julilili42/papers huggingface dataset:
Black holes, gravitational waves and fundamental physics: a roadmap
2019-06-20

The grand challenges of contemporary fundamental physics—dark matter, dark energy, vacuum energy, inflation and early universe cosmology, singularities and the hierarchy problem—all involve gravity as a key component. And of all gravitational phenomena, black holes stand out in their elegant simplicity, while harbouring some of the most remarkable predictions of General Relativity: event horizons, singularities and ergoregions.&#13;\\n&#13;\\nThe hitherto invisible landscape of the gravitational Universe is being unveiled before our eyes: the historical direct detection of gravitational waves by the LIGO-Virgo collaboration marks the dawn of a new era of scientific exploration. Gravitational-wave astronomy will allow us to test models of black hole formation, growth and evolution, as well as models of gravitational-wave generation and propagation. It will provide evidence for event horizons and ergoregions, test the theory of General Relativity itself, and may reveal the existence of new fundamental fields. The synthesis of these results has the potential to radically reshape our understanding of the cosmos and of the laws of Nature.&#13;\\n&#13;\\nThe purpose of this work is to present a concise, yet comprehensive overview of the state of the art in the relevant fields of research, summarize important open problems, and lay out a roadmap for future progress. This write-up is an initiative taken within the framework of the European Action on 'Black holes, Gravitational waves and Fundamental Physics'.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
2019-06-20

Abstract Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The S ystems B iology M arkup L anguage (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core . The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1 . This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/ .
Arginine dephosphorylation propels spore germination in bacteria
2019-06-20

Significance Dormant bacterial spores can survive long periods of time, withstanding extreme conditions, but can rapidly resume a vegetative life form once nutrients become accessible. The key event of this revival process is termed germination, the earliest phase, lasting only for a few minutes, during which cellular awakening is established. Yet, the molecular events propelling this enigmatic phase remain unknown. Here, we revealed that dephosphorylation of Arg residues on key target proteins triggers germination in the model bacterium B. subtilis . We further demonstrate that Arg dephosphorylation of a ribosome-associated factor reactivates translation, whereas dephosphorylation of the major housekeeping σ factor reinitiates transcription. Our results provide a whole mechanism for spore awakening in bacteria.
The Conscientiousness × Interest Compensation (CONIC) model: Generalizability across domains, outcomes, and predictors.
2019-06-20

Conscientiousness and interest are well-known predictors of academic effort and achievement. As hypothesized by the Conscientiousness × Interest Compensation (CONIC) model, conscientiousness and interest can (partly) compensate for each other, leading to (comparatively) high effort if either conscientiousness or interest is high. The present research (a) provides a test of this prediction across four school subjects, (b) examines whether the compensatory interaction can also be found when academic achievement is the outcome instead of academic effort, and (c) probes for the compensatory interaction when interest is replaced by utility value as a predictor variable. A total of 830 students in Grades 5 to 12 participated in this study. We assessed their conscientiousness and measured task value beliefs, academic effort, and achievement in 4 school subjects (German, English, mathematics, and biology). The predictions of the CONIC model were supported in all 4 subjects. In addition, we found compensatory interactions between conscientiousness and interest in predicting both academic effort and achievement. Furthermore, we observed similar compensatory interactions between conscientiousness and utility value. In sum, the results suggest a broader applicability of the CONIC model than originally proposed. (PsycINFO Database Record (c) 2020 APA, all rights reserved)
Metabolomics in serum of patients with non-advanced age-related macular degeneration reveals aberrations in the glutamine pathway
2019-06-20

Age-related macular degeneration (AMD) is a common, progressive multifactorial vision-threatening disease and many genetic and environmental risk factors have been identified. The risk of AMD is influenced by lifestyle and diet, which may be reflected by an altered metabolic profile. Therefore, measurements of metabolites could identify biomarkers for AMD, and could aid in identifying high-risk individuals. Hypothesis-free technologies such as metabolomics have a great potential to uncover biomarkers or pathways that contribute to disease pathophysiology. To date, only a limited number of metabolomic studies have been performed in AMD. Here, we aim to contribute to the discovery of novel biomarkers and metabolic pathways for AMD using a targeted metabolomics approach of 188 metabolites. This study focuses on non-advanced AMD, since there is a need for biomarkers for the early stages of disease before severe visual loss has occurred. Targeted metabolomics was performed in 72 patients with early or intermediate AMD and 72 control individuals, and metabolites predictive for AMD were identified by a sparse partial least squares discriminant analysis. In our cohort, we identified four metabolite variables that were most predictive for early and intermediate stages of AMD. Increased glutamine and phosphatidylcholine diacyl C28:1 levels were detected in non-advanced AMD cases compared to controls, while the rate of glutaminolysis and the glutamine to glutamate ratio were reduced in non-advanced AMD. The association of glutamine with non-advanced AMD corroborates a recent report demonstrating an elevated glutamine level in early AMD using a different metabolomics technique. In conclusion, this study indicates that metabolomics is a suitable method for the discovery of biomarker candidates for AMD. In the future, larger metabolomics studies could add to the discovery of novel biomarkers in yet unknown AMD pathways and expand our insights in AMD pathophysiology.
Distinguishing Between Biological and Technical Replicates in Hypertension Research on Isolated Arteries
2019-06-20

