julilili42/papers huggingface dataset:
WebLicht: Web-Based LRT Services for German
2010-07-13

This software demonstration presents WebLicht (short for: Web-Based Linguistic Chaining Tool), a web-based service environment for the integration and use of language resources and tools (LRT). WebLicht is being developed as part of the D-SPIN project. We-bLicht is implemented as a web application so that there is no need for users to install any software on their own computers or to concern themselves with the technical details involved in building tool chains. The integrated web services are part of a prototypical infrastructure that was developed to facilitate chaining of LRT services. WebLicht allows the integration and use of distributed web services with standardized APIs. The nature of these open and standardized APIs makes it possible to access the web services from nearly any programming language, shell script or workflow engine (UIMA, Gate etc.) Additionally, an application for integration of additional services is available, allowing anyone to contribute his own web service.
Suppression of adverse angiogenesis in an albumin-based hydrogel for articular cartilage and intervertebral disc regeneration
2010-07-13

An injectable polyethylene glycol-crosslinked albumin gel (AG) supplemented with hyaluronic acid as a matrix for autologous chondrocyte implantation was evaluated with regard to its impact on angiogenesis. Healthy articular cartilage and intervertebral discs (IVD) are devoid of blood vessels, whereas pathological blood vessel formation augments degeneration of both theses tissues. In contrast to human endothelial cells, primary human articular chondrocytes encapsulated in the AG retained their viability. Endothelial cells did not adhere to the gel surface to a significant extent nor did they proliferate in vitro. The AG did not release any diffusible toxic components. Contrary to Matrigel employed as positive control, the AG prevented endothelial chemoinvasion in Transwell filter assays even in the presence of a chemotactic gradient of vascular endothelial growth factor. In ovo, the AG exhibited a barrier function for blood vessels of the chick chorioallantoic membrane. Subcutaneous implantation of human IVD chondrocytes enclosed in the albumin gel into immunodeficient mice revealed a complete lack of angiogenesis inside the gel after two weeks. At the same time, the IVD chondrocytes within the gel remained vital and displayed a characteristic gene expression pattern as judged from aggrecan, collagen type I and type II mRNA levels. In summary, aiming at articular cartilage and IVD regeneration the albumin gel promises to be a beneficial implant matrix for chondrocytes simultaneously exhibiting non-permissive properties for adverse endothelial cells.
Robust optimization based upon statistical theory
2010-07-13

Purpose: Organ movement is still the biggest challenge in cancer treatment despite advances in online imaging. Due to the resulting geometric uncertainties, the delivered dose cannot be predicted precisely at treatment planning time. Consequently, all associated dose metrics (e.g., EUD and maxDose) are random variables with a patient‐specific probability distribution. The method that the authors propose makes these distributions the basis of the optimization and evaluation process. Methods: The authors start from a model of motion derived from patient‐specific imaging. On a multitude of geometry instances sampled from this model, a dose metric is evaluated. The resulting pdf of this dose metric is termed outcome distribution. The approach optimizes the shape of the outcome distribution based on its mean and variance. This is in contrast to the conventional optimization of a nominal value (e.g., PTV EUD) computed on a single geometry instance. The mean and variance allow for an estimate of the expected treatment outcome along with the residual uncertainty. Besides being applicable to the target, the proposed method also seamlessly includes the organs at risk (OARs). Results: The likelihood that a given value of a metric is reached in the treatment is predicted quantitatively. This information reveals potential hazards that may occur during the course of the treatment, thus helping the expert to find the right balance between the risk of insufficient normal tissue sparing and the risk of insufficient tumor control. By feeding this information to the optimizer, outcome distributions can be obtained where the probability of exceeding a given OAR maximum and that of falling short of a given target goal can be minimized simultaneously. Conclusions: The method is applicable to any source of residual motion uncertainty in treatment delivery. Any model that quantifies organ movement and deformation in terms of probability distributions can be used as basis for the algorithm. Thus, it can generate dose distributions that are robust against interfraction and intrafraction motion alike, effectively removing the need for indiscriminate safety margins.
GernEdiT: a graphical tool for germanet development
2010-07-13

