julilili42/papers huggingface dataset:
The Magmatic and Fluid Evolution of the Motzfeldt Intrusion in South Greenland: Insights into the Formation of Agpaitic and Miaskitic Rocks
2008-08-02

The 1275 Ga Motzfeldt intrusive complex in the Gardar failed-rift Province in South Greenland formed from six successively intruding melt batches (SM1^SM6) interpreted to be derived from a common magma source at depth. Five units (SM1^SM5) crystallized an alka-line to peralkaline, miaskitic mineral assemblage of amphibole, clino-pyroxene, feldspar, nepheline, Fe^Ti oxides, zircon, apatite, fluorite and rarely olivine.The last magmatic batch (SM6) is characterized by an agpaitic mineral assemblage of aegirine, nepheline, alkali-feld-spar, eudialyte and rare fluorite or sodalite. Coexisting mafic minerals constrain the crystallization conditions of the miaskitic rocks to about 850^6008C, whereas solidus temperatures below 5008C are indicated by coexisting alkali feldspars in the agpaitic rocks. Oxygen fugacities during the orthomagmatic stage are below the FMQ (fayalite^ magnetite^quartz) buffer (FMQ^05 to ^20)whereas late hema-tite provides evidence of a higher relative oxygen fugacity during
IN DEFENCE OF METAPHYSICAL ANALYTICITY
2008-08-04

Abstract According to the so‐called metaphysical conception of analyticity, analytic truths are true in virtue of meaning (or content) alone and independently of (extralinguistic) facts. Quine and Boghossian have tried to present a conclusive argument against the metaphysical conception of analyticity. In effect, they tried to show that the metaphysical conception inevitably leads into a highly implausible view about the truthmakers of analytic truths. We would like to show that their argument fails, since it relies on an ambiguity of the notion of ‘independence of (extralinguistic) facts’. If one distinguishes between variation independence and existence independence, the unwelcome view about the truthmakers of analytic truths no longer follows. Thus, there is at best a challenge, but no conclusive argument. The door to the metaphysical conception of analyticity is still open. 1
A novel tool to analyze MRI recurrence patterns in glioblastoma
2008-08-04

At least 10% of glioblastoma relapses occur at distant and even contralateral locations. This disseminated growth limits surgical intervention and contributes to neurological morbidity. Preclinical data pointed toward a role for temozolomide (TMZ) in reducing radiotherapy-induced glioma cell invasiveness. Our objective was to develop and validate a new analysis tool of MRI data to examine the clinical recurrence pattern of glioblastomas. MRIcro software was used to map the location and extent of initial preoperative and recurrent tumors on MRI of 63 patients in the European Organisation for Research and Treatment of Cancer (EORTC) 26981/22981/National Cancer Institute of Canada (NCIC) CE.3 study into the same stereotaxic space. This allowed us to examine changes of site and distance between the initial and the recurrent tumor on the group level. Thirty of the 63 patients were treated using radiotherapy, while the other patients completed a radiotherapy-plus-TMZ treatment. Baseline characteristics (median age, KPS) and outcome data (progression-free survival, overall survival) of the patients included in this analysis resemble those of the general study cohort. The patient groups did not differ in the promoter methylation status of methyl guanine methyltransferase (MGMT). Overall frequency of distant recurrences was 20%. Analysis of recurrence patterns revealed no difference between the groups in the size of the recurrent tumor or in the differential effect on the distance of the recurrences from the preoperative tumor location. The data show the feasibility of groupwise recurrence pattern analysis. An effect of TMZ treatment on the recurrence pattern in the EORTC 26981/22981/NCIC CE.3 study could not be demonstrated.
ChemInform Abstract: Benzoazabicyclo[4.3.1] Derivatives by Intramolecular Michael Addition of Piperidinone Enolates to Enoates.
2008-08-04

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Syntheses and Crystal Structures of the Rhenium(VII) Nitride Chlorides ReNCl4 and ReNCl4×H2O.
2008-08-04

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Determination of transport levels of organic semiconductors by UPS and IPS
2008-08-05

