julilili42/papers huggingface dataset:
Sensitivity of Red Sea circulation to sea level and insolation forcing during the last interglacial
2011-04-08

Abstract. This study investigates the response of Red Sea circulation to sea level and insolation changes during termination II and across the last interglacial, in comparison with termination I and the Holocene. Sediment cores from the central and northern part of the Red Sea were investigated by micropaleontological and geochemical proxies. The recovery of the planktonic foraminiferal fauna following high salinities during MIS 6 took place at similar sea-level stand (~50 m below present day), and with a similar species succession, as during termination I. This indicates a consistent sensitivity of the basin oceanography and the plankton ecology to sea-level forcing. Based on planktonic foraminifera, we find that increased water exchange with the Gulf of Aden especially occurred during the sea-level highstand of interglacial MIS 5e. From MIS 6 to the peak of MIS 5e, northern Red Sea SST increased from 21 °C to 25 °C, with about 3 °C of this increase taking place during termination II. Changes in planktonic foraminiferal assemblages indicate that the development of the Red Sea oceanography during MIS 5 was strongly determined by insolation and monsoon strength. The SW Monsoon summer circulation mode was enhanced during the termination, causing low productivity in northern central Red Sea core KL9, marked by high abundance of G. sacculifer, which – as in the Holocene – followed summer insolation. Core KL11 records the northern tip of the intruding intermediate water layer from the Gulf of Aden and its planktonic foraminifera fauna shows evidence for elevated productivity during the sea-level highstand in the southern central Red Sea. By the time of MIS 5 sea-level regression, elevated organic biomarker BIT values suggest denudation of soil organic matter into the Red Sea and high abundances of G. glutinata, and high reconstructed chlorophyll-a values, indicate an intensified NE Monsoon winter circulation mode. Our results imply that the amplitude of insolation fluctuations, and the resulting monsoon strength, strongly influence the Red Sea oceanography during sea-level highstands by regulating the intensity of water exchange with the Gulf of Aden. These processes are responsible for the observation that MIS 5e/d is characterized by higher primary productivity than the Holocene.
AFQ056 treatment of levodopa‐induced dyskinesias: Results of 2 randomized controlled trials
2011-04-11

Abstract Study objectives were to assess the efficacy, safety, and tolerability of AFQ056 in Parkinson's disease patients with levodopa‐induced dyskinesia. Two randomized, double‐blind, placebo‐controlled, parallel‐group, in‐patient studies for Parkinson's disease patients with moderate to severe levodopa‐induced dyskinesia (study 1) and severe levodopa‐induced dyskinesia (study 2) on stable dopaminergic therapy were performed. Patients received 25–150 mg AFQ056 or placebo twice daily for 16 days (both studies). Study 2 included a 4‐day down‐titration. Primary outcomes were the Lang‐Fahn Activities of Daily Living Dyskinesia Scale (study 1), the modified Abnormal Involuntary Movement Scale (study 2), and the Unified Parkinson's Disease Rating Scale–part III (both studies). Secondary outcomes included the Unified Parkinson's Disease Rating Scale–part IV items 32–33. The primary analysis was change from baseline to day 16 on all outcomes. Treatment differences were assessed. Fifteen patients were randomized to AFQ056 and 16 to placebo in study 1; 14 patients were randomized to each group in study 2. AFQ056‐treated patients showed significant improvements in dyskinesias on day 16 versus placebo (eg, Lang‐Fahn Activities of Daily Living Dyskinesia Scale, P = .021 [study 1]; modified Abnormal Involuntary Movement Scale, P = .032 [study 2]). No significant changes were seen from baseline on day 16 on the Unified Parkinson's Disease Rating Scale‐part III in either study. Adverse events were reported in both studies, including dizziness. Serious adverse events (most commonly worsening of dyskinesias, apparently associated with stopping treatment) were reported by 4 AFQ056‐treated patients in study 1, and 3 patients (2 AFQ056‐treated patient and 1 in the placebo group) in study 2. AFQ056 showed a clinically relevant and significant antidyskinetic effect without changing the antiparkinsonian effects of dopaminergic therapy. © 2011 Movement Disorder Society
Long-Term Follow-Up and Outcome of Liver Transplantation From Anti-Hepatitis C Virus-Positive Donors: A European Multicentric Case-Control Study
2011-04-11

