julilili42/papers huggingface dataset:
Identification of a Highly Immunogenic HLA-A*01-Binding T Cell Epitope of WT1
2006-12-15

Abstract Purpose: The transcription factor Wilms tumor protein 1 (WT1) belongs to a new generation of tumor antigens, as it is essential for tumor cell proliferation and is highly expressed in various hematologic and solid malignancies. The aim of this study was to apply a modified reverse immunology strategy to identify immunogenic epitopes of WT1 which could be useful for immunotherapy. Experimental Design: Potential HLA-A*01 epitopes predicted by a MHC binding algorithm were screened for recognition by peripheral blood mononuclear cells (PBMC) from patients with spontaneous T cell responses using intracellular cytokine cytometry. Epitope processing was shown by proteasomal cleavage. Epitope-specific T cells were generated from CD4+CD25+ regulatory T cell–depleted PBMC. Results: One of five predicted HLA-A*01-binding candidate epitopes showed high immunogenicity as 5 of 14 patients with hematologic malignancies had WT1.317-327–reactive T cells ranging from 0.4% to 1.5% of CD3+CD8+ T cells. Proteasomal degradation assays indicated the cleavage of WT1.317-327. The depletion of regulatory T cells from PBMCs enabled the rapid expansion of WT1.317-327–specific CTL, whereas no CTL could be generated from unfractionated PBMC. WT1.317-327–specific CTL efficiently lysed an autologous WT1-expressing tumor cell line but not HLA-A*01–negative WT1-expressing tumor cells. Immunogenicity of the epitope across histologies was verified by the demonstration of spontaneous ex vivo WT1.317-327–specific T cell responses in two of six patients with HLA-A*01–positive melanoma or lung cancer. Conclusion: In this study, a modified reverse immunology strategy was employed to identify a first immunogenic HLA-A*01–restricted T cell epitope of the tumor antigen WT1, which is of considerable interest for use in vaccination trials.
Successful vaccination against Onchocerca ochengi infestation in cattle using live Onchocerca volvulus infective larvae
2006-12-15

SUMMARY Epidemiological evidence has led to the hypothesis that the concurrent and predominant transmission of Onchocerca ochengi by Simulium damnosum s.l. in sub‐Saharan Africa could lead to the protection of humans against onchocerciasis caused by Onchocerca volvulus (zooprophylaxis). To gain support for this hypothesis, we investigated whether exposure to O. volvulus could protect cattle from O. ochengi . Gudali calves were vaccinated with live O. volvulus ‐infective larvae and subsequently challenged with O. ochengi‐ infective larvae whilst raised in a fly‐proof house. Post‐challenge adult parasite and microfilaria development, IgG1 and lgG2 subclass antibodies response to Ov10/Ov11 recombinant Onchocerca antigens, and peripheral blood lymphocyte proliferative responses to O. ochengi crude antigens were studied over a 1‐year period. The vaccinated‐challenged animals had 83–87% less adult O. ochengi parasites than non‐vaccinated‐challenged animals. IgG1 and lgG2 antibodies to Ov10/Ov11 recombinant Onchocerca antigens were invoked by non‐vaccinated‐challenged animals but not by most (80%) of the vaccinated‐challenged animals. These findings support the idea of cross‐protection (zooprophylaxis) due to inoculation of humans with O. ochengi ‐infective larvae under natural transmission conditions in endemic areas.
CORRELATIONS IN HOT ASYMMETRIC NUCLEAR MATTER
2006-12-15

The single-particle spectral functions in asymmetric nuclear matter are computed using the ladder approximation within the theory of finite temperature Green's functions. The internal energy and the momentum distributions of protons and neutrons are studied as a function of the density and the asymmetry of the system. The proton states are more strongly depleted when the asymmetry increases, whereas the occupation of the neutron states is enhanced compared to the symmetric case. Preliminary results for the entropy and the free energy are also presented.
Influence of Wall Teichoic Acid on Lysozyme Resistance inStaphylococcus aureus
2006-12-16

ABSTRACT Staphylococcus aureus peptidoglycan (PG) is completely resistant to the hydrolytic activity of lysozyme. Here we show that modifications in PG by O acetylation, wall teichoic acid, and a high degree of cross-linking contribute to this resistance.
Unexpected course of a Williamson ether synthesis
2006-12-17

