julilili42/papers huggingface dataset:
Effective Chemokine Secretion by Dendritic Cells and Expansion of Cross-Presenting CD4−/CD8+Dendritic Cells Define a Protective Phenotype in the Mouse Model of Coxsackievirus Myocarditis
2008-06-13

ABSTRACT Enteroviruses such as coxsackievirus B3 (CVB3) are able to induce lethal acute and chronic myocarditis. In resistant C57BL/6 mice, CVB3 myocarditis is abrogated by T-cell-dependent mechanisms, whereas major histocompatibility complex (MHC)-matched permissive A.BY/SnJ mice develop chronic myocarditis based on virus persistence. To define the role of T-cell-priming dendritic cells (DCs) in the outcome of CVB3 myocarditis, DCs were analyzed in this animal model in the course of CVB3 infection. In both mouse strains, DCs were found to be infectible with CVB3; however, formation of infectious virions was impaired. In DCs derived from C57BL/6 mice, significantly higher quantities of interleukin-10 (IL-10) and the proinflammatory cytokines IL-6 and tumor necrosis factor alpha were measured compared to those from A.BY/SnJ mice. Additionally, the chemokines interferon-inducible protein 10 (IP-10) and RANTES were secreted by DCs from resistant C57BL/6 mice earlier in infection and at significantly higher levels. The protective role of IP-10 in CVB3 myocarditis was confirmed in IP-10 −/− mice, which had increased myocardial injury compared to the immunocompetent control animals. Also, major differences in resistant and permissive mice were found in DC subsets, with C57BL/6 mice harboring more cross-priming CD4 − CD8 + DCs. As CD4 − CD8 + DCs are known to express 10 times more Toll-like receptor 3 (TLR3) than other DC subsets, we followed the course of CVB3 infection in TLR3 −/− mice. These mice developed a fulminant acute myocarditis and secreted sustained low amounts of type I interferons; secretion of IP-10 and RANTES was nearly abrogated in DCs. We conclude that MHC-independent genetic factors involving DC-related IP-10 secretion and TLR3 expression are beneficial in the prevention of chronic coxsackievirus myocarditis.
Efficient linear-scaling calculation of response properties: Density matrix-based Laplace-transformed coupled-perturbed self-consistent field theory
2008-06-13

A density matrix-based Laplace reformulation of coupled-perturbed self-consistent field (CPSCF) theory is presented. It allows a direct, instead of iterative, solution for the integral-independent part of the density matrix-based CPSCF (D-CPSCF) equations [J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 127, 054103 (2007)]. In this way, the matrix-multiplication overhead compared to molecular orbital-based solutions is reduced to a minimum, while at the same time, the linear-scaling behavior of D-CPSCF theory is preserved. The present Laplace-based equation solver is expected to be of general applicability.
Inertial modes of rigidly rotating neutron stars in Cowling approximation
2008-06-13

In this article, we investigate inertial modes of rigidly rotating neutron stars, i.e. modes for which the Coriolis force is dominant. This is done using the assumption of a fixed spacetime (Cowling approximation). We present frequencies and eigenfunctions for a sequence of stars with a polytropic equation of state, covering a broad range of rotation rates. The modes were obtained with a nonlinear general relativistic hydrodynamic evolution code. We further show that the eigenequations for the oscillation modes can be written in a particularly simple form for the case of arbitrary fast, but rigid rotation. Using these equations, we investigate some general characteristics of inertial modes, which are then compared to the numerically obtained eigenfunctions. In particular, we derive a rough analytical estimate for the frequency as a function of the number of nodes of the eigenfunction, and find that a similar empirical relation matches the numerical results with unexpected accuracy. We investigate the slow rotation limit of the eigenequations, obtaining two different sets of equations describing pressure and inertial modes. For the numerical computations we only considered axisymmetric modes, while the analytic part also covers nonaxisymmetric modes. The eigenfunctions suggest that the classification of inertial modes by the quantum numbers of the leading term of a spherical harmonic decomposition is artificial in the sense that the largest term is not strongly dominant, even in the slow rotation limit. The reason for the different structure of pressure and inertial modes is that the Coriolis force remains important in the slow rotation limit only for inertial modes. Accordingly, the scalar eigenequation we obtain in that limit is spherically symmetric for pressure modes, but not for inertial modes.
TheLmgpi15gene, encoding a component of the glycosylphosphatidylinositol anchor biosynthesis pathway, is required for morphogenesis and pathogenicity inLeptosphaeria maculans
2008-06-13

