julilili42/papers huggingface dataset:
A generic RNA-pulsed dendritic cell vaccine strategy for renal cell carcinoma
2005-07-26

Abstract We present a generic dendritic cell (DC) vaccine strategy for patients with renal cell carcinoma (RCC) based on the use of RNA as a source of multiplex tumor-associated antigens (TAAs). Instead of preparing RNA from tumor tissue of each individual RCC patient, we propose to substitute RNA prepared from a well characterized highly immunogenic RCC cell line (RCC-26 tumor cells) as a generic source of TAAs for loading of DCs. We demonstrate here that efficient RNA transfer can be achieved using lipofection of immature DCs, which are subsequently matured with a cytokine cocktail to express high levels of MHC and costimulatory molecules as well as the chemokine receptor CCR7. Neither RNA itself nor the lipid component impacted on the phenotype or the cytokine secretion of mature DCs. Following RNA loading, DCs derived from HLA-A2-positive donors were able to activate effector-memory cytotoxic T lymphocytes (CTLs) specific for a TAA ligand expressed by the RCC-26 cell line. CTL responses to RNA-loaded DCs reached levels comparable to those stimulated directly by the RCC-26 tumor cells. Furthermore, DCs expressing tumor cell RNA primed naïve T cells, yielding T cell lines with cytotoxicity and cytokine secretion after contact with RCC tumor cells. RCC-26 cell lines are available as good manufacturing practice (GMP)-certified reagents enabling this source of RNA to be easily standardized and adapted for clinical testing. In addition, well defined immune monitoring tools, including the use of RNA expressing B cell lines, are available. Thus, this DC vaccine strategy can be directly compared with an ongoing gene therapy trial using genetically-engineered variants of the RCC-26 cell line as vaccines for RCC patients with metastatic disease.
Synthese und Struktur von [(Ph3PAu)3NPPh3][PF6]2, einem Gold(I)‐phosphoraniminato‐Komplex
2005-07-26

Abstract Synthesis and Crystal Structure of [(Ph 3 PAu) 3 NPPh 3 ][PF 6 ] 2 , a Gold(I) Phosphoraneiminato Complex The photolytic reaction of Ph 3 PAuN 3 with Cr(CO) 6 in THF yields the phosphoraneiminato complex [(Ph 3 PAu) 3 NPPh 3 ] 2+ in low yield as well as the cluster cation [(Ph 3 PAu) 8 ] 2+ as the main product. The phosphoraneiminato complex crystallizes from CH 2 Cl 2 with [PF 6 ] − ions as [(Ph 3 PAu) 3 NPPh 3 ][PF 6 ] 2 ·CH 2 Cl 2 in the triclinic space group with a = 1200.8(1), b = 1495.6(2), 2053.5(5), α = 86.97(2)°, β = 82.79(1)°, γ = 81.87(2)°, and Z = 2. The phosphoraneiminato ligand bridges through its N atom three Au atoms, which itself are connected to each other by weak aurophilic interactions.
Synthese und Kristallstruktur von 2‐Azido‐4,6‐dichloro‐s‐triazin
2005-07-26

Abstract Synthesis and Crystal Structure of 2‐Azido‐4,6‐dichloro‐ s ‐triazine Single crystals of 2‐azido‐4,6‐dichloro‐ s ‐triazine were obtained from a reaction between cyanuric chloride and sodium azide. The structure of this compound was determined by single crystal X‐ray diffraction. 2‐Azido‐4,6‐dichloro‐ s ‐triazine crystallizes in the orthorhombic space group Pbca (no. 61), Z = 8, a = 746.48(8) pm, b = 952.6(1) pm, c = 2001.6(2) pm. The crystal structure contains (C 3 N 3 )(N 3 )Cl 2 molecules being arranged in a tape‐like fashion, with tapes running along a‐axis direction. The tapes are combined with each other by interlocking azide‐ligands including an angle of approximately 90°. This arrangement leads to the formation of corrugated layers in the crystal structure.
NMR Spectroscopic Investigation of the β‐Silyl Effect in Carbocations
2005-07-26

