julilili42/papers huggingface dataset:
The MoSGrid Science Gateway – A Complete Solution for Molecular Simulations
2014-05-01

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.
The MERLIN corpus: Learner language and the CEFR
2014-05-01

The MERLIN corpus is a written learner corpus for Czech, German, and Italian that has been designed to illustrate the Common European Framework of Reference for Languages (CEFR) with authentic learner data. The corpus contains 2,290 learner texts produced in standardized language certifications covering CEFR levels A1–C1. The MERLIN annotation scheme includes a wide range of language characteristics that enable research into the empirical foundations of the CEFR scales and provide language teachers, test developers, and Second Language Acquisition researchers with concrete examples of learner performance and progress across multiple proficiency levels. For computational linguistics, it provide a range of authentic learner data for three target languages, supporting a broadening of the scope of research in areas such as automatic proficiency classification or native language identification. The annotated corpus and related information will be freely available as a corpus resource and through a freely accessible, didactically-oriented online platform.
A Test of a Model of Glaucomatous Damage of the Macula With High-Density Perimetry: Implications for the Locations of Visual Field Test Points
2014-05-01

The model can be used to determine the optimal locations for adding test points to the commonly used VF test pattern (24-2). It does not seem necessary to adjust the location of VF test points based upon interindividual differences in the fovea-to-disc axis.
Cranial Morphology of Theriosuchus sympiestodon (Mesoeucrocodylia, Atoposauridae) and the Widespread Occurrence of Theriosuchus in the Late Cretaceous of Europe
2014-05-01

We present a detailed morphological description of the type-locality cranial material of Theriosuchus sympiestodon Martin, Rabi, and Csiki, 2010 from the Maastrichtian Densuş-Ciula Formation of the Haţeg Basin, Romania together with new material of isolated cranial elements and teeth from various sites of the same general area. The recognition of several individuals of distinct sizes allows for an assessment of ontogenetic variation in this taxon. New material, consisting of isolated teeth and an incomplete maxilla with in situ teeth, coming from various late Campanian/early Maastrichtian sites in southern France is referable to ? Theriosuchus sp. and hints to a rare but widespread distribution of Theriosuchus in the Late Cretaceous European archipelago.
Enhanced Passive Bat Rabies Surveillance in Indigenous Bat Species from Germany - A Retrospective Study
2014-05-01

In Germany, rabies in bats is a notifiable zoonotic disease, which is caused by European bat lyssaviruses type 1 and 2 (EBLV-1 and 2), and the recently discovered new lyssavirus species Bokeloh bat lyssavirus (BBLV). As the understanding of bat rabies in insectivorous bat species is limited, in addition to routine bat rabies diagnosis, an enhanced passive surveillance study, i.e. the retrospective investigation of dead bats that had not been tested for rabies, was initiated in 1998 to study the distribution, abundance and epidemiology of lyssavirus infections in bats from Germany. A total number of 5478 individuals representing 21 bat species within two families were included in this study. The Noctule bat (Nyctalus noctula) and the Common pipistrelle (Pipistrellus pipistrellus) represented the most specimens submitted. Of all investigated bats, 1.17% tested positive for lyssaviruses using the fluorescent antibody test (FAT). The vast majority of positive cases was identified as EBLV-1, predominately associated with the Serotine bat (Eptesicus serotinus). However, rabies cases in other species, i.e. Nathusius' pipistrelle bat (Pipistrellus nathusii), P. pipistrellus and Brown long-eared bat (Plecotus auritus) were also characterized as EBLV-1. In contrast, EBLV-2 was isolated from three Daubenton's bats (Myotis daubentonii). These three cases contribute significantly to the understanding of EBLV-2 infections in Germany as only one case had been reported prior to this study. This enhanced passive surveillance indicated that besides known reservoir species, further bat species are affected by lyssavirus infections. Given the increasing diversity of lyssaviruses and bats as reservoir host species worldwide, lyssavirus positive specimens, i.e. both bat and virus need to be confirmed by molecular techniques.
Major, minor, and trace element composition of pyromorphite-group minerals as recorder of supergene weathering processes from the Schwarzwald mining district, SW Germany
2014-05-01

More than 150 samples of pyromorphite, mimetite, vanadinite, and minerals of the hedyphane-group (which collectively are summarized here under the term PyGM for pyromorphite-group minerals) from the Schwarzwald mining district, southwest Germany, have been analyzed by electron microprobe and LA-ICP-MS. In this largest study of its kind, the relations of PyGM composition to host rock and fluid compositions and the amount of solid solution between the various end-members were investigated. In addition, we report the colors of the many analyzed mineral compositions. Here is a list of the most important results.
Point and Interval Estimation on the Degree and the Angle of Polarization: A Bayesian Approach
2014-05-01