Perivascular adipose tissue (PVAT) is implicated in the pathophysiology of cardiovascular disease, especially in obese individuals in which the quantity of renal and visceral PVAT is markedly increased. The control of arterial tone by PVAT has emerged as a relatively new field of experimental hypertension research. The discovery of this prototype of vasoregulation has been mostly inferred from data obtained using wire myography. Currently, there is a major discussion on distinguishing between biological vs. technical replicates in biomedical studies, which resulted in numerous guidelines being published on planning studies and publishing data by societies, journals, and associations. Experimental study designs are determined depending on how the experimentator distinguishes between biological vs. technical replicates. These definitions determine the ultimate standards required for making submissions to certain journals. In this article, we examine possible outcomes of different experimental study designs on PVAT control of arterial tone using isolated arteries. Based on experimental data, we determine the sample size and power of statistical analyses for such experiments. We discuss whether n-values should correspond to the number of arterial rings and analyze the resulting effects if those numbers are averaged to provide a single N-value per animal, or whether the hierarchical statistical method represents an alternative for analyzing such kind of data. Our analyses show that that the data (logEC50) from (+) PVAT to (–) PVAT arteries are clustered. Intraclass correlation (ICC) was 31.4%. Moreover, it appeared that the hierarchical approach was better than regular statistical tests as the analyses revealed by a better goodness of fit (v2-2LL test). Based on our results, we propose to use at least three independent arterial rings from each from three animals or at least seven arterial rings from each from two animals for each group, i.e., (+) PVAT vs. (–) PVAT. Finally, we discuss a clinical situation where distinguishing between biological vs. technical replicates can lead to absurd situations in clinical decision makings. We conclude that discrimination between biological vs. technical replicates is helpful in experimental studies but is difficult to implement in everyday’s clinical practice.
Media, fake news, and debunking
2019-06-20

We construct a modified Hotelling‐type model of two media providers, each of whom can issue fake and/or real news and each of whom can invest in the debunking of their rival’s fake news. The model assumes that consumers have an innate preference for one provider or the other and value real news. However, that valuation varies according to their bias favouring one provider or the other. We demonstrate a unique subgame perfect Nash equilibrium in which only one firm issues fake news and we show, in this setting, that increased polarisation of consumers (represented by a wider distribution) increases the prevalence of both fake news and debunking expenditures and is welfare‐reducing. We also show, inter alia , that a stronger preference by consumers for their preferred provider lowers both fake news and debunking. Finally, we compare monopoly and duopoly market structures in terms of ‘fake news’ provision and show that a public news provider can be welfare‐improving.
Planar graphs of bounded degree have bounded queue number
2019-06-20

A queue layout of a graph consists of a linear order of its vertices and a partition of its edges into queues, so that no two independent edges of the same queue are nested. The queue number of a graph is the minimum number of queues required by any of its queue layouts. A long-standing conjecture by Heath, Leighton and Rosenberg states that the queue number of planar graphs is bounded.This conjecture has been partially settled in the positive for several sub- families of planar graphs (most of which have bounded treewidth).
The Retinal Basis of Vertebrate Color Vision
2019-06-21

The jawless fish that were ancestral to all living vertebrates had four spectral cone types that were probably served by chromatic-opponent retinal circuits. Subsequent evolution of photoreceptor spectral sensitivities is documented for many vertebrate lineages, giving insight into the ecological adaptation of color vision. Beyond the photoreceptors, retinal color processing is best understood in mammals, especially the blue ON system, which opposes short- against long-wavelength receptor responses. For other vertebrates that often have three or four types of cone pigment, new findings from zebrafish are extending older work on teleost fish and reptiles to reveal rich color circuitry. Here, horizontal cells establish diverse and complex spectral responses even in photoreceptor outputs. Cone-selective connections to bipolar cells then set up color-opponent synaptic layers in the inner retina, which lead to a large variety of color-opponent channels for transmission to the brain via retinal ganglion cells.
Pedogenic and microbial interrelation in initial soils under semiarid climate on James Ross Island, Antarctic Peninsula region
2019-06-21