1-Aryl-2-trialkylsilyl-substituted vinyl cations are characterized in solution by NMR spectroscopy. The NMR chemical shift data reveal the stabilization of the positive charge by a β-silyl substituent. The order of hyperconjugative stabilization of a positive charge by β-substituents is H < alkyl < silyl. The β-silyl effect is dependent on the electron demand of the carbocation and decreases with better electron donating α-substituents. NMR spectroscopy is a suitable tool to investigate the competition between π-resonance and σ-hyperconjugation in these type of carbocations.
The Conformational Preference of the Methyl Group in 1‐Methyl‐1‐Silacyclohexane
2005-07-26

The conformational equilibrium of the title compound has been investigated experimentally in the gas phase by gas electron diffraction and in solution at low temperatures by 13C NMR, and theoretically by quantum chemical calculations. Both experimental methods result in a preference of the equatorial position of the methyl group, 68(7)% in the gas phase at 298 K and 74(1)% in solution at 110K. The calculations predict 66% equatorial conformer at room temperature.
N, O‐Dimethyl‐N‐Silylhydroxylamine, a Compound with Steeply Pyramidal Nitrogen Coordination
2005-07-26

N, O-Dimethyl-N-silylhydroxylamine, H3SiMeNOMe, has been prepared by reaction of HMeNOMe with H3SiBr and 2, 6-lutidine as an auxiliary base. The solution NMR data indicate aggregation of the compound. H3SiMeNOMe decomposes at ambient temperature and formation of methylnitrene is probably a first step in the mechanism. The energy of H3SiMeNOMe relative to its potential rearrangement isomer MeHN-H2Si-OMe has been estimated by ab initio calculations to be 289 kJ mol-1. The molecular structure of H3SiMeNOMe has been determined by gas-phase electron diffraction and by ab initio calculations. H3SiMeNOMe possesses a steeply pyramidal nitrogen atom. Hence it is the first silylamine reported with a typically pyramidal nitrogen coordination for electronic reasons. Results of an NBO analysis are discussed to rationalize the bonding situation.
Exploiting the Capture Effect for Collision Detection and Recovery
2005-07-27

In this paper we evaluate a technique to detect and recover messages from packet collisions by exploiting the capture effect. It can differentiate between collisions and packet loss and can identify the nodes involved in the collisions. This information is provided at virtually no extra cost and can produce significant improvements in existing collision mediation schemes. We characterize this technique using controlled collision experiments and evaluate it in real world flooding experiments on a 36-node sensor network.
Accurate Prediction of Power Consumption in Sensor Networks
2005-07-27

Energy consumption is a crucial characteristic of sensor networks and their applications as sensor nodes are commonly battery-driven. Although recent research focuses strongly on energy-aware applications and operating systems, energy consumption is still a limiting factor. Once sensor nodes are deployed, it is challenging and sometimes even impossible to change batteries. As a result, erroneous lifetime prediction causes high costs and may render a sensor network, useless before its purpose is fulfilled. In this paper, we present AEON (accurate prediction of power consumption), a novel evaluation tool to quantitatively predict energy consumption of sensor nodes and whole sensor networks. Our energy model, based on measurements of node current draw and the execution of real code, enables accurate prediction of the actual energy consumption of sensor nodes. Consequently, it prevents erroneous assumptions on node and network lifetime. Moreover, our detailed energy model allows us to compare different low power and energy aware approaches in terms of energy efficiency. Thus, it enables a highly precise estimation of the overall lifetime of a sensor network.
LC–NMR coupling technology: recent advancements and applications in natural products analysis
2005-07-27

Abstract An overview of recent advances in nuclear magnetic resonance (NMR) coupled with separation technologies and their application in natural product analysis is given and discussed. The different modes of LC–NMR operation are described, as well as how technical improvements assist in establishing LC–NMR as an important tool in the analysis of plant‐derived compounds. On‐flow, stopped‐flow and loop‐storage procedures are mentioned, together with the new LC–SPE–NMR configuration. The implementation of mass spectrometry in LC–NMR is also useful on account of the molecular weight and fragmentation information that it provides, especially when new plant species are studied. Cryogenic technology and capillary LC–NMR are the other important recent developments. Since the plant kingdom is endless in producing potential drug candidates, development and optimization of LC–NMR techniques convert the study of natural products to a less‐time‐consuming task, speeding up identification. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Infrared behavior of the ghost-gluon vertex in Landau gauge Yang-Mills theory
2005-07-27

