julilili42/papers huggingface dataset:
Freehand Real-Time MRI-Guided Lumbar Spinal Injection Procedures at 1.5 T: Feasibility, Accuracy, and Safety
2009-03-20

We accept the hypothesis that freehand real-time MRI-guided lumbar spinal injection procedures are feasible, accurate, and safe when performed with a clinical open-bore 1.5-T MRI system. We note that real-time MRI guidance has the additional advantage of a complete absence of patient and operator exposure to ionizing radiation.
Large‐conductance calcium‐activated potassium channels in purkinje cell plasma membranes are clustered at sites of hypolemmal microdomains
2009-03-20

Abstract Calcium‐activated potassium channels have been shown to be critically involved in neuronal function, but an elucidation of their detailed roles awaits identification of the microdomains where they are located. This study was undertaken to unravel the precise subcellular distribution of the large‐conductance calcium‐activated potassium channels (called BK, KCa1.1, or Slo1 ) in the somatodendritic compartment of cerebellar Purkinje cells by means of postembedding immunogold cytochemistry and SDS‐digested freeze‐fracture replica labeling (SDS‐FRL). We found BK channels to be unevenly distributed over the Purkinje cell plasma membrane. At distal dendritic compartments, BK channels were scattered over the plasma membrane of dendritic shafts and spines but absent from postsynaptic densities. At the soma and proximal dendrites, BK channels formed two distinct pools. One pool was scattered over the plasma membrane, whereas the other pool was clustered in plasma membrane domains overlying subsurface cisterns. The labeling density ratio of clustered to scattered channels was about 60:1, established in SDS‐FRL. Subsurface cisterns, also called hypolemmal cisterns, are subcompartments of the endoplasmic reticulum likely representing calciosomes that unload and refill Ca 2+ independently. Purkinje cell subsurface cisterns are enriched in inositol 1,4,5‐triphosphate receptors that mediate the effects of several neurotransmitters, hormones, and growth factors by releasing Ca 2+ into the cytosol, generating local Ca 2+ sparks. Such increases in cytosolic [Ca 2+ ] may be sufficient for BK channel activation. Clustered BK channels in the plasma membrane may thus participate in building a functional unit (plasmerosome) with the underlying calciosome that contributes significantly to local signaling in Purkinje cells. J. Comp. Neurol. 515:215–230, 2009. © 2009 Wiley‐Liss, Inc.
Does Export Openness Increase Firm‐level Output Volatility?
2009-03-20

Abstract There is a widespread concern that increased trade may lead to increased instability and thus risk at the firm level. Greater export openness can indeed affect firm‐level volatility by changing the exposure and the reaction of firms to macroeconomic developments. The net effect is ambiguous from a theoretical point of view. This paper provides firm‐level evidence on the link between openness and volatility. Using comprehensive data on more than 21,000 German manufacturing firms for the period 1980–2001, we analyse the evolution of firm‐level output volatility and the link between volatility and export openness. Our paper has three main findings. First, firm‐level output volatility is significantly higher than the level of aggregate volatility, but it displays similar patterns. Second, increased export openness lowers firm‐level output volatility. This effect is primarily driven by variations along the extensive margin, i.e. by the distinction between exporters and non‐exporters. Variations along the intensive margin, i.e. the volume of exports, tend to have a dampening impact on volatility as well. Third, small firms are more volatile than large firms.
Influence of oxygen and carbogen breathing on renal oxygenation measured by T2*‐weighted imaging at 3.0 T
2009-03-20

