julilili42/papers huggingface dataset:
Segment-based tetrahedral meshing and rendering
2006-11-29

We present a meshing and rendering framework for large unstructured tetrahedral meshes which is based on a collection of segments that form a multi resolution model. Each segment contains several thousand tetrahedra and covers either a part of the original tetrahedral mesh or a simplified version of the mesh. The mesh can be adapted locally at run time to viewing and classification parameters by replacing segments with other segments. Dependencies between segments are stored in a hierarchical graph and ensure a consistent mesh at any time. So, we extend the concept of multi-triangulations from triangle meshes to tetrahedral meshes and show how hierarchical segments can be constructed easily for huge tetrahedral meshes.The segments are stored in a simple, but efficient compressed format which not only saves disc space but also allows for an easy calculation of the incidency information between segments at decompression time. A visualization system exploits the multi-triangulation to increase the interactivity of direct volume rendering, isosurface extraction and vector field visualization such that large meshes can be explored on standard PCs.
The Assembly Pathway of the 19S Regulatory Particle of the Yeast 26S Proteasome
2006-11-30

The 26S proteasome consists of the 20S proteasome (core particle) and the 19S regulatory particle made of the base and lid substructures, and it is mainly localized in the nucleus in yeast. To examine how and where this huge enzyme complex is assembled, we performed biochemical and microscopic characterization of proteasomes produced in two lid mutants, rpn5-1 and rpn7-3, and a base mutant ΔN rpn2, of the yeast Saccharomyces cerevisiae. We found that, although lid formation was abolished in rpn5-1 mutant cells at the restrictive temperature, an apparently intact base was produced and localized in the nucleus. In contrast, in ΔN rpn2 cells, a free lid was formed and localized in the nucleus even at the restrictive temperature. These results indicate that the modules of the 26S proteasome, namely, the core particle, base, and lid, can be formed and imported into the nucleus independently of each other. Based on these observations, we propose a model for the assembly process of the yeast 26S proteasome.
Religious individualization: new challenges to education for tolerance
2006-11-30

The focus of this article is on the relationship between tolerance and individualized religion as the most common type of adolescent religion in many western countries. Drawing on a number of qualitative studies conducted by the author with children and adolescents in Germany, as well as on other larger studies conducted by others, the author identifies a number of problem areas, for example, in Christian adolescents' views of Islam, and discusses the consequences of individualized religion for tolerance education. Different models of religious education in Germany and other European countries are considered. Special emphasis is given to the following question: if and under what conditions can religion and religious education become sources of tolerance? The author suggests that the model of co‐operative dialogical religious education has the potential to support religious identities and, at the same time, to foster dialogical openness.
Dynamics of Oscillatory Activity during Auditory Decision Making
2006-11-30

Perceptual decision making requires the comparison and integration of sensory evidence to generate a behavioral response. We used magnetoencephalography to investigate the temporal dynamics of decision making during an auditory task that required forced-choice decisions about whether a pair of syllables S1 and S2 differed either in their acoustic patterns or in the perceived position of their sound sources. Conditions with easy and difficult decisions were created by varying the similarity of S1 and S2. Statistical probability mapping showed enhanced gamma-band activity (GBA) over posterior parietal cortex for spatial and over left inferior frontal cortex for pattern changes (at approximately 120 to 220 ms after S2 onset). Activations were stronger for easy than difficult decisions. GBA over dorsolateral prefrontal cortex was more pronounced at approximately 280 to 430 ms for easy than difficult decisions regardless of type of change, possibly reflecting decision-relevant networks that integrate information from higher sensory areas representing the perceptual alternatives. Sensorimotor beta desynchronization as a measure of motor preparation peaked at approximately 460 ms for easy and at approximately 520 ms for difficult decisions, thus reflecting the reaction time difference between both conditions. In summary, the analysis of oscillatory activity in magnetoencephalogram served to elucidate the temporal dynamics of perceptual decision making in humans.
On superselection rules in Bohm–Bell theories
2006-11-30

