julilili42/papers huggingface dataset:
Root inoculation with a forest soil streptomycete leads to locally and systemically increased resistance against phytopathogens in Norway spruce
2007-12-10

Soil streptomycetes are commonly antagonistic against plant pathogens. However, interactions involving increased defense responses in the host plant, leading to suppression of plant disease development, have not yet been detailed. Here, the mechanisms were studied of disease suppression by Streptomyces sp. GB 4-2 against Heterobasidion root and butt rot in Norway spruce (Picea abies) seedlings. GB 4-2 promoted mycelial growth of the phytopathogenic fungus, germination rate of fungal spores, extension of germ tubes and early colonization of outer cortical layers of the plant root. Reduced colonization of the inner cortical cell layers was accompanied by the induction of cell wall appositions, and increased xylem formation in the vascular cylinder emerged after bacterium-fungus coinoculation. Bacterial treatment led to decreased water content in roots and needles and increased photosynthetic yield (F(v)/F(m)) and peroxidase activities in needles. The infection of needles by Botrytis cinerea was reduced by bacterial pretreatment. Complex interactions of GB 4-2 with Norway spruce and Heterobasidion abietinum were discovered. The bacterium promoted the growth of the phytopathogenic fungus but induced plant defense responses. Host responses indicate that GB 4-2 induces both local and systemic defense responses in Norway spruce.
Endoscopic treatment of gastric perforation caused by acute necrotizing pancreatitis using over-the-scope clips: a case report
2007-12-10

Gastric perforation is a rare complication after acute necrotizing pancreatitis. We describe endoscopic closure of a gastric perforation that appeared 4 days after surgical necrosectomy including splenectomy due to necrotizing pancreatitis, using the over-the-scope clip (OTSC) system (Ovesco Endoscopy GmbH, Tübingen, Germany). The clips, which are made of nitinol, are loaded onto an application cap which is mounted on the distal tip of the endoscope. The lesion was closed with two clips and the patient recovered well without reinterventions. The lesions showed normal healing on follow-up.
MR measurement of blood flow in the parotid gland without contrast medium: a functional study before and after gustatory stimulation
2007-12-10

Abstract Purpose To investigate the feasibility of blood flow imaging in the parotid gland using the arterial spin labeling (ASL) technique for assessment of functional changes in the parotid gland after gustatory stimulation. Materials and Methods Anatomical and ASL imaging of the parotid gland was performed in eight healthy volunteers before and after gustatory stimulation over a period of 17 min. All measurements were carried out in a 1.5 T whole‐body MR unit. ASL and data recording were performed with an adapted FAIR TrueFISP (flow‐sensitive alternating inversion‐recovery true fast imaging with steady precession) technique. Maps of estimated tissue blood inflow in both parotid glands were derived using a simplified model and the extended Bloch equations. Results Delineation of the parotid glands was possible on FAIR TrueFISP images in all cases. In the 160 s period immediately after stimulation, a significant (P &lt; 0.01) mean increase of 62% in the estimated parotid blood flow was observed. Estimated baseline blood flow before gustatory stimulation ranged from 226 to 500 mL/min/100 g (mean ± SD 335 ± 86). These rates increased in the 160 s immediately after stimulation to 404–772 mL/min/100 g (mean 542 ± 108). In all volunteers, blood flow returned to near baseline values within the observation period. No statistically significant difference between the right and left parotid was observed in baseline and peak blood flow. Conclusion ASL FAIR TrueFISP is feasible for functional characterization of the parotid glands. Assessment of changes in blood flow in the parotid gland could serve as a diagnostic tool in patients suffering from xerostomia. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Data in generative grammar: The stick and the carrot
2007-12-11

Abstract This paper is intended to lay out for broader discussion some arguments for the importance of data in work in generative syntax. These are accepted by many linguists, but a significant number of others still seem reluctant to accept them. The basic claim is that it is no longer tenable for syntactic theories to be constructed on the evidence of a single person's judgements, and that real progress can only be made when syntacticians begin to think more carefully about the empirical basis of their work and apply the minimum standards we propose. We advance two groups of reasons for syntacticians to do this, negative and positive. The negative ‘stick’ group concerns the inadequacy of current practice. We argue that linguists are producing unsatisfactory work with these methods. Data quality is a limiting factor: a theory can only ever be as good as its data base. The positive ‘carrot’ group concerns the descriptive and theoretical advantages which become available with more empirically adequate data. We hope to tempt linguists to adopt new methods by showing them the insights which better data makes available.
Biosynthetic Investigations of Lactonamycin and Lactonamycin Z: Cloning of the Biosynthetic Gene Clusters and Discovery of an Unusual Starter Unit
2007-12-11

