julilili42/papers huggingface dataset:
Comparison of the electronic structure of different perylene‐based dye‐aggregates
2012-04-19

Abstract Aggregates of functionalized polycyclic aromatic molecules like perylene derivatives differ in important optoelectronic properties such as absorption and emission spectra or exciton diffusion lengths. Although those differences are well known, it is not fully understood if they are caused by variations in the geometrical orientation of the molecules within the aggregates, variations in the electronic structures of the dye aggregates or interplay of both. As this knowledge is of interest for the development of materials with optimized functionalities, we investigate this question by comparing the electronic structures of dimer systems of representative perylene‐based chromophores. The study comprises dimers of perylene, 3,4,9,10‐perylene tetracarboxylic acid bisimide (PBI), 3,4,9,10‐perylene tetracarboxylic acid dianhydride (PTCDA), and diindeno perylene (DIP). Potential energy curves (PECs) and characters of those electronic states are investigated which determine the optoelectronic properties. The computations use the spin‐component‐scaled approximate coupled‐cluster second‐order method (SCS‐CC2), which describes electronic states of predominately neutral excited (NE) and charge transfer (CT) character equally well. Our results show that the characters of the excited states change significantly with the intermolecular orientation and often represent significant mixtures of NE and CT characters. However, PECs and electronic structures of the investigated perylene derivatives are almost independent of the substitution patterns of the perylene core indicating that the observed differences in the optoelectronic properties mainly result from the geometrical structure of the dye aggregate. It also hints at the fact that optical properties can be computed from less‐substituted model compounds if a proper aggregate geometry is chosen. © 2012 Wiley Periodicals, Inc.
Mutations in the GM1 Binding Site of Simian Virus 40 VP1 Alter Receptor Usage and Cell Tropism
2012-04-19

ABSTRACT Polyomaviruses are nonenveloped viruses with capsids composed primarily of 72 pentamers of the viral VP1 protein, which forms the outer shell of the capsid and binds to cell surface oligosaccharide receptors. Highly conserved VP1 proteins from closely related polyomaviruses recognize different oligosaccharides. To determine whether amino acid changes restricted to the oligosaccharide binding site are sufficient to determine receptor specificity and how changes in receptor usage affect tropism, we studied the primate polyomavirus simian virus 40 (SV40), which uses the ganglioside GM1 as a receptor that mediates cell binding and entry. Here, we used two sequential genetic screens to isolate and characterize viable SV40 mutants with mutations in the VP1 GM1 binding site. Two of these mutants were completely resistant to GM1 neutralization, were no longer stimulated by incorporation of GM1 into cell membranes, and were unable to bind to GM1 on the cell surface. In addition, these mutant viruses displayed an infection defect in monkey cells with high levels of cell surface GM1. Interestingly, one mutant infected cells with low cell surface GM1 more efficiently than wild-type virus, apparently by utilizing a different ganglioside receptor. Our results indicate that a small number of mutations in the GM1 binding site are sufficient to alter ganglioside usage and change tropism, and they suggest that VP1 divergence is driven primarily by a requirement to accommodate specific receptors. In addition, our results suggest that GM1 binding is required for vacuole formation in permissive monkey CV-1 cells. Further study of these mutants will provide new insight into polyomavirus entry, pathogenesis, and evolution.
A pilot study for clinical feasibility of the near-harmonic 2D referenceless PRFS thermometry in liver under free breathing using MR-guided LITT ablation data
2012-04-19

The application of the near-harmonic 2D referenceless MRT method was feasible in a clinical scenario of MR-guided laser-induced thermal therapy (LITT) ablation in liver and permitted accurate prediction of the thermal lesion under free breathing in conscious patients, obviating the need for a controlled breathing under general anaesthesia.
Isotope fractionation between dissolved and suspended particulate Fe in the oxic and anoxic water column of the Baltic Sea
2012-04-19

