julilili42/papers huggingface dataset:
Electronic Structure of FePc and Interface Properties on Ag(111) and Au(100)
2012-04-30

The electronic structure of iron phthalocyanine (FePc) and interface properties on Ag(111) and Au(100) are investigated by photoexcited electron spectroscopies: photoemission (XPS and UPS) and X-ray absorption spectroscopy (XAS or NEXAFS). Valence band structures with Fe character were identified using resonant photoemission. The strength and nature of the interaction at the interface depend clearly on the substrate. A strong interaction of the central metal atom of the phthalocyanine occurs on Ag(111), whereas no significant changes of the electronic situation were found for FePc on Au(100). Resonant photoemission data show that for FePc on Ag(111) the formed interface states close to the Fermi level are determined by the interaction between Fe 3d states and substrate related states. On the other hand, also the nitrogen atom of FePc is involved in the interaction.
Minimally invasive percutaneous nephrolitholapaxy (PCNL) as an effective and safe procedure for large renal stones
2012-04-30

Study Type – Therapy (case series) Level of Evidence 4 What's known on the subject? and What does the study add? The minimally invasive percutaneous nephrolitholapaxy (MIP) has shown high efficacy and safety for the management of small renal stones. It was initially developed to overcome a gap between the minimally invasive extracorporeal shockwave lithotripsy and invasive conventional percutaneous nephrolitholapaxy (PCNL) in the management of low stone burden but there is debate as to whether the MIP is also effective for larger stones. The present study shows the high efficacy and safety of MIP, which is comparable to conventional PCNL in the treatment of stones of &gt;20 mm, including complex staghorn stones. OBJECTIVE To evaluate the safety and efficacy of minimally invasive percutaneous nephrolitholapaxy (MIP) in the management of large and complex renal calculi. PATIENTS AND METHODS From January 2007 to March 2011, 73 patients with 83 renal units with large renal stones (&gt;20 mm in diameter) were retrospectively evaluated. Stones were classified into simple (isolated renal pelvis or isolated calyceal stones) or complex (partial or complete staghorn stones, renal pelvis stones with accompanying calyceal stones). Stone‐free rate, complications according to the modified Clavien system, decrease in haemoglobin, creatinine level, operative duration and hospital stay were compared for simple and complex renal calculi. RESULTS The mean ( sd ) stone size was 36.7 (23.37) mm and mean operative duration was 99.2 (48.3) min. In all, 65 cases (78.3%) were stone‐free after the first procedure and another 14 needed an auxiliary procedure (four second‐look percutaneous nephrolitholapaxy, nine ureterorenoscopy, and one extracorporeal shockwave lithotripsy) to become stone‐free, resulting in a 95.2% stone‐free rate. Complications occurred in 22 procedures (26.5%), 17 of them were Clavien Grade 1 or 2 (20.5%), five were Grade 3 (6%). There were no Grade 4 or 5 complications. The only significant difference between complex and simple stones was the stone‐free rate (96.9% vs 66.7%, P = 0.001). CONCLUSION The MIP technique is effective and safe for larger stones with low morbidity, good success rate and reasonable operative duration.
Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands
2012-04-30

DNA methylation of CpG islands plays a crucial role in the regulation of gene expression. More than half of all human promoters contain CpG islands with a tissue-specific methylation pattern in differentiated cells. Still today, the whole process of how DNA methyltransferases determine which region should be methylated is not completely revealed. There are many hypotheses of which genomic features are correlated to the epigenome that have not yet been evaluated. Furthermore, many explorative approaches of measuring DNA methylation are limited to a subset of the genome and thus, cannot be employed, e.g., for genome-wide biomarker prediction methods. In this study, we evaluated the correlation of genetic, epigenetic and hypothesis-driven features to DNA methylation of CpG islands. To this end, various binary classifiers were trained and evaluated by cross-validation on a dataset comprising DNA methylation data for 190 CpG islands in HEPG2, HEK293, fibroblasts and leukocytes. We achieved an accuracy of up to 91% with an MCC of 0.8 using ten-fold cross-validation and ten repetitions. With these models, we extended the existing dataset to the whole genome and thus, predicted the methylation landscape for the given cell types. The method used for these predictions is also validated on another external whole-genome dataset. Our results reveal features correlated to DNA methylation and confirm or disprove various hypotheses of DNA methylation related features. This study confirms correlations between DNA methylation and histone modifications, DNA structure, DNA sequence, genomic attributes and CpG island properties. Furthermore, the method has been validated on a genome-wide dataset from the ENCODE consortium. The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/.
Synthesis and Characterization of N-[2-P(i-Pr)2-4-methylphenyl]2– (PNP) Pincer Tin(IV) and Tin(II) Complexes
2012-04-30