In this paper, we present a comprehensive discussion on the determination of transport levels of organic semiconductors using a combination of UV and inverse photoemission spectroscopies (UPS and IPS, respectively). We discuss the key question of how the spectra should be evaluated to obtain the correct values for the transport levels. Our evaluation results in much smaller exciton binding energies than generally assumed, ranging from 0.1 to 0.4 eV for CuPc, PTCDA and Alq3. Moreover, we find that polarization effects, vibrations, experimental resolution and inhomogeneous broadening contribute very little to the position and width of the broad photoelectron spectroscopy (PES) and IPS signals. Thus, we suggest a model that explains much of the broadening as a result of dynamic charge delocalization. We discuss our data in analogy to those obtained for inorganic semiconductors (IOSCs), which are presented in a separate paper.
Retinoblastoma and Its Binding Partner MSI1 Control Imprinting in Arabidopsis
2008-08-06

Parental genomic imprinting causes preferential expression of one of the two parental alleles. In mammals, differential sex-dependent deposition of silencing DNA methylation marks during gametogenesis initiates a new cycle of imprinting. Parental genomic imprinting has been detected in plants and relies on DNA methylation by the methyltransferase MET1. However, in contrast to mammals, plant imprints are created by differential removal of silencing marks during gametogenesis. In Arabidopsis, DNA demethylation is mediated by the DNA glycosylase DEMETER (DME) causing activation of imprinted genes at the end of female gametogenesis. On the basis of genetic interactions, we show that in addition to DME, the plant homologs of the human Retinoblastoma (Rb) and its binding partner RbAp48 are required for the activation of the imprinted genes FIS2 and FWA. This Rb-dependent activation is mediated by direct transcriptional repression of MET1 during female gametogenesis. We have thus identified a new mechanism required for imprinting establishment, outlining a new role for the Retinoblastoma pathway, which may be conserved in mammals.
Dielectric Function of the QCD Vacuum
2008-08-06

It is shown that the inverse of the ghost form factor in the Hamilton approach to Yang-Mills theory in Coulomb gauge can be interpreted as the color dielectric function of the QCD vacuum. Furthermore, the horizon condition to the ghost form factor implies that in the infrared the QCD vacuum is a perfect color diaelectric medium and therefore a dual superconductor. The dielectric function is explicitly calculated within a previously developed variational approach, using a specific ansatz for the vacuum wave functional.
Pregnancy‐Associated Malaria Affects Toll‐Like Receptor Ligand–Induced Cytokine Responses in Cord Blood
2008-08-06

P. falciparum infection history during pregnancy appears to have a pronounced effect on neonatal innate immune responses. The observed effects may have profound implications for the outcome of newly encountered infections in early life.
Arabidopsis has Two Functional Orthologs of the Yeast V‐ATPase Assembly Factor Vma21p
2008-08-06

How individual protein subunits assemble into the higher order structure of a protein complex is not well understood. Four proteins dedicated to the assembly of the V 0 subcomplex of the V‐adenosine triphosphatase (V‐ATPase) in the endoplasmic reticulum (ER) have been identified in yeast, but their precise mode of molecular action remains to be identified. In contrast to the highly conserved subunits of the V‐ATPase, orthologs of the yeast assembly factors are not easily identified based on sequence similarity. We show in this study that two ER‐localized Arabidopsis proteins that share only 25% sequence identity with Vma21p can functionally replace this yeast assembly factor. Loss of AtVMA21a function in RNA interference seedlings caused impaired cell expansion and changes in Golgi morphology characteristic for plants with reduced V‐ATPase activity, and we therefore conclude that AtVMA21a is the first V‐ATPase assembly factor identified in a multicellular eukaryote. Moreover, VMA21p acts as a dedicated ER escort chaperone, a class of substrate‐specific accessory proteins so far not identified in higher plants.
Structure of the Head of the Bartonella Adhesin BadA
2008-08-07