A semi-perturbative calculation of the ghost-gluon vertex in Landau gauge Yang-Mills theory in four and three Euclidean space-time dimensions is presented. Non-perturbative gluon and ghost propagators are employed, which have previously been calculated from a truncated set of Dyson--Schwinger equations and which are in qualitative and quantitative agreement with corresponding lattice results. Our results for the ghost-gluon vertex show only relatively small deviations from the tree-level one in agreement with recent lattice data. In particular, we do not see any sign for a singular behaviour of the ghost-gluon vertex in the infrared.
The Family of Serratia Type Pore Forming Toxins
2005-07-27

The Serratia marcescens hemolysin represents the prototype of a growing family of pore forming toxins. The available bacterial genome sequences reveal Serratia hemolysin homologues in additional species. However, only S. marcescens hemolysin has been studied in great molecular detail. This family of toxins has nothing in common with the pore forming toxins of E. coli type (RTX toxins), the Staphylococcus aureus alpha-toxin or the thiol activated toxin of group A beta-hemolytic streptococci (Streptolysin O). Studies on erythrocytes, eukaryotic cells and artificial black lipid membranes, have shown that the mechanism of pore formation of ShlA is different form other pore forming toxins. The S. marcescens hemolysin proteins ShlB and ShlA, exhibit protein sequence homologues in Proteus mirabilis, Haemophilus ducreyi, Yersinia pestis, Yersinia enterocolitica, Edwardsiella tarda, Photorhabdus luminescens and Xylella fastidiosa . The family of Serratia type pore forming toxins show a unique secretory mechanism which has been described as a two partner secretion system (TPSS) or type V-secretion system. Not only Serratia type pore forming toxins are secreted via TPSS but also adhesins from Bordetella pertussis, Erwinia chrysanthemi and Haemophilus influenzae. The uniqueness of the Serratia family is underlined by the fact that activation of ShlA by ShlB strictly requires phosphatidylethanolamine as a cofactor. And, quite unusual, ShlA undergoes a conformational change during activation.
Determination of regulatory phosphorylation sites in nanogram amounts of a synthetic fragment of ZAP‐70 using microprobe NMR and on‐line coupled capillary HPLC–NMR
2005-07-27

Abstract The protein kinase ZAP‐70 is involved in T‐cell activation and interacts with tyrosine‐phosphorylated peptide sequences known as immunoreceptor tyrosine activation motif s (ITAMs). We have studied the regulatory phosphorylation sites in the tryptic fragment containing amino acids 485–496 (ALGADDSYYTAR). The four possible peptides with phosphorylation at none, one, or both of the Y‐492 and Y‐493 tyrosines were specifically synthesized and analyzed by 1 H/ 13 C–NMR at 600 MHz using a capillary HPLC–NMR microprobe. Unambiguous discrimination of the peptides was possible via effect of chemical shifts of phosphorylation on the aromatic tyrosine protons. With the microprobe and the detection volume of 1.5 μl, it was possible to perform structure elucidation with the very small amounts available for the various peptides. For the syringe injection, 15 μg of the analyte were used (corresponding to ca 2 mg in classical 5‐mm tubes). Capillary HPLC–NMR spectra were recorded in the stopped‐flow mode from less than 400 ng of each peptide, using 1D and 2D techniques ( 1 H, 1 H–COSY‐90, 1 H/ 13 C–HSQC, and 1 H/ 13 C–HMBC). Copyright © 2005 John Wiley &amp; Sons, Ltd.
Monitoring of environmentally monolithic metal-oxide relevant gases by a digital microsensor array
2005-07-27

In this paper, measurements of environmentally relevant gases (CO, CH/sub 4/ and NO/sub 2/) with a novel single-chip digital microhotplate array are presented. The array consists of three tin-oxide-coated microhotplates with integrated MOS-transistor heaters and specifically designed circuitry. The programmable digital temperature controllers enable individual regulation of the microhotplate temperatures in continuous or dynamic mode. Nanocrystalline tin-oxide thick films with different Pd dopings (undoped, 0.2 wt% and 3 wt%) were tested. Excellent discrimination between the three gases was achieved with detection limits of less than 1 ppm for CO, 100 ppm for CH/sub 4/ (40% RH) and 10 ppb of NO/sub 2/ (30%/70% RH).
Mycorrhiza helper bacteriumStreptomycesAcH 505 induces differential gene expression in the ectomycorrhizal fungusAmanita muscaria
2005-07-28