We do not recommend the indiscriminate use of anti-HCV-positive donors, especially if HCV-RNA positive, as the use of this kind of graft could be linked to an advanced stage of fibrosis, the main risk factor we observed for earlier hepatitis C recurrence.
Evolution of inclined planets in three-dimensional radiative discs
2011-04-11

While planets in the solar system only have a low inclination with respect to\\nthe ecliptic there is mounting evidence that in extrasolar systems the\\ninclination can be very high, at least for close-in planets. One process to\\nalter the inclination of a planet is through planet-disc interactions. Recent\\nsimulations considering radiative transport have shown that the evolution of\\nmigration and eccentricity can strongly depend on the thermodynamic state of\\nthe disc. We extend previous studies to investigate the planet-disc\\ninteractions of fixed and moving planets on inclined and eccentric orbits. We\\nalso analyse the effect of the disc's thermodynamic properties on the orbital\\nevolution of embedded planets in detail. The protoplanetary disc is modelled as\\na viscous gas where the internally produced dissipation is transported by\\nradiation. For locally isothermal discs, we confirm previous results and find\\ninclination damping and inward migration for planetary cores. For low\\ninclinations i &lt; 2 H/r, the damping is exponential, while di/dt is proportional\\nto i^-2 for larger i. For radiative discs, the planetary migration is very\\nlimited, as long as their inclination exceeds a certain threshold. If the\\ninclination is damped below this threshold, planetary cores with a mass up to\\napproximately 33 Earth masses start to migrate outwards, while larger cores\\nmigrate inwards right from the start. The inclination is damped for all\\nanalysed planet masses. In a viscous disc an initial inclination of embedded\\nplanets will be damped for all planet masses. This damping occurs on timescales\\nthat are shorter than the migration time. If the inclination lies beneath a\\ncertain threshold, the outward migration in radiative discs is not handicapped.\\nOutward migration is strongest for circular and non-inclined orbits.\\n
Orientational Ordering of Nonplanar Phthalocyanines on Cu(111): Strength and Orientation of the Electric Dipole Moment
2011-04-11

In order to investigate the orientational ordering of molecular dipoles and the associated electronic properties, we studied the adsorption of chlorogallium phthalocyanine molecules (GaClPc, Pc=C32N8H16(-2) on Cu(111) by using the x-ray standing wave technique, photoelectron spectroscopy, and quantum mechanical calculations. We find that for submonolayer coverages on Cu(111) the majority of GaClPc molecules adsorb in a Cl-down configuration by forming a covalent bond to the substrate. For bilayer coverages the x-ray standing wave data indicate a coexistence of the Cl-down and Cl-up configurations on the substrate. The structural details established for both cases and supplementary calculations of the adsorbate system allow us to analyze the observed change of the work function.
Perioperative Outcome of Patients with Esophageal Atresia and Tracheo-esophageal Fistula Undergoing Open Versus Thoracoscopic Surgery
2011-04-12

Thoracoscopic repair of EA with TEF is justified because of a comparable perioperative outcome to open surgery, competitive operating times, decreased trauma to the thoracic cavity, and improved cosmesis despite skeptical considerations. Complication rates are not higher than in children operated on through a thoracotomy. However, a learning curve has to be taken into account and large experience in minimal invasive surgery is mandatory for this procedure. Larger series have to be expected for a more objective evaluation of perioperative as well as long-term outcomes. To our opinion, the thoracoscopic approach appears to be favorable and could be a future standard.
Non-AIDS Associated Kaposi's Sarcoma: Clinical Features and Treatment Outcome
2011-04-12

Unlike KS in AIDS patients, non-AIDS associated KS is a rather localized process which rarely involves lymph nodes or organs. It is mostly seen in elderly males from Mediterranean or Eastern European countries and in most cases responsive on local or systemic therapeutic strategies.
Recovery of cortical functioning in abstinent alcohol-dependent patients: Prefrontal brain oxygenation during verbal fluency at different phases during withdrawal
2011-04-12

Our results are compatible with an increase in frontal brain activity from alcohol dependence over abstinence up to normal functioning. However, as cross-sectional designs do not allow to assess causal relations, results have to be considered preliminary and longitudinal studies are needed to further elucidate recovery processes in alcohol dependence.
Exploring the self-directed anger of the stigmatized
2011-04-12