Random insertional mutagenesis was used to investigate pathogenicity determinants in Leptosphaeria maculans. One tagged nonpathogenic mutant, termed m20, was analysed in detail here. The mutant phenotype was investigated by microscopic analyses of infected plant tissues and in vitro growth assays. Complementation and silencing experiments were used to identify the altered gene. Its function was determined by bioinformatics analyses, cell biology experiments and functional studies. The mutant was blocked at the invasive growth phase after an unaffected initial penetration stage, and displayed a reduced growth rate and an aberrant hyphal morphology in vitro. The T-DNA insertion occurred in the intergenic region between two head-to-tail genes, leading to a complex deregulation of their expression. The unique gene accounting for the mutant phenotype was suggested to be the orthologue of the poorly conserved Saccharomyces cerevisiae gpi15, which encodes for one component of the glycosylphosphatidylinositol (GPI) anchor biosynthesis pathway. Consistent with this predicted function, a functional translational fusion with the green fluorescent protein (GFP) was targeted to the endoplasmic reticulum. Moreover, the mutant exhibited an altered cell wall and addition of glucosamine relieved growth defects. It is concluded that the GPI anchor biosynthetic pathway is required for morphogenesis, cell wall integrity and pathogenicity in Leptosphaeria maculans.
Excess glycaemic excursions after an oral glucose tolerance test compared with a mixed meal challenge and self‐measured home glucose profiles: is the OGTT a valid predictor of postprandial hyperglycaemia and vice versa?
2008-06-16

Introduction: Postprandial hyperglycaemia is often assumed in individuals with high glucose excursions during an oral glucose tolerance test (OGTT), but the relationship between glucose levels during the OGTT and after a mixed meal is yet unclear. We addressed whether (i) glucose concentrations after an oral glucose load are similar to those after a test meal or under daily life conditions and (ii) impaired glucose tolerance (IGT) predicts postprandial hyperglycaemia. Patients and Methods: A total of 60 subjects with normal (NGT), IGT or diabetic (DM) glucose tolerance were examined with an OGTT, a mixed meal challenge (3433 kJ) and a self‐determined 10‐point home glucose profile. Results: There was a significant correlation between the 120‐min OGTT glucose levels and the glycaemic excursions after the test meal and during everyday conditions. However, glucose excursions during the OGTT exceeded those after the test meal and during everyday conditions by ∼20 and ∼30% respectively. Likewise, insulin and C‐peptide levels rose to higher levels after oral glucose compared with mixed meal ingestion. The mean self‐determined diurnal glucose levels were already 10% higher in subjects with IGT compared with NGT subjects (p &lt; 0.0001). Conclusions: Glucose levels reached after an oral glucose challenge and during real life are correlated to some extent, but the absolute levels of glycaemia greatly differ between both conditions. Therefore, ‘postchallenge’ glucose levels measured during an OGTT might be used as a predictor of ‘postprandial hyperglycaemia’, but caution should be taken when both terms are used synonymously. Furthermore, subjects with IGT during an OGTT already exhibit increased postprandial glucose levels under real‐life conditions. This suggests that IGT should already be considered an overt disease condition rather than merely a high‐risk situation.
Geoarchaeological and chronostratigraphical investigations of open‐air sites in the Geelbek Dunes, South Africa
2008-06-16

