julilili42/papers huggingface dataset:
L‐3‐hydroxyacyl‐CoA dehydrogenase II protects in a model of Parkinson's disease
2004-06-28

Abstract The neurotoxin 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine (MPTP) impairs mitochondrial respiration and damages dopaminergic neurons as seen in Parkinson's disease (PD). Here, we report that L ‐3‐hydroxyacyl‐CoA dehydrogenase type II/amyloid binding alcohol dehydrogenase (HADH II/ABAD), a mitochondrial oxidoreductase enzyme involved in neuronal survival, is downregulated in PD patients and in MPTP‐intoxicated mice. We also show that transgenic mice with increased expression of human HADH II/ABAD are significantly more resistant to MPTP than their wild‐type littermates. This effect appears to be mediated by overexpression of HADH II/ABAD mitigating MPTP‐induced impairment of oxidative phosphorylation and ATP production. This study demonstrates that HADH II/ABAD modulates MPTP neurotoxicity and suggests that HADH II/ABAD mimetics may provide protective benefit in the treatment of PD. Ann Neurol 2004;56:51–60
Chandra and FUSE spectroscopy of the hot bare stellar core H 1504+65
2004-06-29

H 1504+65 is an extremely hot hydrogen-deficient white dwarf with an effective temperature close to 200 000 K. We present new FUV and soft X-ray spectra obtained with FUSE and Chandra, which confirm that H 1504+65 has an atmosphere primarily composed of carbon and oxygen. The Chandra LETG spectrum (60-160 Å) shows a wealth of photospheric absorption lines from highly ionized oxygen, neon, and - for the first time identified in this star - magnesium and suggests relatively high Ne and Mg abundances. This corroborates an earlier suggestion that H 1504+65 represents a naked C/O stellar core or even the C/O envelope of an O-Ne-Mg white dwarf.
Under stress, the absence of intermediate filaments from Muller cells in the retina has structural and functional consequences
2004-06-30

In epithelial and muscle cells, intermediate filaments (IFs) are important for resistance to mechanical stress. The aim of this study was to elucidate whether IFs are also important for providing resistance to mechanical stress in the Müller cells of the retina and whether this has any pathophysiological consequences. We used mice deficient in IF proteins glial fibrillary acidic protein and/or vimentin (GFAP–/–, Vim–/– and GFAP–/–Vim–/–), and stress on the retina was applied by excision of the eyes immediately post mortem (compared with in situ fixation) or by inducing a neovascular response to oxygen-induced retinopathy (OIR). The structure of unchallenged retinas was normal, but mechanical stress caused local separation of the inner limiting membrane (ILM) and adjacent tissue from the rest of the retina in GFAP–/–Vim–/– mice and, to a lesser extent, in Vim–/– mice. This detachment occurred within the endfeet of Müller cells, structures normally rich in IFs but IF-free in GFAP–/–Vim–/– mice. Hypoxia-induced neovascularization was comparable in all groups of mice with respect to the retinal surface area occupied by new vessels. However, the vessels traversed the ILM and penetrated the vitreous body less frequently than in wild-type retinas (31-55% in Vim–/–, 66-79% in GFAP–/–Vim–/–). We conclude that IFs are important for maintaining the mechanical integrity of Müller-cell endfeet and the inner retinal layers under a mechanical challenge. Furthermore, the absence of IFs in Müller cells leads to an abnormal response of the vascular system to ischemia, specifically decreased ability of newly formed blood vessels to traverse the ILM.
Numerical study of the thm effects on the near-field safety of a hypothetical nuclear waste \\nrepository - bmt1 of the decovalex iii project. part 1: conceptualization and characterization of \\nthe problems and summary of results
2004-06-30

Geological disposal of the spent nuclear fuel uses often the concept of multiple barrier systems. In order to predict the performance of these barriers, mathematical models have been developed, verified and validated against analytical solutions, laboratory tests and field experiments within the international DECOVALEX III project. These models in general consider the full coupling of thermal (T), hydraulic (H) and mechanical (M) processes that would prevail in the geological media around the repository. For Bench Mark Test no. 1 (BMT1) of the DECOVALEX III project, seven multinational research teams studied the implications of coupled THM processes on the safety of a hypothetical nuclear waste repository at the near-fiel and are presented in three accompany papers in this issue. This paper is the first of the three companion papers, which provides the conceptualization and characterization of the BMT1 as well as some general conclusions based on the findings of the numerical studies. It also shows the process of building confidence in the mathematical models by calibration with a reference T-H-M experiment with realistic rock mass conditions and bentonite properties and measured outputs of thermal, hydraulic and mechanical variables.
Convergence for stabilisation of degenerately convex minimisation problems
2004-06-30

