely, in the tubulointerstitium during rejection.Conclusions and clinical relevance: The established marker set contains peptides related to tubulointerstitial infiltration seen in acute rejection. The set of urinary peptide markers will be used for early diagnosis of acute kidney allograft rejection marker in a multicenter phase III prospective study.
Exploring sequence requirements for C3/C4 carboxylate recognition in the Pseudomonas aeruginosa cephalosporinase: Insights into plasticity of the AmpC β‐lactamase
Authors: Drawz Sarah M. , Taracila Magdalena , Caselli Emilia , Prati Fabio , Bonomo Robert A. 
Published: March 2011

AbstractIn Pseudomonas aeruginosa, the chromosomally encoded class C cephalosporinase (AmpC β‐lactamase) is often responsible for high‐level resistance to β‐lactam antibiotics. Despite years of study of these important β‐lactamases, knowledge regarding how amino acid sequence dictates function of the AmpC Pseudomonas‐derived cephalosporinase (PDC) remains scarce. Insights into structure‐function relationships are crucial to the design of both β‐lactams and high‐affinity inhibitors. In order to understand how PDC recognizes the C3/C4 carboxylate of β‐lactams, we first examined a molecular model of a P. aeruginosa AmpC β‐lactamase, PDC‐3, in complex with a boronate inhibitor that possesses a side chain that mimics the thiazolidine/dihydrothiazine ring and the C3/C4 carboxylate characteristic of β‐lactam substrates. We next tested the hypothesis generated by our model, i.e. that more than one amino acid residue is involved in recognition of the C3/C4 β‐lactam carboxylate, and engineered alanine variants at three putative carboxylate binding amino acids. Antimicrobial susceptibility testing showed that the PDC‐3 β‐lactamase maintains a high level of activity despite the substitution of C3/C4 β‐lactam carboxylate recognition residues. Enzyme kinetics were determined for a panel of nine penicillin and cephalosporin analog boronates synthesized as active site probes of the PDC‐3 enzyme and the Arg349Ala variant. Our examination of the PDC‐3 active site revealed that more than one residue could serve to interact with the C3/C4 carboxylate of the β‐lactam. This functional versatility has implications for novel drug design, protein evolution, and resistance profile of this enzyme.
Structural biology of gram‐positive bacterial adhesins
Authors: Vengadesan Krishnan , Narayana Sthanam V. L. 
Published: March 2011

AbstractThe structural biology of Gram‐positive cell surface adhesins is an emerging field of research, whereas Gram‐negative pilus assembly and anchoring have been extensively investigated and are well understood. Gram‐positive surface proteins known as MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) and individual proteins that assemble into long, hair‐like organelles known as pili have similar features at the primary sequence level as well as at the tertiary structural level. Some of these conserved features are essential for their transportation from the cytoplasm and for cell wall anchoring. More importantly, the MSCRAMMs and the individual pilins are assembled with building blocks that are variants of structural modules used for human immunoglobulins. MSCRAMMs target the host's extracellular matrix proteins, such as collagen, fibrinogen, and fibronectin, and they have received considerable attention from structural biologists in the last decade, who have primarily been interested in understanding their interactions with host tissue. The recent focus is on the newly discovered pili of Gram‐positive bacteria, and in this review, we highlight the advances in understanding of the individual pilus constituents and their associations and stress the similarities between the individual pilins and surface proteins.
NMR reveals novel mechanisms of protein activity regulation
Authors: Kalodimos Charalampos G. 
Published: March 2011

AbstractNMR spectroscopy is one of the most powerful tools for the characterization of biomolecular systems. A unique aspect of NMR is its capacity to provide an integrated insight into both the structure and intrinsic dynamics of biomolecules. In addition, NMR can provide site‐resolved information about the conformation entropy of binding, as well as about energetically excited conformational states. Recent advances have enabled the application of NMR for the characterization of supramolecular systems. A summary of mechanisms underpinning protein activity regulation revealed by the application of NMR spectroscopy in a number of biological systems studied in the lab is provided.
A career pathway in protein folding: From model peptides to postreductionist protein science
Authors: Gierasch Lila M. 
Published: March 2011

AbstractThis review discusses the inherent challenge of linking “reductionist” approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments—“postreductionist” approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.
An alternative view of the proposed alternative activities of hemopexin
Authors: Mauk Marcia R. , Smith Ann , Grant Mauk A. 
Published: March 2011

