julilili42/papers huggingface dataset:
Combined molecular and morphological data for improving phylogenetic hypothesis in Dacrymycetes
2013-09-01

We analyzed the DNA sequences of four gene regions, 28S and 18S rDNA, the ITS region and rpb2, to obtain a high resolution phylogenetic tree of Dacrymycetes. In addition, we comparatively studied micro- and macromorphological characteristics of representative species. The traditional generic classification based on morphological characteristics was not reflected by our molecular phylogenies. Ancestral state reconstructions indicated that the morphology of basidia and clamp connections are evolutionarily stable. In contrast, basidiocarps and basidiospore septation patterns appear variable. Dacrymyces unisporus shares the dolipores with non-perforate parenthesomes typical of other dacrymycetous taxa but is a unique species having predominantly non-bifurcate basidia and subglobose to ovoid basidiospores with transverse and longitudinal septa. In molecular phylogenies this species is a member of Dacrymycetes but always occupies a sister position in relation to the rest of the Dacrymycetes. Based on our results we propose a new genus, Unilacryma, for D. unisporus. For proper accommodation of this taxon, we introduce the family Unilacrymaceae and the order Unilacrymales.
Terrain classification with conditional random fields on fused 3D LIDAR and camera data
2013-09-01

For a mobile robot to navigate safely and efficiently in an outdoor environment, it has to recognize its surrounding terrain. Our robot is equipped with a low-resolution 3D LIDAR and a color camera. The data from both sensors are fused to classify the terrain in front of the robot. Therefore, the ground plane is divided into a grid and each cell is classified as either asphalt, cobblestones, grass or gravel. We use height and intensity features for the LIDAR data and Local ternary patterns for the image data. By additionally taking into account the context-sensitive nature of the terrain, the results can be improved significantly. We present a method based on Conditional Random Fields and compare it with a Markov Random Field based approach. We show that the Conditional Random Field model is better suited for our task. We achieve an average true positive rate of 94.2% for classifying the grid cells into the four terrain classes.
True or false? Activations of language-related areas in patients with disorders of consciousness
2013-09-01

Twenty-nine patients with Unresponsive Wakefulness Syndrome (UWS), 26 patients in Minimally Conscious State (MCS), and 21 healthy control individuals matched in age and social environment (patients' relatives) were presented with 80 short sentences half of which were factually correct, and the other half factually incorrect. The diagnosis was made on the basis of repeated neurological examinations as well as the standardized assessment using a Coma Recovery Scale-Revised (CRS-R). fMRI blood oxygen level dependent signal was recorded in an event-related design time-locked to the end word of the sentences. In the contrast "incorrect-minus-correct" significant activations in the relevant brain regions were obtained in 17 (81%) controls and in 16 (29%) patients. Among patients, the 16 responders had a significantly longer time since accident than the 39 non-responders. Responders and non-responders did not differ in terms of the diagnosis (UWS vs. MCS), age, CRS-R score, or the degree of brain atrophy. The data concur with the results of several earlier studies on UWS/MCS patients, with the difference that the critical stimuli in those studies were semantically incongruent or ambiguous propositions rather than factually false ones in the present experiment. The hypothesis is discussed that the differential response of brain language areas to factually correct and incorrect statements does not require conscious perception of the statements.
OCT A-Scan based lung tumor tissue classification with Bidirectional Long Short Term Memory networks
2013-09-01

This paper presents a novel method for lung tumor tissue classification using Bidirectional Long Short Term Memory networks (BLSTMs). Samples are obtained through Optical Coherence Tomography (OCT) from real soft tissue specimen and represented as data sequences. Such sequences are learned with BLSTMs, which are able to recognize even non-uniformly compressed temporal encoded patterns in sequential data in both forward and backward time-direction. Our experiments indicate that BLSTMs are a suitable choice for this classification task, since they outperform other recurrent architectures. Furthermore, the presented findings lead to promising future investigations in the field of OCT based tissue analysis.
The Science of Exoplanets and Their Systems
2013-09-01