Linear polarization measurements provide access to two quantities, the degree (DOP) and the angle of polarization (AOP). The aim of this work is to give a complete and concise overview of how to analyze polarimetric measurements. We review interval estimations for the DOP with a frequentist and a Bayesian approach. Point estimations for the DOP and interval estimations for the AOP are further investigated with a Bayesian approach to match observational needs. Point and interval estimations are calculated numerically for frequentist and Bayesian statistics. Monte Carlo simulations are performed to clarify the meaning of the calculations. Under observational conditions, the true DOP and AOP are unknown, so that classical statistical considerations - based on true values - are not directly usable. In contrast, Bayesian statistics handles unknown true values very well and produces point and interval estimations for DOP and AOP, directly. Using a Bayesian approach, we show how to choose DOP point estimations based on the measured signal-to-noise ratio. Interval estimations for the DOP show great differences in the limit of low signal-to-noise ratios between the classical and Bayesian approach. AOP interval estimations that are based on observational data are presented for the first time. All results are directly usable via plots and parametric fits.
Robust and efficient volumetric occupancy mapping with an application to stereo vision
2014-05-01

A map of occupied and free space in a robot's environment is a common prerequisite for navigational tasks. Although the first methods for occupancy mapping relied on a 2D grid representation, 3D volumetric approaches are becoming increasingly popular. In this paper we present a new volumetric mapping approach that is based on the OctoMap method. We designed this method to be more robust against measurement errors, in particular against high temporally or spatially correlated errors usually received from a stereo vision system. For this purpose, we define a probability measure that a voxel is currently visible. An update of a voxel's occupancy probability then happens with respect to this visibility probability, allowing us to neglect measurements for voxels that are actually unobservable. Finally, we model the depth error of a stereo vision sensor, and take care of this error when performing a map update. By evaluation we show that our method produces maps with far less erroneous artifacts compared to OctoMap. Our maps also require less memory, and due to an optimized update reduction, our method is also faster than OctoMap when processing dense range measurement data.
Finding a Tradeoff between Accuracy and Rater's Workload in Grading Clustered Short Answers
2014-05-01

In this paper we investigate the potential of answer clustering for semi-automatic scoring of short answer questions for German as a foreign language. We use surface features like word and character n-grams to cluster answers to listening comprehension exercises per question and simulate having human graders only label one answer per cluster and then propagating this label to all other members of the cluster. We investigate various ways to select this single item to be labeled and find that choosing the item closest to the centroid of a cluster leads to improved (simulated) grading accuracy over random item selection. Averaged over all questions, we can reduce a teacher’s workload to labeling only 40 % of all different answers for a question, while still maintaining a grading accuracy of more than 85%.
A Direct Synthesis of a Strongly Zwitterionic 6,6'-Diaminofulvalene
2014-05-01

Upon reaction of the dipyrido-anellated guanidinium salt 1 with one equivalent of CpNa we were able to synthesize the dipyrido-anellated diaminofulvalene 4 in one step in 33% isolated yield. This shortens the initial route that applies a literature-known fulvalene synthesis via uronium salt 3 by two steps and avoids the need for a sacrificial equivalent of CpNa. Although the X-ray structure analysis reveals a shorter exocyclic double bond than observed in the diaminofulvalene V, a theoretical analysis based upon DFT calculations shows a stronger zwitterionic character for the dipyridofulvalene 4.
IMA901 for Metastatic Renal Cell Carcinoma in the Context of new Approaches to Immunotherapy
2014-05-01

The promising option of immunotherapy for metastatic renal cell carcinoma has evolved from rather unspecific approaches to a specific activation of an anti-tumor T-cell response. The latest step is a synthetic peptide vaccine called IMA901, which demonstrated a clear association between a provoked T-cell response and a prolonged overall survival. The results of IMA901 for the treatment of metastatic renal cell carcinoma are discussed together with new approaches to immunotherapy, such as local and systemic immunomodulation with adjuvants, checkpoint inhibitors, classical chemotherapeutics, such as cyclophosphamide or tyrosine kinase inhibitors. The capability of theses substances to modulate leukocytes subsets, such as myeloid-derived suppressor cells, Tregs or Th17 cells, are outlined together with the possibility to combine them with tumor vaccination strategies to achieve a higher cancer specificity and immunogenicity.
Visual SLAM for autonomous MAVs with dual cameras
2014-05-01