ABSTRACT The antibiotics lactonamycin and lactonamycin Z provide attractive leads for antibacterial drug development. Both antibiotics contain a novel aglycone core called lactonamycinone. To gain insight into lactonamycinone biosynthesis, cloning and precursor incorporation experiments were undertaken. The lactonamycin gene cluster was initially cloned from Streptomyces rishiriensis . Sequencing of ca. 61 kb of S. rishiriensis DNA revealed the presence of 57 open reading frames. These included genes coding for the biosynthesis of l -rhodinose, the sugar found in lactonamycin, and genes similar to those in the tetracenomycin biosynthetic gene cluster. Since lactonamycin production by S. rishiriensis could not be sustained, additional proof for the identity of the S. rishiriensis cluster was obtained by cloning the lactonamycin Z gene cluster from Streptomyces sanglieri . Partial sequencing of the S. sanglieri cluster revealed 15 genes that exhibited a very high degree of similarity to genes within the lactonamycin cluster, as well as an identical organization. Double-crossover disruption of one gene in the S. sanglieri cluster abolished lactonamycin Z production, and production was restored by complementation. These results confirm the identity of the genetic locus cloned from S. sanglieri and indicate that the highly similar locus in S. rishiriensis encodes lactonamycin biosynthetic genes. Precursor incorporation experiments with S. sanglieri revealed that lactonamycinone is biosynthesized in an unusual manner whereby glycine or a glycine derivative serves as a starter unit that is extended by nine acetate units. Analysis of the gene clusters and of the precursor incorporation data suggested a hypothetical scheme for lactonamycinone biosynthesis.
Immunologic activity of schistosomal and bacterial TLR2 ligands in Gabonese children
2007-12-11

SUMMARY Schistosomes carry lipid moieties that interact with the immune system. To understand the consequence of interactions in terms of polarizing the cytokine profiles, the effect of two Toll‐like receptor‐2 (TLR2) activating schistosomal lipid fractions was studied on whole blood from Gabonese children living in a schistosomiasis endemic area. One fraction contained lysophosphatidylserine [monoacylglycerophosphoserine (lysoGPSer)] plus diacylphosphatidylserine [diacylglycerophosphoserine (GPSer)] while the other contained lysoGPSer and only a trace of GPSer. The effect of these schistosomal lipid fractions was compared with the known bacterial TLR2 ligands PAM 3 CSK 4 and MALP‐2. PAM 3 CSK 4 and MALP‐2 had preferential IL‐10‐activating capacities, while the fraction containing lysoGPSer plus GPSer had a strong TNF‐α‐inducing capacity. The fraction containing lysoGPSer was neutral with respect to pro‐ vs. anti‐inflammatory effects. When Th1 and Th2 cytokines were analysed, the schistosomal lipid fraction containing lysoGPSer plus GPSer showed a stronger Th2 response compared to PAM 3 CSK 4 , MALP‐2 and lysoGPSer alone. Therefore, the study indicates that not only TLR2 ligands derived from bacteria or from parasites can generate distinct cytokine profiles but also that the composition of lipid entities reaching the immune system can be important in leading to different immune outcomes. This information may be important for exploitation of immune modulatory molecules.
Ca-rich Ilvaite-Epidote-Hydrogarnet Endoskarns: a Record of Late-Magmatic Fluid Influx into the Persodic Ilimaussaq Complex, South Greenland
2007-12-12