A scientific forum on "The Future Science of Exoplanets and Their Systems," sponsored by Europlanet and the International Space Science Institute (ISSI) and co-organized by the Center for Space and Habitability (CSH) of the University of Bern, was held during December 5 and 6, 2012, in Bern, Switzerland. It gathered 24 well-known specialists in exoplanetary, Solar System, and stellar science to discuss the future of the fast-expanding field of exoplanetary research, which now has nearly 1000 objects to analyze and compare and will develop even more quickly over the coming years. The forum discussions included a review of current observational knowledge, efforts for exoplanetary atmosphere characterization and their formation, water formation, atmospheric evolution, habitability aspects, and our understanding of how exoplanets interact with their stellar and galactic environment throughout their history. Several important and timely research areas of focus for further research efforts in the field were identified by the forum participants. These scientific topics are related to the origin and formation of water and its delivery to planetary bodies and the role of the disk in relation to planet formation, including constraints from observations as well as star-planet interaction processes and their consequences for atmosphere-magnetosphere environments, evolution, and habitability. The relevance of these research areas is outlined in this report, and possible themes for future ISSI workshops are identified that may be proposed by the international research community over the coming 2-3 years.
Real time face tracking and pose estimation using an adaptive correlation filter for human-robot interaction
2013-09-01

In this paper, we present a real time algorithm for mobile robots to track human faces and estimate face poses accurately, even when humans move freely and far away from the camera or go through different illumination conditions in uncontrolled environments. We combine the algorithm of an adaptive correlation filter with a Viola-Jones object detection to track the face as well as the facial features including the two external eye corners and the nose. These facial features provide geometric cues to estimate the face pose robustly. In our method, the depth information from a Microsoft Kinect camera is used to estimate the face size and improve the performance of tracking facial features. Our method is shown to be robust and fast in uncontrolled environments.
Do oval posts improve fracture resistance of teeth with oval root canals?
2013-09-01

Abstract Aim To determine whether the use of oval posts increases fracture resistance of root canal treated teeth with oval‐shaped canals. Methods Extracted mandibular premolars with similar dimensions were decoronated. After root canal treatment, standardized post space preparations were performed to simulate the presence of oval‐shaped root canal morphologies. Specimens were randomly assigned to 3 groups ( n = 3 × 24). In group SFP (small fiber post), circular posts with a cervical diameter of 1.5 mm were used without additional form‐congruent post space preparation. In group LFP (large fiber post), a circular post space preparation was performed to adapt posts with a cervical diameter of 1.9 mm. In group OFP (oval fiber post), oval posts with a long cervical diameter of 1.9 mm and short cervical diameter of 1.3 mm were utilized without additional post space preparation. Posts were cemented with dual‐cure resin. All specimens were restored with standardized direct composite crowns. After thermo‐mechanical loading in a computer‐controlled masticator, all specimens underwent fracture resistance testing. Means and standard deviations were calculated. Data were analyzed using the K ruskal– W allis test (α = 0.05). Results The highest mean fracture load was observed in group OFP (273N ± 51), the lowest in group LFP (258N ± 72). K ruskal– W allis indicated no significant differences in fracture resistance among the three experimental groups. Conclusions Within the limitations of this laboratory study, oval posts did not reveal increased fracture resistance of root canal‐treated premolars with oval‐shaped root canals compared with circular posts.
Following a quadrotor with another quadrotor using onboard vision
2013-09-01

We consider a leader-following problem with two flying robots with different sensor configurations. The follower is equipped with a camera to detect the leader robot. The platforms are based on the low-cost Parrot AR. Drone quadrotor modified for on-board sensing and computing. Our approach relies on detecting artificial passive markers on the leader quadrotor to compute the relative distance between the vehicles. We solve the perspective-n-point problem using an algorithm based on the inscribed angle theorem that runs efficiently on resource-limited platforms. We validate the position estimation algorithm and leader-following controllers with autonomously flown figures.
Developmental residue and developmental novelty - different modes of adipose-fin formation during ontogeny
2013-09-01