Abstract. James Ross Island (JRI) offers the exceptional opportunity to study microbial-driven pedogenesis without the influence of vascular plants or faunal activities (e.g., penguin rookeries). In this study, two soil profiles from JRI (one at Santa Martha Cove – SMC, and another at Brandy Bay – BB) were investigated, in order to gain information about the initial state of soil formation and its interplay with prokaryotic activity, by combining pedological, geochemical and microbiological methods. The soil profiles are similar with respect to topographic position and parent material but are spatially separated by an orographic barrier and therefore represent windward and leeward locations towards the mainly southwesterly winds. These different positions result in differences in electric conductivity of the soils caused by additional input of bases by sea spray at the windward site and opposing trends in the depth functions of soil pH and electric conductivity. Both soils are classified as Cryosols, dominated by bacterial taxa such as Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes and Chloroflexi. A shift in the dominant taxa was observed below 20 cm in both soils as well as an increased abundance of multiple operational taxonomic units (OTUs) related to potential chemolithoautotrophic Acidiferrobacteraceae. This shift is coupled by a change in microstructure. While single/pellicular grain microstructure (SMC) and platy microstructure (BB) are dominant above 20 cm, lenticular microstructure is dominant below 20 cm in both soils. The change in microstructure is caused by frequent freeze–thaw cycles and a relative high water content, and it goes along with a development of the pore spacing and is accompanied by a change in nutrient content. Multivariate statistics revealed the influence of soil parameters such as chloride, sulfate, calcium and organic carbon contents, grain size distribution and pedogenic oxide ratios on the overall microbial community structure and explained 49.9 % of its variation. The correlation of the pedogenic oxide ratios with the compositional distribution of microorganisms as well as the relative abundance certain microorganisms such as potentially chemolithotrophic Acidiferrobacteraceae-related OTUs could hint at an interplay between soil-forming processes and microorganisms.
The YIN and YANG of lipoproteins in developing and preventing infectious arthritis by Staphylococcus aureus
2019-06-21

Rapid bone destruction often leads to permanent joint dysfunction in patients with septic arthritis, which is mainly caused by Staphylococcus aureus (S. aureus). Staphylococcal cell wall components are known to induce joint inflammation and bone destruction. Here, we show that a single intra-articular injection of S. aureus lipoproteins (Lpps) into mouse knee joints induced chronic destructive macroscopic arthritis through TLR2. Arthritis was characterized by rapid infiltration of neutrophils and monocytes. The arthritogenic effect was mediated mainly by macrophages/monocytes and partially via TNF-α but not by neutrophils. Surprisingly, a S. aureus mutant lacking Lpp diacylglyceryl transferase (lgt) caused more severe joint inflammation, which coincided with higher bacterial loads of the lgt mutant in local joints than those of its parental strain. Coinjection of pathogenic S. aureus LS-1 with staphylococcal Lpps into mouse knee joints caused improved bacterial elimination and diminished bone erosion. The protective effect of the Lpps was mediated by their lipid moiety and was fully dependent on TLR2 and neutrophils. The blocking of CXCR2 on neutrophils resulted in total abrogation of the protective effect of the Lpps. Our data demonstrate that S. aureus Lpps elicit innate immune responses, resulting in a double-edged effect. On the one hand, staphylococcal Lpps boost septic arthritis. On the other hand, Lpps act as adjuvants and activate innate immunity, which could be useful for combating infections with multiple drug-resistant strains.
Gender and Outcomes following Guided De-Escalation of Antiplatelet Treatment in Acute Coronary Syndrome Patients: The TROPICAL-ACS Gender Substudy
2019-06-21