GernEdiT (short for: GermaNet Editing Tool) offers a graphical interface for the lexicographers and developers of GermaNet to access and modify the underlying GermaNet resource. GermaNet is a lexical-semantic wordnet that is modeled after the Princeton Word-Net for English. The traditional lexicographic development of GermaNet was error prone and time-consuming, mainly due to a complex underlying data format and no opportunity of automatic consistency checks. GernEdiT replaces the earlier development by a more userfriendly tool, which facilitates automatic checking of internal consistency and correctness of the linguistic resource. This paper presents all these core functionalities of GernEdiT along with details about its usage and usability. 1
ABCC2 and Clinical Outcome of Tamoxifen Therapy
2010-07-13

TO THE EDITOR: The study by Kiyotani et al is another important contribution to the field of tamoxifen (TAM) pharmacogenomics in favor of CYP2D6 genetic testing for the improvement of TAM response in postmenopausal Japanese patients with breast cancer. In addition, for the first time, the authors identified a significant association between the rs3740065 G allele (intron 29, IVS29 154A G) of the ABC efflux drug transporter ABCC2 (multidrug related protein [MRP2]) and longer recurrence-free survival compared with individuals carrying the A allele in their study population of 282 patients. Because TAM-resistant MCF-7 cells express higher levels of ABCC2 than nonresistant MCF-7 cells, it has been suggested that ABCC2 induction could play a role in TAM resistance. On these grounds, Kiyotani et al speculated that the rs3740065 variant may be associated with increased ABCC2 expression and enhanced transport activity, thereby lowering the exposure of breast cancer cells to endoxifen, the active metabolite of TAM. However, in their study, the G allele was associated with longer recurrence-free survival, which would rather indicate a lower expression of ABCC2 and, hence, reduced transporter activity in breast cancer cells, resulting in higher intracellular endoxifen levels. Recently, a systematic DNA sequencing study that included 236 healthy individuals of Japanese ethnic background showed that a common promoter variant in ABCC2 ( 1774delG) is in strong linkage disequilibrium with rs3740065. Moreover, functional studies revealed that the 1774delG variation decreased ABCC2 promoter activity by 36% and that the promoter carrying the 1774delG allele had a defect in chenodeoxycholic acid–induced induction of promoter activity. Finally, a haplotype containing the 1774delG polymorphism showed a strong association with cholestatic or mixedtype hepatitis. We, therefore, propose that it is the 1774delG variant that can explain the findings of an association between ABCC2 and TAM outcome reported by Kiyotani et al. Unfortunately, the authors did not include the 1774delG variant in their investigation. Therefore, the issue of ABCC2 variants that predict clinical outcome must await more specific studies.
Activation of Hypoxia Inducible Factor 1 Is a General Phenomenon in Infections with Human Pathogens
2010-07-14

Activation of HIF-1 is a general phenomenon in infections with human pathogenic bacteria, viruses, fungi and protozoa. HIF-1-regulated pathways might be an attractive target to modulate the course of life-threatening infections.
A novel staphylococcal internalization mechanism involves the major autolysin Atl and heat shock cognate protein Hsc70 as host cell receptor
2010-07-14