The adipose fin is a structure with questionable function, for a long time even regarded as a rudimentary element without any function. A comparative study of adipose fin development revealed two different modes: a salmoniform-type where the adipose fin develops directly from the larval fin fold simultaneously with the other median fins. And a characiform-type where the adipose fin develops anew after the reduction of the larval fin fold. Compared to the first mode the latter starts late in ontogeny, when all other median fins already have their shape, fin rays and colouration. The characiform-type of adipose fin development contradicts the view that this structure is just a larval fin fold remainder. It also disputes the hypothesis of the adipose fin as a structure without any function. Such a hypothesis cannot explain a systematically widely distributed structure which even exhibits different modes of ontogenetic development in different taxa. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Methodological aspects on hypoxia PET acquisition and image processing.
2013-09-01

Tumor hypoxia is one of the main factors compromising the effectiveness of radiotherapy. As a consequence, non-invasive hypoxia imaging with positron emission tomography (PET) is very promising with regard to its potential to provide a functional basis for patient stratification or therapy modification. This review article aims at providing a comprehensive overview of different methodologies for hypoxia PET image acquisition protocols as well as data processing and analysis as used in recent studies and clinical trials. Furthermore, different physical and also technical aspects that may induce ambiguities and limitations into hypoxia PET image acquisition and interpretation are discussed in the context of this article. In the future, dedicated hypoxia PET image acquisition protocols and methodologies for processing, analysis and interpretation of hypoxia PET data are necessary to allow for comparison of hypoxia PET image data acquired in different study centers and enable for the definition of multicenter trials on hypoxia PET imaging and hypoxia-based treatment interventions.
Treatment of pyoderma gangrenosum with topical factor XIII
2013-09-01

Pyoderma gangrenosum (PG) is a severe ulcerative skin disease. Despite systemic immunosuppressive therapy, PG ulcers often progress and can develop into life-threatening conditions. In this case series, we treated 6 patients suffering from recalcitrant PG with topical coagulation factor XIII, which has been shown to exert beneficial effects on tissue regeneration and wound healing. All 6 patients showed a positive response to treatment with a marked reduction in wound size that was maintained during a 3-month follow-up period. The treatment was well tolerated with no remarkable adverse effects or complications. Topical factor XIII has potential in combination with standard immunosuppressive therapy for the treatment of PG.
User-friendly metaworkflows in quantum chemistry
2013-09-01

The Science Gateway MoSGrid (Molecular Simulation Grid) allows to build up quantum chemical metaworkflows. End users mostly request complex workflows which are dissected into smaller workflows: Those can be combined freely to larger metaworkflows. Herein, we describe important general quantum chemical workflows which serve as toolbox for the real use case of a spectroscopic analysis as example for an end user desired metaworkflow. All workflow features are implemented via WS-PGRADE and submitted to UNICORE. The workflows are stored in the MoSGrid repository and ported to the SHIWA repository.
Loop closure detection using depth images
2013-09-01

We investigate the question whether loop closure detection using depth images is feasible using currently available depth features. For this reason, we collected a benchmark dataset consisting of a total number of 15 logfiles with several loops in various environments, implemented a modular and easily extensible loop closure detector and used this to evaluate the adequacy of state-of-the art depth features on our benchmark dataset. To allow for a fair comparison, we determined the best values for the sometimes large number of user-chosen parameters using a large-scale grid search. Since our benchmark dataset contains both depth and RGB images, we can compare the performance relying on depth features with the performance achieved when using intensity image features.
Accelerated model-based robustness testing of state machine implementations
2013-09-01