Trimeric autotransporter adhesins (TAAs) are a major class of proteins by which pathogenic proteobacteria adhere to their hosts. Prominent examples include Yersinia YadA, Haemophilus Hia and Hsf, Moraxella UspA1 and A2, and Neisseria NadA. TAAs also occur in symbiotic and environmental species and presumably represent a general solution to the problem of adhesion in proteobacteria. The general structure of TAAs follows a head-stalk-anchor architecture, where the heads are the primary mediators of attachment and autoagglutination. In the major adhesin of Bartonella henselae, BadA, the head consists of three domains, the N-terminal of which shows strong sequence similarity to the head of Yersinia YadA. The two other domains were not recognizably similar to any protein of known structure. We therefore determined their crystal structure to a resolution of 1.1 A. Both domains are beta-prisms, the N-terminal one formed by interleaved, five-stranded beta-meanders parallel to the trimer axis and the C-terminal one by five-stranded beta-meanders orthogonal to the axis. Despite the absence of statistically significant sequence similarity, the two domains are structurally similar to domains from Haemophilus Hia, albeit in permuted order. Thus, the BadA head appears to be a chimera of domains seen in two other TAAs, YadA and Hia, highlighting the combinatorial evolutionary strategy taken by pathogens.
Cyclic Guanosine Monophosphate-dependent Protein Kinase I Promotes Adhesion of Primary Vascular Smooth Muscle Cells
2008-08-07

The cyclic guanosine monophosphate (cGMP)/cGMP-dependent protein kinase type I (cGKI) pathway regulates many cellular functions. The current study shows that 8-Br-cGMP stimulates the number of attached primary but not that of subcultured murine vascular smooth muscle cells (VSMCs). These effects of 8-Br-cGMP require the presence of cGKI. In agreement with previous studies, cGKI inhibited the number of cells in repeatedly passaged murine VSMCs. Activation of the cGMP/cGKI pathway in freshly isolated primary VSMCs slightly decreased apoptosis and strongly increased cell adhesion. The stimulation of cell adhesion by cGKI involves an inhibition of the RhoA/Rho kinase pathway and increased exposure of β 1 and β 3 integrins on the cell surface. Together, these results identify a novel proadhesive function of cGMP/cGKI signaling in primary VSMCs and suggest that the opposing effects of this pathway on VSMC number depend on the phenotypic context of the cells.
Mutants with aberrant numbers of gametic cells shed new light on old questions
2008-08-07

Abstract In contrast to animals, plant gametes form in distinct haploid generations, termed gametophytes. The female gametophyte of Arabidopsis consists of two gametic cells, the egg and central cell, which are flanked by accessory cells. The gametic cells differ with respect to morphology, molecular attributes and, importantly, their fate: whereas the egg cell, upon fertilisation, gives rise to the embryo, the central cell forms the endosperm. To ensure correct endosperm formation, not only the egg cell but also the central cell has to fuse with a sperm cell. The respective sperm cell pair is delivered by a single pollen tube. In some plant species, the two male gametes appear to express a different bias towards the female gametes. Such a preference consequently determines their respective contribution to either embryo or endosperm development. In Arabidopsis and many other species the sperm cells are indistinguishable and it has been discussed whether they possess an inherent preference for either of the female gametes. The recent isolation of mutants that form an aberrant number of either male or female gametes stimulates discussion, albeit with different results. Furthermore, some data indicate that the central cell is competent to initiate endosperm formation without a paternal contribution. These data support the theory that the endosperm is of gametophytic rather than sporophytic origin.
Highly Multiplexed Genotyping of Thiopurine S-Methyltransferase Variants Using MALDI-TOF Mass Spectrometry: Reliable Genotyping in Different Ethnic Groups
2008-08-08