Does social identification protect or harm targets of discrimination? Two studies ( N = 52, N = 94) tested the prediction that perceived legitimacy moderates the impact of social identification on negative responses to discrimination. Results confirm that when discrimination is perceived as illegitimate, identification is negatively related to self-directed anger ( buffering effect) because identification provides a feeling of in-group support. However, when discrimination is perceived as legitimate, identification is positively related to self-directed anger ( exacerbating effect) because the internalized social identity is perceived as legitimate target for the negative treatment. Legitimacy is measured and manipulated among different low-status groups. The legitimization and internalization of discrimination driven by self-directed anger are discussed.
Changes in chemical composition and nanostructure of SiC thin films prepared by PECVD during thermal annealing
2011-04-12

Abstract Silicon carbide (SiC) thin films were deposited on silicon (Si) using plasma enhanced chemical vapor deposition (PECVD). Annealing was done in a rapid thermal annealing furnace at a temperature of 1300 °C. As‐deposited and annealed Si‐rich and stoichiometric SiC thin films were investigated by analytical transmission electron microscopy (AEM). TEM‐energy‐dispersive X‐ray spectroscopy was used to quantify the chemical composition of the SiC thin films with high accuracy. The chemical composition of the near stoichiometric SiC thin film changed during annealing from Si 0.4 C 0.6 to Si 0.5 C 0.5 due to diffusion of Si from the Si substrate into the film. The Si‐rich Si 1– x C x film had the identical chemical composition of Si 0.8 C 0.2 before and after annealing. As‐deposited films show nanoporosity within the bulk film. During annealing, v‐shaped defect structures were formed at the interface of the stoichiometric SiC thin film to the Si substrate. Diffraction patterns revealed that as‐deposited films were amorphous. During annealing the crystallization of 3C‐SiC occurred in near‐stoichiometric SiC thin films, whereas in Si‐rich Si 1– x C x thin films two phases, namely Si and 3C‐SiC, crystallized. Low‐loss and core‐loss electron energy loss spectroscopy (EELS) verified the diffraction results. In the low‐loss spectra of the near stoichiometric SiC thin film, a plasmon peak located at 20.2 eV before and at 22.3 eV after annealing was detected. The low‐loss spectra of the Si‐rich Si 1– x C x thin film showed an asymmetric plasmon peak with two maxima located at 18.5 and 25.0 eV in the as‐deposited film and 18.6 and 24.3 eV in the annealed Si‐rich Si 1– x C x film. The 18.5 eV plasmon peaks is assigned to Si and the 25 eV plasmon peak is attributed to the SiC phase.
Estimation of radiation exposure of retrospective gated and prospective triggered 128-slice triple-rule-out CT angiography
2011-04-13

Background CT has become an important role in the differential diagnosis of acute chest pain to exclude an aortic dissection, pulmonary embolism and acute coronary artery syndrome. However, the additional radiation exposure is a cause of concern and dose saving strategies should be applied, if possible. Purpose To estimate effective dose of retrospective gated and prospective ECG-triggered triple-rule-out computed tomography angiography (TRO-CTA). Material and Methods An Alderson-Rando-phantom equipped with thermoluminescent dosimeters was used for dose measurements. Exposure was performed on a 128-slice single source scanner. The following scan parameters were used (retrospective ECG-gated): 120 kV, 190 mAs/rot., collimation 128x0.6 mm, rotation time 0.3 s. Protocols with a simulated heart rate (HR) of 60 and 100 bpm were performed using the standard ECG-pulsing as well as MinDose. Additionally, a prospective triggered TRO-CTA was acquired (HR 60 bpm). Results The estimated effective dose of retrospective ECG-gated TRO-CTA ranged from 7.4–13.4 mSv and from 10.1–17.5 mSv for men and women, respectively. Due to radiosensitive breast tissue, women received a significant increased effective dose of up to 64.7% ± 0.03% (p = 0.028) compared to men. MinDose reduces radiation exposure of up to 33.0% ± 6.5% in comparison to standard ECG-pulsing (p &lt; 0.001). The effective dose increased significantly with lower heart rates (p &lt; 0.001). Prospective ECG-triggered TRO-CTA showed an effective dose of 5.9 mSv and 8.2 mSv for men and women, respectively. Compared to retrospective ECG-gated TRO-CTA a significant dose reduction was observed (p &lt; 0.001). Conclusion Due to the significant different dose exposure, scan protocols should be specifically adapted in a patient- and problem-oriented manner.
On expedient properties of common biological score functions for multi-modality, adaptive and 4D dose optimization
2011-04-13