Abstract The aim of the study was to assess the influence of carbogen (95% O 2 , 5% CO 2 ) or pure oxygen breathing on renal oxygenation measured by blood oxygenation level dependent (BOLD) magnetic resonance imaging at 3.0 T. Seven healthy young volunteers (median age 25, range 23–35 years) participated in the study. A T2*‐weighted fat‐saturated spoiled gradient‐echo sequence was implemented on a 3.0 T whole‐body imager (TE/TR = 27.9 ms/49 ms, excitation angle 20°) with an acquisition time of approximately 5.3 s. A total of 100 images were acquired during 22 min. A block design was applied for gas administration: 4 min room air, 4 min carbogen/oxygen, 4 min room air, 4 min carbogen/oxygen and 6 min room air. A compartment model was fitted to the data sets accounting for time‐dependent increase/decrease of renal oxygenation as well as baseline changes of the scanner. T2*‐weighted images showed good image quality without notable artefacts or distortions. Mean relative signal increase due to carbogen breathing was 2.73% (95% confidence interval: 1.34–5.54) in the right kidney and 3.76% (1.53–9.20) in the left kidney, while oxygen breathing led to a signal enhancement of 3.20% (2.57–3.98) in the right kidney and 3.16% (1.83–5.45) in the left kidney. No statistical difference was found between carbogen and oxygen breathing or between the oxygenation of the right and the left kidney. A significant difference was found in the characteristic time constant for the signal increase with a faster saturation taking place for oxygen breathing. Renal tissue oxygenation is clearly influenced by carbogen or oxygen breathing. The changes can be assessed by T2*‐weighted MRI at high field strengths. The effects are in the expected range for the BOLD effect of 3–4% at 3.0 T. The proposed technique might be interesting for the assessment of renal tissue oxygenation and its regulation in patients with kidney diseases. Copyright © 2009 John Wiley &amp; Sons, Ltd.
Role of the Hydrogen Bonding Heteroatom−Lys53 Interaction between the p38α Mitogen-Activated Protein (MAP) Kinase and Pyridinyl-Substituted 5-Membered Heterocyclic Ring Inhibitors
2009-03-20

In the framework of investigating the role of heteroatoms in pyridinyl-substituted 5-membered (hetero)cycles as potential p38alpha MAP kinase inhibitor scaffolds, cyclopentene, pyrrole, furan, and imidazole analogues were synthesized and tested with respect to their ability to inhibit p38alpha MAP kinase. The vicinal pyridine/4-fluorophenyl pharmacophore was conserved, such as in the prototypical imidazole inhibitor SB203580. The strength of the HB interaction was calculated and compared to the biological data.
Agrin, Aquaporin-4, and Astrocyte Polarity as an Important Feature of the Blood-Brain Barrier
2009-03-23

The blood-brain barrier (BBB) does not exclusively refer to brain endothelial cells, which are the site of the barrier proper. In the past few years, it has become increasingly clear that BBB endothelial cells depend considerably on the brain microenvironment to a degree exceeding the environmental influence in other organs. The concept of the BBB has been continuously developed over the decades, culminating now in the recognition that endothelial cell function in the brain is not limited to simply mediating energy and oxygen transfer between blood and neural tissue. Endothelial cells are rather “Janus-headed beings” that are active partners of both luminal molecules and cells, as well as subendothelial cells such as pericytes, astrocytes, and neurons. In this overview, the authors present and discuss both the role of astroglial cells in managing the BBB and aspects of pathological alterations in the brain as far as the BBB is involved. After a brief introduction of the BBB that describes the structure and function of the brain capillary endothelial cells, the authors report on both the water channel protein aquaporin-4 (AQP4) in astrocytes and the extracellular matrix between astrocytes/pericytes and endothelial cells. The AQP4 has an important impact on the homeostasis in the brain parenchyma; however, the mechanistic cascade from the composition of the astrocyte membrane to the maintenance of BBB properties in the endothelial cells, including their tight junction formation, is still completely unknown.
Symmetry Detection Using Feature Lines
2009-03-23

Abstract In this paper, we describe a new algorithm for detecting structural redundancy in geometric data sets. Our algorithm computes rigid symmetries, i.e., subsets of a surface model that reoccur several times within the model differing only by translation, rotation or mirroring. Our algorithm is based on matching locally coherent constellations of feature lines on the object surfaces. In comparison to previous work, the new algorithm is able to detect a large number of symmetric parts without restrictions to regular patterns or nested hierarchies. In addition, working on relevant features only leads to a strong reduction in memory and processing costs such that very large data sets can be handled. We apply the algorithm to a number of real world 3D scanner data sets, demonstrating high recognition rates for general patterns of symmetry.
Continuum‐based Strain Limiting
2009-03-23