Abstract Background: To avoid severe hematotoxicity in patients, determination of the TPMT (thiopurine S-methyltransferase) genotype before commencing thiopurine therapy has become accepted. Methods: We used MALDI-TOF mass spectrometry (MS) based on Sequenom iPLEX® technology to develop novel multiplex assays for comprehensive testing of TPMT. Two assays, a 15-plex and a 7-plex assay, consisting of multiplex PCR, shrimp alkaline phosphatase treatment, primer extension, and MALDI-TOF MS analysis, allow detection of all currently known functionally relevant 24 TPMT alleles (TPMT*2 to *18, *20 to *23). Previously identified variant DNA samples and newly constructed synthetic templates were used as quality controls. Results: Assay evaluation performed on a panel of 586 genomic DNA samples previously genotyped by other methods (denaturing HPLC, sequencing) resulted in 100% agreement. Analyses of the distribution of TPMT alleles in 116 samples from a Ghanaian population revealed a TPMT*8 allele frequency of 3.4%. In a Korean population of 118 unrelated individuals, we found a TPMT*6 allele frequency of 1.3%. Conclusions: The newly developed multiplex MALDI-TOF MS assay allows efficient genotyping for all currently known functional TPMT variants. To achieve the most accurate prediction of TPMT phenotype, molecular diagnosis of TPMT should include all these variants.
ChemInform Abstract: Heterocycles [h]‐Fused onto 4‐Oxoquinoline‐3‐carboxylic Acid. Part 5. Synthesis and Antibacterial Activity of Some New 2,3‐Disubstituted 7‐Oxo‐7,10‐dihydropyrido[2,3‐f]quinoxaline‐8‐carboxylic Acids and Esters.
2008-08-08

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Formal Total Synthesis of Neopeltolide.
2008-08-08

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Neutralization of tumor-derived soluble Glucocorticoid-Induced TNFR-Related Protein ligand increases NK cell anti-tumor reactivity
2008-08-09

Abstract NK cell anti-tumor reactivity is governed by a balance of activating and inhibitory receptors including various TNF receptor (TNFR) family members. Here we report that human tumor cells release a soluble form of the TNF family member Glucocorticoid-Induced TNFR-Related Protein (GITR) ligand (sGITRL), which can be detected in cell culture supernatants. Tumor-derived sGITRL concentration-dependently reduced NK cell cytotoxicity and IFN-γ production, which could be overcome by neutralization of sGITRL using a GITR-Ig fusion protein. Although sGITRL did not induce apoptosis in NK cells, it diminished nuclear localized RelB, indicating that sGITRL negatively modulates NK cell NF-κB activity. Furthermore, we detected substantial levels of sGITRL in sera of patients with various malignancies, but not in healthy controls. Presence of sGITRL-containing patient serum in cocultures with tumor cells significantly reduced NK cell cytotoxicity and IFN-γ production, which could again be restored by neutralization of sGITRL. The strong correlation of tumor incidence and elevated sGITRL levels indicates that sGITRL is released from cancers in vivo, leading to impaired NK cell immunosurveillance of human tumors. Our data suggest that determination of sGITRL levels might be implemented as a tumor marker in patients, and GITRL neutralization may be used to improve immunotherapeutic strategies relying on NK cell reactivity.
VEGF-dependent induction of CD62E on endothelial cells mediates glioma tropism of adult haematopoietic progenitor cells
2008-08-09

Haematopoietic progenitor cells (HPC) are attracted by experimental gliomas in vivo. This attraction is further enhanced by irradiation or hypoxic preconditioning of the glioma cells. Adhesive interactions might be critical to the preferential accumulation of HPC within the glioma tissue. Here, we studied the interactions of HPC with endothelial cells. Exposure of human cerebral endothelial cells (SV-HCEC), human microvascular endothelial cells (HMEC) and brain tumour endothelial cells derived from human glioblastomas (BTEC) to supernatants of glioma cells and primary glioma cells (SN-G) induced the expression of E-selectin (CD62E). CD62E expression was further enhanced when the glioma cells had been exposed to irradiation or hypoxia prior to the collection of supernatants, as well as by irradiation or exposure to hypoxia of the endothelial cells. Vascular cell adhesion molecule 1 (VCAM-1) was constitutively expressed on SV-HCEC, HMEC and BTEC, but was not modulated by SN-G, irradiation or hypoxia. Transendothelial HPC migration was enhanced after CD62E induction in vitro. Neutralizing antibodies to CD62E strongly reduced the homing of lin(-)Sca-1(+)c-kit(+) cells to orthotopic SMA-560 gliomas in vivo. Tissue microarray sampling normal brain tissue and astrocytomas of WHO grades II-IV revealed a selective expression of CD62E on endothelial cells of tumour vessels. SN-G-induced CD62E expression on endothelial cells in vitro required transforming growth factor (TGF)-beta signalling in glioma cells and vascular endothelial growth factor (VEGF)/VEGF receptor 2 (VEGF-R2) signalling in endothelial cells. Further, we observed a nuclear factor kappa B-dependent activation of the CD62E promoter peaking at 12 h after VEGF-R2 activation by glioma-derived VEGF. Taken together, we identify glioma cell-induced CD62E expression on endothelial cells as one mediator of the glioma tropism of HPC.
Perception-motivated interpolation of image sequences
2008-08-09