N-[2-P(i-Pr)(2)-4-methylphenyl](2)(-) (PNP) pincer complexes of tin(IV) and tin(II), [(PNP)SnCl(3)] (2) and [(PNP)SnN(SiMe(3))(2)] (3), respectively, were prepared and characterized by X-ray diffraction, solution and solid state NMR spectroscopy, and (119)Sn Mössbauer spectroscopy. Furthermore, (119)Sn cross polarization magic angle spinning NMR spectroscopic data of [Sn(NMe(2))(2)](2) are reported. Compound 2 is surprisingly stable toward air, but attempts to substitute chloride ligands caused decomposition.
Controlling the interaction of photons and single quantum systems in an optical microresonator
2012-04-30

Small optical microresonators are structures which confine light to volumes with dimensions on the order of one wavelength and provide an important means for controlling light-matter interaction in integrated optics. In this Paper, we would like to present our work on the study of the interaction of single quantum emitters or nanoparticles located in the confined optical field of a single-mode microresonator. The interaction possibilities between a general photonic system and a quantum system are discussed, with special focus on the effect of resonant microcavities. For the case of the optical microresonator used in our experiments, we present a model based on the transfer matrix method which can analytically describe the radiative enhancement of even complex resonator geometries. This allows not only the optimization of resonator geometries, but gives accurate information on the radiative processes occurring in the cavity, allowing the extraction of information normally inaccessible in optical measurements.
A quantitative index of land-use intensity in grasslands: Integrating mowing, grazing and fertilization
2012-05-01

Land use is increasingly recognized as a major driver of biodiversity and ecosystem functioning in many current research projects. In grasslands, land use is often classified by categorical descriptors such as pastures versus meadows or fertilized versus unfertilized sites. However, to account for the quantitative variation of multiple land-use types in heterogeneous landscapes, a quantitative, continuous index of land-use intensity (LUI) is desirable. Here we define such a compound, additive LUI index for managed grasslands including meadows and pastures. The LUI index summarizes the standardized intensity of three components of land use, namely fertilization, mowing, and livestock grazing at each site. We examined the performance of the LUI index to predict selected response variables on up to 150 grassland sites in the Biodiversity Exploratories in three regions in Germany (Alb, Hainich, Schorfheide). We tested the average Ellenberg nitrogen indicator values of the plant community, nitrogen and phosphorus concentration in the aboveground plant biomass, plant-available phosphorus concentration in the top soil, and soil C/N ratio, and the first principle component of these five response variables.\\n\\nThe LUI index significantly predicted the principal component of all five response variables, as well as some of the individual responses. Moreover, vascular plant diversity decreased significantly with LUI in two regions (Alb and Hainich).\\n\\nInter-annual changes in management practice were pronounced from 2006 to 2008, particularly due to variation in grazing intensity. This rendered the selection of the appropriate reference year(s) an important decision for analyses of land-use effects, whereas details in the standardization of the index were of minor importance. We also tested several alternative calculations of a LUI index, but all are strongly linearly correlated to the proposed index.\\n\\nThe proposed LUI index reduces the complexity of agricultural practices to a single dimension and may serve as a baseline to test how different groups of organisms and processes respond to land use. In combination with more detailed analyses, this index may help to unravel whether and how land-use intensities, associated disturbance levels or other local or regional influences drive ecological processes.
Coupled polar-axial magnetar oscillations
2012-05-01

