julilili42/papers huggingface dataset:
A computational model for measuring discourse complexity
2019-08-02

In past studies, the few quantitative approaches to discourse structure were mostly confined to the presentation of the frequency of discourse relations. However, quantitative approaches should take into account both hierarchical and relational layers in the discourse structure. This study considers these factors and addresses the issue of how discourse relations and discourse units are related. It draws upon the available corpora of discourse structure (rhetorical structure theory-discourse treebank (RST-DT)) from a new perspective. Since an RST tree can be converted into a syntactic dependency tree, the data extracted from the RST-DT can be useful for calculating the discourse distance in much the same way as syntactic dependency distance is calculated. Discourse distance is also applicable to measuring the depth of the human processing of discourse. Furthermore, the data derived from the RST-DT are also easily converted into network data. This study finds that discourse structure has its discourse distance minimum and each type of RST relations has its range of discourse distance. The frequency distribution of discourse data basically follows the power law on several levels, while a network approach reveals how discourse units are arranged spatially in regular patterns. The two methods are mutually complementary in revealing the interaction between discourse relations and discourse units in a comprehensive manner, as well as in revealing how people process and comprehend discourse dynamically. Accordingly, we propose merging the two methods so as to yield a computational model for assessing discourse complexity and comprehension.
No Word is an Island—A Transformation Weighting Model for Semantic Composition
2019-08-02

Composition models of distributional semantics are used to construct phrase representations from the representations of their words. Composition models are typically situated on two ends of a spectrum. They either have a small number of parameters but compose all phrases in the same way, or they perform word-specific compositions at the cost of a far larger number of parameters. In this paper we propose transformation weighting (TransWeight), a composition model that consistently outperforms existing models on nominal compounds, adjective-noun phrases, and adverb-adjective phrases in English, German, and Dutch. TransWeight drastically reduces the number of parameters needed compared with the best model in the literature by composing similar words in the same way.
The Kids Obesity Prevention Program: Cluster Randomized Controlled Trial to Evaluate a Serious Game for the Prevention and Treatment of Childhood Obesity (Preprint)
2019-08-02

<sec> <title>BACKGROUND</title> Health games provide opportunities for the treatment and prevention of childhood obesity. We developed a motion-controlled serious game for children that addresses 3 core topics of nutrition, physical activity, and stress coping. It is the first serious game that extensively targets the dietary energy density principle (DED-P) in relation to nutrition. The game is intended to provide an additional educational component for the prevention and treatment of obesity in children. </sec> <sec> <title>OBJECTIVE</title> The Kids Obesity Prevention study aimed to evaluate the newly developed game and to evaluate how well children are able to understand and apply the DED-P. </sec> <sec> <title>METHODS</title> This cluster randomized controlled trial collected data from 82 primary school children aged 9 to 12 years and their parents at baseline (T0), at 2 weeks after study commencement (T1), and at the 4-week follow-up (T2). The dropout rate was 3.6%. The intervention group (IG) played the game within 2 weeks (2 sessions with different game modules). One part of the game involves selection of food with the lower energy density when presented with a pair of foods. This allows assessment of whether the children have understood the DED-P and whether they can apply it to unknown foods under time pressure. The control group (CG) received a brochure about the food pyramid concept and physical activity. The primary outcome was the gain in knowledge (nutrition and stress coping) and measured with a pretested questionnaire. The secondary outcomes were the maintenance of knowledge, application of the DED-P, feelings during game play, game acceptance, and behavioral measures (physical activity, media consumption, and dietary intake). </sec> <sec> <title>RESULTS</title> The knowledge score ranging from 0 to 100 increased from T0 (IG: 53 [SD 10], CG: 50 [SD 11]) to T1 (IG: 69 [SD 11], CG: 52 [SD 12]) in IG versus CG (&lt;i&gt;P&lt;/i&gt;&amp;lt;.001). At T2, the knowledge score of IG remained at the same level as that of T1. Game data showed that after DED-P education, the classification under time pressure of unknown versus known food pairs according to their DED category was similar (hit rate around 70%). Overall, 95% of the children liked the game very much or much. No group changes were observed at the behavioral level. </sec> <sec> <title>CONCLUSIONS</title> The Kids Obesity Prevention program sustainably increased knowledge in the areas of nutrition and stress coping, and children were able to apply the DED-P. </sec> <sec> <title>CLINICALTRIAL</title> ClinicalTrials.gov NCT02551978; https://clinicaltrials.gov/ct2/show/NCT02551978 </sec>
Impact of C-reactive protein on osteo-/chondrogenic transdifferentiation and calcification of vascular smooth muscle cells
2019-08-03

