julilili42/papers huggingface dataset:
Reconstruction of short-term palaeoceanographic changes during the formation of the Late Albian ‘Niveau Breistroffer’ black shales (Oceanic Anoxic Event 1d, SE France)
2005-06-21

The Niveau Breistroffer black shale succession in the Vocontian Basin (SE France) is the regional equivalent of the widely distributed Late Albian Oceanic Anoxic Event 1d. The studied black shale-rich interval at the Col de Palluel section is 6.28 m thick and comprises four black shale units with up to 2.5 wt% total organic carbon (TOC) intercalated with marlstones. Calcareous nannofossil, palynomorph, planktic Foraminifera and stable isotopic data from the Niveau Breistroffer succession suggest that short-term climate changes influenced its deposition, with relatively warm and humid climate during black shale formation in comparison with relatively cool and dry climatic conditions during marlstone deposition. An increase in the terrigenous/marine ratio of palynomorphs indicates enhanced humidity and higher runoff during black shale formation. A nutrient index based on calcareous nannofossils and the abundance pattern of small (63–125 μm) hedbergellid Foraminifera show short-term changes in the productivity of the surface water. Surface-water productivity was reduced during black shale formation and increased during marlstone deposition. A calcareous nannofossil temperature index and bulk-rock oxygen isotope data indicate relative temperature changes, with warmer surface waters for black shale samples. At these times, warm–humid climate and reduced surface-water productivity were accompanied by greater abundances of ‘subsurface’-dwelling calcareous nannofossils (nannoconids) and planktic Foraminifera (rotaliporids). These taxa presumably indicate more stratified surface-water conditions. We suggest that the formation of the Niveau Breistroffer black shales occurred during orbitally induced increase in monsoonal activity that led to increasing humidity during periods of black shale formation. This, in turn, caused a decrease in low-latitude deep-water formation and probably an increase in surface-water stratification. The combination of these two mechanisms caused depleted O 2 concentrations in the bottom water that increased the preservation potential of organic matter.
Modeling the resonant planetary system GJ 876
2005-06-21

The evolution of the GJ 876 system using two-dimensional hydrodynamical simulations including viscous heating and radiative cooling was discussed. It was found that the relaxed disk remained circular in all models for low planet-to-star mass ratio q2, but becomes eccentric for high mass ratios for those models with fixed temperature structure. A more comprehensive set of numerical calculations treating the evolution of two planets interacting with their protoplanetary disk was presented with special emphasis on the resonant system GJ 876. The results show that it was possible to reduce the final values of the eccentricities close to the observed values.
Age determination of Ordovician magmatism in NE Sardinia and its bearing on Variscan basement evolution
2005-06-21

A newly discovered pre-Variscan cover–basement relationship in NE Sardinia is defined by differences in structural and metamorphic histories. The oldest metamorphic fabrics in the basement are absent from a series of metaplutons that are inferred to be comagmatic with metavolcanic rocks in the cover. Cover and basement are further distinguished by contrasting metapelite compositions. Superimposed metamorphism is represented by pre-Variscan garnet and Variscan plagioclase porphyroblasts that appear in the field as a ‘mixed’ garnet + albite zone. In situ U–Pb zircon dating of meta-igneous rocks from cover and basement by laser-ablation inductively coupled plasma-mass spectrometry gives ages of 458 ± 7 Ma for the Tanaunella orthogneiss, 456 ± 14 Ma for the Lodè orthogneiss, and 474 ± 13 Ma for the Lula porphyroid. The internal Sardinian Variscides thus incorporate a mid-Ordovician magmatic belt developed upon an older basement; correlation is proposed with a tectonostratigraphic domain that is at present exposed in the Alps. Within the mid-Ordovician peri-Gondwanan realm, the internal Sardinian Variscides appear to have developed along an active margin, whereas the foreland correlates with the Ibero-Aquitaine domain and is related to the evolution of a passive margin during rifting and detachment of Avalonia to form the Rheic Ocean.
Current treatment and prognosis in children with functionally univentricular hearts
2005-06-21

