julilili42/papers huggingface dataset:
Extending BART to provide a coreference resolution system for German
2010-05-01

We present a flexible toolkit-based approach to automatic coreference resolution on German text. We start with our previous work aimed at reimplementing the system from Soon et al. (2001) for English, and extend it to duplicate a version of the state-of-the-art proposal from Klenner and Ailloud (2009). Evaluation performed on a benchmarking dataset, namely the TüBa-D/Z corpus (Hinrichs et al., 2005b), shows that machine learning based coreference resolution can be robustly performed in a language other than English. 1.
New treatments in the management of type 2 diabetes: a critical appraisal of saxagliptin
2010-05-01

Saxagliptin is a novel dipeptidyl peptidase-4 inhibitor (DPP-4 inhibitor) for the treatment of type 2 diabetes, with a duration profile for once daily dosing. It is highly selective for DPP-4 in comparison to other enzymes of the dipeptidyl peptidase family. DPP-4 inhibitors elevate plasma concentrations of the incretin hormones glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP). This effect results in a glucose-dependent stimulation of insulin secretion and an inhibition of glucagon secretion without an intrinsic risk for hypoglycemia. In comparison to sulfonylureas and thiazolidinediones that promote weight gain, DPP-4 inhibitors are weight neutral. Saxagliptin has been approved by the FDA for the US and by the EMEA for Europe in 2009. Clinical trials showed a dose-dependent inhibition of DPP-4 by saxagliptin in doses ranging from 2.5 to 100 mg daily without serious side effects. Type 2 diabetic patients receiving 5 mg to 10 mg saxagliptin once daily had a significant lowering of HbA(1c) and glycemic parameters along with good tolerability and safety. Saxagliptin has demonstrated a good efficacy for glycemic parameters in various patient populations either in monotherapy or in combination with metformin and other oral antidiabetic drugs as well as a favorable cardiovascular profile. With its high selectivity for DPP-4 and its clinical and cardiovascular profile, saxagliptin is an attractive novel DPP-4 inhibitor.
Creating a Coreference Resolution System for Italian
2010-05-01

This paper summarizes our work on creating a full-scale coreference resolution (CR) system for Italian, using BART – an open-source modular CR toolkit initially developed for English corpora. We discuss our experiments on language-specific issues of the task. As our evaluation experiments show, a language-agnostic system (designed primarily for English) can achieve a performance level in high forties (MUC F-score) when re-trained and tested on a new language, at least on gold mention boundaries. Compared to this level, we can improve our F-score by around 10 % introducing a small number of language-specific changes. This shows that, with a modular coreference resolution platform, such as BART, one can straightforwardly develop a family of robust and reliable systems for various languages. We hope that our experiments will encourage researchers working on coreference in other languages to create their own full-scale coreference resolution systems – as we have mentioned above, at the moment such modules exist only for very few languages other than English. 1.
Pulsations and planets: The asteroseismology‐extrasolar‐planet connection
2010-05-01

Abstract The disciplines of asteroseismology and extrasolar planet science overlap methodically in the branch of high‐precision photometric time series observations. Light curves are, amongst others, useful to measure intrinsic stellar variability due to oscillations, as well as to discover and characterize those extrasolar planets that transit in front of their host stars, periodically causing shallow dips in the observed brightness. Both fields ultimately derive fundamental parameters of stellar and planetary objects, allowing to study for example the physics of various classes of pulsating stars, or the variety of planetary systems, in the overall context of stellar and planetary system formation and evolution. Both methods typically also require extensive spectroscopic follow‐up to fully explore the dynamic characteristics of the processes under investigation. In particularly interesting cases, a combination of observed pulsations and signatures of a planet allows to characterize a system's components to a very high degree of completeness by combining complementary information. The planning of the relevant space missions has consequently converged with respect to science cases, where at the outset there was primarily a coincidence in instrumentation and techniques. Whether space‐ or ground‐based, a specific type of stellar pulsations can themselves be used in an innovative way to search for extrasolar planets. Results from this additional method at the interface of stellar pulsation studies and exoplanet hunts in a beyond‐mainstream area are presented (© 2010 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Pattern-Based Extraction of Negative Polarity Items from Dependency-Parsed Text
2010-05-01