Frequently, radiotherapy treatments are comprised of several dose distributions computed or optimized in different patient geometries. Therefore, the need arises to compute the comprehensive biological effect or physical figure of merit of the combined dose of a number of distinct geometry instances. For that purpose the dose is typically accumulated in a reference geometry through deformation fields obtained from deformable image registration. However, it is difficult to establish precise voxel-by-voxel relationships between different anatomical images in many cases. In this work, the mathematical properties of commonly used score functions are exploited to derive an upper boundary for the maximum effect for normal tissue and a lower boundary for the minimum effect for the target of accumulated doses on multiple geometry instances.
Mesoscopic cross-film cryotrons: Vortex trapping and dc-Josephson-like oscillations of the critical current
2011-04-13

We investigate theoretically and experimentally the transport properties of a\\nplain Al superconducting strip in the presence of a single straight\\ncurrent-carrying wire, oriented perpendicular to the superconducting strip. It\\nis well known that the critical current of the superconducting strip, Ic, in\\nsuch cryotron--like system can be tuned by changing the current in the control\\nwire, Iw. We demonstrated that the discrete change in the number of the pinned\\nvortices/antivortices inside the narrow and long strip nearby the\\ncurrent-carrying wire results in a peculiar oscillatory dependence of Ic on Iw.\\n
Hepatic Glucokinase Expression Is Associated with Lipogenesis and Fatty Liver in Humans
2011-04-14

Abstract Background/Aims: Glucokinase (GCK) phosphorylates glucose to form glucose 6-phosphate and thereby regulates hepatic glucose disposal and activates hepatic lipogenesis. Hepatic GCK activity is regulated on the level of GCK mRNA expression and by the inhibitory glucokinase regulatory protein. In this study, we aimed to investigate the relation between GCK mRNA expression and markers of lipogenesis as well as liver fat content in human liver biopsies. Additionally, we investigated whether genetic variation in the liver specific GCK promoter determines liver fat content in humans. Methods: Hepatic mRNA expression and liver triglyceride content was analyzed in 50 human liver biopsies. In a second cohort of 330 individuals, liver fat was precisely measured by 1H magnetic resonance spectroscopy. Results: Hepatic GCK mRNA expression is associated with triglyceride content in human liver biopsies (r = 0.50, P = 0.0002). Furthermore, hepatic GCK mRNA expression is associated with lipogenic gene expression (fatty acid synthase, r = 0.49, P = 0.0003; acetyl-coenzyme A carboxylase-α, r = 0.44, P = 0.0015, and acetyl-coenzyme A carboxylase-β, r = 0.48, P = 0.0004) and the de novo lipogenesis index (r = 0.36, P = 0.01). In support of these findings, the single-nucleotide polymorphism rs2041547 in the liver-specific GCK promoter is associated with liver fat content in prediabetic individuals (P = 0.047). Conclusions: In this study, we demonstrate for the first time that GCK mRNA expression is associated with markers of de novo lipogenesis and liver triglyceride content in humans. This suggests that increased GCK activity may induce fatty liver and its metabolic and hepatic consequences in humans. Thus, the widely used approach to nonspecifically activate β-cell and hepatic GCK to treat diabetes mellitus is therefore questionable and may cause serious side effects.
Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules
2011-04-14