For more than 30 years Fontan-type procedures have been performed for surgical treatment in patients with functionally univentricular hearts. Advances in proper patient selection, staging of the Fontan palliation, and modifications of the surgical technique resulted in continuous improvement of the surgical results during the past two decades. However, increasing experience with medium term and long term follow-up of the Fontan circulation has drawn attention to a number of sequelae and chronic complications affecting a significant number of patients.
Noradrenaline Transmission within the Ventral Bed Nucleus of the Stria Terminalis Is Critical for Fear Behavior Induced by Trimethylthiazoline, a Component of Fox Odor
2005-06-22

The bed nucleus of the stria terminalis (BNST) is involved in the mediation of fear behavior in rats. A previous study of our laboratory demonstrated that temporary inactivation of the BNST blocks fear behavior induced by exposure to trimethylthiazoline (TMT), a component of fox odor. The present study investigates whether noradrenaline release within the BNST is critical for TMT-induced fear behavior. First, we confirmed previous studies showing that the ventral BNST is the part of the BNST that receives the densest noradrenaline innervation. Second, using in vivo microdialysis, we showed that noradrenaline release within the BNST is strongly increased during TMT exposure, and that this increase can be blocked by local infusions of the α 2 -receptor blocker clonidine. Third, using intracerebral injections, we showed that clonidine injections into the ventral BNST, but not into neighboring brain sites, completely blocked TMT-induced potentiation of freezing behavior. The present data clearly show that the noradrenergic innervation of the ventral BNST is important for the full expression of behavioral signs of fear to the predator odor TMT.
Differential Regulation of β-Chemokines in Children with Plasmodium falciparum Malaria
2005-06-22

ABSTRACT Chemokines regulate the host immune response to a variety of infectious pathogens. Since the role of chemokines in regulating host immunity in children with Plasmodium falciparum malaria has not previously been reported, circulating levels of β-chemokines (MIP-1α, MIP-1β, and RANTES) and their respective transcriptional profiles in ex vivo peripheral blood mononuclear cells (PBMCs) were investigated. Peripheral blood MIP-1α and MIP-1β levels were significantly elevated in mild and severe malaria, while RANTES levels decreased with increasing disease severity. β-Chemokine gene expression profiles in blood mononuclear cells closely matched those of circulating β-chemokines, illustrating that PBMCs are a primary source for the observed pattern of β-chemokine production during acute malaria. Statistical modeling revealed that none of the chemokines was significantly associated with either parasitemia or anemia. Additional investigations in healthy children with a known history of malaria showed that children with prior severe malaria had significantly lower baseline RANTES production than children with a history of mild malaria, suggesting inherent differences in the ability to produce RANTES in these two groups. Baseline MIP-1α and MIP-1β did not significantly differ between children with prior severe malaria and those with mild malaria. Additional in vitro experiments in PBMCs from healthy, malaria-naïve donors revealed that P. falciparum -derived hemozoin (Hz; malarial pigment) and synthetic Hz (β-hematin) promote a similar pattern of β-chemokine gene expression. Taken together, the results presented here demonstrate that children with severe malaria have a distinct profile of β-chemokines characterized by increased circulating levels of MIP-1α and MIP-1β and decreased RANTES. Altered patterns of circulating β-chemokines result, at least in part, from Hz-induced changes in β-chemokine gene expression in blood mononuclear cells.
Carbon Isotope Fractionation in the Reductive Dehalogenation of Carbon Tetrachloride at Iron (Hydr)Oxide and Iron Sulfide Minerals
2005-06-22