We present a method for image interpolation which is able to create high-quality, perceptually convincing transitions between recorded images. By implementing concepts derived from human vision, the problem of a physically correct image interpolation is relaxed to an image interpolation that is perceived as physically correct by human observers. We find that it suffices to focus on exact edge correspondences, homogeneous regions and coherent motion to compute such solutions. In our user study we confirm the visual quality of the proposed image interpolation approach. We show how each aspect of our approach increases the perceived quality of the interpolation results, compare the results obtained by other methods and investigate the achieved quality for different types of scenes.
Identification and Characterization of Metabolically Benign Obesity in Humans
2008-08-11

A metabolically benign obesity that is not accompanied by insulin resistance and early atherosclerosis exists in humans. Furthermore, ectopic fat in the liver may be more important than visceral fat in the determination of such a beneficial phenotype in obesity.
Convergent finite element discretizations of the nonstationary incompressible magnetohydrodynamics system
2008-08-11

The incompressible MHD equations couple Navier-Stokes equations with Maxwell's equations to describe the flow of a viscous, incompressible, and electrically conducting fluid in a Lipschitz domain . We verify convergence of iterates of different coupling and decoupling fully discrete schemes towards weak solutions for vanishing discretization parameters. Optimal first order of convergence is shown in the presence of strong solutions for a splitting scheme which decouples the computation of velocity field, pressure, and magnetic fields at every iteration step.
Fixed‐Dose Pyronaridine‐Artesunate Combination for Treatment of Uncomplicated Falciparum Malaria in Pediatric Patients in Gabon
2008-08-11

Pyronaridine-artesunate is a promising novel artemisinin-combination therapy for pediatric patients with uncomplicated Plasmodium falciparum malaria, and the development of both the tablet and the granule coformulations is warranted.
Influence of aquifer and streambed heterogeneity on the distribution of groundwater discharge
2008-08-11

Abstract. The spatial distribution of groundwater fluxes through a streambed can be highly variable, most often resulting from a heterogeneous distribution of aquifer and streambed permeabilities along the flow pathways. In a previous study, observed temperature profiles in the streambed of a small stream in Germany were used to calibrate the subsurface parameters of a groundwater flow and heat transport model of the stream-aquifer system. Based on the model results, we defined four scenarios to simulate and assess the interplay of aquifer and streambed heterogeneity on the distribution of groundwater fluxes through the streambed: (a) a homogeneous low-K streambed within a heterogeneous aquifer; (b) a heterogeneous streambed within a homogeneous aquifer; (c) a well connected heterogeneous low-K streambed within a heterogeneous aquifer; and (d) a poorly connected heterogeneous low-K streambed within a heterogeneous aquifer. The results showed that the aquifer has a stronger influence on the distribution of groundwater fluxes through the streambed than the streambed itself. However, a homogeneous low-K streambed, a case often implemented in regional-scale groundwater flow models, resulted in a strong homogenization of fluxes, which may have important implications for the estimation of peak mass flows. The simulation results with heterogeneous low-K streambeds, whether or not well connected to the aquifer, were similar to the results of the base case scenario without a separate parameterization of the streambed, despite the lower permeability. We conclude that predictions of water flow and solute transport may significantly benefit from heterogeneous distributions of both aquifer and streambed properties in numerical simulation models.