Endoskarn assemblages involving the Ca-silicates ilvaite, epidote and Ca-rich garnet occur along fracture zones in the persodic Ilímaussaq intrusion, South Greenland. The 1·16 Ga intrusion solidified at a depth of about 3–4 km, below a cover of sandstones and pillow-basalts of the Eriksfjord Formation. In contrast to typical skarn assemblages, the Ilímaussaq endoskarns contain albite as a main phase and they did not form in metacarbonate rocks, as these are completely lacking in the vicinity of Ilímaussaq. Instead, they record late- to post-magmatic interaction of possibly external Ca-rich fluids with the alkaline to agpaitic magmatic rocks. Accordingly, endoskarn textures clearly reflect the magmatic textures of the precursor rocks. Phase relations in two endoskarn varieties with epidote + albite + andradite-rich garnet ± ilvaite ± retrograde prehnite suggest their formation at about 500°C at high oxygen fugacities slightly above the hematite–magnetite oxygen buffer [FMQ (fayalite–magnetite–quartz) + 5 to FMQ + 7] with later small modifications as a result of fluid influx or cooling of the original fluid at about 300–350°C (formation of prehnite) and at about 200–250°C (oxygen isotopic re-equilibration of the albite). One model for the formation of the observed assemblages is the decomposition of Ca-bearing minerals, such as primary eudialyte, clinopyroxene or ternary feldspar, and redistribution of the Ca by a metasomatizing late-magmatic fluid. Stable isotope (O, H) investigations, however, favour a model in which seawater was the metasomatizing fluid, which entered the Eriksfjord basalts above the intrusion, reacted with them (spilitization) and brought about 10−3 mol/l Ca along fractures into the metasomatized rocks. Fluid–rock interaction in the Eriksfjord basalts is documented by abundant chlorite–epidote–quartz assemblages; high fluid/rock ratios allowed the fluid to retain its seawater oxygen isotope composition.
Recent progress constraining the nuclear equation of state from astrophysics and heavy-ion reactions
2007-12-13

The quest for the nuclear equation of state (EoS) at high densities and/or extreme isospin is one of the longstanding problems of nuclear physics. Ab initio calculations for the nuclear many-body problem make predictions for the density and isospin dependence of the EoS far away from the saturation point of nuclear matter. On the other hand, in recent years substantial progress has been mode to constrain the EoS both, from the astrophysical side and from accelerator based experiments. Heavy ion experiments support a soft EoS at moderate densities while recent neutron star observations require a ``stiff'' high density behavior. Both constraints are discussed and shown to be in agreement with the predictions from many-body theory.
A data-driven approach to pronominal anaphora resolution for German
2007-12-13

This paper reports on a hybrid architecture for computational anaphora resolution (CAR) of German that combines a rule-based pre-filtering component with a memory-based resolution module (using the Tilburg Memory Based Learner – TiMBL). The data source is provided by the TuBa-D/Z treebank of German newspaper text (Telljohann et al. 04) that is annotated with anaphoric relations. The CAR experiments performed on these treebank data corroborate the importance of modelling aspects of discourse structure for robust, data-driven anaphora resolution. The best result with an F-measure of 0.734 achieved by these experiments outperforms the results reported by (Schiehlen 04), the only other study of German CAR that is based on newspaper treebank data.
Neutron capture cross section of76Ge
2007-12-13

We have measured the neutron capture cross section of 76Ge by means of the activation technique. Neutrons were produced via the 7Li(p, n)7Be reaction, which offered the possibility of simulating a quasi-stellar neutron spectrum for kT = 25 keV, thus allowing us to measure the Maxwellian averaged cross section directly. The stellar cross section extrapolated to kT = 30 keV was found to be 12.4 ± 0.7 mbarn. This result carries a considerably smaller uncertainty than previous data.
Trehalose and anhydrobiosis in tardigrades – evidence for divergence in responses to dehydration
2007-12-14

To withstand desiccation, many invertebrates such as rotifers, nematodes and tardigrades enter a state known as anhydrobiosis, which is thought to require accumulation of compatible osmolytes, such as the non‐reducing disaccharide trehalose to protect against dehydration damage. The trehalose levels of eight tardigrade species comprising Heterotardigrada and Eutardigrada were observed in five different states of hydration and dehydration. Although many species accumulate trehalose during dehydration, the data revealed significant differences between the species. Although trehalose accumulation was found in species of the order Parachela (Eutardigrada), it was not possible to detect any trehalose in the species Milnesium tardigradum and no change in the trehalose level has been observed in any species of Heterotardigrada so far investigated. These results expand our current understanding of anhydrobiosis in tardigrades and, for the first time, demonstrate the accumulation of trehalose in developing tardigrade embryos, which have been shown to have a high level of desiccation tolerance.
A Novel Polymorphism in the Promoter Region ofERBB4Is Associated with Breast and Colorectal Cancer Risk
2007-12-15