MHC class II molecules (MHC II) play a pivotal role in the cell-surface presentation of antigens for surveillance by T cells. Antigen loading takes place inside the cell in endosomal compartments and loss of the peptide ligand rapidly leads to the formation of a non-receptive state of the MHC molecule. Non-receptiveness hinders the efficient loading of new antigens onto the empty MHC II. However, the mechanisms driving the formation of the peptide inaccessible state are not well understood. Here, a combined approach of experimental site-directed mutagenesis and computational modeling is used to reveal structural features underlying "non-receptiveness." Molecular dynamics simulations of the human MHC II HLA-DR1 suggest a straightening of the α-helix of the β1 domain during the transition from the open to the non-receptive state. The movement is mostly confined to a hinge region conserved in all known MHC molecules. This shift causes a narrowing of the two helices flanking the binding site and results in a closure, which is further stabilized by the formation of a critical hydrogen bond between residues αQ9 and βN82. Mutagenesis experiments confirmed that replacement of either one of the two residues by alanine renders the protein highly susceptible. Notably, loading enhancement was also observed when the mutated MHC II molecules were expressed on the surface of fibroblast cells. Altogether, structural features underlying the non-receptive state of empty HLA-DR1 identified by theoretical means and experiments revealed highly conserved residues critically involved in the receptiveness of MHC II. The atomic details of rearrangements of the peptide-binding groove upon peptide loss provide insight into structure and dynamics of empty MHC II molecules and may foster rational approaches to interfere with non-receptiveness. Manipulation of peptide loading efficiency for improved peptide vaccination strategies could be one of the applications profiting from the structural knowledge provided by this study.
Inhibitory effects of glycosaminoglycans on basal and stimulated transforming growth factor- 1 expression in mesangial cells: biochemical and structural considerations
2011-04-14

A number of glycosaminoglycan (GAG) species related to heparin, dermatan sulfate (DeS) and chondroitin sulfate were tested for their ability to interfere with the physiological expression and/or pathological overexpression of the TGF-β1 gene. The influence of the molecular weight, molecular weight distribution, degree of sulfation and location of the sulfate groups was examined in an attempt to unveil fine relationships between structure and activity. The nature of the polysaccharide plays a major part, heparins proving able to inhibit both basal and stimulated TGF-β1 gene expression, DeSs being essentially inactive and chondroitin sulfates only inhibiting stimulated TGF-β1 gene expression. Within this frame, the particular physical and chemical properties of some GAGs appear to further modulate TGF-β1 gene response. Judging from our investigation, chondroitin sulfates seem the most promising for potential pharmacological applications in disorders characterized by fibrogenic TGF-β1 overexpression.
Quantifying the Link between Anatomical Connectivity, Gray Matter Volume and Regional Cerebral Blood Flow: An Integrative MRI Study
2011-04-15

Connectivity and perfusion are systematically linked throughout a number of brain regions, thus we discuss these results as a starting point for further research on the role of homology in the formation of functional connectivity networks and on how structure/function relationships can manifest in the form of such trait interdependency.
The Transcription Factor Evi-1 Is Overexpressed, Promotes Proliferation, and Is Prognostically Unfavorable in Infratentorial Ependymomas
2011-04-15

Abstract Purpose: Ependymomas are glial tumors of presumably radial glial origin that share morphologic similarities with ependymal cells. The molecular genetics of ependymomas of supratentorial, infratentorial, and spinal location is heterogeneous. We aimed at identifying pathways operative in the development of infratentorial ependymomas. Experimental Design: To do so, gene expression profiles of tumor cells laser microdissected from infratentorial ependymomas (n = 15) were compared with that of nonneoplastic ependymal cells laser microdissected from autopsy tissue (n = 7). Results: Among 31 genes significantly overexpressed (&amp;gt;5-fold) in ependymomas, transcription factor EVI1 (ecotropic viral integration site 1) showed the highest overexpression (35-fold). Evi-1 protein expression could be confirmed in formalin-fixed, paraffin-embedded samples of 26 of 28 infratentorial ependymomas but only in 7 of 47 nonependymal glial tumors (P &amp;lt; 0.001). Furthermore, MDS1/EVI1 fusion transcripts were detectable in 17 of 28 infratentorial ependymomas and significantly correlated with MGMT (O6-methylguanine-DNA-methyltransferase) promoter hypermethylation (P &amp;lt; 0.05). In primary infratentorial ependymoma cells, transfection with EVI1-specific siRNAs resulted in significant growth inhibition [48 hours: 87% ± 2% and 74% ± 10% as compared with control (mean ± SD; P &amp;lt; 0.001)]. The prognostic role of EVI1 could further be validated in an independent cohort of 39 infratentorial and 26 supratentorial ependymomas on the basis of mRNA expression profiling. Although in supratentorial ependymomas EVI1 expression status had no prognostic impact, in infratentorial ependymomas, high EVI1 expression was associated with shorter overall survival and progression-free survival. Conclusions: To conclude, the transcription factor Evi-1 is overexpressed in infratentorial ependymomas, promotes proliferation of ependymal tumor cells, and is prognostically unfavorable. Clin Cancer Res; 17(11); 3631–7. ©2011 AACR.