We study coupled axial and polar axisymmetric oscillations of a neutron star\\nendowed with a strong magnetic field, having both poloidal and toroidal\\ncomponents. The toroidal component of the magnetic field is driving the\\ncoupling between the polar and axial oscillations. The star is composed of a\\nfluid core as well as a solid crust. Using a two dimensional general\\nrelativistic simulation and a magnetic field B = 10^16 G, we study the change\\nin the polar and axial spectrum caused by the coupling. We find that the axial\\nspectrum suffers a dramatic change in its nature, losing its continuum\\ncharacter. In fact, we find that only the 'edges' of the continua survive,\\ngenerating a discrete spectrum. As a consequence the crustal frequencies, that\\nin our previous simulation could be absorbed by the continua, if they were\\nembedded inside it, are now long living oscillations. They may lose their\\nenergy only in the very special case that they are in resonance with the\\n'edges' of the continua.\\n
Standardizing a Component Metadata Infrastructure
2012-05-01

This paper describes the status of the standardization efforts of a Component Metadata approach for describing Language Resources with metadata. Different linguistic and Language &amp;amp; Technology communities as CLARIN, META-SHARE and NaLiDa use this component approach and see its standardization of as a matter for cooperation that has the possibility to create a large interoperable domain of joint metadata. Starting with an overview of the component metadata approach together with the related semantic interoperability tools and services as the ISOcat data category registry and the relation registry we explain the standardization plan and efforts for component metadata within ISO TC37/SC4. Finally, we present information about uptake and plans of the use of component metadata within the three mentioned linguistic and L&amp;amp;T communities.
Chimeric FLS2 Receptors Reveal the Basis for Differential Flagellin Perception in Arabidopsis and Tomato
2012-05-01

The flagellin receptor of Arabidopsis thaliana, At-FLAGELLIN SENSING2 (FLS2), has become a model for mechanistic and functional studies on plant immune receptors. Here, we started out with a comparison of At-FLS2 and the orthologous tomato (Solanum lycopersicum) receptor Sl-FLS2. Both receptors specifically responded to picomolar concentrations of the genuine flg22 ligand but proved insensitive to >10(6)-fold higher concentrations of CLV3 peptides that have recently been reported as a second type of ligand for At-FLS2. At-FLS2 and Sl-FLS2 exhibit species-specific differences in the recognition of shortened or sequence-modified flg22 ligands. To map the sites responsible for these species-specific traits on the FLS2 receptors, we performed domain swaps, substituting subsets of the 28 leucine-rich repeats (LRRs) in At-FLS2 with the corresponding LRRs from Sl-FLS2. We found that the LRRs 7 to 10 of Sl-FLS2 determine the high affinity of Sl-FLS2 for the core part RINSAKDD of flg22. In addition, we discovered importance of the LRRs 19 to 24 for the responsiveness to C-terminally modified flagellin peptides. These results indicate that ligand perception in FLS2 is a complex molecular process that involves LRRs from both the outermost and innermost LRRs of the FLS2 ectodomain.
SFRP1CpG island methylation locus is associated with renal cell cancer susceptibility and disease recurrence
2012-05-01

Loss of the secreted Fzd-related protein 1 (SFRP1) and concurrent alteration of the SFRP1/WNT pathway are frequently observed in human cancers such as in renal cell cancer (RCC). Whether methylation of a SFRP1 CpG island locus in normal human solid tissues is associated with increased tissue specific cancer risk has not been determined to date. Here we measure the cancer risk attributable to SFRP1 DNA methylation in renal tissue. Pyrosequencing of bisulfite treated DNA was used for a case-control study including 120 normal-appearing renal tissues of autopsy specimens and 72 normal-appearing tissues obtained from tumor adjacent areas, and a cross sectional study of 96 RCCs. Association of methylation with demographic risk factor age, clinicopathological parameters and course of patients was investigated. We show significant hypermethylation of a SFRP1 CpG island locus in normal-appearing renal tissues from RCC patients compared with normal-appearing autopsy kidney tissues. Inter quartile analysis revealed a 6-, 13- and 11-fold increased cancer risk for the second, third and fourth quartiles of methylation in the age matched subgroup of tissues (p = 0.001, p = 1.3E-6, p = 6.9E-6). Methylation in autopsy tissues increased with age and methylation in tumors was an independent predictor of recurrence free survival. SFRP1 DNA methylation, accumulates with age in normal-appearing kidney tissues and is associated with increased renal cancer risk, suggesting this CGI sub region as an epigenetic susceptibility locus for RCC. Our data underline the need to further analyze the tissue specific risks conferred by methylated loci for the development of human cancers.
Using depth in visual simultaneous localisation and mapping
2012-05-01