The meaning of superselection rules in Bohm-Bell theories (i.e., quantum theories with particle trajectories) is different from that in orthodox quantum theory. More precisely, there are two concepts of superselection rule, a weak and a strong one. Weak superselection rules exist both in orthodox quantum theory and in Bohm-Bell theories and represent the conventional understanding of superselection rules. We introduce the concept of strong superselection rule, which does not exist in orthodox quantum theory. It relies on the clear ontology of Bohm-Bell theories and is a sharper and, in the Bohm-Bell context, more fundamental notion. A strong superselection rule for the observable G asserts that one can replace every state vector by a suitable statistical mixture of eigenvectors of G without changing the particle trajectories or their probabilities. A weak superselection rule asserts that every state vector is empirically indistinguishable from a suitable statistical mixture of eigenvectors of G. We establish conditions on G for both kinds of superselection. For comparison, we also consider both kinds of superselection in theories of spontaneous wavefunction collapse.
Earnings‐related Severance Pay
2006-11-30

Abstract. In an efficiency wage economy, lump‐sum severance pay from which shirkers can be excluded raises employment. However, severance payments are usually related to wages. It is shown that earnings‐related, mandated severance pay will have ambiguous employment effects if effort can be varied continuously. A substitution of the earnings‐related for the lump‐sum component reduces employment. Thus, the prevalent form of severance payments in OECD countries might have less advantageous employment effects than previously conjectured.
Drug-Eluting and Bare Nitinol Stents for the Treatment of Atherosclerotic Lesions in the Superficial Femoral Artery:Long-term Results From the SIROCCO Trial
2006-12-01

These data demonstrate that the sirolimus-eluting and the bare SMART stent are effective, safe, and free from restenosis in a majority of patients for up to 24 months. Because the restenosis rate in the bare stent group is unexpectedly low, no significant difference could be found between the sirolimus-eluting and the bare SMART stents.
Phytotoxicity and Innate Immune Responses Induced by Nep1-Like Proteins
2006-12-01

Abstract We show that oomycete-derived Nep1 (for necrosis and ethylene-inducing peptide1)–like proteins (NLPs) trigger a comprehensive immune response in Arabidopsis thaliana, comprising posttranslational activation of mitogen-activated protein kinase activity, deposition of callose, production of nitric oxide, reactive oxygen intermediates, ethylene, and the phytoalexin camalexin, as well as cell death. Transcript profiling experiments revealed that NLPs trigger extensive reprogramming of the Arabidopsis transcriptome closely resembling that evoked by bacteria-derived flagellin. NLP-induced cell death is an active, light-dependent process requiring HSP90 but not caspase activity, salicylic acid, jasmonic acid, ethylene, or functional SGT1a/SGT1b. Studies on animal, yeast, moss, and plant cells revealed that sensitivity to NLPs is not a general characteristic of phospholipid bilayer systems but appears to be restricted to dicot plants. NLP-induced cell death does not require an intact plant cell wall, and ectopic expression of NLP in dicot plants resulted in cell death only when the protein was delivered to the apoplast. Our findings strongly suggest that NLP-induced necrosis requires interaction with a target site that is unique to the extracytoplasmic side of dicot plant plasma membranes. We propose that NLPs play dual roles in plant pathogen interactions as toxin-like virulence factors and as triggers of plant innate immune responses.
Structural and thermoelectric properties of epitaxially grown Bi2Te3 thin films and superlattices
2006-12-01