Compound-specific isotope analysis (CSIA) is used increasingly in contaminant hydrology in the attempt to assess the nature as well as the extent of in situ transformation reactions. Potentially, variations of stable isotope ratios along a contaminant plume may be used to quantify in situ degradation. In the present study, the abiotic dehalogenation of CCl4 by Fe(II) present at the surface of different iron minerals has been characterized in terms of the reaction rates and carbon isotopic fractionation (delta13C) of carbon tetrachloride (CCl4) as well as the yields and isotopic signatures of chloroform (CHCl3), one of the main transformation products. The abiotic reductive dehalogenation of CCl4 was associated with substantial carbon isotopic enrichment effects. The observed enrichment factors, e, correlated neither with the surface-normalized reaction rate constants nor with the type of products formed but fell into two distinctly different ranges for the two principal groups of minerals studied. With iron (hydr)oxide minerals (goethite, hematite, lepidocrocite, and magnetite) and with siderite, the e-values for CCl4 dehalogenation were remarkably similar (-29 +/- 3 per thousand). Because this value matches well with the theoretical estimates for the cleavage of an aliphatic C-Cl bond, we suggest that dissociative electron transfer to CCl4 controls the reaction rates for this group of iron minerals. Conversely, CCl4 transformation by different preparations of the iron sulfide mackinawite was accompanied by a significantly lower carbon istotopic fractionation (e = -15.9 +/- 0.3 per thousand), possibly due to the presence of nonfractionating rate-determining steps or a significantly different transition state structure of the reaction. Isotopically sensitive branching of the reaction pathways (i.e., the effect of different product distributions on isotope fractionation of CCl4) did not play a significant role in our systems. The extensive data set presented in this study opens new perspectives toward an improved understanding of the factors that determine reaction mechanisms and isotopic fractionation of dehalogenation reactions by Fe(II) at iron containing minerals.
Regional and subtype selective changes of neurotransmitter receptor density in a rat transgenic for the Huntington's disease mutation
2005-06-22

Abstract Huntington's disease (HD) is an autosomal dominantly inherited progressive neurodegenerative disorder caused by a CAG/polyglutamine repeat expansion in the gene encoding the huntingtin protein. We have recently generated a rat model transgenic for HD, which displays a slowly progressive phenotype resembling the human adult‐onset type of disease. In this study we systematically assessed the distribution and density of 17 transmitter receptors in the brains of 2‐year‐old rats using quantitative multi‐tracer autoradiography and high‐resolution positron emission tomography. Heterozygous animals expressed increased densities of M 2 acetylcholine (increase of 148 ± 16% of controls; p &gt; 0.001; n = 7), nicotine (increase of 149 ± 16% of controls; p &gt; 0.01; n = 6), and α 2 noradrenergic receptors (increase of 141 ± 15% of controls; p &gt; 0.001; n = 6), respectively. Densities of these receptors were decreased in homozygous animals. Decreases of receptor density in both hetero‐ and homozygous animals were found for M 1 acetylcholine, 5‐HT 2A serotonin, A 2A adenosine, D 1 and D 2 dopamine, and GABA A receptors, respectively. Other investigated receptor systems showed small changes or were not affected. The present data suggest that the moderate increase of CAG/polyglutamine repeat expansions in the present rat model of Huntington's disease is characterized by subtype‐selective and region‐specific changes of neuroreceptor densities. In particular, there is evidence for a contribution of predominantly presynaptically localized cholinergic and noradrenergic receptors in the response to Huntington's disease pathology.
Magnetic Resonance Elastography of the Breast
2005-06-22

A good separation exists between benign and malignant lesions in elasticity, corresponding with specific signal intensity and morphologic data. Further clinical studies with a larger number of patients are needed for extended validation.
Intense Cholesterol Lowering Therapy with a HMG-CoA Reductase Inhibitor does not Improve Nitric Oxide Dependent Endothelial Function in Type-2-Diabetes
2005-06-23

Disturbances in nitric oxide (NO) metabolism resulting in endothelial dysfunction play a central role in the pathogenesis of atherosclerosis in hypercholesterolemia and in individuals with type 2 diabetes. It is unclear whether lipid lowering therapy with HMG-CoA-reductase inhibitors might improve endothelial function in subjects with type 2 diabetes as it is demonstrated in non-diabetic subjects with hypercholesterolemia. We examined the influence of 0.2 mg and 0.8 mg cerivastatin on endothelial function in a multicenter, randomised, double-blind, and three-arm placebo-controlled clinical trial. Endothelial function was assessed by nitric oxide-dependent flow mediated vasodilatation (FMD) of the brachial artery. A total of 103 patients with type 2 diabetes were enrolled in the study. Bayer Company undertook a voluntary action to withdraw cerivastatin from market, therefore the study was terminated earlier. At this point 77 patients were randomised, of which 58 completed the study (mean age 60 +/- 8 years, HbA1c 7.4 +/- 0.9 %). At baseline mean FMD was disturbed in all three therapy arms (5.18 +/- 2.31 % in the placebo group, 3.88 +/- 1.68 in the 0.2-mg cerivastation group, and 4.86 +/- 2.25 in the 0.8-mg cerivastatin group). Despite a significant reduction in cholesterol and LDL-cholesterol-levels after 12 weeks of treatment (decrease in LDL-cholesterol - 26.8 +/- 13.9 % in the 0.2-mg group and - 40.3 +/- 16.0 % in the 0.8-mg group, p = 0.0001, ANCOVA) there was no difference in flow mediated vasodilatation (p = 0.52 and p = 0.56 vs. placebo, respectively, ANCOVA). HbA1c, CRP, and HDL-cholesterol did not change during the study. Furthermore no difference in safety profile between cerivastatin and placebo was found. Despite a significant improvement in lipid profile under statin therapy, no improvement of endothelial dysfunction in terms of nitric oxide bioavailability could be detected.
The roothairless1 Gene of Maize Encodes a Homolog of sec3, Which Is Involved in Polar Exocytosis
2005-06-24