We present a method of utilizing depth information as provided by RGBD sensors for robust real-time visual simultaneous localisation and mapping (SLAM) by augmenting monocular visual SLAM to take into account depth data. This is implemented based on the feely available software "Parallel Tracking and Mapping" by Georg Klein. Our modifications allow PTAM to be used as a 6D visual SLAM system even without any additional information about odometry or from an inertial measurement unit.
Synthesis of glycosylated metal phthalocyanines and naphthalocyanines
2012-05-01

The first part of this review summarizes methods for the syntheses of mono-, di-, and tetra-substituted glycosylated phthalonitriles, which are the main starting materials for the preparation of the corresponding glycosylated metal phthalocyanines. In the second part the preparation of symmetrically and unsymmetrically tetra- and octa- glycosylated zinc phthalocyanines in which the sugar is attached either anomerically or via another one of its OH -groups to the phthalocyanine macrocycle as well as other structurally different glycosylated metal phthalocyanines are reviewed.
Transmission of cochlear distortion products as slow waves: A comparison of experimental and model data
2012-05-01

There is a long-lasting question of how distortion products (DPs) arising from nonlinear amplification processes in the cochlea are transmitted from their generation sites to the stapes. Two hypotheses have been proposed: (1) the slow-wave hypothesis whereby transmission is via the transverse pressure difference across the cochlear partition and (2) the fast-wave hypothesis proposing transmission via longitudinal compression waves. Ren with co-workers have addressed this topic experimentally by measuring the spatial vibration pattern of the basilar membrane (BM) in response to two tones of frequency f1 and f2. They interpreted the observed negative phase slopes of the stationary BM vibrations at the cubic distortion frequency fDP = 2f1 − f2 as evidence for the fast-wave hypothesis. Here, using a physically based model, it is shown that their phase data is actually in accordance with the slow-wave hypothesis. The analysis is based on a frequency-domain formulation of the two-dimensional motion equation of a nonlinear hydrodynamic cochlea model. Application of the analysis to their experimental data suggests that the measurement sites of negative phase slope were located at or apical to the DP generation sites. Therefore, current experimental and theoretical evidence supports the slow-wave hypothesis. Nevertheless, the analysis does not allow rejection of the fast-wave hypothesis.
Visual terrain classification by flying robots
2012-05-01

In this paper we investigate the effectiveness of SURF features for visual terrain classification for outdoor flying robots. A quadrocopter fitted with a single camera is flown over different terrains to take images of the ground below. Each image is divided into a grid and SURF features are calculated at grid intersections. A classifier is then used to learn to differentiate between different terrain types. Classification results of the SURF descriptor are compared with results from other texture descriptors like Local Binary Patterns and Local Ternary Patterns. Six different terrain types are considered in this approach. Random forests are used for classification on each descriptor. It is shown that SURF features perform better than other descriptors at higher resolutions.
Aggressiveness in different presentations of cluster headache: Results from a controlled multicentric study
2012-05-01