Degenerate variational problems often result from a relaxation technique in effective numerical simulation of nonconvex minimisation problems. The relaxed energy density is the convex envelope of the original one and so convex but not strictly convex. Hence strong convergence of straightforward finite element approximations cannot be expected but is relevant in many applications. This paper establishes a modified discretization by stabilisation and proves its convergence in strong norms.
Demonstration of antibodies to the chitin-binding mistletoe lectin (cbML) in tumor patients before and during therapy with an aqueous mistletoe extract.
2004-06-30

Mistletoe extracts exert immunomodulatory properties in vivo and in vitro, and these effects have been related mainly to mistletoe lectin 1 (ML-1). Recently, a new chitin-binding mistletoe lectin (cbML) has been isolated and structurally characterized in these extracts. Aim of the present study was, therefore, to evaluate whether this cbML also affects immunocompetent cells and can for instance activate B-cells to produce anti-cbML-specific antibodies. Sera from patients with different tumors who were treated with the mistletoe extract ABNOBAviscum Mali (AM) 4 for at least 18 weeks were analysed before therapy and after 3, 6, 9, 12, 18, and 24 weeks. Sera were tested by ELISA against ML-1, -3, and cbML, isolated from a single mistletoe plant collected from an apple tree (Malus domestica). Eight of the 26 patients (31%) had IgG anti-cbML antibodies already before therapy, while only four had anti-ML-1 and -3 antibodies. Of the 18 anti-cbML negative patients before therapy 54% developed these antibodies during therapy, and there was a significant increase in anti-cbML antibody titers. In contrast, anti-ML-1 or -3-antibodies developed in almost 100% of the 25 patients being negative before therapy. These data indicate that cbML can induce immunological responses in patients treated with mistletoe extracts, although it seems to have lower antigenicity. Interestingly, anti-cbML antibodies can be observed in a low incidence also in individuals, not having yet received mistletoe therapy.
Integrated Study of Single Anthropogenic Particles—Magnetic and Environmental Implications
2004-06-30

Environmental Context. Industrial metal production, thermoelectric power plants, and similar technologies can release a large amount of particles (with sizes up to the millimetre scale) of heavy metals into the local surrounds. Up to 10% of these particles are strongly magnetic and easily detectable above the background magnetism. A map of the regional magnetic signals, which would be relatively simple and cheap to produce, provides a guide to pollution ‘hotspots’. But it’s not that simple: The authors integrate chemistry, microscopy, and magnetism studies of single particles of sediments from the Danube River to show rock magnetic parameters established for natural rocks cannot be directly used on environmental man-made particles. Abstract. The presence of significant amounts of strongly magnetic phases in anthropogenic particulate industrial emissions allows the use of magnetic methods for fast and cheap detection of environmental pollution. The aim of our study is to check the validity of some of the constitutive magnetic parameters and their ratios used for estimation of grain sizes and distance from the pollution source. The results from our integrated magnetic, microscopic, and microchemical study on large, single, anthropogenic particles show that classical rock magnetic parameters (Mrs/Mr, Bcr/Bc) for mineral magnetic characterization cannot be directly applied to the anthropogenic phases. This results from their inhomogeneous composition, often with dendritic exsolution of iron oxides within an aluminosilicate matrix.
Assembly of the Pamirs: Age and origin of magmatic belts from the southern Tien Shan to the southern Pamirs and their relation to Tibet
2004-07-01