Abstract. Fe isotope ratios and concentrations of dissolved Fe (Fedis, &lt; 0.45 μm) and of suspended particulate Fe (FeSPM) from a depth profile in the Eastern Gotland Basin, Baltic Sea, show a sharp gradient in δ56Fedis across the suboxic interface with δ56Fedis = −0.4 ‰ in the euxinic deep basin and δ56Fedis = +0.3 ‰ in the oxic upper water column. The isotopic gradient overlaps with a strong concentration gradient of Fedis, a concentration maximum in FeSPM and lower δ56FeSPM values than δ56Fedis. These features indicate preferential loss of light Fe isotopes into suspended iron-oxyhydroxides (FeIOH) during typical oxidative precipitation across the redox interface in the marine environment. The sign of the fractionation, Δ56FeFe_IOH–Fe(II)(aq) &lt; 0 ‰, is in contrast to similar, mostly non-marine redox environments, where Δ56FeFe_IOH–Fe(II)(aq) &gt; 0 ‰. The difference appears to be the result of isotope exchange dominated by reaction kinetics in the marine water column, rather than equilibrium fractionation generally inferred for oxidative Fe precipitation elsewhere. High residual δ56Fedis immediately above the suboxic interface and throughout the oxic water column suggest that any potential Fe export from reducing waters or sediments into the open water column is enriched in the heavy isotopes. Within the suboxic to euxinic deep basin the decreasing δ56FeSPM trend with depth and a generally low δ56Fedis are comparable to trends in marine anoxic sediment profiles indicative of microbial reductive Fe dissolution. This confirms supply of dissolved Fe to the euxinic water column mainly from reductive dissolution of settling particles.
Electrodynamic Coupling of Electric Dipole Emitters to a Fluctuating Mode Density within a Nanocavity
2012-04-20

We investigate the impact of rotational diffusion on the electrodynamic coupling of fluorescent dye molecules (oscillating electric dipoles) to a tunable planar metallic nanocavity. Fast rotational diffusion of the molecules leads to a rapidly fluctuating mode density of the electromagnetic field along the molecules' dipole axis, which significantly changes their coupling to the field as compared to the opposite limit of fixed dipole orientation. We derive a theoretical treatment of the problem and present experimental results for rhodamine 6G molecules in cavities filled with low and high viscosity liquids. The derived theory and presented experimental method is a powerful tool for determining absolute quantum yield values of fluorescence.
Factors influencing heterogeneity of radiation-induced DNA-damage measured by the alkaline comet assay
2012-04-20

Abstract Background To investigate whether different conditions of DNA structure and radiation treatment could modify heterogeneity of response. Additionally to study variance as a potential parameter of heterogeneity for radiosensitivity testing. Methods Two-hundred leukocytes per sample of healthy donors were split into four groups. I: Intact chromatin structure; II: Nucleoids of histone-depleted DNA; III: Nucleoids of histone-depleted DNA with 90 mM DMSO as antioxidant. Response to single (I-III) and twice (IV) irradiation with 4 Gy and repair kinetics were evaluated using %Tail-DNA. Heterogeneity of DNA damage was determined by calculation of variance of DNA-damage (V) and mean variance (Mvar), mutual comparisons were done by one-way analysis of variance (ANOVA). Results Heterogeneity of initial DNA-damage (I, 0 min repair) increased without histones (II). Absence of histones was balanced by addition of antioxidants (III). Repair reduced heterogeneity of all samples (with and without irradiation). However double irradiation plus repair led to a higher level of heterogeneity distinguishable from single irradiation and repair in intact cells. Increase of mean DNA damage was associated with a similarly elevated variance of DNA damage (r = +0.88). Conclusions Heterogeneity of DNA-damage can be modified by histone level, antioxidant concentration, repair and radiation dose and was positively correlated with DNA damage. Experimental conditions might be optimized by reducing scatter of comet assay data by repair and antioxidants, potentially allowing better discrimination of small differences. Amount of heterogeneity measured by variance might be an additional useful parameter to characterize radiosensitivity.
Reference values for three‐dimensional surface cephalometry in children aged 3–6 years
2012-04-20