Multi-quantum-well structures of Bi2Te3 are predicted to have a high thermoelectric figure of merit ZT. Bi2Te3 thin films and Bi2Te3∕Bi2(Te0.88Se0.12)3 superlattices (SLs) were grown epitaxially by molecular beam epitaxy on BaF2 substrates with periods of 12 and 6nm, respectively. Reflection high-energy electron diffraction confirmed a layer-by-layer growth, x-ray diffraction yielded the lattice parameters and SL periods and proved epitaxial growth. The in-plane transport coefficients were measured and the thin films and SL had power factors between 28 and 35μW∕cmK2. The lattice thermal conductivity varied between 1.60W∕mK for Bi2Te3 thin films and 1.01W∕mK for a 10nm SL. The best figures of merit ZT were achieved for the SL; however, the values are slightly smaller than those in bulk materials. Thin films and superlattices were investigated in plan view and cross section by transmission electron microscopy. In the Bi2Te3 thin film and SL the dislocation density was found to be 2×1010cm−2. Bending of the SL with amplitudes of 30nm (12nm SL) and 15nm (6nm SL) and a wavelength of 400nm was determined. Threading dislocations were found with a density greater than 2×109cm−2. The superlattice interfaces are strongly bent in the region of the threading dislocations, undisturbed regions have a maximum lateral sie of 500nm. Thin films and SL showed a structural modulation [natural nanostructure (nns)] with a wavelength of 10nm and a wave vector parallel to (1,0,10). This nns was also observed in Bi2Te3 bulk materials and turned out to be of general character for Bi2Te3. The effect of the microstructure on the thermoelectric properties is discussed. The microstructure is governed by the superlattice, the nns, and the dislocations that are present in the films. Our results indicate that the microstructure directly affects the lattice thermal conductivity. Thermopower and electrical conductivity were found to be negatively correlated and no clear dependence of the two quantities on the microstructure could be found.
Voices of the dead: complex nonlinear vocal signals from the larynx of an ultrasonic frog
2006-12-01

SUMMARY Most anurans are highly vocal but their vocalizations are stereotyped and simple with limited repertoire sizes compared with other vocal vertebrates,presumably because of the limited mechanisms for fine vocal motor control. We recently reported that the call of the concaveeared torrent frog (Amolops tormotus Fei) is an exception in its seemingly endless variety, musical warbling quality, extension of call frequency into the ultrasonic range and the prominence of subharmonics, chaos and other nonlinear features. We now show that the major spectral features of its calls, responsible for this frog's vocal diversity, can be generated by forcing pressurized air through the larynx of euthanized males. Laryngeal specializations for ultrasound appear to include very thin portions of the medial vocal ligaments and reverse sexual size dimorphism of the larynx - being smaller in males than in females. The intricate morphology of the vocal cords, which changes along their length,suggests that nonlinear phenomena probably arise from complex nonlinear oscillatory regimes of separate elastically coupled masses. Amolopsis thus the first amphibian for which the intrinsic nonlinear dynamics of its larynx - a relatively simple and expedient mechanism - can account for the species' call complexity, without invoking sophisticated neuromuscular control.
Enhanced mixing and reaction through flow focusing in heterogeneous porous media
2006-12-01

Transverse dispersion across adjacent streamlines can control the amount of mixing and reaction between one or more contaminants and a limiting substrate along the fringes of groundwater plumes. Streamlines in groundwater converge and diverge in heterogeneous porous media, depending on the permeability distribution. When flow is focused in a high‐permeability zone, the distance required for a solute to cross a given number of streamlines decreases, and the time allowed for mixing and reaction is reduced. Because the first effect outweighs the latter, the overall result is an enhancement of transverse mixing and reaction. Here we develop a conceptual model of heterogeneous two‐dimensional structures facilitating flow focusing. We use the conceptual model to develop simple analytical expressions quantifying the extent to which mixing and reaction are enhanced when flow focusing occurs and compare these to results of numerical simulations. Significant enhancement of transverse mixing and reaction by flow focusing is observed; for the cases considered, flow focusing enhances the amount of reaction by a factor ranging from 1.8 to 11.9. The relatively simple analytical expressions demonstrate that the fraction of the domain height made up by high‐permeability inclusions, the fraction of flow that passes through the inclusions, and the fringe bypassing of inclusions determine the amount of mixing and reaction enhancement for the permeability distributions considered. These results partially explain why field‐scale dispersivities are larger than laboratory derived dispersivities, where homogeneous and isotropic sediments are typically used. Further work is needed to verify the theoretical results presented here with laboratory and field experiments and to expand the relatively simple analytical expressions to consider more heterogeneous three‐dimensional permeability fields.
Thrombospondins deployed by thrombopoietic cells determine angiogenic switch and extent of revascularization
2006-12-01