Magmatic rocks and depositional setting of associated volcaniclastic strata along a north‐south traverse spanning the southern Tien Shan and eastern Pamirs of Kyrgyzstan and Tajikistan constrain the tectonics of the Pamirs and Tibet. The northern Pamirs and northwestern Tibet contain the north facing Kunlun suture, the south facing Jinsha suture, and the intervening Carboniferous to Triassic Karakul–Mazar subduction accretion system; the latter is correlated with the Songpan‐Garze–Hoh Xi system of Tibet. The Kunlun arc is a composite early Paleozoic to late Paleozoic‐Triassic arc. Arc formation in the Pamirs is characterized by ∼370–320 Ma volcanism that probably continued until the Triassic. The cryptic Tanymas suture of the southern northern Pamirs is part of the Jinsha suture. A massive ∼≤227 Ma batholith stitches the Karakul–Mazar complex in the Pamirs. There are striking similarities between the Qiangtang block in the Pamirs and Tibet. Like Tibet, the regional structure of the Pamirs is an anticlinorium that includes the Muskol and Sares domes. Like Tibet, the metamorphic rocks in these domes are equivalents to the Karakul–Mazar–Songpan‐Garze system. Granitoids intruding the Qiangtang block yield ∼200–230 Ma ages in the Pamirs and in central Tibet. The stratigraphy of the eastern Pshart area in the Pamirs is similar to the Bangong‐Nujiang suture zone in the Amdo region of eastern central Tibet, but a Triassic ocean basin sequence is preserved in the Pamirs. Arc‐type granitoids that intruded into the eastern Pshart oceanic‐basin–arc sequence (∼190–160 Ma) and granitoids that cut the southern Qiangtang block (∼170–160 Ma) constitute the Rushan‐Pshart arc. Cretaceous plutons that intruded the central and southern Pamirs record a long‐lasting magmatic history. Their zircons and those from late Miocene xenoliths show that the most distinct magmatic events were Cambro‐Ordovician (∼410–575 Ma), Triassic (∼210–250 Ma; likely due to subduction along the Jinsha suture), Middle Jurassic (∼147–195 Ma; subduction along Rushan‐Pshart suture), and mainly Cretaceous. Middle and Late Cretaceous magmatism may reflect arc activity in Asia prior to the accretion of the Karakoram block and flat‐slab subduction along the Shyok suture north of the Kohistan‐Ladakh arc, respectively. Before India and Asia collided, the Pamir region from the Indus‐Yarlung to the Jinsha suture was an Andean‐style plate margin. Our analysis suggests a relatively simple crustal structure for the Pamirs and Tibet. From the Kunlun arc in the north to the southern Qiangtang block in the south the Pamirs and Tibet likely have a dominantly sedimentary crust, characterized by Karakul–Mazar–Songpan‐Garze accretionary wedge rocks. The crust south of the southern Qiangtang block is likely of granodioritic composition, reflecting long‐lived subduction, arc formation, and Cretaceous‐Cenozoic underthrusting.
Detection and Typing of Human Papillomavirus by E6 Nested Multiplex PCR
2004-07-01

ABSTRACT A nested multiplex PCR (NMPCR) assay that combines degenerate E6/E7 consensus primers and type-specific primers was evaluated for the detection and typing of human papillomavirus (HPV) genotypes 6/11, 16, 18, 31, 33, 35, 39, 42, 43, 44, 45, 51, 52, 56, 58, 59, 66, and 68 using HPV DNA-containing plasmids and cervical scrapes ( n = 1,525). The performance of the NMPCR assay relative to that of conventional PCR with MY09-MY11 and GP5+-GP6+ primers, and nested PCR with these two primer sets (MY/GP) was evaluated in 495 cervical scrapes with corresponding histologic and cytologic findings. HPV prevalence rates determined with the NMPCR assay were 34.7% (102 of 294) in the absence of cervical intraepithelial neoplasia (CIN 0), 94.2% (113 of 120) in the presence of mild or moderate dysplasia (CIN I/II), and 97.8% (44 of 45) in the presence of severe dysplasia (CIN III). The combination of all four HPV detection methods applied in the study was taken as “gold standard”: in all three morphological subgroups the NMPCR assay had significantly ( P &lt; 0.0001) higher sensitivities than the MY09-MY11 and GP5+-GP6+ assays and sensitivities comparable or equal to those of the MY/GP assay. All 18 HPV genotypes investigated were detected among the clinical samples. The ratio of high- to low-risk HPV genotypes increased from 4:1 (80 of 103) in CIN 0 to 19:1 (149 of 157) in CIN I to III. Multiple infections were detected in 47.9% (124 of 259) of the patients. In conclusion, the novel NMPCR method is a sensitive and useful tool for HPV DNA detection, especially when exact HPV genotyping and the identification of multiple HPV infections are required.
What is the best hydration regimen to prevent contrast media-induced nephrotoxicity?
2004-07-01