The interaction between the mycorrhiza helper bacteria Streptomyces nov. sp. 505 (AcH 505) and Streptomyces annulatus 1003 (AcH 1003) with fly agaric (Amanita muscaria) and spruce (Picea abies) was investigated. The effects of both bacteria on the mycelial growth of different ectomycorrhizal fungi, on ectomycorrhiza formation, and on fungal gene expression in dual culture with AcH 505 were determined. The fungus specificities of the streptomycetes were similar. Both bacterial species showed the strongest effect on the growth of mycelia at 9 wk of dual culture. The effect of AcH 505 on gene expression of A. muscaria was examined using the suppressive subtractive hybridization approach. The responsive fungal genes included those involved in signalling pathways, metabolism, cell structure, and the cell growth response. These results suggest that AcH 505 and AcH 1003 enhance mycorrhiza formation mainly as a result of promotion of fungal growth, leading to changes in fungal gene expression. Differential A. muscaria transcript accumulation in dual culture may result from a direct response to bacterial substances.
Eye-witness memory and the writing of the Gospels
2005-07-28

For the last several decades, Graham Stanton has worked primarily in Gospels and Jesus research. Following in his footsteps, these reflections concentrate on how the 'history of Jesus', of which we have only fragmentary knowledge, is related to the four Gospels as the oldest narrative reports about him.
Maintenance of Embryonic Auxin Distribution for Apical-Basal Patterning by PIN-FORMED–Dependent Auxin Transport inArabidopsis
2005-07-29

Abstract Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.
On the applicability of Fick's law to diffusion in inhomogeneous systems
2005-07-29

Two alternative expressions exist for the diffusive flux in inhomogeneous systems: Fick's law and the Fokker–Planck law. Here we re-examine the origin of these expressions and perform numerical and physical experiments to shed light on this duality. We conclude that in general the Fokker–Planck expression should be conceded preference, in spite of the fact that Fick's law seems to be more popular.
Stereospecific Synthesis of Chiral 2,3‐Dihydro‐1,4‐benzodithiine and Methyl‐2,3‐dihydro‐1,4‐benzodithiine Derivatives and their Toxic Effects on Trypanosoma brucei
2005-07-29

Abstract Preparation of chiral 2,3‐dihydro‐1,4‐benzodithiine and methyl‐2,3‐dihydro‐1,4‐benzodithiine derivatives with known absolute configurations from the easily accessible chiral synthons benzyl 4‐ O ‐trifloxy‐2,3‐anhydro‐β‐ L ‐ribopyranoside and benzyl 4‐ O ‐trifloxy‐2,3‐anhydro‐α‐ D ‐ribopyranoside is described. These compounds showed significant in vitro toxicity of the bloodstream form of Trypanosoma brucei with an IC 50 of 11 μ M . The parasites' energy metabolism and consumption of oxygen were found to be affected during incubation.
Shp2 Is Required for Protein Kinase C-dependent Phosphorylation of Serine 307 in Insulin Receptor Substrate-1
2005-07-30

The function of insulin receptor substrate-1 (IRS-1), a key molecule of insulin signaling, is modulated by phosphorylation at multiple serine/threonine residues. Phorbol ester stimulation of cells induces phosphorylation of two inhibitory serine residues in IRS-1, i.e. Ser-307 and Ser-318, suggesting that both sites may be targets of protein kinase C (PKC) isoforms. However, in an in vitro system using a broad spectrum of PKC isoforms (alpha, beta1, beta2, delta, epsilon, eta, mu), we detected only Ser-318, but not Ser-307 phosphorylation, suggesting that phorbol ester-induced phosphorylation of this site in intact cells requires additional signaling elements and serine kinases that link PKC activation to Ser-307 phosphorylation. As we have observed recently that the tyrosine phosphatase Shp2, a negative regulator of insulin signaling, is a substrate of PKC, we studied the role of Shp2 in this context. We found that phorbol ester-induced Ser-307 phosphorylation is reduced markedly in Shp2-deficient mouse embryonic fibroblasts (Shp2-/-) whereas Ser-318 phosphorylation is unaltered. The Ser-307 phosphorylation was rescued by transfection of mouse embryonic fibroblasts with wild-type Shp2 or with a phosphatase-inactive Shp2 mutant, respectively. In this cell model, tumor necrosis factor-alpha-induced Ser-307 phosphorylation as well depended on the presence of Shp2. Furthermore, Shp2-dependent phorbol ester effects on Ser-307 were blocked by wortmannin, rapamycin, and the c-Jun NH2-terminal kinase (JNK) inhibitor SP600125. This suggests an involvement of the phosphatidylinositol 3-kinase/mammalian target of rapamycin cascade and of JNK in this signaling pathway resulting in IRS-1 Ser-307 phosphorylation. Because the activation of these kinases does not depend on Shp2, it is concluded that the function of Shp2 is to direct these activated kinases to IRS-1.
A hardware architecture for multi-resolution volume rendering
2005-07-30