We describe a new method for extracting Negative Polarity Item candidates (NPI candidates) from dependency-parsed German text corpora. Semi-automatic extraction of NPIs is a challenging task since NPIs do not have uniform categorical or other syntactic properties that could be used for detecting them; they occur as single words or as multi-word expressions of almost any syntactic category. Their defining property is of a semantic nature, they may only occur in the scope of negation and related semantic operators. In contrast to an earlier approach to NPI extraction from corpora, we specifically target multi-word expressions. Besides applying statistical methods to measure the co-occurrence of our candidate expressions with negative contexts, we also apply linguistic criteria in an attempt to determine to which degree they are idiomatic. Our method is evaluated by comparing the set of NPIs we found with the most comprehensive electronic list of German NPIs, which currently contains 165 entries. Our method retrieved 142 NPIs, 114 of which are new. 1.
New treatments in the management of type 2 diabetes: a critical appraisal of saxagliptin
2010-05-01

New treatments in the management of type 2 diabetes: a critical appraisal of saxagliptin Baptist GallwitzDept Medicine IV, T&uuml;bingen University, Otfried-M&uuml;ller-Str, 10, 72076 T&uuml;bingen, GermanyAbstract: Saxagliptin is a novel dipeptidyl peptidase-4 inhibitor (DPP-4 inhibitor) for the treatment of type 2 diabetes, with a duration profile for once daily dosing. It is highly selective for DPP-4 in comparison to other enzymes of the dipeptidyl peptidase family. DPP-4 inhibitors elevate plasma concentrations of the incretin hormones glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP). This effect results in a glucose-dependent stimulation of insulin secretion and an inhibition of glucagon secretion without an intrinsic risk for hypoglycemia. In comparison to sulfonylureas and thiazolidinediones that promote weight gain, DPP-4 inhibitors are weight neutral. Saxagliptin has been approved by the FDA for the US and by the EMEA for Europe in 2009. Clinical trials showed a dose-dependent inhibition of DPP-4 by saxagliptin in doses ranging from 2.5 to 100 mg daily without serious side effects. Type 2 diabetic patients receiving 5 mg to 10 mg saxagliptin once daily had a significant lowering of HbA1c and glycemic parameters along with good tolerability and safety. Saxagliptin has demonstrated a good efficacy for glycemic parameters in various patient populations either in monotherapy or in combination with metformin and other oral antidiabetic drugs as well as a favorable cardiovascular profile. With its high selectivity for DPP-4 and its clinical and cardiovascular profile, saxagliptin is an attractive novel DPP-4 inhibitor.Keywords: type 2 diabetes, diabetes therapy, DPP-4 inhibitors, incretin based therapy, GLP-1, saxagliptin
Utilization of AFFX spike-in control probes to monitor sample identity throughout Affymetrix GeneChip Array processing
2010-05-01

Microarrays evolved from a highly specialized technique into a standard molecular biology method that is widely used for whole-genome gene expression profiling. One of the most important aspects of this method is sample identity, that is, whether the expression profile recorded from an array actually derives from the indicated sample. Several potential steps in the protocol exist where a mix-up of samples may occur. With the increasing size of microarray studies, it is important to ensure that each expression profile is assigned to the correct sample. Errors at this level almost certainly lead to erroneous results and can even cause a complete failure of the microarray study. We developed a system that utilizes probes already present on commercially available Affymetrix arrays to unambiguously correlate the recorded expression profile with the input sample RNA. A set of eight spike-in controls were generated, which can be added to sample RNA in different combinations to generate an "on-chip identifier" that passes through the entire array processing protocol and results in a sample-specific hybridization pattern. This pattern can then be used to monitor whether each array was hybridized with the correct sample. The spike-in controls did not have any negative effect on RNA integrity or any detectable influence on the expression values of the remaining probes on the array; therefore, these controls represent an inexpensive and easily adaptable system to guarantee high-quality results from microarray experiments.
Term and Collocation Extraction by Means of Complex Linguistic Web Services.
2010-05-01