In this paper, we present an approach for accelerating model-based robustness testing of state-based software components. We use the Z3 SAT solver to derive executable test cases fully automatically from a state model based on a UML Statechart. The test cases are paths along the Statechart comprising states and transitions. The main advantage of our approach is an accelerated execution of the test cases by refining already reached states as starting points for further test cases using reverse execution. Furthermore, the presented approach is able to check whether a correct target state has been reached or not when executing the path-based test cases using runtime verification and therefore increases the test significance. The runtime verification is done without instrumenting the source code of the component under test.
Robust real-time detection of multiple balls on a mobile robot
2013-09-01

In this paper, we present a robust method for detecting multiple balls without using color information. The method builds upon the boosted Haar classifier approach introduced by Viola et al. [11] and is applied onto an image from a catadioptric camera without performing rectification of the image. We compare the method with one based on a classical color segmentation approach. Originally both methods have been developed for the participation on the 2012 "SICK robot day", an international robotics competition. The task was to collect balls with a robot and put them into dedicated perches within a certain amount of time. Both methods showed to be robust during the competition. Our team placed second out of fifteen contenders.
Collact.Me: Conceptual Framework for Extracting Domain-Specific Content from Twitter
2013-09-01

In the last decade, social networks like Facebook and Twitter increasingly became important parts of people's lives. A rapidly growing number of users of these social networks create tremendous amounts of information, such as social text and multimedia feeds. In this context finding specific information and keeping it accessible becomes more and more a challenge. In parallel information filtering, topic modeling and quality has become subject of researchers in the field of social network analysis. Here we introduce Collact. Me, a conceptual framework to extract and classify microblogging content in an automated manner. Domain-specific data from social Twitter streams are collected from which topic models are created. The training data is used to build classifiers that allow computationally efficient multi-label classification. Results are presented and visualized using a novel dot-plot chart, which displays quantities of classified tweets of user-defined topics in a temporal fashion. We applied Collact. Me to selected bioinformatics topics. Our results show that our framework helps users to identify and interpret the level of attention of topics and to understand the relations between different topics as well as indications of emerging patterns. http://collact.me.
Heterocycles [f]-Fused onto Quinolones. Synthesis of Novel Dioxo-Nethylpyrano[ 2,3-f ]- and [3,2-f ]quinoline-10-carboxylic Acids
2013-09-01

A model N-ethyl-1,10-dioxo-3-phenylpyrano[3,2- f ]quinoline-9-carboxylic acid (8) and the isomeric (2-substituted) pyrano[2,3- f ]quinoline-9-carboxylic acids (6 and 7) were prepared from the corresponding 6/7-aminochromen-4-ones via the Gould-Jacobs reaction. The new tricyclic heterocycles 6-8 exhibit moderate antibacterial activity (MIC=16 - 64 μgmL -1 ) against E. coli and S. aureus
A Bochner-type representation of positive definite mappings on the dual of a compact group
2013-09-01

For an arbitrary compact group G with dual space Σ(G) a Bochner-type bijection is established between positive definite mappings on Σ(G) and central bounded measures on G.This bijection defined by the generalized Fourier transformation is based on the comparative study of three kinds of function algebras: the coefficient algebra, the algebra of convergent Fourier series, and the central Fourier algebra of G.
Vehicle model based outlier detection for automotive visual odometry
2013-09-01

In this paper we present a novel outlier detection scheme for image feature based ego-motion estimation in automotive applications. It is based on a restrictive motion model, describing the relationship between road vehicle motion and camera motion. The model also enables the integration of ESP sensor data, such as measured longitudinal velocity and yaw-rate. In this way a high precision camera motion prediction is realized, which is used to identify erroneous feature correspondences. High costs of standard methods like the iterative random sample consensus (RANSAC) [1] are thereby avoided.
CXCR1 is dispensable for allergy-driven airway leukocyte recruitment in vivo
2013-09-01