Abstract Purpose: The receptor tyrosine kinase ERBB4/HER4 plays a role in cell division, migration, differentiation, as well as apoptosis, and is frequently overexpressed in breast and colorectal tumors. To understand the role of genetic variations in the regulation of ERBB4 expression, we identified new polymorphisms and investigated their functional implication and risk association with breast and colorectal cancer. Experimental Design: We screened colorectal tumors from 92 patients for genetic variants at the ERBB4 ATG −1000 bp 5′-regulatory region by denaturing high-performance liquid chromatography and sequencing. Variants were subjected to DNA-protein interaction analyses (electrophoretic mobility shift assay), reporter gene assays in breast cancer cell lines MDA134 and MDA157, and immunohistochemical analyses of breast tumors. We established genotype frequencies within a breast cancer case-control collection (1,021 cases, 1,015 population-based controls) and a colorectal cancer case-control collection (459 cases, 569 blood donors) using matrix-assisted laser desorption ionization/time of flight mass spectrometry. Adjusted odds ratios (OR) and 95% confidence intervals (CI) were assessed by multivariate logistic regression. Results: We identified five new germ line variants −815 A&amp;gt;T, −782 G&amp;gt;T, −638 insTC, −267 C&amp;gt;G, and −219 del10bp. Two variants showed in vitro functional effects. The −782T allele showed lower protein binding affinity and lower promoter activity compared with the −782G allele, however, the −815T allele showed higher protein binding affinity and higher promoter activity. The −782T variant was identified as a risk allele for breast and colorectal cancer (OR, 1.59; 95% CI, 1.06-2.34 and OR, 2.21; 95% CI, 1.22-3.99, respectively). Conclusion: The ERBB4 −782 G&amp;gt;T polymorphism, by virtue of its in vitro functional implication and incidence, is a risk factor for breast and colorectal cancer.
Cardiac computed tomography: indications, applications, limitations, and training requirements: Report of a Writing Group deployed by the Working Group Nuclear Cardiology and Cardiac CT of the European Society of Cardiology and the European Council of Nuclear Cardiology
2007-12-16

As a consequence of improved technology, there is growing clinical interest in the use of multi-detector row computed tomography (MDCT) for non-invasive coronary angiography. Indeed, the accuracy of MDCT to detect or exclude coronary artery stenoses has been high in many published studies. This report of a Writing Group deployed by the Working Group Nuclear Cardiology and Cardiac CT (WG 5) of the European Society of Cardiology and the European Council of Nuclear Cardiology summarizes the present state of cardiac CT technology, as well as the currently available data concerning its accuracy and applicability in certain clinical situations. Besides coronary CT angiography, the use of CT for the assessment of cardiac morphology and function, evaluation of perfusion and viability, and analysis of heart valves is discussed. In addition, recommendations for clinical applications of cardiac CT imaging are given and limitations of the technique are described.
Sperm length and quality in sperm-dependent parthenogens
2007-12-17

Is the male function of parthenogenetic hermaphrodites a historic remnant or an adaptive investment? In the first case, one would expect the male function to be ‘degraded’ and, in the second case, fully functional, despite being reduced. To answer this question, we investigated sperm morphology and quality in the hermaphroditic planarian Schmidtea polychroa. Parthenogenetic forms of this species are sperm-dependent and require allosperm to trigger embryogenesis. Although there is generally no genetic paternal contribution, occasional fertilization of parthenogenetic eggs has been reported, leading to genetic changes in an otherwise apomictic lineage (‘occasional sex’). Comparing two locations, one with pure clonality and one with occasional sexuality, revealed substantial differences in both sperm length and fertility: Occasional sex appears to be coupled with longer sperm and higher sperm quality. We discuss the implications of these results for the maintenance of the male function in sperm-dependent parthenogens. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 81–87.
Platelet-Derived Stromal Cell–Derived Factor-1 Regulates Adhesion and Promotes Differentiation of Human CD34 + Cells to Endothelial Progenitor Cells
2007-12-18