The Williamson ether synthesis between the sodium salt of methyl mandelate and methyl αbromophenylacetate was reinvestigated.In addition to the expected ether product cis-dimethyl 2,3-diphenyloxirane-2,3-dicarboxylate, methyl phenylacetate and methyl phenylglyoxylate were obtained.Their formation is explained by an initial α-elimination producing an α-oxo-carbene from the α-bromoester.This is followed by a hydride transfer from the sodium salt of methyl mandelate to the carbenic intermediate furnishing the enolate of methyl phenylacetate as reduction product and methyl phenylglyoxylate as oxidation product.Finally, the methyl phenylglyoxylate reacts with the enolate of the α-bromoester in a diastereospecific Darzens condensation to the cis-oxirane (cis-conformation confirmed by single crystal structure analysis).In this series of parallel and sequential reactions, the sodium salt of methyl mandelate displays 3 modes of action: nucleophile (ether synthesis), base (α-elimination) and hydride donor (redox process).
Lactobacillus fermentum attenuates the proinflammatory effect of Yersinia enterocolitica on human epithelial cells
2006-12-19

Our results lead to the conclusion that L. fermentum inhibits the Y. enterocolitica-induced IL-8 production by a possibly secreted phospholipid of <10 kDa molecular weight. These data suggest that L. fermentum may have probiotic properties modulating intestinal inflammatory responses and might offer new therapeutic strategies in the treatment of intestinal inflammatory diseases.
Extracellular domain splice variants of a transforming protein tyrosine phosphatase α mutant differentially activate Src‐kinase dependent focus formation
2006-12-19

The extracellular domains of receptor‐type protein‐tyrosine phosphatases (PTPs) contain a diverse range of protein modules like fibronectin‐ or immunoglobulin‐like structures. These are frequently expressed in a tissue‐ and development specific manner as splice variants. The extracellular domain of PTPα is rather short and heavily glycosylated. Two splice variants are known, which it differs by an exon encoding nine amino acids within the extracellular domain. We have analyzed the expression pattern of both variants and found that the smaller form is ubiquitously expressed while the larger form was found at an increased level only in brain, some skeletal muscle and differentiating cells like granule neurons, adipocytes and myotubes. The phosphatase activity of both forms was similar when tested in vitro using para‐nitrophenylphosphate as a substrate and in a transient expression system with the substrates c‐Fyn or c‐Src. In a quantitative focus formation assay the capability of the larger form to activate Src‐dependent focus formation in intact cells was increased more than twofold whereas the capability to dephosphorylate the insulin receptor in a BHK cell system was similar. We conclude that the two splice variants of PTPα are expressed differentially and regulate c‐Src activity in different ways.
A Concise and Optimized Four‐Step Approach Toward 2‐(Aryl‐)alkylsulfanyl‐, 4(5)‐Aryl‐, 5(4)‐Heteroaryl‐Substituted Imidazoles Using Alkyl‐ or Arylalkyl Thiocyanates.
2006-12-19

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Fourier synthesis of optical potentials for atomic quantum gases
2006-12-20

We demonstrate a scheme for the Fourier synthesis of periodic optical\\npotentials with asymmetric unit cells for atoms. In a proof of principle\\nexperiment, an atomic Bose-Einstein condensate is exposed to either symmetric\\nor sawtooth-like asymmetric potentials by superimposing a conventional standing\\nwave potential of spatial periodicity with a fourth-order lattice\\npotential of periodicity. The high periodicity lattice is realized\\nusing dispersive properties of multiphoton Raman transitions. Future\\napplications of the demonstrated scheme could range from the search for novel\\nquantum phases in unconventionally shaped lattice potentials up to\\ndissipationless atomic quantum ratchets.\\n
Analysis ofBartonellaAdhesin A Expression Reveals Differences between VariousB. henselaeStrains
2006-12-20