Chemokines recruit inflammatory cells to sites of inflammation. Human CXCL8 (Interleukin 8) represents the prototypical chemokine for neutrophil migration by binding to the G-protein coupled chemokine receptors CXCR1 (IL-8RA, CD181) and CXCR2 (IL-8RB, CD182). While the role of CXCR2 has been investigated in detail by genetic deletion or pharmacologic inhibition, the distinct contribution of CXCR1 remains incompletely understood. The murine homologue of human CXCR1 has recently been identified. Here we studied the role of CXCR1 in leukocyte recruitment by using recently generated CXCR1 knock-out mice and in vivo models of airway inflammation (ovalbumin and house dust mite models of allergic asthma), infection-triggered cell recruitment and chemotaxis. In contrast to human CXCR1, murine CXCR1 was dispensable for the recruitment of neutrophils, monocytes, dendritic cells or T cells in models of allergic or bacterial inflammation. These studies demonstrate that CXCR1 is dispensable for allergy-driven airway leukocyte recruitment and inflammatory cell migration in vivo. The functional role of murine CXCR1 in cell recruitment and pulmonary inflammation remains to be solved in future studies.
A facility for soft proton irradiation of X-ray detectors and instrument testing for future space missions
2013-09-01

Orbital soft protons (from tens of keV to a few MeV) can seriously degrade the performance of astronomical X-ray detectors. This paper briefly describes an irradiation setup for large detectors at the accelerator facility of the University of Tübingen. Main advantages are a high flux uniformity over a large area as well as a precise monitoring system for the applied spectrum and fluence. Recent modifications of this setup that enable measurements of the small angle scattering efficiency of Wolter-type X-ray mirror shells are presented.
Evaluation of terahertz emission from intrinsic josephson junctions using a high-T<inf>c</inf> superconductor grain boundary Josephson junction
2013-09-01

To evaluate terahertz emission from intrinsic Josephson junctions, we use a YBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sub> grain boundary Josephson junction as a detector. Shapiro steps on the current-voltage characteristics of the detector were clearly observed and their positions moved with the bias voltage of the emitter accordingly. Analyzing the current-voltage characteristics of the detector, we found that the emission was tuned over a wide frequency range, e.g., between 496.6 GHz and 540 GHz, at a temperature of 24 K.
P21: Analysing the human serological response for HCV and eight other pathogens with a multiplexed antigen array
2013-09-01

Hepatitis C is a major public health problem with high incidence in regions such as Egypt and other Mediterranean countries. We are developing hepatitis C virus (HCV) specific serological assays within the FP7-HEALTH granted project ‘Spontaneous clearance in patients acutely infected with HCV-immune profiling, novel biomarkers and X-omics approaches (SPHINX)’. HCV is classified into six genotypes, each with numerous subtypes. Genotypes 1, 2, and 3 are common throughout the United States and Europe. HCV genotype 4 (HCVg4) is common in the Middle East and in Africa, where it is responsible for more than 80% of all HCV infections, and has recently spread to several European countries. Egypt has the highest prevalence of HCV worldwide and the highest prevalence of HCVg4 (1). The aim of this project is the development and validation of a multiplexed bead-based serological assay for HCV, with special attention to HCVg4. For the identification of the serological response against HCV, antigens from different HCV genotypes are used. HCVg4 specific fusion proteins were generated to monitor the serological response. In addition we have included other HCV genotype-specific probes and pathogen specific antigens to cover the serological response against hepatitis A, hepatitis B, hepatitis D, hepatitis E, Epstein Barr, cytomegalovirus, Helicobacter pylori and Toxo-plasma gondii. We will show results from chronic and acutely infected HCV patients generated with our multiplexed serological assay. 1. Sanaa M. Kamal and Imad A. Nasser. Hepatitis C Genotype 4: What We Know and What We Don't Yet Know. Hepatology 2008; 47: 1371–1383.