Möller M., Schaupp E., Massumi‐Möller N., Zeyher C., Godt A., Berneburg M. Reference values for three‐dimensional surface cephalometry in children aged 3–6 years Orthod Craniofac Res 2012; 15 : 103–116. © 2012 John Wiley &amp; Sons A/S Structured Abstract Objective – This prospective cross‐sectional study design was performed to define reference values for the facial surfaces of 3–6‐year‐old boys and girls using three‐dimensional surface cephalometry. Material and Methods – A total of 2290 standardized three‐dimensional facial images from 3 to 6‐year‐old preschool children were separated by gender and assigned to four age categories. All children were Caucasian and revealed no evidence of dentofacial abnormalities. On each image, 31 cephalometric landmarks were marked, resulting in 35 (19 frontal, six lateral, 10 paired) distances and eight angles. Differences between age groups and genders were calculated and significances detected. Results – A base table with reference values was compiled, which indicated that boys showed higher values than age‐matched girls and that measured distances increased with age. Conclusion – The mean values from this study could be compiled as a reference table for three‐dimensional facial analysis in Caucasian children aged 3–6 years. Such a reference table could be used in comparative studies with other populations or children with craniofacial malformations.
Synthetic Biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production
2012-04-21

The supply of precursors, which are subsequently incorporated into the final product, is often already organized in a modular manner in nature and may directly be exploited for Synthetic Biology. Here we report examples for the synthesis of building blocks and possibilities to modify and optimize antibiotic biosynthesis, exemplary for the synthesis of the manipulation of the synthesis of the glycopeptide antibiotic balhimycin.
Leukodystrophies in Patients with Adult-Onset Ataxia: Frequency and Phenotype (P05.020)
2012-04-22

Objective: We aimed to determine the frequency of leukodystrophies and its phenotypic spectrum in patients with ataxia of unknown cause. Background A broad spectrum of heterogeneous neurological disorders including lysosomal storage disorders present with chronic progressive cerebellar ataxia. Identifying the underlying etiology is important as it sometimes allows for initiation of pharmacological treatment. Design/Methods: We prospectively studied 107 index patients who presented with adult-onset cerebellar ataxia consistent with autosomal recessive inheritance. Patients were screened for lysosomal enzyme deficiencies including metachromatic leukodystrophy, GM1-Gangliosidosis, Tay-Sachs and Sandhoff9 disease, and Krabbe disease. If clinical evidence was suggestive of other types of leukodystrophies, additional genetic or metabolic testing was performed. Clinical characterization included neurological and psychiatric features and MR-imaging. Results: Screening for lysosomal disorders detected one patient with late-onset Tay Sachs disease and one with metachromatic leukodystrophy. Both patients presented with cognitive deficits and psychiatric comorbidity beside ataxia. Additonal tests revealed two patients with Nieman Pick disease type C, one with cerebrotendinous xanthomatosis, and one with leukencephalopathy with brain stem and spinal cord involvement and lactate elevation. All of them presented with additional signs like cognitive dysfunction, pyramidal affection and/or peripheral neuropathy. Conclusions: Leukodystrophies were responsible for 6% of cryptic ataxia in our series. The concomitant occurrence of cerebellar ataxia with cognitive dysfunction, psychiatric comorbidities, spasticity and/or neuropathy should prompt screening for lysosomal storage disorders. Hyperintensity of cerebral white matter on MR FLAIR images is not an obligate marker in adult-onset leukodystrophies. Supported by: German Ministry of Research and Education (BMBF) grant 01GM0838. Disclosure: Dr. Muller vom Hagen has nothing to disclose. Dr. Synofzik has received personal compensation for activities with Volkswagen Foundation, the Movement Disorder Society, and Fresenius Kabi. Dr. Schicks has nothing to disclose. Dr. Krageloh-Mann has nothing to disclose. Dr. Schoels has received research support from Deutsche Forschungsgemeinschaft, German Research Council, Leukonet, mitoNET, EUROSPA, RISCA, and the HSP-Selbsthilfegruppe Deutschland eV.
Molecular interactions of ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS, a LOB domain protein regulating shoot-borne root initiation in maize (Zea maysL.)
2012-04-23