AbstractHemopexin is a plasma protein that plays a well‐established biological role in sequestering heme that is released into the plasma from hemoglobin and myoglobin as the result of intravascular or extravascular hemolysis as well as from skeletal muscle trauma or neuromuscular disease. In recent years, a variety of additional biological activities have been attributed to hemopexin, for example, hyaluronidase activity, serine protease activity, pro‐inflammatory and anti‐inflammatory activity as well as suppression of lymphocyte necrosis, inhibition of cellular adhesion, and binding of divalent metal ions. This review examines the challenges involved in the purification of hemopexin from plasma and in the recombinant expression of hemopexin and evaluates the questions that these challenges and the characteristics of hemopexin raise concerning the validity of many of the new activities proposed for this protein. As well, an homology model of the three‐dimensional structure of human hemopexin is used to reveal that the protein lacks the catalytic triad that is characteristic of many serine proteases but that hemopexin possesses two highly exposed Arg‐Gly‐Glu sequences that may promote interaction with cell surfaces.
Quantum flavor oscillations extended to the Dirac theory
Authors: Bernardini A.E. , Guzzo M.M. , Nishi C.C. 
Published: March 2011

AbstractFlavor oscillations by itself and its coupling with chiral oscillations and/or spin‐flipping are the most relevant quantum phenomena of neutrino physics. This report deals with the quantum theory of flavor oscillations in vacuum, extended to fermionic particles in the several subtle aspects of the first quantization and second quantization theories. At first, the basic controversies regarding quantum‐mechanical derivations of the flavor conversion formulas are reviewed based on the internal wave packet (IWP) framework. In this scenario, the use of the Dirac equation is required for a satisfactory evolution of fermionic mass‐eigenstates since in the standard treatment of oscillations the mass‐eigenstates are implicitly assumed to be scalars and, consequently, the spinorial form of neutrino wave functions is not included in the calculations. Within first quantized theories, besides flavor oscillations, chiral oscillations automatically appear when we set the dynamic equations for a fermionic Dirac‐type particle. It is also observed that there is no constraint between chiral oscillations, when it takes place in vacuum, and the process of spin‐flipping related to the helicity quantum number, which does not take place in vacuum. The left‐handed chiral nature of created and detected neutrinos can be implemented in the first quantized Dirac theory in presence of mixing; the probability loss due to the changing of initially left‐handed neutrinos to the undetected right‐handed neutrinos can be obtained in analytic form. These modifications introduce correction factors proportional to mν2/Eν2 that are very difficult to be quantified by the current phenomenological analysis. All these effects can also be identified when the non‐minimal coupling with an external (electro)magnetic field in the neutrino interacting Lagrangian is taken into account. In the context of a causal relativistic theory of a free particle, one of the two effects should be present in flavor oscillations: (a) rapid oscillations or (b) initial flavor violation. Concerning second quantized approaches, a simple second quantized treatment exhibits a tiny but inevitable initial flavor violation without the possibility of rapid oscillations. Such effect is a consequence of an intrinsically indefinite but approximately well defined neutrino flavor. Within a realistic calculation in pion decay, including the quantum field treatment of the creation process with finite decay width, it is possible to quantify such violation. The violation effects are shown to be much larger than loop induced lepton flavor violation processes, already present in the standard model in the presence of massive neutrinos with mixing. For the implicitly assumed fermionic nature of the Dirac theory, the conclusions of this report lead to lessons concerning flavor mixing, chiral oscillations, interference between positive and negative frequency components of Dirac equation solutions, and the field formulation of quantum oscillations.
Charged dilatonic black holes and their transport properties
Authors: Goutéraux B. , Kim B.S. , Meyer R. 
Published: March 2011

AbstractWe briefly explain the consistency conditions imposed on the effective holographic theories, which are parameterized by two real exponents (γ,δ) that control the IR dynamics. The general scaling of DC resistivity with temperature at low temperature and AC conductivity at low frequency across the whole (γ,δ) plane are explained. There is a codimension‐one region where the DC resistivity is linear in the temperature. For massive carriers, it is shown that when the scalar operator is not the dilaton, the DC resistivity scales as the heat capacity (and entropy) for (2+1)‐dimensional systems. Regions are identified where the theory at finite density is a Mott‐like insulator. This contribution is based on (C. Charmousis, et al. J. High Energy Phys. 1011, 151 (2010)) [1] with emphasis on the transport properties of charged dilatonic black holes with potential.
Free energy of ABJM theory
Authors: Smedbäck M. 
Published: March 2011