Abstract We present Continuum‐based Strain Limiting (CSL) – a new method for limiting deformations in physically‐based cloth simulations. Despite recent developments for nearly inextensible materials, the efficient simulation of general biphasic textiles and their anisotropic behavior remains challenging. Many approaches use soft materials and enforce limits on edge elongations, leading to discretization‐dependent behavior. Moreover, they offer no explicit control over shearing and stretching unless specifically aligned meshes are used. Based on a continuum deformation measure, our method allows accurate control over all strain components using individual thresholds. We impose deformation limits element‐wise and cast the problem as a 6×6 system of linear equations. CSL can be combined with any cloth simulator and, as a velocity filter, integrates seamlessly into standard collision handling.
Coverage dependent adsorption dynamics in hyperthermal organic thin film growth
2009-03-23

We have examined the dynamics of adsorption of diindenoperylene (DIP) on SiO2 and SiO2 modified with an interfacial organic layer using in situ real time synchrotron x-ray scattering, focusing on the effects of coverage. On both surfaces we observe a substantial increase in the probability of adsorption with increasing coverage, which is most dramatic at the highest incident kinetic energies. On the initially uncovered surfaces, we observe a smooth decrease in the probability of adsorption with increasing incident kinetic energy, indicative of trapping-mediated adsorption. Once both surfaces are covered by DIP, the effects of incident kinetic energy are greatly reduced, and trapping is very efficient over the range of kinetic energies examined. Possible reasons for efficient trapping at high coverage and at high incident kinetic energy include more efficient momentum transfer due to mass matching, and possibly direct molecular insertion. Comparison to results on another small-molecule, pentacene, suggests that this behavior should be common to hyperthermal growth of a variety of other small-molecule thin films.
Monitoring Coordination during Bimanual Movements: Where Is the Mastermind?
2009-03-23

Abstract One remarkable aspect of the human motor repertoire is the multitude of bimanual actions it contains. Still, the neural correlates of coordinated movements, in which the two hands share a common goal, remain debated. To address this issue, we designed two bimanual circling tasks that differed only in terms of goal conceptualization: a “coordination” task that required movements of both hands to adapt to each other to reach a common goal and an “independent” task that imposed a separate goal to each hand. fMRI allowed us to pinpoint three areas located in the right hemisphere that were more strongly activated in the coordination condition: the superior temporal gyrus (STG), the SMA, and the primary motor cortex (M1). We then used transcranial magnetic stimulation (TMS) to disrupt transiently the function of those three regions to determine their causal role in bimanual coordination. Right STG virtual lesions impaired bimanual coordination, whereas TMS to right M1 enhanced hand independence. TMS over SMA, left STG, or left M1 had no effect. The present study provides direct insight into the neural correlates of coordinated bimanual movements and highlights the role of right STG in such bimanual movements.
SBML2LaTEX: Conversion of SBML files into human-readable reports
2009-03-23

Abstract Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization. Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX. Contact: andreas.draeger@uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
Partition Behavior of Polycyclic Aromatic Hydrocarbons Between Aged Coal Tar and Water
2009-03-23