We present a web service-based environment for the use of linguistic resources and tools to address issues of terminology and language varieties. We discuss the architecture, corpus representation formats, components and a chainer supporting the combination of tools into task-specific services. Integrated into this environment, single web services also become part of complex scenarios for web service use. Our web services take for example corpora of several million words as an input on which they perform preprocessing, such as tokenisation, tagging, lemmatisation and parsing, and corpus exploration, such as collocation extraction and corpus comparison. Here we present an example on extraction of single and multiword items typical of a specific domain or typical of a regional variety of German. We also give a critical review on needs and available functions from a user’s point of view. The work presented here is part of ongoing experimentation in the D-SPIN project, the German national counterpart of CLARIN. 1.
Kernel-based estimation of the applicability domain of QSAR models
2010-05-01

Machine learning techniques have become a valuable tool to assess molecular properties without the need of in vitro experiments. Most of these methods do not give any information if a molecule that is predicted can be sufficiently described by the knowledge contained in the model. Thus, the estimation of the reliability of a model-based prediction is an important question in machine learning based QSAR modeling. One approach to solve this problem is to describe the portion of the chemical space used during the training phase of a model. Any molecule included in the same subspace is then considered as a structure for which the model is regarded as valid. This concept of the description of the subspace in which a model is regarded as reliable is known as the estimation of the applicability domain of this model [1]. Most machine learning approaches for QSAR rely on a vectorial representation of the molecules. The applicability domain is expressed as a subspace of the vector space with one dimension for each descriptor used. This concept can be not directly applied to kernel-based techniques like support vector machines. These methods rely on an implicit feature space that is only defined by the applied kernel similarity and with unknown dimensions. The applicability domain of a kernel-based model therefore has to be defined by means of the kernel. Consequently, this allows to use structured similarity measures, like the Optimal Assignment Kernel [2] and its extension [3], instead of a numerical encoding. Thus, it is possible to describe the complex chemical structure of many drugs better than it would be using descriptors. In this work, several approaches to define the applicability domain of a QSAR model by means of a kernel are presented and compared to each other. The approach is to extend the concept of a kernel density estimation to incorporate further information contained in a trained model. This can be achieved by using a weighted average kernel similarity of a predicted molecule to the training data set. The weights can be obtained either by exploiting the knowledge contained in the learned model or by approaches that describe the feature space structure using the kernel.
Rescoring of docking poses using force field-based methods
2010-05-01

Existing protein-ligand docking methods computationally screen thousands to millions of organic molecules against protein structures, trying to find those with complementary shapes and highest binding free energies. To allow large molecular databases to be screened rapidly, simple and approximative scoring functions are used as a fast filter, resulting in low hit rates. Therefore, docking hit lists are commonly rescored in a final step by more rigorous and time-consuming methods to gain a more accurate final list of ranked compounds. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) or generalized Born surface area (MM-GBSA) methods are currently considered to be suitable techniques for rescoring. These physically realistic approaches incorporate more sophisticated models for solvation and electrostatic interactions than most scoring functions. Hence, they can discriminate more reliably between correct and incorrect docking poses. A high-throughput rescoring protocol using force field-based methods has been proposed by Brown and Muchmore [1]. They used 18 in-house urokinase-ligand crystal structures and their corresponding experimentally determined binding free energies as a test set. On the basis of this rescoring protocol we tested several molecular dynamics simulation protocols in combination with different MM-PBSA, and MM-GBSA calculation procedures using Amber 10 [2] and Gromacs 4 [3]. Considering performance and accuracy, our best rescoring protocol performs similarly to the one described by Brown and Muchmore [1]. It has a comparable run-time and achieves a correlation between experimental and rescored values of 0.88 compared to 0.87. However, we used urokinase-ligand complexes generated using the docking program Glide [4] instead of crystal structures. Additionally, this shows that our rescoring protocol improves the correlation of 0.57 between experimental values and Glide scores significantly to 0.88, thereby achieving a more accurate list of ranked compounds. The protocol will be incorporated into BALLView [5], an open-source molecular viewer and modeling tool. Thus, it will be available free of charge and can be conveniently used to rescore (docked) protein-ligand complexes.
Relationship between Thiopurine metabolite levels and endoscopic improvement in patients with postoperative moderate to severe endoscopic recurrence of Crohn's disease
2010-05-01