ABSTRACT Bartonella henselae causes cat scratch disease and the vasculoproliferative disorders bacillary angiomatosis and peliosis hepatis in humans. One of the best known pathogenicity factors of B. henselae is Bartonella adhesin A (BadA), which is modularly constructed, consisting of head, neck/stalk, and membrane anchor domains. BadA is important for the adhesion of B. henselae to extracellular-matrix proteins and endothelial cells (ECs). In this study, we analyzed different B. henselae strains for BadA expression, autoagglutination, fibronectin (Fn) binding, and adhesion to ECs. We found that the B. henselae strains Marseille, ATCC 49882, Freiburg 96BK3 (FR96BK3), FR96BK38, and G-5436 express BadA. Remarkably, BadA expression was lacking in a B. henselae ATCC 49882 variant, in strains ATCC 49793 and Berlin-1, and in the majority of bacteria of strain Berlin-2. Adherence of B. henselae to ECs and Fn reliably correlated with BadA expression. badA was present in all tested strains, although the length of the gene varied significantly due to length variations of the stalk region. Sequencing of the promoter, head, and membrane anchor regions revealed only minor differences that did not correlate with BadA expression, apart from strain Berlin-1, in which a 1-bp deletion led to a frameshift in the head region of BadA. Our data suggest that, apart from the identified genetic modifications (frameshift deletion and recombination), other so-far-unknown regulatory mechanisms influence BadA expression. Because of variations between and within different B. henselae isolates, BadA expression should be analyzed before performing infection experiments with B. henselae.
Absence of Toll-Like Receptor 4 Signaling Results in Delayed Yersinia enterocolitica YopP-Induced Cell Death of Dendritic Cells
2006-12-20

ABSTRACT In an initial period (≤4 h) Toll-like receptor 4 (TLR4) signaling is required for Yersinia enterocolitica YopP-induced dendritic cell (DC) death. Later (&gt;4 h), DC die independent of TLR4 signaling. In TLR4-deficient DC caspase 8 cleavage is delayed, indicating that TLR4 signaling accelerates caspase 8 activation, leading to DC death.
Nitrogen Metabolism in <i>Streptomyces coelicolor</i>: Transcriptional and Post-Translational Regulation
2006-12-21

Glutamine synthetases (GS) are key enzymes of nitrogen metabolism. Most bacteria contain only one type of GS enzyme encoded by &lt;i&gt;glnA&lt;/i&gt;. &lt;i&gt;Streptomyces coelicolor&lt;/i&gt;, the model organism for Gram-positive streptomycetes, however is characterized by two functional GS &lt;i&gt;(&lt;/i&gt;&lt;i&gt;glnA&lt;/i&gt;, &lt;i&gt;glnII&lt;/i&gt;&lt;i&gt;)&lt;/i&gt; involved in nitrogen assimilation. In addition, three GS-like genes were identified which do not exhibit GS enzyme activity. The control of nitrogen assimilation and metabolism is mediated by transcriptional and post-translational regulation systems. The OmpR-like regulators GlnR and GlnRII are involved in transcriptional control of important nitrogen metabolism genes &lt;i&gt;(&lt;/i&gt;&lt;i&gt;glnA&lt;/i&gt;, &lt;i&gt;glnII&lt;/i&gt;, &lt;i&gt;amtB&lt;/i&gt;, &lt;i&gt;glnK&lt;/i&gt;, &lt;i&gt;glnD&lt;/i&gt;&lt;i&gt;)&lt;/i&gt;. Although GlnR and GlnRII share identical binding regions, their physiological impact is different. GSI activity is modulated post-translationally by the adenylyltransferase GlnE in response to the nitrogen concentration whereas no post-translational modifications of GSII are known. The PII/GlnD system also responds to changes in nitrogen conditions. The adenylyltransferase GlnD, which resembles the uridylyltransferase of &lt;i&gt;Enterobacteriaceae&lt;/i&gt;, modifies PII under low-nitrogen conditions. Furthermore, PII is processed at its N-terminus in response to an ammonium shock. Apparently the function of the PII protein of &lt;i&gt;S. coelicolor&lt;/i&gt; is different from that of the PII proteins of &lt;i&gt;Enterobacteriaceae&lt;/i&gt;.
Hydration of Oligo(ethylene glycol) Self-Assembled Monolayers Studied Using Polarization Modulation Infrared Spectroscopy
2006-12-21

The interaction with water of protein-resistant monolayers (SAMs), self-assembled from (triethylene glycol) terminated thiol HS(CH2)11(OCH2CH2)3OMe solutions, was studied using in and ex situ polarization-modulated Fourier transform infrared spectroscopy. In particular, shifts in the position of the characteristic C-O-C stretching vibration were observed after the monolayers had been exposed to water. The shift in frequency increased when the SAM was observed in direct contact with a thin layer of water. It was found that the magnitude of the shift also depended on the surface coverage of the SAM. These findings suggest a rather strong interaction of oligo(ethylene glycol) SAMs with water and indicate the penetration of water into the upper region of the monolayer.
Carbon Catabolite Repression of Sucrose Utilization in <i>Staphylococcus xylosus</i>: Catabolite Control Protein CcpA Ensures Glucose Preference and Autoregulatory Limitation of Sucrose Utilization
2006-12-21