Staphylococcus aureus and Staphylococcus epidermidis can cause serious chronic and recurrent infections that are difficult to eradicate. An important pathogenicity factor in these infections caused by S. aureus is its ability to be internalized by non-professional phagocytes thereby evading the host immune system and antibiotic treatment. Here, we report a novel mechanism involved in staphylococcal internalization by host cells, which is mediated by the major autolysin/adhesins Atl and AtlE from S. aureus and S. epidermidis respectively. In a flow cytometric internalization assay, atl and atlE mutants are significantly reduced in their capacities to be internalized by endothelial cells. Moreover, pre-incubation of endothelial cells with recombinant Atl dose-dependently inhibited internalization. As putative Atl-host cell receptor, the heat shock cognate protein Hsc70 was identified by mass spectrometry. The importance of Hsc70 in internalization was demonstrated by the inhibition of S. aureus internalization with anti-Hsc70 antibodies. In conclusion, this novel Atl- or AtlE-mediated internalization mechanism may represent a 'back-up' mechanism in S. aureus internalization, while it may represent the major or even sole mechanism involved in the internalization of coagulase-negative staphylococci and thus may play an important role in the pathogenesis of chronic and relapsing infections with these serious pathogens.
NMDA-receptor antagonist and morphine decrease CRPS-pain and cerebral pain representation
2010-07-14

A combination therapy of morphine with an NMDA-receptor antagonist might be more effective than morphine without a NMDA-receptor antagonist for the relief of neuropathic pain in patients with complex regional pain syndrome (CRPS). In order to test the efficacy of this combination therapy we performed a double-blind randomized placebo-controlled study on patients suffering from CRPS of the upper extremity. We used functional magnetic resonance imaging during movement of the affected and unaffected upper hand before and after a treatment regimen of 49 days that contrasted morphine and an NMDA-receptor antagonist with morphine and placebo. We postulated superior pain relief for the combination therapy and concomitant changes in brain areas associated with nociceptive processing. Only the combination therapy reduced pain at rest and during movement, and disability. After treatment, activation in the contralateral primary somatosensory (cS1) and anterior cingulate cortex was significantly reduced when the affected hand was moved. Pain relief during therapy was related to decreased activation in cS1 and secondary somatosensory cortex (S2). Our data suggest that the combination of morphine with an NMDA-receptor antagonist significantly affects the cerebral processing of nociceptive information in CRPS. The correlation of pain relief and decrease in cortical activity in cS1 and S2 is in accordance with the expected impact of the NMDA-receptor antagonist on cerebral pain processing with emphasis on sensory-discriminative aspects of pain.
SemEval-2010 Task 1: Coreference Resolution in Multiple Languages
2010-07-15

This paper presents the SemEval-2010 task on Coreference Resolution in Multiple Languages. The goal was to evaluate and compare automatic coreference resolution systems for six different languages (Catalan, Dutch, English, German, Italian, and Spanish) in four evaluation settings and using four different metrics. Such a rich scenario had the potential to provide insight into key issues concerning coreference resolution: (i) the portability of systems across languages, (ii) the relevance of different levels of linguistic information, and (iii) the behavior of scoring metrics. 1
Repeated Reading of Syllables Among Finnish-Speaking Children With Poor Reading Skills
2010-07-15

Abstract The study evaluated the effect of repeated reading on reading speed among 36 Finnish-speaking poor readers in Grades 4 to 6. A switching replications design was applied: Group A (n = 20) received training first, and during this period Group B (n = 16) acted as a control group. After a midpoint test, the design was switched. The training material consisted of syllables, which were practiced during 10 training sessions for a total of 50 times. The reading speed of the trained syllables increased more during training than during the control period. During training, the reading speed of pseudowords containing the trained syllables improved significantly. This improvement was found both in a computer task and in a list-reading task, which had a lower congruency with the training method than the computer task. Finally, training did not induce changes in a control (text reading) task that assessed general reading speed. Notes 1One child had a reading speed above the 10th percentile; however, he was included in the participant group as his performance was low (< 25th percentile) and the teacher reported that he had reading problems in a regular classroom situation. a n = 20. b n = 16.
Epidemiology of parasitic co-infections during pregnancy in Lambaréné, Gabon
2010-07-15

This study shows a high burden of parasitic infections with substantial degree of parasitic co-infections in pregnant women in a Central African region. This may have implications for immunological studies and operational research involving pregnant women.
BART: A Multilingual Anaphora Resolution System
2010-07-15