Introduction: Endoscopic recurrence of Crohn's disease (CD) after curative ileocecal resection, which is reported in up to 70% of patients within 1 year, precedes clinical relapse. Azathioprine (AZA) reduces the risk of both clinical and endoscopic recurrence. Aim: To evaluate the association between thiopurine metabolite levels and endoscopic improvement in CD patients with moderate to severe postoperative endoscopic recurrence. Methods: Patients treated with AZA within the AZT-2 study, a prospective double-blinded trial comparing 2.0–2.5mg/kg/d AZA versus 4.0g/d mesalamine for prevention of clinical relapse in patients with postoperative moderate to severe endoscopic recurrence, were included. Ileocolonoscopy was performed at baseline and at week 52 or at premature discontinuation (median 364 days, range: 176–381). Red blood cell concentrations (RBC) of 6-thioguanine nucleotides (6-TGN), 6-methyl-mercaptopurine ribonucleotides (6-MMPR), and 6-methyl-thioguanine nucleotides (6-MTGN) were measured by high-performance liquid chromatography assay. A cut-off value of 6-TGN of ≥235pmol/8×108 RBC was used as established in literature. 6-MMPR and 6-MTGN levels below and above the median were considered low and high, respectively. Endoscopic improvement was defined as a reduction of the endoscopic score according to Rutgeerts by at least one point, and mucosal healing as endoscopic score of i0 (=no lesions). Results: Endoscopic data were available on 31 patients treated with azathioprine (f/m=13/18, median age: 32 years, median AZA dose: 2.24mg/kg/d) for median 358 days. At last observation, the median levels of 6-TGN (n=26), 6-MMPR (n=27), and 6-MTGN (n=26) were 139.7, 1696.1 and 70.1pmol/8×108 RBC, respectively. Overall, endoscopic score improved from i3-i4 to i0-i2 (p=0.004). Mucosal healing was achieved in 6/31 (19.4%) of patients. High 6-TGN levels (n=8) were associated with a significantly higher drop in the Rutgeerts score than low 6-TGN (n=18) levels (median drop of 3 vs. 1, p=0.023). There was no difference concerning mucosal healing (p=0.33). Furthermore, there was no correlation between 6-MMPR and 6-MTGN levels and endoscopic improvement. Conclusion: Our data suggest that high 6-TGN levels may linked to endoscopic improvement in patients with postoperative endoscopic recurrence of CD.
Language technology challenges of a "small" language (Catalan)
2010-05-01

In this paper, we present a brief snapshot of the state of affairs in computational processing of Catalan and the initiatives that are starting to take place in an effort to bring the field a step forward, by making a better and more efficient use of the already existing resources and tools, by bridging the gap between research and market, and by establishing periodical meeting points for the community. In particular, we present the results of the First Workshop on the Computational Processing of Catalan, which succeeded in putting together a fair representation of the research in the area, and received attention from both the industry and the administration. Aside from facilitating communication among researchers and between developers and users, the Workshop provided the organizers with valuable information about existing resources, tools, developers and providers. This information has allowed us to go a step further by setting up a “harvesting” procedure which will hopefully build the seed of a portal-catalogue-observatory of language resources and technologies in Catalan
Prevalence Of Diastolic Dysfunction And Association With Peak Vo2 In Obese Patients Without History Of Heart Disease
2010-05-01