Abstract The roothairless1 (rth1) mutant is impaired in root hair elongation and exhibits other growth abnormalities. Unicellular root hairs elongate via localized tip growth, a process mediated by polar exocytosis of secretory vesicles. We report here the cloning of the rth1 gene that encodes a sec3 homolog. In yeast (Saccharomyces cerevisiae) and mammals, sec3 is a subunit of the exocyst complex, which tethers exocytotic vesicles prior to their fusion. The cloning of the rth1 gene associates the homologs of exocyst subunits to an exocytotic process in plant development and supports the hypothesis that exocyst-like proteins are involved in plant exocytosis. Proteomic analyses identified four proteins that accumulate to different levels in wild-type and rth1 primary roots. The preferential accumulation in the rth1 mutant proteome of a negative regulator of the cell cycle (a prohibitin) may at least partially explain the delayed development and flowering of the rth1 mutant.
A new quality-of-life measure for men experiencing involuntary childlessness
2005-06-24

The TLMK provides information about the quality-of-life in men experiencing involuntary childlessness and was found to be easy to administer and acceptable to patients. It may be used to assess patients' baseline and ongoing quality-of-life during fertility treatment and as an outcome variable in the evaluation of integrated psychological counselling.
Factors Influencing Reaction Time during Automated Kinetic Perimetry on the Tubingen Computer Campimeter
2005-06-24

Reaction time during automated kinetic perimetry varies considerably. This study shows that the factors of age, the subject examined, his or her daily condition, the course within one examination period, and the stimulus location and luminance are of relevance. For a much more reliable prediction of individual RTs and thus a precise assessment of local kinetic thresholds, application of some additional kinetic stimuli (RT time vectors) within the intact visual field areas is necessary.
Metabolic Engineering of Aminocoumarins: Inactivation of the Methyltransferase Gene cloP and Generation of New Clorobiocin Derivatives in a Heterologous Host
2005-06-24

Abstract Aminocoumarin antibiotics are highly potent inhibitors of bacterial gyrase and represent a class of antibiotics that are very suitable for the generation of new compounds by metabolic engineering. In this study, the putative methyltransferase gene cloP in the biosynthetic gene cluster of clorobiocin was inactivated. Expression of the modified gene cluster in the heterologous host Streptomyces coelicolor M512 gave three new aminocoumarin antibiotics. The structures of the new compounds were elucidated by MS and 1 H NMR, and their antibacterial activities were determined. All three compounds lacked clorobiocin's methyl group at 4‐OH of the deoxysugar moiety, noviose. They differed from each other in the position of the 5‐methylpyrrole‐2‐carbonyl group, which was found to be attached to either 2‐OH, 3‐OH or 4‐OH of noviose. Attachment at 4‐OH resulted in the highest antibacterial activity. This is the first time that an aminocoumarin antibiotic acylated at 4‐OH in noviose has been detected.
A coherent state description of the shape phase transition in even–even Gd isotopes
2005-06-24

Three versions of the coherent state model, called CSM, CSM2 and GCSM, are used to describe excitation energies and intraband as well as interband transition probabilities of three interacting bands, ground, beta and gamma, in the even–even isotopes 150–160Gd. Common features and differences in the predictions of the three formalisms are commented. All of them yield results which are in fairly good agreement with the available data. New signatures for the transition U(5)–SU(3) are pointed out. It turns out that for some properties this transition is state dependent. Also, there are some properties indicating that in the isotope chain considered there are more than two phases, satisfying the U(5) and SU(3) symmetries, respectively. The formalisms employed here confirm that 154Gd exhibits features which are specific to the X(5) symmetry.
Evolutionary algorithms for the self-organized evolution of networks
2005-06-25