Abstract The Geelbek Dunes located north of Cape Town, South Africa, are an active, northward migrating dune field. Interdunal deflation hollows temporarily expose former land surfaces that are associated with archaeological sites. These open‐air sites shed light on large‐scale patterns of Middle and Later Stone Age settlement and augment the information gained from well‐stratified, but spatially limited caves, rock shelters, and coastal shell middens. Based on paleopedological and sedimentological parameters, three former land surfaces were identified and associated with different assemblages. A chronostratigraphy of the various land surfaces was established by applying optically stimulated luminescence (OSL) dating. The youngest former land surface is represented by a dune generation (AD2) which stabilized at a maximum of 5 ka. An older dune generation (AD1) shows a more heterogeneous age pattern where deposition started at ca. 27 ka with a maximum estimated age of stabilization at ca. 10 ka. Both of these dune generations overlie a weathered calcrete complex of Middle to Late Pleistocene age. While the third dune generation (AD0) was observed between underlying calcrete layers, samples taken from this unit could not be dated. © 2008 Wiley Periodicals, Inc.
Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics on Human Language Technologies: Student Research Workshop
2008-06-16

Welcome to the ACL-08: HLT Student Research Workshop! The Student Research Workshop is now an established tradition at ACL conferences and provides a venue for student researchers investigating topics in Computational Linguistics and Natural Language Processing to present their work and receive feedback. New this year was encouraging researchers in Information Retrieval to be involved, both reviewers and authors. We received a total of 27 submissions coming from 11 different countries, and accepted 12 of them. 5 will be presented orally, and 7 as posters, during a common poster session with the main conference. A total of 61 students and senior researchers agreed to serve on the program committee, which allowed us to assign 5 reviewers per paper. We would like to thank the reviewers for understanding the spirit of the Student ResearchWorkshop and giving careful and constructive reviews. We hope their comments will be helpful to all the students who submitted their work. All presenters received financial support from the U.S. National Science Foundation to assist them in their travel to Columbus.
Molecular determinants of ammonia and urea conductance in plant aquaporin homologs
2008-06-17

Aquaporins and/or aquaglyceroporins regulate the permeability of plant membranes to water and small, uncharged molecules. Using molecular simulations with a plant plasma membrane aquaporin tetramer, the residues in the channel constriction region were identified as the crucial determinants of ammonia and urea conductance. The impact of these residues was experimentally verified using AtPIP2;1 pore mutants. Several, but not all, mutants with a NIP‐like selectivity filter promoted yeast growth on urea or ammonia as sole sources of nitrogen. TIP‐like mutants conducted urea but not NH 3 , and a residue without direct contact to the pore lumen was critical for conduction in the mutants.
Hepatitis A virus protein 2B suppresses beta interferon (IFN) gene transcription by interfering with IFN regulatory factor 3 activation
2008-06-17

Hepatitis A virus (HAV) antagonizes the innate immune response by inhibition of retinoic acid-inducible gene I-mediated and melanoma differentiation-associated gene 5-mediated beta interferon (IFN- β ) gene expression. This study showed that this is due to an interaction of HAV with mitochondrial antiviral signalling protein (MAVS)-dependent signalling, in which the viral non-structural protein 2B and the protein intermediate 3ABC recently suggested in this context seem to be involved, cooperatively affecting the activities of MAVS and the kinases TANK-binding kinase 1 (TBK1) and the inhibitor of NF- κ B kinase ε (IKKε). In consequence, interferon regulatory factor 3 (IRF-3) is not activated. As IRF-3 is necessary for IFN- β transcription, inhibition of this factor results in efficient suppression of IFN- β synthesis. This ability might be of vital importance for HAV, which is an exceptionally slow growing virus sensitive to IFN- β , as it allows the virus to establish infection and maintain virus replication for a longer period of time.
Formation of Spirocyclic Compounds from Heck Cyclizations Invoking Cyclic Enamides
2008-06-17

The palladium-mediated transformation of 3,4-dihydro-2(1H)-pyridinones 12 featuring a (2-bromophenyl)ethyl substituent in the 5-position produces spirocyclic products, imides 14 and amides 15. The formation of these products can be explained by insertion of the enamide double bond into the initial aryl-Pd bond followed by oxidation or reduction of the organopalladium intermediate. Alternatively, formation of these spiro compounds might proceed via acyliminium ion intermediates.
Ordovician metagranitoid from the Anatolide‐Tauride Block, northwest Turkey: geodynamic implications
2008-06-18