Abstract Coal tar aged in a large-scale, artificial aquifer experiment for five years was subsequently investigated for leaching behavior of polycyclic aromatic hydrocarbons (PAHs). After five years, the initially liquid coal tar had solidified and formed segregated particles with a grain size similar to that of the sandy aquifer material. The composition of the aged coal tar (ACT) with regard to PAHs was remarkably different from that of the original bulk coal tar (BCT), because most of the low-molecular-weight compounds had been depleted. Equilibrium aqueous-phase concentrations of 17 PAHs leaching from the aquifer material containing the ACT were measured from consecutive equilibration steps at increasing temperatures of between 25 and 100C using accelerated solvent extraction. The results showed 2-to 5,000-fold lower concentrations than those from BCT, indicating dramatic changes of dissolution behavior of PAHs from coal tar after the five-year aging period. Predictions based on Raoult's law with the subcooled liquid solubilities substantially overestimated the equilibrium aqueous-phase concentrations of the PAHs from ACT, whereas the estimations were reasonable if the solid solubilities were employed instead. The enthalpies of phase transfer from ACT to water were determined based on the van't Hoff equation. The resulting values agreed with the dissolution enthalpies of pure solid rather than subcooled liquid PAHs.
Switching Akt: from survival signaling to deadly response
2009-03-24

Abstract Akt, a protein kinase hyperactivated in many tumors, plays a major role in both cell survival and resistance to tumor therapy. A recent study, 1 along with other evidences, shows interestingly, that Akt is not a single‐function kinase, but may facilitate rather than inhibit cell death under certain conditions. This hitherto undetected function of Akt is accomplished by its ability to increase reactive oxygen species and to suppress antioxidant enzymes. The ability of Akt to down‐regulate antioxidant defenses uncovers a novel Achilles' heel, which could be exploited by oxidant therapies in order to selectively eradicate tumor cells that express high levels of Akt activity.
Effects of Native Organic Material and Water on Sorption Properties of Reference Diesel Soot
2009-03-24

Soot has been considered as a potentially important sorbent for organic contaminants in soils, sediments, and aerosols. This paper demonstrates that native (authigenic) extractable organic material (EOM) and surface-covering water on soot may have a substantial influence on sorption properties of the soot. Sorption isotherms were determined for apolar and weakly polar sorbates (n-octane, cyclooctane, n-propylbenzene, naphthalene) from an aqueous solution to a standard reference material of diesel soot (SRM 2975) in the original state and after extraction with methanol. For all sorbates tested, removal of EOM from soot by methanol caused the sorption isotherms to be more nonlinear (decrease of Freundlich exponents by 0.19-0.25) compared to the untreated soot. The changes in the isotherms depend on both sorbate structure and sorbate concentration and can be accounted for by two opposing roles that EOM could have on the sorption properties of soot (i) enhancing the overall sorption by absorbing the sorbate into the EOM phase, and (ii) attenuating the sorbate adsorption to the soot carbon surface through sorption competition or site blockage. The n-alkane-to-cycloalkane sorption coefficient ratios (Kn/Kc) indicated that the removal of EOM altered the sorption mode for alkanes from absorption to adsorption. A comparison of the sorption isotherms measured in aqueous suspensions with the soot-air sorption coefficients reported for SRM 2975 in the literature showed that sorption to "soot in water" is significantly weaker than sorption to "soot in air", indicating that complete surface coverage with water suppresses the sorption by soot.
CGADL: An Architecture Description Language for Coarse-Grained Reconfigurable Arrays
2009-03-24

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The high degree of freedom in the design of coarse-grained reconfigurable arrays imposes new challenges on their description and modeling. In this paper, we introduce an architecture description language targeted to describe coarse-grained reconfigurable architecture templates. It comprises innovative key features to allow fast modeling and analysis of such architectures, i.e.: representation of processing element array (ir)regularities, and flexible and concise description of interconnection network. We demonstrate that the proposed language enables a formal validation of the described template, and it eases the analysis and estimation of hardware costs earlier in the design phase. Finally, we show how we automatically generate a SystemC-based simulator of the described architecture. Our results suggest that the semantic and technical innovations of the proposed architecture description language may have a positive impact on the productivity of the design phase. </para>
Recursion in XQuery
2009-03-24

We introduce a controlled form of recursion in XQuery, an inflationary fixed point operator, familiar from the context of relational databases. This operator imposes restrictions on the expressible types of recursion, but it is sufficiently versatile to capture a wide range of interesting use cases, including Regular XPath and its core transitive closure operator. While the optimization of general user-defined recursive functions in XQuery appears elusive, we describe how inflationary fixed points can be efficiently evaluated, provided that the recursive XQuery expressions are distributive. We test distributivity syntactically and algebraically, and provide experimental evidence that XQuery processors can benefit substantially from this mode of evaluation.
Time-point and dosage of gene inactivation determine the tumor spectrum in conditional Ptch knockouts
2009-03-25