BART (Versley et al., 2008) is a highly modular toolkit for coreference resolution that supports state-of-the-art statistical approaches and enables efficient feature engineering. For the SemEval task 1 on Coreference Resolution, BART runs have been submitted for German, English, and Italian. BART relies on a maximum entropy-based classifier for pairs of mentions. A novel entitymention approach based on Semantic Trees is at the moment only supported for English. 1
Targeting glutathione by dimethylfumarate protects against experimental malaria by enhancing erythrocyte cell membrane scrambling
2010-07-15

The balance between GSH-levels and oxidative stress is critical for cell survival. The GSH-levels of erythrocytes are dramatically decreased during infection with Plasmodium spp. We therefore investigated the consequences of targeting GSH for erythrocyte and Plasmodium survival in vitro and in vivo using dimethylfumarate (DMF) at therapeutically established dosage. We first show that noninfected red blood cells (RBC) exposed to DMF undergo changes typical of apoptosis or eryptosis, such as cell shrinkage and cell membrane scrambling with subsequent phosphatidylserine (PS) exposure. DMF did not induce appreciable hemolysis. DMF-triggered PS exposure was mediated by intracellular GSH depletion and reversed by the antioxidative N-acetyl-l-cysteine. DMF treatment controlled intraerythrocyte DNA amplification and in vitro parasitemia of Plasmodium falciparum -infected RBC. In vivo, DMF treatment had no effect on RBC count or GSH levels in noninfected mice. Consistent with its effects on infected RBC, DMF treatment abrogated parasitemia and enhanced the survival of mice infected with Plasmodium berghei from 0% to 60%. In conclusion, DMF sensitizes the erythrocytes to the effect of Plasmodium infection on PS exposure, thus accelerating the clearance of infected erythrocytes. Accordingly, DMF treatment favorably influences the clinical course of malaria. As DMF targets mechanisms within the host cell, it is not likely to generate resistance of the pathogen.
Interaction of the Papillomavirus E8∧E2C Protein with the Cellular CHD6 Protein Contributes to Transcriptional Repression
2010-07-15

ABSTRACT Expression of the E6 and E7 oncogenes of high-risk human papillomaviruses (HPV) is controlled by cellular transcription factors and by viral E2 and E8∧E2C proteins, which are both derived from the HPV E2 gene. Both proteins bind to and repress the HPV E6/E7 promoter. Promoter inhibition has been suggested to be due to binding site competition with cellular transcription factors and to interactions of different cellular transcription modulators with the different amino termini of E2 and E8∧E2C. We have now identified the cellular chromodomain helicase DNA binding domain 6 protein (CHD6) as a novel interactor with HPV31 E8∧E2C by using yeast two-hybrid screening. Pull-down and coimmunoprecipitation assays indicate that CHD6 interacts with the HPV31 E8∧E2C protein via the E2C domain. This interaction is conserved, as it occurs also with the E8∧E2C proteins expressed by HPV16 and -18 and with the HPV31 E2 protein. Both RNA knockdown experiments and mutational analyses of the E2C domain suggest that binding of CHD6 to E8∧E2C contributes to the transcriptional repression of the HPV E6/E7 oncogene promoter. We provide evidence that CHD6 is also involved in transcriptional repression but not activation by E2. Taken together our results indicate that the E2C domain not only mediates specific DNA binding but also has an additional role in transcriptional repression by recruitment of the CHD6 protein. This suggests that repression of the E6/E7 promoter by E2 and E8∧E2C involves multiple interactions with host cell proteins through different protein domains.
Evolvability of between-year seed dormancy in populations along an aridity gradient
2010-07-15