Abstract We report a Middle Ordovician metagranitoid from the northern margin of the Anatolide‐Tauride Block, the basement of which is generally characterized by voluminous Latest Proterozoic to Early Cambrian granitoids. The Ordovician metagranitoid forms an ∼400‐m‐thick body in the marbles and micaschists of the Tavşanlı Zone. The whole sequence was metamorphosed in the blueschist facies during the Late Cretaceous ( c. 80 Ma). Zircons from the metagranitoid give a Middle Ordovician Pb‐Pb evaporation age of 467.0 ± 4.5 Ma interpreted as the age of crystallization of the parent granitic magma. The micaschists underlying the metagranitoid yield Cambro‐Ordovician (530–450 Ma) and Carboniferous ( c. 310 Ma) detrital zircon ages indicating that the granitoid is a pre‐ or syn‐metamorphic tectonic slice. The Ordovician metagranitoid represents a remnant of the crystalline basement of the Anatolide‐Tauride Block and provides evidence for Ordovician magmatism at the northern margin of Gondwana. Prismatic Carboniferous detrital zircons in the micaschists indicate that during the Triassic, the northern margin of the Anatolide‐Tauride Block was close to Variscan terranes.
Hip Abductor Weakness is not the Cause for Iliotibial Band Syndrome
2008-06-18

Muscular deficits in the hip abductors are presumed to be a major factor in the development of Iliotibial Band Syndrome in runners. No definite relationship between muscular weakness of the hip abductors and the development of Iliotibial Band Syndrome or different ratios between hip adduction to abduction have been reported so far. Isokinetic measurements were taken from 10 healthy runners and 10 runners with Iliotibial Band Syndrome. Primary outcome variables were concentric, eccentric, and isometric peak torque of the hip abductors and adductors at 30 degrees/s, and a concentric endurance quotient at the same angle velocity. Differences in muscle strength of the hip abductors between healthy (CO) and injured runners (ITBS) were not statistically significant in any of the muscle functions tested. Both groups showed the same strength differences between hip adduction and abduction, and increased strength in hip adduction. Weakness of hip abductors does not seem to play a role in the etiology of Iliotibial Band Syndrome in runners, since dynamic and static strength measurements did not differ between groups, and differences between hip abduction and adduction were the same. Strengthening of hip abductors seems to have little effect on the prevention of Iliotibial Band Syndrome in runners.
Down-regulation of CD28, TCR-zeta (zeta) and up-regulation of FAS in peripheral cytotoxic T-cells of primary breast cancer patients.
2008-06-18

The significant up-regulation of CD95 and down-regulation of TCR zeta and CD28 in peripheral cytotoxic T-cells of breast cancer patients leads to the hypothesis of systemic immunosuppression, which could open the door for tumor cell dissemination via the blood stream and which is the subject of ongoing studies.
Eugen Müller (1905–1976)
2008-06-18

Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2046/2008/o200700066_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Comparison of Maize (Zea maysL.) F1-Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends
2008-06-19

Abstract The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1 plants compared to their homozygous parental inbred plants. Heterosis is manifested during the early stages of root development in maize. The goal of this study was to identify nonadditive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two-step strategy was used. First, a microarray preselection of nonadditively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high-throughput quantitative real-time (qRT)–PCR experiments. Initial microarray experiments identified 1941 distinct microarray features that displayed nonadditive gene expression in at least 1 of the 12 analyzed hybrids compared to the midparent value of their parental inbred lines. Most nonadditively expressed genes were expressed between the parental values (&amp;gt;89%). Comparison of these 1941 genes with nonadditively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance. This finding suggests organ-specific patterns of nonadditively expressed genes. qRT–PCR analyses of 64 of the 1941 genes in four different hybrids revealed conserved patterns of nonadditively expressed genes in different hybrids. Subsequently, 22 of the 64 genes that displayed nonadditive expression in all four hybrids were analyzed in 12 hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all 12 hybrids and might thus play a protective role in heterosis-related antioxidative defense in the primary root of maize hybrids. The findings of this study are consistent with the hypothesis that both global expression trends and the consistent differential expression of specific genes contribute to the organ-specific manifestation of heterosis.
The immunoadhesin glycoprotein VI-Fc regulates arterial remodelling after mechanical injury in ApoE−/− mice
2008-06-19