Rootless concerning crown and seminal roots ( Rtcs ) encodes a LATERAL ORGAN BOUNDARIES domain (LBD) protein that regulates shoot-borne root initiation in maize ( Zea mays L.). GREEN FLUORESCENT PROTEIN (GFP)-fusions revealed RTCS localization in the nucleus while its paralogue RTCS-LIKE (RTCL) was detected in the nucleus and cytoplasm probably owing to an amino acid exchange in a nuclear localization signal. Moreover, enzyme-linked immunosorbent assay (ELISA) experiments demonstrated that RTCS primarily binds to LBD DNA motifs. RTCS binding to an LBD motif in the promoter of the auxin response factor (ARF) ZmArf34 and reciprocally, reciprocal ZmARF34 binding to an auxin responsive element motif in the promoter of Rtcs was shown by electrophoretic mobility shift assay experiments. In addition, comparative qRT-PCR of wild-type versus rtcs coleoptilar nodes suggested RTCS-dependent activation of ZmArf34 expression. Consistently, luciferase reporter assays illustrated the capacity of RTCS, RTCL and ZmARF34 to activate downstream gene expression. Finally, RTCL homo- and RTCS/RTCL hetero-interaction were demonstrated in yeast-two-hybrid and bimolecular fluorescence complementation experiments, suggesting a role of these complexes in downstream gene regulation. In summary, the data provide novel insights into the molecular interactions resulting in crown root initiation in maize.
WebCAGe -- A Web-Harvested Corpus Annotated with GermaNet Senses
2012-04-23

This paper describes an automatic method for creating a domain-independent senseannotated corpus harvested from the web. As a proof of concept, this method has been applied to German, a language for which sense-annotated corpora are still in short supply. The sense inventory is taken from the German wordnet GermaNet. The web-harvesting relies on an existing mapping of GermaNet to the German version of the web-based dictionary Wiktionary. The data obtained by this method constitute
Visualising Linguistic Evolution in Academic Discourse
2012-04-23

The present paper describes procedures to visualise diachronic language changes in academic discourse to support analysis. These changes are reflected in the distribution of different lexico-grammatical features according to register. Findings about register differences are relevant for both linguistic applications (e.g., discourse analysis and translation studies) and NLP tasks (notably automatic text classification). 1
Estimating and visualizing language similarities using weighted alignment and force-directed graph layout
2012-04-23

The paper reports several studies about quantifying language similarity via phonetic alignment of core vocabulary items (taken from Wichman’s Automated Similarity Judgement Program data base). It turns out that weighted alignment according to the Needleman-Wunsch algorithm yields best results. For visualization and data exploration purposes, we used an implementation of the Fruchterman-Reingold algorithm, a version of force directed graph layout. This software projects large amounts of data points to a two- or three-dimensional structure in such a way that groups of mutually similar items form spatial clusters. The exploratory studies conducted along these ways lead to suggestive results that provide evidence for historical relationships beyond the traditionally recognized language families.
Localization of superconductivity in superconductor–electromagnet hybrids
2012-04-23

We investigate the nucleation of superconductivity in a superconducting Al strip under the influence of the magnetic field generated by a current-carrying Nb wire,perpendicularly oriented and located underneath the strip. The inhomogeneous magnetic field, induced by the\\nNb wire, produces a spatial modulation of the critical temperature Tc, leading to a controllable localization of the superconducting order parameter (OP) wavefunction. We demonstrate that close to the phase boundary Tc(Bext) the localized OP solution can be displaced reversibly by either applying an external perpendicular magnetic field B_ext or by changing the amplitude of the inhomogeneous field.
Functional T Cells Targeting NY-ESO-1 or Melan-A Are Predictive for Survival of Patients With Distant Melanoma Metastasis
2012-04-24