Background: The hypothalamus has been discussed as a pivotal structure for both cluster headache (CH) and aggressiveness, but little is known about the extent of self-reported aggressiveness in patients with CH. Patients and methods: Twenty-six patients with chronic, 25 with active episodic and 22 with episodic CH outside the active period were examined interictally with a validated questionnaire quantifying factors of aggression and compared with 24 migraine patients and 31 headache-free volunteers. Results: The ANOVA was significant for the subscale ‘self-aggression/depression’ ( F 4, 123 = 5.771, p &lt; 0.001) with significant differences between chronic and episodic CH and healthy volunteers. No significant changes were found for other subscales and the sum scale ( F 4, 123 &lt; 1.421, p &gt; 0.230). Especially in the clinically most affected group of patients (chronic CH and active episodic CH), high levels of “self-aggression/depression” correlate with higher prevalence of depressive symptoms and higher impairment measured on an emotional and functional level. Discussion: Self-aggressive and depressive cognitions with highest scores in chronic CH seem to be reactive as they correlate with depressive symptoms and impairment. They should be considered as an important therapeutic target since they impair the patient’s life significantly.
Decrease of CD44-positive cells correlates with tumor response to chemotherapy in patients with gastrointestinal cancer.
2012-05-01

We were able to monitor changes of CD44 expression after chemotherapy and detected a correlation between the CD44 decrease and the patients' response to treatment. Our findings show that CD44 detection helps to monitor chemotherapy response in patients with gastrointestinal cancer.
Sparse regularized regression identifies behaviorally-relevant stimulus features from psychophysical data
2012-05-01

As a prerequisite to quantitative psychophysical models of sensory processing it is necessary to learn to what extent decisions in behavioral tasks depend on specific stimulus features, the perceptual cues. Based on relative linear combination weights, this study demonstrates how stimulus-response data can be analyzed in this regard relying on an L1-regularized multiple logistic regression, a modern statistical procedure developed in machine learning. This method prevents complex models from over-fitting to noisy data. In addition, it enforces “sparse” solutions, a computational approximation to the postulate that a good model should contain the minimal set of predictors necessary to explain the data. In simulations, behavioral data from a classical auditory tone-in-noise detection task were generated. The proposed method is shown to precisely identify observer cues from a large set of covarying, interdependent stimulus features—a setting where standard correlational and regression methods fail. The proposed method succeeds for a wide range of signal-to-noise ratios and for deterministic as well as probabilistic observers. Furthermore, the detailed decision rules of the simulated observers were reconstructed from the estimated linear model weights allowing predictions of responses on the basis of individual stimuli.
Using Run-Time Reconfiguration to Implement Fault-Tolerant Coarse Grained Reconfigurable Architectures
2012-05-01

Triple modular redundancy (TMR) is a common method to implement fault-tolerant circuits. Traditionally, TMR is realized by triplication of components. In order to reduce the area overhead of TMR another approach was proposed on coarse grained reconfigurable architectures (CGRAs). In that approach spare functional units (FUs) are used for redundant computation of results. However, it was not shown that this approach is workable for any application. In this work we close that gap. We mapped several multipoint fast Fourier transform on a CGRA of different array sizes and analyzed the ratio of spare FUs to used FUs. If the number of spare FUs is not sufficient to find a fault-tolerant application mapping, we propose to use run-time reconfiguration to extend the number of spare FUs in the time domain. We compared this strategy with the traditional approach in terms of area and throughput. The comparing results show that run-time reconfiguration can be a suitable method for decreasing the area overhead of TMR, however at the expense of lower throughput.
Holaaa!! writin like u talk is kewl but kinda hard 4 NLP
2012-05-01

We present work in progress aiming to build tools for the normalization of User-Generated Content (UGC). As we will see, the task requires the revisiting of the initial steps of NLP processing, since UGC (micro-blog, blog, and, generally, Web 2.0 user texts) presents a number of non-standard communicative and linguistic characteristics, and is in fact much closer to oral and colloquial language than to edited text. We present and characterize a corpus of UGC text in Spanish from three different sources: Twitter, consumer reviews and blogs. We motivate the need for UGC text normalization by analyzing the problems found when processing this type of text through a conventional language processing pipeline, particularly in the tasks of lemmatization and morphosyntactic tagging, and finally we propose a strategy for automatically normalizing UGC using a selector of correct forms on top of a pre-existing spell-checker.