GPVI-Fc preferentially bound to sites of vascular injury and was able to inhibit neointima formation after wire-induced vascular injury in ApoE(-/-) mice. Thus, soluble GPVI-Fc might be also a promising compound to attenuate lesion progression after plaque rupture.
How to monitor elusive lizards: comparison of capture–recapture methods on giant day geckos ( Gekkonidae , Phelsuma madagascariensis grandis ) in the Masoala rainforest exhibit, Zurich Zoo
2008-06-19

Abstract Rapid and reliable estimation of population size is needed for the efficient monitoring of animal populations of conservation concern. Unfortunately, technical advances in this area have not been paralleled in uptake in conservation, which may be due to difficulties in implementation or the lack of general guidelines for application. Here we tested five different methods used to estimate population size [capture–mark–recapture (CMR), finite‐mixture models, model averaging of finite‐mixture models, accumulation curve methods (ACM), and the line transect method (LT)] using extensive capture–recapture data of the giant day gecko ( Gekkonidae , Phelsuma madagascariensis grandis , Gray 1870) at the Masoala rainforest exhibit, Zurich Zoo. When the complete data were analyzed [30 sessions (and 27 sessions for the LT)], all methods except the LT produced similar estimates of population size. The simple ACM gave a small coefficient of variation (CV), but did not cover the most likely value of population size at moderate sampling effort. Nevertheless, the ACM was the only method that showed a reasonable convergence when subsets of data were used. CMR and Pledger models included the reference value in their confidence intervals (CI) after 25 and 30 sessions, respectively. Although model averaging did slightly improve the estimate, the CV was still high for the full dataset. Our method of using subsets of data to test the robustness of estimates is simple to apply and could be adopted more widely in such analyzes to evaluate sensitivity to method of evaluation. In conclusion, simple accumulation methods showed similar efficiency to more complex statistical models, and are likely to be sufficiently precise for most conservation monitoring purposes.
Sodic Pyroxene and Sodic Amphibole as Potential Reference Materials for In Situ Lithium Isotope Determinations by SIMS
2008-06-20

Two large pegmatitic crystals of sodic pyroxene (aegirine) and sodic amphibole (arfvedsonite) from the agpaitic igneous Ilímaussaq Complex, south Greenland were found to be suitable as reference materials for in situ Li isotope determinations. Lithium concentrations determined by SIMS and micro‐drilled material analysed by MC‐ICP‐MS generally agreed within analytical uncertainty. The arfvedsonite crystal was homogeneous with [Li] = 639 ± 51 μg g −1 (2s, n = 69, MC‐ICP‐MS and SIMS results). The aegirine crystal shows strongly developed sector zoning, which is a common feature of aegirines. Using qualitative element mapping techniques (EPMA), the homogeneous core of the crystal was easily distinguished from the outermost sectors of the crystals. The core had a mean [Li] of 47.6 ± 3.6 μg g −1 (2s, n = 33) as determined by SIMS. The seven micro‐drilled regions measured by solution MC‐ICP‐MS returned slightly lower concentrations (41–46 μg g −1 ), but still overlap with the SIMS data within uncertainty. Based on MC‐ICP‐MS and SIMS analyses, the variation in δ 7 Li was about 1‰ in each of the two crystals, which is smaller than that in widely used glass reference materials, making these two samples suitable to serve as reference materials. There was, however, a significant offset between the results of MC‐ICP‐MS and SIMS. The latter deviated from the MC‐ICP‐MS results by −6.0 ± 1.9‰ (2s) for the amphibole and by −3.9 ± 1.9‰ (2s) for the aegirine. This indicates the presence of a significant matrix effect in SIMS determinations of Li isotopes for amphibole and pyroxene relative to the basalt glasses used for calibration. Based on the MC‐ICP‐MS results, mean δ 7 Li values of +0.7 ± 1.2‰ (2s, n = 10) for the arfvedsonite crystal and of −3.7 ± 1.2‰ (2s, n = 7) for the core of the aegirine crystal were calculated. Adopting these values, SIMS users can correct for the specific IMF (instrumental mass fractionation) of the ion probe used. We propose that these two crystals serve as reference materials for in situ Li isotope determinations by SIMS and pieces of these two crystals are available from the first author upon request.