This paper extends a monocular visual simultaneous localization and mapping (SLAM) system to utilize two cameras with non-overlap in their respective field of views (FOVs). We achieve using it to enable autonomous navigation of a micro aerial vehicle (MAV) in unknown environments. The methodology behind this system can easily be extended to multi-camera rigs, if the onboard computation capability allows this. We analyze the iterative optimizations for pose tracking and map refinement of the SLAM system in multicamera cases. This ensures the soundness and accuracy of each optimization update. Our method is more resistant to tracking failure than conventional monocular visual SLAM systems, especially when MAVs fly in complex environments. It also brings more flexibility to configurations of multiple cameras used onboard of MAVs. We demonstrate its efficiency with both autonomous flight and manual flight of a MAV. The results are evaluated by comparisons with ground truth data provided by an external tracking system.
Modeling substrate-bacteria-grazer interactions coupled to substrate transport in groundwater
2014-05-01

Models of microbial dynamics coupled to solute transport in aquifers typically require the introduction of a bacterial capacity term to prevent excessive microbial growth close to substrate-injection boundaries. The factors controlling this carrying capacity, however, are not fully understood. In this study, we propose that grazers or bacteriophages may control the density of bacterial biomass in continuously fed porous media. We conceptualize the flow-through porous medium as a series of retentostats, in which the dissolved substrate is advected with water flow whereas the biomasses of bacteria and grazers are considered essentially immobile. We first model a single retentostat with Monod kinetics of bacterial growth and a second-order grazing law, which shows that the system oscillates but approaches a stable steady state with nonzero concentrations of substrate, bacteria, and grazers. The steady state concentration of the bacteria biomass is independent of the substrate concentration in the inflow. When coupling several retentostats in a series to mimic a groundwater column, the steady state bacteria concentrations thus remain at a constant level over a significant travel distance. The one-dimensional reactive transport model also accounts for substrate dispersion and a random walk of grazers influenced by the bacteria concentration. These dispersive-diffusive terms affect the oscillations until steady state is reached, but hardly the steady state value itself. We conclude that grazing, or infection by bacteriophages, is a possible explanation of the maximum biomass concentration frequently needed in bioreactive transport models. Its value depends on parameters related to the grazers or bacteriophages and is independent of bacterial growth parameters or substrate concentration, provided that there is enough substrate to sustain bacteria and grazers.
Restrictive Immigration Policy in Germany: Pains and Gains Foregone?
2014-05-01

Many European countries restrict immigration from new EU member countries. The rationale is to avoid adverse wage and employment effects. We quantify these effects for Germany. Following Borjas (in Q J Econ CXVIII(4): 1335–1374, 2003), we estimate a structural model of labor demand, based on elasticities of substitution between workers with different experience levels and education. We allow for unemployment which we model in a price-wage-setting framework. Simulating a counterfactual scenario without restrictions for migration from new EU members countries in Germany, we find moderate negative wage and employment effects for incumbent foreigners, but positive effects for natives. Our results indicate that for the native German population as a whole the immigration restrictions are not welfare enhancing.
Note: Artificial neural networks for the automated analysis of force map data in atomic force microscopy
2014-05-01

Force curves recorded with the atomic force microscope on structured samples often show an irregular force versus indentation behavior. An analysis of such curves using standard contact models (e.g., the Sneddon model) would generate inaccurate Young's moduli. A critical inspection of the force curve shape is therefore necessary for estimating the reliability of the generated Young's modulus. We used a trained artificial neural network to automatically recognize curves of “good” and of “bad” quality. This is especially useful for improving the analysis of force maps that consist of a large number of force curves.
Impact of Perioperative Immunosuppressive Medication on Surgical Outcome in Crohn’s Disease (CD)
2014-05-01

Abstract Introduction: Patients with Crohn’s disease [CD] carry an 80 − 90 % lifetime risk of undergoing surgery. Many of these patients are on immunosuppressive medication at the time of surgery. The aim of this study was to evaluate the effect of immunosuppression on the surgical outcome in CD patients. Methods: We retrospectively analyzed 484 consecutive abdominal operations for CD from 1995 to 2008 for surgical complications. Results: A total of 241 operations (= 49.8 %) were performed under perioperative immunosuppression (corticoids and thiopurine). The overall complication rate was 18.6 %, the major complication rate was 8.7 % and the anastomotic leakage rate was 3.3 %. No differences were observed between patients without immunosuppression compared to those with immunosuppression. Patients with colo-rectal resections showed a higher complication rate than patients with small bowel resection independently of immunosuppression. Conclusion: Nearly 50 % of the patients undergoing abdominal surgery for CD are receiving immunosuppressive medication during surgery. However, perioperative immunosuppression with corticoids, thiopurine or the combination of both does not significantly alter the surgical complication rate. Therefore the decision of a required surgery should not be delayed due to the fact that the patient is under immunosuppressive medication.
Development of smart feature selection for advanced virtual metrology
2014-05-01

