julilili42/papers huggingface dataset:
TRUST
2017-04-21

Context. The radiative transport of photons through arbitrary three-dimensional (3D) structures of dust is a challenging problem due to the anisotropic scattering of dust grains and strong coupling between different spatial regions. The radiative transfer problem in 3D is solved using Monte Carlo or Ray Tracing techniques as no full analytic solution exists for the true 3D structures. Aims. We provide the first 3D dust radiative transfer benchmark composed of a slab of dust with uniform density externally illuminated by a star. This simple 3D benchmark is explicitly formulated to provide tests of the different components of the radiative transfer problem including dust absorption, scattering, and emission. Methods. The details of the external star, the slab itself, and the dust properties are provided. This benchmark includes models with a range of dust optical depths fully probing cases that are optically thin at all wavelengths to optically thick at most wavelengths. The dust properties adopted are characteristic of the diffuse Milky Way interstellar medium. This benchmark includes solutions for the full dust emission including single photon (stochastic) heating as well as two simplifying approximations: One where all grains are considered in equilibrium with the radiation field and one where the emission is from a single effective grain with size-distribution-averaged properties. A total of six Monte Carlo codes and one Ray Tracing code provide solutions to this benchmark. Results. The solution to this benchmark is given as global spectral energy distributions (SEDs) and images at select diagnostic wavelengths from the ultraviolet through the infrared. Comparison of the results revealed that the global SEDs are consistent on average to a few percent for all but the scattered stellar flux at very high optical depths. The image results are consistent within 10%, again except for the stellar scattered flux at very high optical depths. The lack of agreement between different codes of the scattered flux at high optical depths is quantified for the first time. Convergence tests using one of the Monte Carlo codes illustrate the sensitivity of the solutions to various model parameters. Conclusions. We provide the first 3D dust radiative transfer benchmark and validate the accuracy of this benchmark through comparisons between multiple independent codes and detailed convergence tests.
Radium-223 for primary bone metastases in patients with hormone-sensitive prostate cancer after radical prostatectomy
2017-04-21

Radium-223 dichloride (Ra-223) is the first bone-targeting agent showing improvement in overall survival in patients with castration-resistant prostate cancer (CRPC) and bone metastases. We aimed to assess feasibility of Ra-223 treatment in patients with metastatic hormone-sensitive prostate cancer (mHSPC). Ten patients with primary bone metastases received Ra-223 following radical prostatectomy (RP). Changes in alkaline phosphatase (ALP) and prostate-specific antigen (PSA) were recorded, while pain intensity was evaluated using the self-reporting Brief Pain Inventory (BPI) questionnaire. Bone scintigraphy (BS) was performed to assess treatment response. Seven patients completed six cycles of Ra-223. Discontinuation was due to leuko- and lymphopenia, progressive lymph node metastasis or newly diagnosed liver metastasis. Treatment-related adverse events occurred in three patients and included leuko- and lymphopenia, fatigue, abdominal discomfort and nausea. Overall, a median decrease of 28% in ALP and a median decrease of 83% in PSA were noted at follow-up. However, PSA progressed in five patients at follow-up. Improvement of pain was observed in all patients (median decrease of 36% after 3 cycles and of 40% at the end of therapy). On BS, three patients showed remission, four had stable disease, and one showed progressive disease at follow-up. Our results suggest that Ra-223 for primary bone metastases in patients with mHSPC after RP is feasible and alleviates pain. ALP, rather than PSA, may be a good marker for assessing treatment response. Ra-223 could therefore be taken into consideration as part of a multimodal approach for carefully selected patients with advanced prostate cancer.
Nanodiscs for INPHARMA NMR Characterization of GPCRs: Ligand Binding to the Human A2A Adenosine Receptor
2017-04-21

Abstract G‐protein‐coupled‐receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure‐based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A 2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back‐calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A 2A R with the low‐affinity ligand 3‐pyrrolidin‐1‐ylquinoxalin‐2‐amine was determined based on the X‐ray structure of ligand ZM‐241,358 in complex with a modified A 2A R.
Researching non-formal religious education: The example of the European study on confirmation work
2017-04-21