While the evolution of biological networks can be modeled sensefully as a series of mutation and selection, evolution of other networks such as the social network in a city or the network of streets in a country is not determined by selection since there is no alternative network with which these singular networks have to compete. Nonetheless, these singular networks do evolve due to dynamic changes of vertices and edges. In this article we present a formal, analyzable framework for the evolution of singular networks. We show that the careful design of adaptation rules can lead to the emergence of network topologies with satisfying performance in polynomial time while other adaptation rules yield exponential runtime. We further show by example how the framework could be applied to some ad-hoc communication scenarios.
Identifying valid solutions for the inference of regulatory networks
2005-06-25

In this paper, we address the problem of finding gene regulatory networks from experimental DNA microarray data. The problem often is multi-modal and therefore appropriate optimization strategies become necessary. We propose to use a clustering based niching evolutionary algorithm to maintain diversity in the optimization population to prevent premature convergence and to raise the probability of finding the global optimum by identifying multiple alternative networks than standard algorithms. With this set of alternatives, the identification of the true solution has then to be addressed in a second post-processing step.
Why simulating evolutionary processes is just as interesting as applying them
2005-06-25

Evolutionary algorithms are very efficient tools to find a near-optimum solution in many cases. Until now they have been mostly used to find results but in this article we argue that evolutionary algorithms can also be used to simulate the evolution of complex systems. We model complex systems as networks in which agents are connected by edges if they interact with each other. It is known that many networks of this kind exhibit stable properties despite the dynamic processes they are subject to. We show here how evolutionary processes on complex systems can be modeled with a new kind of evolutionary algorithm which we have presented in [8]. We will show that some evolutionary processes within this framework yield networks with stable properties in reasonable time. An understanding of what kind of evolutionary processes will produce what kind of network properties in what time is vital to transfer evolutionary processes to technical ad-hoc networks in order to improve their flexibility and stability in quickly changing environments.
Long Chain CoA Esters as Competitive Antagonists of Phosphatidylinositol 4,5-Bisphosphate Activation in Kir Channels
2005-06-26

Long chain fatty acid esters of coenzyme A (LC-CoA) are potent activators of ATP-sensitive (K(ATP)) channels, and elevated levels have been implicated in the pathophysiology of type 2 diabetes. This stimulatory effect is thought to involve a mechanism similar to phosphatidylinositol 4,5-bisphosphate (PIP2), which activates all known inwardly rectifying potassium (Kir) channels. However, the effect of LC-CoA on other Kir channels has not been well characterized. In this study, we show that in contrast to their stimulatory effect on K(ATP) channels, LC-CoA (e.g. oleoyl-CoA) potently and reversibly inhibits all other Kir channels tested (Kir1.1, Kir2.1, Kir3.4, Kir7.1). We also demonstrate that the inhibitory potency of the LC-CoA increases with the chain length of the fatty acid chain, while both its activatory and inhibitory effects critically depend on the presence of the 3'-ribose phosphate on the CoA group. Biochemical studies also demonstrate that PIP2 and LC-CoA bind with similar affinity to the C-terminal domains of Kir2.1 and Kir6.2 and that PIP2 binding can be competitively antagonized by LC-CoA, suggesting that the mechanism of LC-CoA inhibition involves displacement of PIP2. Furthermore, we demonstrate that in contrast to its stimulatory effect on K(ATP) channels, phosphatidylinositol 3,4-bisphosphate has an inhibitory effect on Kir1.1 and Kir2.1. These results demonstrate a bi-directional modulation of Kir channel activity by LC-CoA and phosphoinositides and suggest that changes in fatty acid metabolism (e.g. LC-CoA production) could have profound and widespread effects on cellular electrical activity.
Molecular and systemic mechanisms of general anaesthesia: the ‘multi-site and multiple mechanisms’ concept
2005-06-27

Clinical anaesthesia is based on drug actions at multiple anatomical sites in the brain. The finding that amnesia, hypnosis and immobility involve distinct molecular targets opens new avenues for developing improved therapeutic strategies in anaesthesia.