Medial vascular calcification occurs during the aging process and is strongly accelerated by chronic kidney disease (CKD). Elevated C-reactive protein (CRP) levels are associated with vascular calcification, cardiovascular events and mortality in CKD patients. CRP is an important promoter of vascular inflammation. Inflammatory processes are critically involved in initiation and progression of vascular calcification. Thus, the present study explored a possible impact of CRP on vascular calcification. We found that CRP promoted osteo-/chondrogenic transdifferentiation and aggravated phosphate-induced osteo-/chondrogenic transdifferentiation and calcification of primary human aortic smooth muscle cells (HAoSMCs). These effects were paralleled by increased cellular oxidative stress and corresponding pro-calcific downstream-signaling. Antioxidants or p38 MAPK inhibition suppressed CRP-induced osteo-/chondrogenic signaling and mineralization. Furthermore, silencing of Fc fragment of IgG receptor IIa (FCGR2A) blunted the pro-calcific effects of CRP. Vascular CRP expression was increased in the klotho-hypomorphic mouse model of aging as well as in HAoSMCs during calcifying conditions. In conclusion, CRP augments osteo-/chondrogenic transdifferentiation of vascular smooth muscle cells through mechanisms involving FCGR2A-dependent induction of oxidative stress. Thus, systemic inflammation may actively contribute to the progression of vascular calcification.
Identification of the Secreted Proteins Originated from Primary Human Hepatocytes and HepG2 Cells
2019-08-03

The liver plays a pivotal role in whole-body carbohydrate, lipid, and protein metabolism. One of the key regulators of glucose and lipid metabolism are hepatokines, which are found among the liver secreted proteins, defined as liver secretome. To elucidate the composition of the human liver secretome and identify hepatokines in primary human hepatocytes (PHH), we conducted comprehensive protein profiling on conditioned medium (CM) of PHH. Secretome profiling using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS) identified 691 potential hepatokines in PHH. Subsequently, pathway analysis assigned these proteins to acute phase response, coagulation, and complement system pathways. The secretome of PHH was compared to the secreted proteins of the liver hepatoma cell line HepG2. Although the secretome of PHH and HepG2 cells show a high overlap, the HepG2 secretome rather mirrors the fetal liver with some cancer characteristics. Collectively, our study represents one of the most comprehensive secretome profiling approaches for PHH, allowing new insights into the composition of the secretome derived from primary human material, and points out strength and weakness of using HepG2 cell secretome as a model for the analysis of the human liver secretome.
Representation of uncertainty in macaque visual cortex
2019-08-03

Uncertainty is intrinsic to perception. Neural circuits which process sensory information must therefore also represent the reliability of this information. How they do so is a topic of debate. We propose a view of visual cortex in which average neural response strength encodes stimulus features, while cross-neuron variability in response gain encodes the uncertainty of these features. To test our theory, we studied spiking activity of neurons in macaque V1 and V2 elicited by repeated presentations of stimuli whose uncertainty was manipulated in distinct ways. We show that gain variability of individual neurons is tuned to stimulus uncertainty, that this tuning is invariant to the source of uncertainty, and that it is specific to the features encoded by these neurons. We demonstrate that this behavior naturally arises from known gain-control mechanisms, and derive how downstream circuits can jointly decode stimulus features and their uncertainty from sensory population activity.
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
2019-08-05

Abstract We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent “core” of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s cities.
The results of biodiversity-ecosystem functioning experiments are realistic
2019-08-05