Background— Peripheral homing of progenitor cells in areas of diseased organs is critical for tissue regeneration. The chemokine stromal cell–derived factor-1 (SDF-1) regulates homing of CD34 + stem cells. We evaluated the role of platelet-derived SDF-1 in adhesion and differentiation of human CD34 + cells into endothelial progenitor cells. Methods and Results— Adherent platelets express substantial amounts of SDF-1 and recruit CD34 + cells in vitro and in vivo. A monoclonal antibody to SDF-1 or to its counterreceptor, CXCR4, inhibits stem cell adhesion on adherent platelets under high arterial shear in vitro and after carotid ligation in mice, as determined by intravital fluorescence microscopy. Platelets that adhere to human arterial endothelial cells enhance the adhesion of CD34 + cells on endothelium under flow conditions, a process that is inhibited by anti-SDF-1. During intestinal ischemia/reperfusion in mice, anti-SDF-1 and anti-CXCR4, but not isotype control antibodies, abolish the recruitment of CD34 + cells in microcirculation. Moreover, platelet-derived SDF-1 binding to CXCR4 receptor promotes platelet-induced differentiation of CD34 + cells into endothelial progenitor cells, as verified by colony-forming assays in vitro. Conclusions— These findings imply that platelet-derived SDF-1 regulates adhesion of stem cells in vitro and in vivo and promotes differentiation of CD34 + cells to endothelial progenitor cells. Because tissue regeneration depends on recruitment of progenitor cells to peripheral vasculature and their subsequent differentiation, platelet-derived SDF-1 may contribute to vascular and myocardial regeneration.
Impact of Bidirectional Charge Transfer and Molecular Distortions on the Electronic Structure of a Metal-Organic Interface
2007-12-18

Interface energetics are of fundamental importance in organic and molecular electronics. By combining complementary experimental techniques and first-principles calculations, we resolve the complex interplay among several interfacial phenomena that collectively determine the electronic structure of the strong electron acceptor tetrafluoro-tetracyanoquinodimethane chemisorbed on copper. The combination of adsorption-induced geometric distortion of the molecules, metal-to-molecule charge transfer, and molecule-to-metal back transfer leads to a net increase of the metal work function.
ITS Evolution in Platanus (Platanaceae): Homoeologues, Pseudogenes and Ancient Hybridization
2007-12-18

Broad ITS data sets that cover intra- and interindividual variability reveal past and ongoing speciation processes in Platanus. Evolutionary pathways can be visualized with splits graphs, but not with bifurcating trees.
4-[4-(4-Fluorophenyl)-2-methyl-5-oxo-2,5-dihydroisoxazol-3-yl]-1-methylpyridinium iodide–4-[3-(4-fluorophenyl)-2-methyl-5-oxo-2,5-dihydroisoxazol-4-yl]-1-methylpyridinium iodide (0.6/0.4)
2007-12-18

The crystal structure of the title compound, C(16)H(16)FN(2)O(2) (+)·I(-), was determined as part of a study of the biological activity of isoxazolone derivatives as p38 mitogen-activated protein kinase (MAPK) inhibitors. The X-ray crystal structure of 4-[4-(4-fluoro-phenyl)-2-methyl-5-oxo-2,5-dihydro-isoxazol-3-yl]-1-methyl-pyridinium iodide showed the presence of the regioisomer 4-[3-(4-fluoro-phenyl)-2-methyl-5-oxo-2,5-dihydro-isoxazol-4-yl]-1-methyl-pyridinium iodide. The synthesis of the former compound was achieved by reacting 4-(4-fluoro-phenyl)-3-(4-pyridyl)isoxazol-5(2H)-one after treatment with Et(3)N in dimethyl-formamide, with iodo-methane. The unexpected formation of the regioisomer could be explained by a rearrangement occurring via aziridine of the isoxazolone compound. The regioisomers have site occupancies of 0.632 (4)/0.368 (4). The two six members rings make a dihedral angle of 66.8 (2)°.
Migration to Apoptotic “Find-me” Signals Is Mediated via the Phagocyte Receptor G2A
2007-12-19

Phagocytosis of apoptotic cells is fundamentally important throughout life, because non-cleared cells become secondarily necrotic and release intracellular contents, thus instigating inflammatory and autoimmune responses. Secreted "find-me" and exposed "eat-me" signals displayed by the dying cell in concert with the phagocyte receptors comprise the phagocytic synapse of apoptotic cell clearance. In this scenario, lysophospholipids (lysoPLs) are assumed to act as find-me signals for the attraction of phagocytes. However, both the identity of the lyso-PLs released from apoptotic cells and the nature of the phagocyte receptor are largely unknown. By a detailed analysis of the structural requirements we show here that lysophosphatidylcholine (lysoPC), but none of the lysoPC metabolites or other lysoPLs, represents the essential apoptotic attraction signal able to trigger a phagocyte chemotactic response. Furthermore, using RNA interference and expression studies, we demonstrate that the G-protein-coupled receptor G2A, unlike its relative GPR4, is involved in the chemotaxis of monocytic cells. Thus, our study identifies lysoPC and G2A as the crucial receptor/ligand system for the attraction of phagocytes to apoptotic cells and the prevention of autoimmunity.