In this paper we propose a hardware accelerated ray-casting architecture for multi-resolution volumetric datasets. The architecture is targeted at rendering very large datasets with limited voxel memory resources for both cases where the working set of a frame does or does not fit into the voxel memory. We describe the multi-resolution model used to organize the volume data, especially the wavelet based compression scheme. An efficient hardware implementation of the wavelet decompression is presented and the considerations for volume memory management are discussed. By incorporating the wavelet decompression in hardware a multiple of the decompression bandwidth compared to a PC can be achieved We also show that the impact of our multi-resolution scheme on the actual ray-casting pipeline is minimal.
GEOGRAPHICAL PATTERNS IN BIOLOGICALLY AVAILABLE STRONTIUM, CARBON AND OXYGEN ISOTOPE SIGNATURES IN PREHISTORIC SW GERMANY*
2005-08-01

In order to interpret strontium and oxygen isotope values in Neolithic human skeletons analysed previously, we begin to map the biologically available strontium, carbon and oxygen isotopic signatures of prehistoric southern Germany by analysing tooth enamel of pigs from archaeological sites distributed around the region. The mapping shows a marked upland–lowland difference in biologically available 87 Sr/ 86 Sr values, ranging between 0.7086 and 0.7103 in the sedimentary lowlands, and from 0.710 to as high as 0.722 in the crystalline uplands of the Odenwald, the Black Forest and the Bavarian Forest. In addition, carbon isotopes in the carbonate fraction of pig enamel were generally about 1–2 more enriched in 13 C in the uplands. Despite the expected depletion of 18 O with altitude, oxygen isotopes in pig enamel showed little correlation with site altitude, although for pig samples not older than the Iron Age there was some geographical correlation with δ 18 O patterns in modern precipitation.
Sisterhood and tonal scaling*
2005-08-01

Abstract. This paper discusses central aspects of the effects of hierarchical structure on tonal scaling in intonation. The core results of a number of phonetic studies on this topic, by Ladd, by van den Berg, Gussenhoven and Rietveld, as well as experimental results of our own, are reviewed. We review the suggestions of this earlier work and argue for an addition to the theory. The principle ‘The deeper the steeper’ says that downstep among sister nodes is relatively larger if these sister‐nodes are relatively more deeply embedded in the prosodic representation.
Coxsackievirus-adenovirus receptor (CAR) is essential for early embryonic cardiac development
2005-08-01

The coxsackievirus-adenovirus receptor (CAR) is a cell contact protein on various cell types with unknown physiological function. It belongs to a subfamily of the immunoglobulin-superfamily of which some members are junctional adhesion molecules on epithelial and/or endothelial cells. CAR is dominantly expressed in the hearts and brains of mice until the newborne phase after which it becomes mainly restricted to various epithelial cells. To understand more about the physiological function of CAR, we have generated CAR-deficient mice by gene targeting. We found that these mice die between E11.5 and E13.5 of embryonal development. Ultrastructural analysis of cardiomyocytes revealed that the density of myofibrils was reduced and that their orientation and bundling was disorganized. In addition, mitochondria were enlarged and glycogen storage strongly enriched. In line with these defects, we observed pericardial edema formation as a clear sign of insufficient heart function. Developmental abnormalities likely to be secondary effects of gene ablation were the persistent singular cardial atrio-ventricular canal and dilatations of larger blood vessels such as the cardinal veins. The secondary nature of these defects was supported by the fact that CAR was not expressed on vascular cells or on cells of the vascular wall. No obvious signs for alterations of the histological organization of the placenta were observed. We conclude that CAR is required for embryonal heart development, most likely due to its function during the organization of myofibrils in cardiomyocytes.