Thrombopoietic cells may differentially promote or inhibit tissue vascularization by releasing both pro- and antiangiogenic factors. However, the molecular determinants controlling the angiogenic phenotype of thrombopoietic cells remain unknown. Here, we show that expression and release of thrombospondins (TSPs) by megakaryocytes and platelets function as a major antiangiogenic switch. TSPs inhibited thrombopoiesis, diminished bone marrow microvascular reconstruction following myelosuppression, and limited the extent of revascularization in a model of hind limb ischemia. We demonstrate that thrombopoietic recovery following myelosuppression was significantly enhanced in mice deficient in both TSP1 and TSP2 (TSP-DKO mice) in comparison with WT mice. Megakaryocyte and platelet levels in TSP-DKO mice were rapidly restored, thereby accelerating revascularization of myelosuppressed bone marrow and ischemic hind limbs. In addition, thrombopoietic cells derived from TSP-DKO mice were more effective in supporting neoangiogenesis in Matrigel plugs. The proangiogenic activity of TSP-DKO thrombopoietic cells was mediated through activation of MMP-9 and enhanced release of stromal cell-derived factor 1. Thus, TSP-deficient thrombopoietic cells function as proangiogenic agents, accelerating hemangiogenesis within the marrow and revascularization of ischemic hind limbs. As such, interference with the release of cellular stores of TSPs may be clinically effective in augmenting neoangiogenesis.
Differential expression of otoferlin in brain, vestibular system, immature and mature cochlea of the rat
2006-12-01

Abstract Mutations of the human otoferlin gene lead to an autosomal recessive nonsyndromic form of prelingual, sensorineural deafness (deafness autosomal recessive 9, DFNB9). Several studies have demonstrated expression of otoferlin in the inner ear and brain, and suggested a role of otoferlin in Ca 2+ ‐triggered exocytosis. So far, otoferlin expression profiles were solely based on the detection of mRNA. Here, we analysed the expression of otoferlin protein and mRNA using immunohistochemistry, in situ hybridization and RT‐PCR in neonatal and mature Wistar rat tissue. In agreement with previous studies, otoferlin expression was found in the brain and in inner and vestibular hair cells. Otoferlin mRNA and protein was, however, also detected in mature outer hair cells of low‐frequency processing cochlear turns and in auditory nerve fibres. In outer, inner and vestibular hair cells, otoferlin was subcellularly localized at a considerable distance from the presumed active release sites. Double‐staining with the synaptic ribbon marker, C‐terminal binding protein 2 (CtBP2), or the presynaptic Ca 2+ ‐channel, Ca v 1.3, both assumed to mark the sites of vesicle fusion and transmitter release, did not colocalize with otoferlin expression and thus do not necessarily support a selected role of otoferlin in Ca 2+ ‐triggered exocytosis. The widespread distribution of otoferlin in neurons, nerve fibres and hair cells, and its subcellular distribution extending beyond the regions of synaptic vesicle fusion, i.e. coenrichment with the cytosolic Golgi matrix protein 130 (GM130) in inner hair cells or the early endosomal autoantigen 1 (EEA1) in outer hair cells support instead the idea of a more ubiquitous role of otoferlin in early/recycling endosome trans ‐Golgi network dynamics.
Cortical Demyelination Can Be Modeled in Specific Rat Models of Autoimmune Encephalomyelitis and Is Major Histocompatability Complex (MHC) Haplotype-Related
2006-12-01