Mutations in Patched (PTCH) have been associated with tumors characteristic both for children [medulloblastoma (MB) and rhabdomyosarcoma (RMS)] and for elderly [basal cell carcinoma (BCC)]. The determinants of the variability in tumor onset and histology are unknown. We investigated the effects of the time-point and dosage of Ptch inactivation on tumor spectrum using conditional Ptch-knockout mice. Ptch heterozygosity induced prenatally resulted in the formation of RMS, which was accompanied by the silencing of the remaining wild-type Ptch allele. In contrast, RMS was observed neither after mono- nor biallelic postnatal deletion of Ptch. Postnatal biallelic deletion of Ptch led to BCC precancerous lesions of the gastrointestinal epithelium and mesenteric tumors. Hamartomatous gastrointestinal cystic tumors were induced by monoallelic, but not biallelic Ptch mutations, independently of the time-point of mutation induction. These data suggest that the expressivity of Ptch deficiency is largely determined by the time-point, the gene dose and mode of Ptch inactivation. Furthermore, they point to key differences in the tumorigenic mechanisms underlying adult and childhood tumors. The latter ones are unique among all tumors since their occurrence decreases rather than increases with age. A better understanding of mechanisms underlying this ontological restriction is of potential therapeutic value.
HESS upper limit on the very high energyγ-ray emission from the globular cluster 47 Tucanae
2009-03-25

Observations of the globular cluster 47 Tucanae (NGC 104), which contains at least 23 ms pulsars, were performed with the HESS telescope system. The observations lead to an upper limit of F(E &lt; 800 GeV) &lt; 6.7 × 10-13 cm-2 s-1 on the integral γ-ray photon flux from 47 Tucanae. Considering millisecond pulsars as the unique potential source of γ-rays in the globular cluster, constraints based on emission models are derived: on the magnetic field in the average pulsar nebula and on the conversion efficiency of spin-down power to γ-ray photons or to relativistic leptons. © 2009 ESO.
The Targeted Oral, Once‐Daily Phosphodiesterase 4 Inhibitor Roflumilast and the Leukotriene Receptor Antagonist Montelukast Do Not Exhibit Significant Pharmacokinetic Interactions
2009-03-25

This nonrandomized, fixed‐sequence, 3‐period study investigated potential pharmacokinetic interactions between the leukotriene receptor antagonist montelukast, approved for the treatment of asthma, and roflumilast, an oral, once‐daily phosphodiesterase 4 inhibitor in clinical development for asthma and chronic obstructive pulmonary disease. Pharmacokinetic interactions are of interest because both drugs may be coadministered and share a common metabolic pathway via cytochrome P450 3A. Single‐dose montelukast (10 mg, po) was administered alone in period 1, followed by repeated once‐daily roflumilast alone (500 μg, po) for 12 days (period 2). In period 3, 500 μg qd roflumilast was coadministered with 10 mg qd montelukast for 8 days. Different pharmacokinetic parameters were evaluated for montelukast alone, for steady‐state roflumilast and its pharmacologically active metabolite roflumilast N‐oxide alone, for single‐dose montelukast when coadministered with steady‐state roflumilast, and for steady‐state roflumilast and its N‐oxide metabolite when coadministered with steady‐state montelukast. The AUC and C max of montelukast were modestly increased by 9% and 8%, respectively, when single‐dose montelukast was coadministered with steady‐state roflumilast. The pharmacokinetics of roflumilast and roflumilast N‐oxide in steady state remained unchanged when repeat‐dose montelukast was coadministered at steady‐state. Concomitant administration of both drugs was well tolerated. These findings suggest that no dose adjustment is warranted for either drug when roflumilast and montelukast are coadministered.