Summary A large body of research shows that biodiversity loss can reduce ecosystem functioning, thus providing support for the conservation of biological diversity 1–4 . Much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments (hereafter: biodiversity experiments), in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured 5–9 . This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly may often be non-random and influenced by external drivers, such as climate or land-use intensification 10–18 . Despite these repeated criticisms, there has been no comprehensive, quantitative assessment of how experimental and real-world plant communities really differ, and whether these differences invalidate the experimental results. Here, we compare data from two of the largest and longest-running grassland biodiversity experiments globally (Jena Experiment, Germany; BioDIV, USA) to related real-world grassland plant communities in terms of their taxonomic, functional, and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments have greater variance in these compositional features than their real-world counterparts, covering almost all of the variation of the real-world communities (82-96%) while also containing community types that are not currently observed in the real world. We then re-analysed a subset of experimental data that included only ecologically-realistic communities, i.e. those comparable to real-world communities. For ten out of twelve biodiversity-ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically-realistic subset of experimental communities. This demonstrates that the results of biodiversity experiments are largely insensitive to the inclusion/exclusion of unrealistic communities. By bridging the gap between experimental and real-world studies, these results demonstrate the validity of inferences from biodiversity experiments, a key step in translating their results into specific recommendations for real-world biodiversity management.
Motives, experiences and psychological strain in medical students engaged in refugee care in a reception center– a mixed-methods approach
2019-08-05

A rather small proportion of the medical students working in the reception center displayed explicit symptoms of psychological strain in terms of secondary traumatic stress. Due to their assignments, students were able to improve their cultural awareness, which they reported to be highly relevant for their future occupation. In view of increasing globalization, theoretical and practical courses on issues of flight and global health might therefore be implemented as an obligatory part of medical curricula.
Computing Tropical Varieties Over Fields with Valuation
2019-08-05

We show how the tropical variety of an ideal over a field K with non-trivial discrete valuation can always be traced back to the tropical variety of an ideal over some dense subring R in its ring of integers. We show that this connection is compatible with the Gröbner polyhedra covering them. Combined with previous works, we thus obtain a framework for computing tropical varieties over general fields with valuations, which relies on the existing theory of standard bases if is generated by elements in .
On the processing of nonwords in word naming and auditory lexical decision
2019-08-05

&lt;p&gt;Nonwords are often used to clarify how lexical pro- cessing takes place in the absence of semantics. This study shows that nonwords are not semantically vac- uous. We used Linear Discriminative Learning [2] to estimate the meanings of nonwords in the MALD database [14] from the speech signal. We show that measures gauging nonword semantics significantly improve model fit for both acoustic durations and RTs. Although nonwords do not evoke meanings that afford conscious reflexion, they do make con- tact with the semantic space, and the angles and dis- tances of nonwords with respect to actual words co- determine articulation and lexicality decisions.&lt;/p&gt;
The ADEP Biosynthetic Gene Cluster in Streptomyces hawaiiensis NRRL 15010 Reveals an Accessory clpP Gene as a Novel Antibiotic Resistance Factor
2019-08-06

Antibiotic acyldepsipeptides (ADEPs) represent a promising new class of potent antibiotics and, at the same time, are valuable tools to study the molecular functioning of their target, ClpP, the proteolytic core of the bacterial caseinolytic protease. Here, we present a straightforward purification procedure for ADEP1 that yields substantial amounts of the pure compound in a time- and cost-efficient manner, which is a prerequisite to conveniently study the antimicrobial effects of ADEP and the operating mode of bacterial ClpP machineries in diverse bacteria. Identification and characterization of the ADEP biosynthetic gene cluster in Streptomyces hawaiiensis NRRL 15010 enables future bioinformatics screenings for similar gene clusters and/or subclusters to find novel natural compounds with specific substructures. Most strikingly, we identified a cluster-associated clpP homolog (named clpP ADEP ) as an ADEP resistance gene. ClpP ADEP constitutes a novel bacterial resistance factor that alone is necessary and sufficient to confer high-level ADEP resistance to Streptomyces across species.
Activated gp130 signaling selectively targets B cell differentiation to induce mature lymphoma and plasmacytoma
2019-08-07

Aberrant activity of the glycoprotein 130 130/JAK/STAT3 (gp130/JAK/STAT3) signaling axis is a recurrent event in inflammation and cancer. In particular, it is associated with a wide range of hematological malignancies, including multiple myeloma and leukemia. Novel targeted therapies have only been successful for some subtypes of these malignancies, underlining the need for developing robust mouse models to better dissect the role of this pathway in specific tumorigenic processes. Here, we investigated the role of selective gp130/JAK/STAT3 activation by generating a conditional mouse model. This model targeted constitutively active, cell-autonomous gp130 activity to B cells, as well as to the entire hematopoietic system. We found that regardless of the timing of activation in B cells, constitutively active gp130 signaling resulted in the formation specifically of mature B cell lymphomas and plasma cell disorders with full penetrance, only with different latencies, where infiltrating CD138+ cells were a dominant feature in every tumor. Furthermore, constitutively active gp130 signaling in all adult hematopoietic cells also led to the development specifically of largely mature, aggressive B cell cancers, again with a high penetrance of CD138+ tumors. Importantly, gp130 activity abrogated the differentiation block induced by a B cell-targeted Myc transgene and resulted in a complete penetrance of the gp130-associated, CD138+, mature B cell lymphoma phenotype. Thus, gp130 signaling selectively provides a strong growth and differentiation advantage for mature B cells and directs lymphomagenesis specifically toward terminally differentiated B cell cancers.
A Minority pulls the sample mean: on the individual prevalence of robust group-level cognitive phenomena – the instance of the SNARC effect
2019-08-07