Purpose To analyze the prognostic relevance of circulating T cells responding to NY-ESO-1, Melan-A, MAGE-3, and survivin in patients with melanoma with distant metastasis. Patients and Methods We examined 84 patients with follow-up after analysis (cohort A), 18 long-term survivors with an extraordinarily favorable course of disease before analysis (&gt; 24 months survival after first occurrence of distant metastases; cohort B), and 14 healthy controls. Circulating antigen-reactive T cells were characterized by intracellular cytokine staining after in vitro stimulation. Results In cohort A patients, the presence of T cells responding to peptides from NY-ESO-1, Melan-A, or MAGE-3 and the M category according to the American Joint Committee on Cancer classification were significantly associated with survival. T cells responding to NY-ESO-1 and Melan-A (hazard ratios, 0.29 and 0.18, respectively) remained independent prognostic factors in Cox regression analysis and were superior to the M category in predicting outcome. Median survival of patients possessing T cells responding to NY-ESO-1, Melan-A, or both was 21 months, compared with 6 months for all others. NY-ESO-1–responsive T cells were detected in 70% of cohort A patients surviving &gt; 18 months and in 50% of cohort B patients. Melan-A responses were found in 42% and 47% of patients in cohorts A and B, respectively. In contrast, the proportion was only 22% for NY-ESO-1 and 23% for Melan-A in those who died within 6 months. Conclusion The presence of circulating T cells responding to Melan-A or NY-ESO-1 had strong independent prognostic impact on survival in advanced melanoma. Our findings support the therapeutic relevance of Melan-A and NY-ESO-1 as targets for immunotherapy.
SEARCH FOR DARK MATTER ANNIHILATION SIGNALS FROM THE FORNAX GALAXY CLUSTER WITH H.E.S.S.
2012-04-24

The Fornax galaxy cluster was observed with the High Energy Stereoscopic System for a total live time of 14.5 hr, searching for very high energy (VHE; E &gt; 100GeV) γ -rays from dark matter (DM) annihilation. No significant signal was found in searches for point-like and extended emissions. Using several models of the DM density distribution, upper limits on the DM velocity-weighted annihilation cross-section _σv_ as a function of the DM particle mass are derived. Constraints are derived for different DM particle models, such as those arising from Kaluza–Klein and supersymmetric models. Various annihilation final states are considered. Possible enhancements of the DM annihilation γ -ray flux, due to DM substructures of the DM host halo, or from the Sommerfeld effect, are studied. Additional γ -ray contributions from internal bremsstrahlung and inverse Compton radiation are also discussed. For a DM particle mass of 1 TeV, the exclusion limits at 95% of confidence level reach values of _σv_95% C.L. ∼ 10−23 cm3 s−1, depending on the DM particle model and halo properties. Additional contribution from DM substructures can improve the upper limits on _σv_ by more than two orders of magnitude. At masses around 4.5 TeV, the enhancement by substructures and the Sommerfeld resonance effect results in a velocityweighted annihilation cross-section upper limit at the level of _σv_95% C.L. ∼10−26 cm3 s−1.
What the Human Brain Likes About Facial Motion
2012-04-24

Facial motion carries essential information about other people's emotions and intentions. Most previous studies have suggested that facial motion is mainly processed in the superior temporal sulcus (STS), but several recent studies have also shown involvement of ventral temporal face-sensitive regions. Up to now, it is not known whether the increased response to facial motion is due to an increased amount of static information in the stimulus, to the deformation of the face over time, or to increased attentional demands. We presented nonrigidly moving faces and control stimuli to participants performing a demanding task unrelated to the face stimuli. We manipulated the amount of static information by using movies with different frame rates. The fluidity of the motion was manipulated by presenting movies with frames either in the order in which they were recorded or in scrambled order. Results confirm higher activation for moving compared with static faces in STS and under certain conditions in ventral temporal face-sensitive regions. Activation was maximal at a frame rate of 12.5 Hz and smaller for scrambled movies. These results indicate that both the amount of static information and the fluid facial motion per se are important factors for the processing of dynamic faces.
Influence of Motor Planning on Distance Perception within the Peripersonal Space
2012-04-24

We examined whether movement costs as defined by movement magnitude have an impact on distance perception in near space. In Experiment 1, participants were given a numerical cue regarding the amplitude of a hand movement to be carried out. Before the movement execution, the length of a visual distance had to be judged. These visual distances were judged to be larger, the larger the amplitude of the concurrently prepared hand movement was. In Experiment 2, in which numerical cues were merely memorized without concurrent movement planning, this general increase of distance with cue size was not observed. The results of these experiments indicate that visual perception of near space is specifically affected by the costs of planned hand movements.