PURPOSE: Diastolic dysfunction (DD) can cause increased pressure und fluid in the blood vessel of the lung which might lead to dyspnea on exertion. Moreover, dyspnea is a common symptom in obese patients. Thus, we sought to evaluate the prevalence of DD in obese patients and to assess whether obese patients with DD have a reduced peak VO2. METHODS: 92 consecutive obese patients (22 female, mean age 42 ±11.7 years [18-70], mean BMI 44.3 ± 8.6 kg/m2 [30.0-74.7]) with normal systolic left ventricular function were included in this study. All patients were evaluated by echocardiography prior to incremental treadmill exercise testing using a walking protocol to determine peak VO2. Diastolic dysfunction was defined as an inversed E/A-ratio derived from transmitral valve flow pattern. RESULTS: DD was observed in 35/92 patients (38%). Mean peak VO2 was 20.2 ± 4.6 mL/kg/min [10-31] with a significant high value in patients with normal diastolic function (21.0 ± 4.8 mL/kg vs. 18.9 ± 4.1 mL/kg, p<0.05). However, after adjustment for age, gender and body mass index, this difference was no longer significant. CONCLUSIONS: Diastolic dysfunction is common in obese patients without history of prior heart disease. However, in a multifactorial model the presence of diastolic dysfunction was not associated with reduced peak VO2 as assessed by treadmill test. Thus, dyspnea in obese patients with diastolic dysfunction might not be explained by a reduced peak VO2.
Polar oscillations in magnetars
2010-05-01

We study polar Alfvén oscillations of relativistic stars endowed with a strong global poloidal dipole magnetic field. Here we focus only on the axisymmetric oscillations which are studied by evolving numerically the 2D perturbation equations. We show that the spectrum of the polar Alfvén oscillations is discrete in contrast to that of axial Alfvén ones. We also show that the typical fluid modes are not significantly affected by the presence of the magnetic field.
PET/CT for the detection and quantification of the β--emitting therapeutic radionuclide Yttrium-90 after liver SIRT
2010-05-01

341 Objectives Yttrium-90 (Y90) bound to microspheres is used for the therapy of malignancies in the liver (Selective Internal Radiotherapy SIRT). Y90 decays in 99.98% by emitting an electron, but has a minor branch to the 0+ excited state with an energy excess of 1.7 MeV. Hence, in 32 out of 1 Mio. decays, internal pair formation leads to the emission of a positron detectable by PET. We would like to present our initial results with PET/CT imaging of Y90. Methods An IEC hot-spheres phantom filled with 3.6 MBq/ml Y90 was imaged using our non-TOF PET/CT scanner (Siemens biograph 16 Hi-Rez, 40 min/bed). In addition, three patients who had undergone SIRT of the liver with 1.500 GBq, 1.013 GBq, and 1.030 GBq Y90 SIRTex spheres, were scanned. Results We were able to detect and quantify Y90 without modifications of the PET/CT instrument itself. The sensitivity for detecting annihilation photons from Y90 decay was 0.72 cps/MBq Y90 using a calibrated activity solution, a reduction in comparison to F18-PET by a factor of 3.4e-5, suggesting a minimum concentration of 1 MBq/ml for image formation. Recovery coefficients were 0.6 or above with spheres ≥ 17 mm. A resolution of 5.2±0.6 mm (336×336 matrix, 8 iterations, 16 subsets) and 7.8±0.5 mm (128×128, 4i8s) could be achieved. In patient scans, we could depict Y90 biodistribution with sufficient resolution and quantify the Y90 concentration in the liver, which was 1.280/1.500 GBq (85.3%) for the first, 0.930/1.013 (91.8%) for the second, and 0.970/1.030 (94.2%) for the third patient. Conclusions Our initial results show the feasibility of Y90-PET/CT after liver SIRT with a potentially higher resolution than bremsstrahlung scintigraphy (planar and SPECT). An accurate quantification of the applied Y90 dose to the liver seems to be possible