Sucrose utilization in &lt;i&gt;Staphylococcus xylosus &lt;/i&gt;is dependent on two genes, &lt;i&gt;scrA&lt;/i&gt; and &lt;i&gt;scrB; &lt;/i&gt;encoding a PTS permease and a sucrose phosphate hydrolase, respectively. The genes are encoded on separate loci and are transcribed from two promoters, P&lt;sub&gt;&lt;i&gt;scrA&lt;/i&gt;&lt;/sub&gt; and P&lt;sub&gt;&lt;i&gt;scrB&lt;/i&gt;&lt;/sub&gt;, both of which are controlled by the repressor ScrR by binding to the operator sequences &lt;i&gt;O&lt;/i&gt;&lt;sub&gt;&lt;i&gt;A&lt;/i&gt;&lt;/sub&gt; and &lt;i&gt;O&lt;/i&gt;&lt;sub&gt;&lt;i&gt;B&lt;/i&gt;&lt;/sub&gt;. In the &lt;i&gt;scrA&lt;/i&gt; promoter region, a catabolite-responsive element &lt;i&gt;(cre)&lt;/i&gt;, operator for the global catabolite control protein CcpA, is also present, but its contribution to &lt;i&gt;scrA&lt;/i&gt; regulation has not been determined. Using an integrative promoter probe plasmid, the activities of the promoters P&lt;sub&gt;&lt;i&gt;scrA&lt;/i&gt;&lt;/sub&gt; and P&lt;sub&gt;&lt;i&gt;scrB&lt;/i&gt;&lt;/sub&gt; were determined under different growth conditions. Both promoters are induced by sucrose and induction is prevented when glucose is also present. Without a functional CcpA, glucose-mediated prevention of induction is lost, clearly demonstrating that CcpA ensures hierarchical sugar utilization with glucose as preferred substrate. Measurements of promoter activities in the absence of a functional ScrR repressor indicated that CcpA also acts upon the operators &lt;i&gt;O&lt;/i&gt;&lt;sub&gt;&lt;i&gt;A&lt;/i&gt;&lt;/sub&gt; and &lt;i&gt;O&lt;/i&gt;&lt;sub&gt;&lt;i&gt;B&lt;/i&gt;&lt;/sub&gt;&lt;i&gt;, &lt;/i&gt;albeit not as efficiently as on the genuine &lt;i&gt;cre&lt;/i&gt; in P&lt;sub&gt;&lt;i&gt;srcA&lt;/i&gt;&lt;/sub&gt;. Besides determining the choice of the carbon source, CcpA has a second effect on sucrose gene expression. When sucrose is the sole carbon source, sucrose catabolism activates carbon catabolite repression and CcpA prevents full induction of the sucrose utilization genes by partially repressing the &lt;i&gt;scrA&lt;/i&gt; promoter. Thus, CcpA-dependent regulation serves as a built-in autoregulatory device to restrict sucrose uptake.
[Dynamics of decapitation after falling in a self-tightening rope noose].
2006-12-22

In decapitation by dropping into a slip noose, it is in principle justified to doubt that suicide is involved. It must hence always be checked whether the dynamics to be inferred from the concrete facts can result in decapitation. Essential characteristics of the dynamics are the deceleration forces (tractional force of the rope) that are determined by the height of the drop, the directional force of the rope and the body mass of the victim as well as the density of the lines of centripetal force acting on the neck. However, the appropriateness of the dynamics must at all events be corroborated by compatible autopsy and scientific criminological findings with regard to the characteristic wound morphology, the intravital signs, the trace analysis and the topography of the fiber ablation traces on the rope that are due to the effect of heat.
Fixation devices for whole-body 18F-FDG PET/CT: Patient perspectives and technical aspects
2006-12-25

Both the technical aspects and patient evaluations favour the use of the vacuum device in whole-body PET/CT examinations. In particular, in time consuming protocols using multiphase CT examination the fixation device leads to excellent co-registration quality and patient compliance.
Isoscalar short-range current in the deuteron induced by an intermediate dibaryon
2006-12-26

A new model for short-range isoscalar currents in the deuteron and in the NN system is developed; it is based on the generation of an intermediate dibaryon which is the basic ingredient for the medium- and short-range NN interaction which was proposed recently by the present authors.This new current model can very well describe the experimental data for the three basic deuteron observables of isoscalar magnetic type, viz. the magnetic moment, the circular polarization of the photon in the process at thermal neutron energies and the structure function B up to Q =60 fm .
A Network Analysis of Changes in Molecular Interactions in Cellular Signaling
2006-12-26