In recent years, a number of histopathologic studies revealed the presence of cortical demyelination in multiple sclerosis (MS). The underlying mechanisms responsible for cortical demyelination are unresolved. Recently, the presence of cortical lesions in autoimmune encephalomyelitis (EAE) induced in marmosets and Lewis rats has been demonstrated. So far, it is not known whether cortical demyelinated lesions are also present in other models of EAE. In this study, we analyzed a large spectrum of different rat strains actively immunized with myelin oligodendrocyte glycoprotein (MOG), a model strongly mimicking MS for cortical demyelination. By using sets of rat strains with the constant EAE-permissive LEW nonmajor histocompatability complex (MHC) genome, but different MHC haplotypes, we demonstrated that considerable cortical demyelination was only found in LEW.1AR1 (RT1) and LEW.1W (RT1) strains. These rat strains have the isotypes and alleles RT1.BD in the MHC II region and RT1.C in the nonclassic MHC I region in common. Because cortical demyelination was most prominent in LEW.1AR1 rats, an additional strong influence is promoted by the RT1.A MHC class I allele. Demyelination was accompanied by microglia infiltration and deposition of immunoglobulins on myelin sheaths. Our study shows that extensive cortical demyelination can be reproducibly induced in certain rat strains by active immunization with MOG. Furthermore, our findings suggest that cortical demyelination in EAE depends on particular combinations of MHC I and class II isotypes and alleles. The mechanisms for this influence and any similar effects in humans will be important to define.
Resveratrol Binds to the Sulfonylurea Receptor (SUR) and Induces Apoptosis in a SUR Subtype-specific Manner
2006-12-01

Sulfonylurea receptors (SURs) constitute the regulatory subunits of ATP-sensitive K+ channels (K(ATP) channels). SUR binds nucleotides and synthetic K(ATP) channel modulators, e.g. the antidiabetic sulfonylurea glibenclamide, which acts as a channel blocker. However, knowledge about naturally occurring ligands of SUR is very limited. In this study, we show that the plant phenolic compound trans-resveratrol can bind to SUR and displace binding of glibenclamide. Electrophysiological measurements revealed that resveratrol is a blocker of pancreatic SUR1/K(IR)6.2 K(ATP) channels. We further demonstrate that, like glibenclamide, resveratrol induces enhanced apoptosis. This was shown by analyzing different apoptotic parameters (cell detachment, nuclear condensation and fragmentation, and activities of different caspase enzymes). The observed apoptotic effect was specific to cells expressing the SUR1 isoform and was not mediated by the electrical activity of K(ATP) channels, as it was observed in human embryonic kidney 293 cells expressing SUR1 alone. Enhanced susceptibility to resveratrol was not observed in pancreatic beta-cells from SUR1 knock-out mice or in cells expressing the isoform SUR2A or SUR2B or the mutant SUR1(M1289T). Resveratrol was much more potent than glibenclamide in inducing SUR1-specific apoptosis. Treatment with etoposide, a classical inducer of apoptosis, did not result in SUR isoform-specific apoptosis. In conclusion, resveratrol is a natural SUR ligand that can induce apoptosis in a SUR isoform-specific manner. Considering the tissue-specific expression patterns of SUR isoforms and the possible effects of SUR mutations on susceptibility to apoptosis, these observations could be important for diabetes and/or cancer research.
Enzymatic Degradation ofβ- and Mixedα,β-Oligopeptides
2006-12-01

One of the main and most astonishing characteristics of peptides comprised of beta-amino acids with proteinogenic side chains is their extraordinarily high stability towards enzymatic degradation. So far, only certain microbial enzymes have been shown to cleave N-terminal beta(3)-homoamino acid residues from peptides. In this work, the L-aminopeptidase-D-amidase/esterase (DmpA) from Ochrobactrum anthropi LMG7991 is compared to two closely related beta-peptidyl aminopeptidases (BapA), which originate from Sphingosinicella strains, and to microsomal leucine aminopeptidase (LAP) as a reference. All four enzymes are aminopeptidases cleaving N-terminal amino acids from small peptides. Degradation experiments reveal that DmpA and both BapA enzymes exhibit unique, but clearly distinct substrate specificities and preferences. DmpA also cleaves beta- and mixed alpha,beta-peptides and amides, but a short side chain of the N-terminal beta-amino acid residue seems to be a prerequisite, since only peptides carrying N-terminal betahGly and beta(3)hAla are hydrolyzed with good efficiencies. Both beta-peptidyl aminopeptidases cleave beta-amino acids from a variety of beta-peptides and mixed alpha,beta-peptides, but they do not accept alpha-amino acids in the N-terminal position. Astonishingly, DmpA exhibited much higher catalytical rates for the mixed dipeptide carnosine (H-betahGly-His-OH) than for any other substrate described until now.