AbstractThe free energy of ABJM theory has previously been computed in the strong and weak coupling limits. In this note, we report on results for the computation of the first non‐vanishing quantum correction to the free energy, from the field theory side. The correction can be expressed in terms of a thermal mass for the scalar fields. This mass vanishes to 1‐loop order, but there is a non‐vanishing result to 2‐loop order. Hence, the leading correction to the free energy is non‐analytic in the 't Hooft coupling constant λ. The reason is that the infrared divergences necessitate a resummation of ring diagrams and a related reorganization of perturbation theory, in which already the leading correction receives contributions from all orders in λ. These results suggest that the free energy interpolates smoothly between weak and strong coupling.
String vacua with massive boson‐fermion degeneracy and non‐singular cosmology
Authors: Florakis I. 
Published: March 2011

AbstractWe discuss marginal deformations of string vacua with Massive boson‐fermion Degeneracy Symmetry (MSDS), in connection to the cosmological evolution of the Universe from an early non‐geometrical era. In particular, we discuss recent results on the stringy mechanism that resolves both Hagedorn divergences and the Initial Singularity problem.
A resilience assessment framework for infrastructure and economic systems: Quantitative and qualitative resilience analysis of petrochemical supply chains to a hurricane
Authors: Vugrin Eric D. , Warren Drake E. , Ehlen Mark A. 
Published: March 2011

AbstractIn recent years, the nation has recognized that critical infrastructure protection should consider not only the prevention of disruptive events but also the processes that infrastructure systems undergo to maintain functionality following disruptions. This more comprehensive approach has been termed critical infrastructure resilience. Given the occurrence of a particular disruptive event, the resilience of a system to that event is the system's ability to reduce efficiently both the magnitude and duration of the deviation from targeted system performance levels. Under the direction of the U. S. Department of Homeland Security's Science and Technology Directorate, Sandia National Laboratories has developed a comprehensive resilience assessment framework for evaluating the resilience of infrastructure and economic systems. The framework includes a quantitative methodology that measures resilience costs that result from a disruption to infrastructure function. The framework also includes a qualitative analysis methodology that assesses system characteristics affecting resilience to provide insight and direction for potential improvements. This article describes the resilience assessment framework and demonstrates the utility of the assessment framework through application to two hypothetical scenarios involving the disruption of a petrochemical supply chain by hurricanes. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Heterolocal Identities? Counter‐Urbanisation, Second Homes, and Rural Consumption in the Era of Mobilities
Authors: Halfacree Keith 
Published: March 2011

ABSTRACTThis paper forms part of a critical engagement with the aspects of the core population geography concept of ‘counterurbanisation’. It argues that contextualising counterurbanisation within the ‘era of mobilities’ has profound consequences for the concept. After introducing the era of mobilities and its implications for social science, migration's central and multiple places within this discourse are outlined. The paper then examines one set of ideas, ‘dynamic heterolocalism’, that facilitates the understanding of the existential significance today of the circulatory expressions of migration. Returning to counterurbanisation, the paper draws into its orbit the consumers of rural second homes, understanding of which has also increasingly adopted a quasi‐heterolocal tone. An inclusive model of what is then recast terminologically as ‘counter‐urbanisation’ posits it as an extremely heterodox concept, potentially embracing not only second‐home owners but also diverse other consumers of rural space or rural sojourners. The paper concludes by reiterating the sustained centrality of ‘rurality’ to counterurbanisation, second‐home consumption, and other expressions of identity within the era of mobilities. Copyright © 2011 John Wiley & Sons, Ltd.
Exciton spectra in thin crystals
Authors: Harper P. G. , Hilder J. A. 
Published: March 2011

AbstractA theory is presented of the observed dependence of exciton series spectra on crystal thickness [2,3]. When the latter is comparable to the Wannier exciton radius the effective confinement of the exciton bound states, by the uncertainty principle, raises the kinetic energy. This confinement is introduced by the boundary condition which requires the Wannier wave function to vanish outside the crystal. Allowance is made for thick crystal anisotropy, and its effects on the binding energy calculated for the low excited states.
Free carrier absorption in n‐type CdTe crystals
Authors: Yamada S. , Kawasaki Y. , Nishida O. 
Published: March 2011

AbstractOptical absorption is investigated in In‐doped n‐type CdTe crystals between 2.5 and 16 μm. The measurements are made at 295 and 473°K. The absorption coefficient increases smoothly with wavelength, and this is almost certainly due to free carrier absorption. From the absorption curves, it is concluded that the electrons are scattered mainly by optical phonons and partially by ionized impurities.
Diffusion concentration distribution near an idealized contact spot
Authors: Cramer K. R. , Richards K. J. 
Published: March 2011

AbstractThe distribution of the concentration of a diffusing substance near an idealized contact spot is determined analytically for unsteady self‐diffusion across only the contact region. The results demonstrate that the influence of the contact spot is restricted to less than ten spot radii in the radial direction and less than four in the axial direction.