Multiprotein complexes play an essential role in the propagation and integration of cellular signals. However, systems level analyses of signaling-dependent changes in the pattern of molecular interactions are still missing. Signaling in T-lymphocytes is one prominent example in which multiprotein complexes orchestrate signal transduction. We implemented peptide microarrays comprising a set of interaction motifs of signaling proteins for network-based analyses of signaling-dependent changes in molecular interactions. Lysates of resting or stimulated cells were incubated on these arrays, and the binding of signaling proteins was detected by immunofluorescence. Signaling-dependent complex formation led to changes of signals on the microarrays in two ways. 1) Masking of a binding site of a signaling protein for a peptide on the array resulted in a signal decrease. 2) Interaction of a protein with a second protein, which in turn binds to a peptide on the array, resulted in a signal increase for the first protein. Dissipation of complexes led to the reverse changes. Competition with peptides corresponding to interaction motifs provided detailed information on the architecture of complexes; lack of individual signaling proteins revealed the functional interdependence of interactions in the network. We show that complex formation through phosphorylation of the scaffolding protein LAT (linker for activation of T-cells) acted as a signal amplifier. PLCgamma1 deficiency increased the resting state levels of LAT-dependent complexes and augmented the recruitment of the phosphatase SHPTP2 into complexes. For the analysis of signaling networks, the parallel detection of changes in interactions enabled the identification of functional interdependencies with minimum a priori knowledge.
Granular elasticity: Stress distributions in silos and under point loads
2006-12-27

An elastic-strain-stress relation, the result of granular elasticity as introduced in the preceding paper, is employed here to calculate the stress distribution (a) in cylindrical silos and (b) under point loads assuming uniform density. In silos, the ratio k{J} between the horizontal and vertical stress is found to be constant (as conjectured by Janssen) and given as k{J}=1-sin phi (with phi the Coulomb yield angle), in agreement with a construction industry standard usually referred to as the Jaky formula. Next, the stress distribution at the bottom of a granular layer exposed to a point force at its top is calculated. The results include both vertical and oblique point forces, which agree well with simulations and experiments using rainlike preparation. Moreover, the stress distribution of a sheared granular layer exposed to the same point force is calculated and again found in agreement with given data.
Granular elasticity: General considerations and the stress dip in sand piles
2006-12-27

Granular materials are predominantly plastic, incrementally nonlinear, preparation-dependent, and anisotropic under shear. Nevertheless, their static stress distribution is well accounted for, in the whole range up to the point of failure, by a judiciously tailored isotropic nonanalytic elasticity theory termed granular elasticity. The first purpose of this paper is to carefully expound this view. Then granular elasticity is employed to consider the stress distribution in two-dimensional sand piles (or sand wedges). Starting from a uniform density, the pressure at the bottom of the pile is found to show a single central peak. It turns into a pressure dip, if some density inhomogeneity, with the center being less compact, is assumed. These two pressure distributions are remarkably similar to recent measurements, made in piles obtained, respectively, by rainlike pouring and funneling. In an accompanying paper, the stress distributions in silos and under point loads, calculated using the same method, are also found to agree with experiments.
Density resummation of perturbation series in a pion gas to leading order in chiral perturbation theory
2006-12-27

The mean field (MF) approximation for the pion matter, being equivalent to the leading ChPT order, involves no dynamical loops and, if self-consistent, produces finite renormalizations only. The weight factor of the Haar measure of the pion fields, entering the path integral, generates an effective Lagrangian which is generally singular in the continuum limit. There exists one parameterization of the pion fields only, for which the weight factor is equal to unity and , respectively. This unique parameterization ensures selfconsistency of the MF approximation. We use it to calculate thermal Green functions of the pion gas in the MF approximation as a power series over the temperature. The Borel transforms of thermal averages of a function of the pion fields with respect to the scalar pion density are found to be . The perturbation series over the scalar pion density for basic characteristics of the pion matter such as the pion propagator, the pion optical potential, the scalar quark condensate , the in-medium pion decay constant , and the equation of state of pion matter appear to be asymptotic ones. These series are summed up using the contour-improved Borel resummation method. The quark scalar condensate decreases smoothly until MeV. The temperature is the maximum temperature admissible for thermalized non-linear sigma model at zero pion chemical potentials. The estimate of is above the chemical freeze-out temperature MeV at RHIC and above the phase transition to two-flavor quark matter MeV, predicted by lattice gauge theories.
ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome
2006-12-28

ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.