Under global climate change, adaptation to new conditions is crucial for plant species persistence. This requires the ability to evolve in traits that are correlated with changing climatic variables. We studied between-year seed dormancy, which correlates with environmental variability, and tested for clinal trends in its evolvability along an aridity gradient in Israel. We conducted a germination experiment under five irrigation levels with two dryland winter annuals (Biscutella didyma, Bromus fasciculatus) from four sites along the gradient. Species differed in means and evolvability of dormancy. Biscutella had high dormancy, which significantly increased with aridity but decreased with higher irrigation. In Bromus, dormancy was low, similar among populations, and only marginally affected by irrigation. Evolvability in Biscutella was high and varied among populations, without a clinal trend along the gradient. Conversely, in Bromus, trait evolvability was low and declined with increasing aridity. We argue that changes in evolvability along climatic gradients depend on the relative intensity of stabilizing selection. This may be high in Bromus and not only depends on environmental stress, but also on variability. Our findings point to the importance of measuring evolvability of climate-related traits across different natural and artificial environments and for many coexisting species.
Attack or call for help? Rapid individual decisions in a group-hunting ant
2010-07-15

Adaptive decision making is an important trait of many animals, especially in the context of foraging. Social animals are able to optimize their foraging behavior individually or on a collective level. In the predatory ant Leptogenys diminuta, scout ants search individually for prey and then decide within seconds whether to attack directly or to recruit a large raiding group for a collective attack. Both strategies have inherent costs and benefits, and the information collected by the scout during prey assessment is crucial for an appropriate reaction. We studied how differences in prey type and size are taken into account by experienced and inexperienced scout ants. Although decisions are made under time pressure and frequently without disturbing the prey, experienced scouts adjusted their raiding strategies in accordance with predicted hypotheses. In contrast, inexperienced scouts preferred a risk-averse strategy by recruiting large raiding groups. After a 4-week learning phase, inexperienced scouts developed raiding strategies equal to experienced scouts, independent of hunting success treatments, suggesting a predetermined behavioral repertoire. Using gas chromatography and mass spectrometry, we studied furthermore whether prey items could be discriminated by chemical cues. Natural prey was distinguishable on a high taxonomic level. In raids on chemically treated dummies, however, responses were not equal to those elicited by real prey. Thus, the ants probably integrate additional information, such as visual or tactile cues, into their decision-making process. Overall, L. diminuta exhibits a remarkably cautious, quick, and adaptive decision-making system in which prey cuticular chemicals are incorporated as informational cues. Copyright 2010, Oxford University Press.
Chunking German: An Unsolved Problem
2010-07-15

uni-tuebingen.de This paper describes a CoNLL-style chunk representation for the Tübingen Treebank of Written German, which assumes a flat chunk structure so that each word belongs to at most one chunk. For German, such a chunk definition causes problems in cases of complex prenominal modification. We introduce a flat annotation that can handle these structures via a stranded noun chunk. 1
Bateman Gradients in Hermaphrodites: An Extended Approach to Quantify Sexual Selection
2010-07-16

Sexual selection is often quantified using Bateman gradients, which represent sex-specific regression slopes of reproductive success on mating success and thus describe the expected fitness returns from mating more often. Although the analytical framework for Bateman gradients aimed at covering all sexual systems, empirical studies are biased toward separate-sex organisms, probably because important characteristics of other systems remain incompletely treated. Our synthesis complements the existing Bateman gradient approach with three essential reproductive features of simultaneous hermaphrodites. First, mating in one sex may affect fitness via the opposite sex, for example, through energetic trade-offs. We integrate cross-sex selection effects and show how they help characterizing sexually mutualistic versus antagonistic selection. Second, male and female mating successes may be correlated, complicating the interpretation of Bateman gradients. We show how to quantify the impact of this correlation on sexual selection and propose a principal component analysis on male and female mating success to facilitate interpretation. Third, self-fertilization is accounted for by adding selfed progeny as a separate category of reproductive success to analyses of Bateman gradients. Finally, using a worked example from the snail Biomphalaria glabrata, we illustrate how the extended analytical framework can enhance our understanding of sexual selection in hermaphroditic animals and plants.