Objectives This prespecified analysis of the TROPICAL-ACS trial aimed to assess the impact of gender on clinical outcomes and platelet reactivity (PR) following guided de-escalation of dual antiplatelet treatment (DAPT) in acute coronary syndrome (ACS) patients. Background Guided de-escalation of DAPT was recently identified as an effective alternative treatment strategy in ACS. Methods We used Cox proportional hazards models and linear regression analysis to assess the interaction of gender with clinical endpoints and PR. Results In both male (n = 2,052) and female (n = 558) patients, the 1-year incidence of the primary endpoint did not differ in guided de-escalation versus control group patients (male: 7.0% vs. 9.0%; hazard ratio [HR], 0.78, 95% confidence interval [CI], 0.57–1.06, p = 0.11; female: 8.4% vs. 9.2%; HR, 0.92, 95% CI, 0.53–1.62, p = 0.76, p int = 0.60). The 1-year incidence of combined ischemic events (male: 2.5% vs. 3.3%; HR, 0.76, 95% CI, 0.46–1.26, p = 0.29; female: 2.2% vs. 2.8%; HR, 0.78,95% CI, 0.27–2.25, p = 0.65, p int = 0.96) as well as Bleeding Academic Research Consortium ≥ 2 bleeding (male: 4.6% vs. 6.0%; HR, 0.77, 95% CI, 0.52–1.12, p = 0.17; female: 6.2% vs. 6.4%; HR, 0.99, 95% CI, 0.51–1.92, p = 0.97, p int = 0.51) was similar in the guided de-escalation versus control group for both male and female patients. Interaction testing revealed no significant impact of gender on PR levels (prasugrel or clopidogrel) across treatment groups (p int = 0.72). Conclusion Guided de-escalation of DAPT appears to be equally safe and effective in women and men. Especially in patients with increased bleeding risk and independent from gender, a guided DAPT de-escalation strategy may be used as an alternative treatment strategy. Clinical Trial Registration URL: https//www.clinicaltrials.gov. Unique Identifier: NCT: 01959451.
Effects of arm weight and target height on hand selection: A low-cost virtual reality paradigm
2019-06-21

We evaluated the ability of a virtual reality (VR) system to reliably detect the reaching frequency midline position of a user; the distinguishing plane between free-choice use of the left and right hand. The paradigm utilized the Leap Motion Hand Tracker along with a custom script written in C# and was realized through a Unity3D application. Stimuli appeared in random locations on the computer screen and required the participant to reach with the hand of their choice to contact them with a virtually coupled hand inside the virtual space. We investigated the effects of two manipulations of effort on the free-choice reaching of either the left or right hand. We varied the height of target positions and applied an additional weight to the non-dominant, left hand. We observed main effects of height and weight on reaching frequency midline positions across the group. We found increased use of the dominant hand as stimuli height increased, as well as a significant increase in overall use of the dominant, right hand when a weighted-glove was worn by the non-dominant, left hand. Our results are in line with previously published research on hand selection from similar paradigms, supporting the use of our VR paradigm in future experiments and applications.
Automated Definition of Skeletal Disease Burden in Metastatic Prostate Carcinoma: A 3D Analysis of SPECT/CT Images
2019-06-21

To meet the current need for skeletal tumor-load estimation in castration-resistant prostate cancer (CRPC), we developed a novel approach based on adaptive bone segmentation. In this study, we compared the program output with existing estimates and with the radiological outcome. Seventy-six whole-body single-photon emission computed tomographies/x-ray computed tomography with 3,3-diphosphono-1,2-propanedicarboxylic acid from mCRPC patients were analyzed. The software identified the whole skeletal volume (SVol) and classified the voxels metastases (MVol) or normal bone (BVol). SVol was compared with the estimation of a commercial software. MVol was compared with manual assessment and with prostate specific antigen (PSA) levels. Counts/voxel were extracted from MVol and BVol. After six cycles of 223RaCl2-therapy every patient was re-evaluated as having progressive disease (PD), stable disease (SD), or a partial response (PR). SVol correlated with that of the commercial software (R = 0,99, p &amp;lt
Teaching English-Chinese textual translation strategies
2019-06-21

Abstract The topic-chain is a typical characteristic used to distinguish Chinese discourse from other languages, such as English. By studying how to make use of the topic-chain, one learns how to decipher English into natural and idiomatic Chinese translation. The idea of using topic-chains to explore English-Chinese (E-C) textual translation is relatively new to translation studies. As such, this paper provides a detailed account of cross-linguistic differences between English and Chinese, with regard to the topic-chain, as well as the differences between the topic-chain model and the approach of thematic progression theory. This study, based on contrastive analysis, constructs a model consisting of specific procedures that are simple and easy to use, thereby making English-Chinese textual translation a more manageable process. Use of topic-chain strategies will promote the efficiency and quality of E-C translation, and allow for Chinese translated text to be more idiomatic. This paper provides an overview of effective textual translation strategies that are useful both for translators and the field of translation studies as a whole. It addresses how to teach translation effectively to students, providing practical theory and practice for pedagogical instruction. Meanwhile, an experiment conducted provides the evidence that topic-chain for pedagogical instruction is significantly valid. The pedagogical design of these strategies emphasizes the training of students’ textual awareness and targets language-sensitive awareness. It is assumed that didactics can help students gain bilingual competence and strengthen their core transfer competence. This study, therefore, is significant not only in exploring the benefits and uses of textual translation studies, but has practical value when applied directly to translation learning and teaching.