In patients with normal renal function, intravenous prehydration seems to be a very effective and feasible method to prevent the decline in GFR after contrast media exposure. Volume expansion given only during the CM exposure appears not to be sufficient enough to prevent renal damage.
Overexpression ofGLUTAMINE DUMPER1Leads to Hypersecretion of Glutamine from Hydathodes of Arabidopsis Leaves[W]
2004-07-01

Abstract Secretion is a fundamental process providing plants with the means for disposal of solutes, improvement of nutrient acquisition, and attraction of other organisms. Specific secretory organs, such as nectaries, hydathodes, and trichomes, use a combination of secretory and retrieval mechanisms, which are poorly understood at present. To study the mechanisms involved, an Arabidopsis thaliana activation tagged mutant, glutamine dumper1 (gdu1), was identified that accumulates salt crystals at the hydathodes. Chemical analysis demonstrated that, in contrast with the amino acid mixture normally present in guttation droplets, the crystals mainly contain Gln. GDU1 was cloned and found to encode a novel 17-kD protein containing a single putative transmembrane span. GDU1 is expressed in the vascular tissues and in hydathodes. Gln content is specifically increased in xylem sap and leaf apoplasm, whereas the content of several amino acids is increased in leaves and phloem sap. Selective secretion of Gln by the leaves may be explained by an enhanced release of this amino acid from cells. GDU1 study may help to shed light on the secretory mechanisms for amino acids in plants.
Endocytosis, membrane recycling and sorting of GPI‐anchored proteins: Trypanosoma brucei as a model system
2004-07-01

Summary In the flagellated protozoon Trypanosoma brucei , endo‐ and exocytosis are restricted to a small area of the plasma membrane, the flagellar pocket. All endosomal compartments and the single Golgi complex are located within the posterior part of the cell between the flagellar pocket and the nucleus. The use of reverse genetic tools, including RNA interference, in combination with quantitative 3D‐fluorescence and electron microscopic techniques has provided an insight into endosomal membrane traffic, which occurs at a very high rate and appears to exhibit a lower level of complexity than in mammalian cells. The flagellate is an excellent model system for studies on endocytosis, sorting and recycling of glycosylphosphatidylinositol‐anchored glycoproteins, because 10 7 molecules of the variant surface glycoprotein form a dense coat at the cell's surface. Because the endocytic rate varies widely at different stages in the parasite's life cycle, trypanosomes may be used for investigating developmental aspects of their endocytic system.
Hydrogen solubility and speciation in natural, gem-quality chromian diopside
2004-07-01

A new technique for performing long duration (up to 300 hours) high-pressure annealing experiments under water-saturated conditions has been developed. This technique has been used to investigate watersolubility and speciation in natural, gem-quality chromian diopside. Capsule design for the technique is a variant of the double-capsule technique, and relies on the use of a semi-permeable Pt membrane, which permits free hydrogen diffusion into samples, but protects samples from reacting with buffer mixtures. The investigation of a natural single crystal of chromian diopside revealed a very unusual annealing behavior: water contents increase sharply after a short annealing period and then decrease slowly to some metastable equilibrium value. The main process that takes place during the annealing experiments is hydrogen diffusion coupled with Fe3+ reduction. This essentially reverses the main mechanism for hydrogen loss from mantle samples during exhumation, and the technique therefore provides sample-specific information on original water contents. Absorption bands at 3646 and 3434 cm-1 in IR spectra from annealed samples suggest two main mechanisms for hydrogen incorporation in the diopside sample: (1) incorporation of hydrogen onto the O2 site, with vibration of the OH dipole in the direction of a nearby O3 site (along the edge of an M2 site), and (2) incorporation of hydrogen onto the O2 site with vibration of the OH dipole toward a nearby O1 site (along a shared M1-M2 edge) or O2 site (along the edge of an M1 site). The ratio of peak heights between the absorption bands at 3646 and 3434 cm-1 is independent of water fugacity but dependent on oxygen fugacity, and appears to provide a measure of the redox state "frozen" into the sample. This ratio could be used to determine whether pyroxenes from upper-mantle xenoliths had experienced concurrent hydrogen-loss and oxidation during exhumation.
Accretion dynamics in neutron star-black hole binaries
2004-07-01