Advanced Process Control is an important research area in Semiconductor Manufacturing to improve process stability crucial for product quality. Actual research focuses on Virtual Metrology (VM) using high sophisticated Machine Learning methods to predict a predefined metrology target based on statistical models trained on historical data. Enhancing physical metrology by predictive models leads to smart future fabs. Enabling scalable VM for fab-wide deployment depends on the extraction of only the most important out of typically hundreds to thousands of available process parameters. High Density Plasma (HDP) Chemical Vapor Deposition appears to be a process area in SM predestinated for application of thus required Data Mining. In low-volume-high-mixture fabrication plants, Knowledge Discovery in Databases is extremely challenging due to complex technology mixtures and reduced availability of data for comparable process steps. In this paper, a new Feature Selection wrapper method has been developed and is investigated to reveal only the most important process parameters for smart VM. Modeling of unknown functional interrelations and selection of these features is achieved to predict the layer thickness of dielectric layers deposited onto a metallization layer of the manufactured wafers with highest accuracy and reliability.
Neuronal Correlates of Non-verbal Numerical Competence in Primates
2014-05-01

Abstract Non-verbal numerical competence, such as the estimation of set size, is rooted in biological primitives that can also be explored in animals. Over the past years, the anatomical substrates and neuronal mechanisms of numerical cognition in primates have been unravelled down to the level of single neurons. Studies with behaviourally-trained monkeys have identified a parietofrontal network of individual neurons selectively tuned to the number of items (cardinal aspect) or the rank of items in a sequence (ordinal aspect). The properties of these neurons’ numerosity tuning curves can explain fundamental psychophysical phenomena, such as the numerical distance and size effect. Functionally overlapping groups of parietal neurons represent not only numerable-discrete quantity (numerosity), but also innumerable-continuous quantity (extent) and relations between quantities (proportions), supporting the idea of a generalized magnitude system in the brain. Moreover, many neurons in the prefrontal cortex establish semantic associations between signs and abstract numerical categories, a neuronal precursor mechanisms that may ultimately give rise to symbolic number processing in humans. These studies establish putative homologies between the monkey and human brain, and demonstrate the suitability of non-human primates as model system to explore the neurobiological roots of the brain’s non-verbal quantification system, which may constitute the phylogenetic and ontogenetic foundation of all further, more elaborate numerical skills in humans.
TICoMS -- A Modular and Message-Based Framework for Monitoring and Control of Medical Devices
2014-05-01

An important aspect of clinical work, especially in the intensive care unit (ICU) is the vigilant observation of patients' vital data on a various number of monitors and displays to allow for rapid decision-making which is often required in critical conditions. Most often, the presented data cannot be collected and used as a whole to aid the decision making by availability and comparison of all relevant data at once. In this paper, a novel approach for handling real-time clinical data is presented. We developed TICoMS (Tübinger ICU Control and Monitoring System), a framework for integration of sensors and effectors into a homogeneous message-based network capable of gathering and distributing real-time data in ICU settings from medical devices. The accumulated data can be presented on a central patient monitoring screen for a fast and extensive overview of the patient's current condition and trends with a homogenous time-base. Furthermore, this framework provides control capabilities for medical devices and is therefore an essential foundation for device interactions that may allow for computer-based support in decision-making or advanced automation in intensive care scenarios.
Combining Dynamic Foot Scanning and Additive Manufacturing for the Production of Insoles: a Case Study
2014-05-01

The development of an insole that is representative of the foot's dynamic nature is crucial for good fit as well as comfort and performance. Additive manufacturing (AM) has the potential to allow the production of such insoles because of its tool-less capabilities and the ability to directly manufacture from CAD models at no extra cost. Research therefore has been undertaken to explore a process of foot capture by using a dynamic scanner for the design and manufacture of insoles using AM. The feet of four individuals were dynamically and statically scanned and from these data, four insole designs were developed for each person. The designs were: footprint, dynamic, average and static. The results indicated that the personalisation process is complex, mainly due to the need to identify and select the point cloud(s) from a large number of frames and manipulate them accordingly, presenting challenges in the design phase. The data from this study have demonstrated that combining dynamic scanning and AM technology is feasible for developing personalised insoles. While traditional footwear/insole is based on static data, this study can be considered as a starting point for the development of personalised insoles by using dynamic scanning and AM.