The aim of cognitive psychology is to obtain insights into human cognition in general. For this purpose, group-studies are typically conducted on representative samples, such that the results can be generalized to the population. Within this approach, individual differences are typically neglected or considered to be error variance. Little is known about the prevalence of group-level phenomena at the individual level. Such information is nevertheless important for claims about the universality of phenomena, as, in theory, significant effects at the group-level can be driven by a minority of participants. Here we used a uniform analysis of 18 existing data sets revealing a well-replicated phenomenon in numerical cognition at the group level, the so-called SNARC (Spatial-Numerical Association of Response Codes) effect, to investigate its prevalence at the individual level. Three methods of analyzing the presence of this effect at the individual level were utilized: one psychometric and two bootstrapping methods. The results suggest that the group-level SNARC effect is driven by a minority of individuals (≤ 45%). Our findings are pertinent to an important theoretical question: whether group-level effects are reflecting general principles of cognition. We discuss advantages and drawbacks of the present methods and their utility in investigating the prevalence of other cognitive phenomena. We posit that testing the presence of robust group-level cognitive effects at the individual level, as well as ensuring their reliable measurement, is an important step towards integrating two traditionally separate experimental and correlational approaches of scientific psychology, as previously proposed by Cronbach in the 1950s.
Where do regional influences matter? The impact of socio-spatial indicators on transitions from secondary school to university
2019-08-07

The paper at hand concentrates on how regional indicators influence school graduates’ transitions to university in and outside their home region. Our paper contributes to the literature in three ways: We include not only study opportunities in the region but focus on three distinct regional factors; namely, the economic situation, the university orientation as well as study opportunities. Furthermore, we quantify the spatial radius in which the three regional indicators affect individuals’ transition to university. Beyond that, the analyses cover a period of 26 years to infer on developments in the relevance of regional factors over time. To do so, geographic information on regions is used and aggregated within travel-time radii. The data is linked to panel data from the German National Educational Panel Study (NEPS). Our findings indicate that, school graduates’ chances to enter university depend on labor-market conditions as well as on university infrastructure. We find that spatial radius matters; significant regional associations can only be observed up to radii of 60-minutes of travel time. Regional influences on the chance to enter university and the place of study increase over time.
Synthesis and Photodimerization of 2- and 2,3-Disubstituted Anthracenes: Influence of Steric Interactions and London Dispersion on Diastereoselectivity
2019-08-07

There is increased evidence that the effect of bulky groups in organic, organometallic, and inorganic chemistry is not only repulsive but can be attractive because of London dispersion interactions. The influence of the size of primary alkyl substituents in 2- and 2,3-positions of anthracenes on the diastereoselectivity (anti vs syn dimer) of the [π<sub>4s</sub> + π<sub>4s</sub>] photoinduced dimerization is investigated. The synthesis of the anthracene derivatives was achieved by Suzuki-Miyaura reaction of 2,3-dibromoanthracene with alkylboronic acids as well as by reduction of anthraquinones that were obtained from 2,3-disubstituted 1,3-butadienes and naphthoquinone followed by dehydrogenation. The mixtures of dianthracene isomers were analyzed with respect to the anti/syn-ratio of the products by X-ray crystallography and nuclear Overhauser effect spectroscopy. While for the 2,3-dimethylanthracene the anti and syn isomers were formed in equal amounts, the anti dimers are the major products in all other cases. A linear correlation (<i>R</i><sup>2</sup> = 0.98) between the steric size (Charton parameter) and the isomeric ratio suggests that the selectivity is dominated by classical repulsive steric effects. An exception is the iso-butyl substituent that produces an increased amount of the syn isomer. It is suggested that this is due to an exalted effect of London dispersion interactions.