We perform three-dimensional, Newtonian hydrodynamic simulations with a nuclear equation of state to investigate the accretion dynamics in neutron star–black hole systems. We find as a general result that non-spinning donor stars yield larger circularization radii than corotating donors. Therefore, the matter from a neutron star without spin will more likely settle into an accretion disc outside the Schwarzschild radius. With the stiff equation of state used we find it hard to form an accretion disc that is promising to launch a gamma-ray burst. In all relevant cases the core of the neutron star survives and keeps orbiting the black hole as a mini neutron star for the rest of the simulation time (up to several hundred dynamical neutron star time-scales). The existence of this mini neutron star leaves a clear imprint on the gravitational wave signal which thus can be used to probe the physics at supranuclear densities.
Activity patterns and habitat preferences of insectivorous bats in a West African forest–savanna mosaic
2004-07-01

We studied activity patterns and habitat use by insectivorous bats in Comoé National Park, Ivory Coast. Bat foraging activity was quantified along five transects representing three different habitat types using acoustic monitoring and captures with mist nets and harp traps. Aerial insect abundance was assessed using a light trap; in addition shrub and tree arthropods were sampled. Bat activity was significantly and positively related to insect availability and ambient temperature, whereas increased visibility of the moon had a negative influence on flight activity. Together, these factors best explained both total bat activity and activity of bats hunting in open space and edge habitats. The interaction between temperature and light intensity was the best predictor of activity by species foraging in obstacle-rich forest habitats, however, the regression model had a low predictive value. Overall, a large proportion ( c . 50%) of the variation in bat activity appeared to be a consequence of transect- and/or habitat-specific influences. We found a significant non-linear relationship between the activity of QCF (quasi-constant frequency) and FM–QCF (frequency modulated – quasi-constant frequency) bats and the phase of the moon, with lowest levels of activity occurring near full moon. We interpret this lunar-phobic behaviour as a reflection of a higher predation risk during moonlit periods. For FM (steep frequency modulated) and CF (constant frequency) bats, no significant correlation was found, although there was a trend suggesting that these bats at least were not negatively affected by bright moonlight. Foraging activity of bats was positively correlated with the abundance of atympanate moths; however, no such correlation was found for tympanate moths.
A process-oriented approach to computing multi-field problems in porous media
2004-07-01

Object-oriented methods are becoming more and more important in order to meet the challenges in scientific computing, such as the treatment of coupled multi-field problems with high spatial resolution. This paper introduces an object-oriented concept for modelling multi-process systems in porous media. The basic idea is the direct representation of a physical process by an object of the numerical code. Because a physical process can be represented by a field variable and an equation system, the process object contains the equation system for the field variable as well as all methods needed for building and solving the equation system. The process object is thus self-configuring and well encapsulated, which are the main advantages of this new approach and thus allows for an easy extension to more complex applications with a higher number of processes. The design and implementation of the object-oriented concept for the presented process objects is described in detail and illustrated by a set of application examples.
Experimental Check of the Gerasimov-Drell-Hearn Sum Rule for H1
2004-07-01

For the first time we checked the fundamental Gerasimov-Drell-Hearn (GDH) sum rule for the proton experimentally in the photon energy range from 0.2-2.9 GeV with the tagged photon facilities at MAMI (Mainz) and ELSA (Bonn). New data of the doubly polarized total cross section difference are presented in the energy range from 1.6 to 2.9 GeV. The contribution to the GDH integral from 0.2-2.9 GeV yields [254+/-5(stat)+/-12(syst)] microb with negative contributions in the Regge regime at photon energies above 2.1 GeV. This trend supports the validity of the GDH sum rule.
Loop Deletions Indicate Regions Important for FhuA Transport and Receptor Functions in Escherichia coli
2004-07-01

ABSTRACT Precise deletions of cell surface-exposed loops of FhuA resulted in mutants of Escherichia coli with distinct phenotypes. Deletion of loop 3 or 11 inactivated ferrichrome transport activity. Deletion of loop 8 inactivated receptor activity for colicin M and the phages T1, T5, and φ80. The loop 7 deletion mutant was colicin M resistant but fully phage sensitive. The loop 4 deletion mutant was resistant to the TonB-dependent phages T1 and φ80 but fully sensitive to the TonB-independent phage T5. The phenotypes of the deletion mutants revealed important sites for the multiple FhuA transport and receptor activities. The ligand binding sites are nonidentical and are distributed among the entire exposed surface. Presumably, FhuA evolved as a ferrichrome transporter and was subsequently used as a receptor by the phages and colicin M, which selected the same as well as distinct loops as receptor sites.