This article discusses the need for researching non-formal religious education as a neglected field of empirical research in religious education. By describing the growing awareness of the theological and educational meaning and importance of non-formal education and by reviewing the literature on research in religious education which appears to be focused somewhat one-sidedly on the formal context of the school and of the school subject of Religious Education, the author creates a background for the presentation of current research on confirmation work in Europe. The author gives an overview on a more than 10-year-long project on confirmation work in nine European countries, with an emphasis on the research design, methods, and main results. The experiences from this project are then discussed from the perspective of research on non-formal religious education. Finally, the author considers implications of this research for religious education and practical theology in general.
The Sensation and the Stimulus: Psychophysics and the Prehistory of the Marburg School
2017-04-21

This paper analyzes the role played by Fechner's psychophysics—the new science meant to measure sensation as a function of the stimulus—in the development of Marburg Neo-Kantianism. It will show how Cohen, in the early 1870s, in order to make sense of Kant's obscure principle of the Anticipations of Perception, resorted to psychophysics' parlance of the relation between stimulus and sensation. By the end of the decade, Cohen's remarks encouraged the early 'Cohen circle' (Stadler, Elsas, Müller) to pursue what were often sophisticated analyses of the problem of the measurability of sensation. This paper argues that in reaction to these contributions, Cohen shifted his interests towards the history of the infinitesimal calculus in his controversial 1883 monograph, Das Princip der Infinitesimal-Methode. This book, with its characteristic amalgam of transcendental philosophy and history of science, paved the way to what, around 1900, would become the "Marburg school" (Natorp, Cassirer, Görland and others). However, it also interrupted a promising discussion in Marburg on the problem of measurability in science.
Methanediide Formation via Hydrogen Elimination in Magnesium versus Aluminium Hydride Complexes of a Sterically Demanding Bis(iminophosphoranyl)methanediide
2017-04-22

Substituted bis(iminophosphoranyl)methanes are CH acidic compounds that can form complexes with formally dianionic central carbon centres. The reaction of H2C(Ph2P=NDip)2 (≡ H2L), Dip = 2,6-diisopropylphenyl, with one equivalent of di-n-butylmagnesium afforded the methanide complex [HLMgnBu] 1. Treatment of Complex 1 with phenylsilane in aromatic solvents at elevated temperatures afforded the methanediide complex [(LMg)2] 2 presumably via the MgH intermediate [(HLMgH)n] (n = 1 or 2). The reaction of 1 with LiAlH4 in diethyl ether yielded the AlH complex [HLAlH2] 3. Alternatively, this complex was also obtained from the reaction of H2L with AlH3∙NMe3. The molecular structures of [HLMgnBu] 1, [(LMg)2] 2, and [HLAlH2] 3 are reported. Complex 3 shows no sign of H2 elimination to a methanediide species at elevated temperatures in contrast to the facile elimination of the putative reaction intermediate [(HLMgH)n] (n = 1 or 2) to form [(LMg)2] 2. The chemical properties of Complex 2 were investigated, and this complex appears to be stable against coordination with strong donor molecules.
Many-Body Quantum Systems and Effective Theories
2017-04-22

In the last years, substantial progress has been made in many areas of mathematical physics. The goal of this workshop was to bring together researchers working on analytic and probabilistic aspects of many-body quantum systems and quantum statistical mechanics, to discuss recent developments, exchange ideas and propose new challenges and research directions. Among the questions addressed during the workshop were the derivation of effective equations, the analysis of physically interesting nonlinear partial differential equations emerging from microscopic theories, the study of open quantum systems in and out of equilibrium, and the investigation of the ground state properties and of the dynamics of quantum spin systems.
A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R
2017-04-24

This paper describes and summarizes approaches for visualization and statistical analysis using data from <i>Ralstonia solanacearum</i> infection experiments based on methods and concepts that are broadly applicable. Members of the <i>R. solanacearum</i> species complex cause bacterial wilt disease. Bacterial wilt is a lethal plant disease and has been studied for over 100 years. During this time various methods to quantify disease and different ways to analyze the generated data have been employed. Here, I aim to provide a general background on three distinct and commonly used measures of disease: the area under the disease progression curve, longitudinal recordings of disease severity and host survival. I will discuss how one can proceed with visualization, statistical analysis, and interpretation using different datasets while revisiting the general concepts of statistical analysis. Datasets and R code to perform all analyses discussed here are included in the supplement.
Efficient 2D and 3D Facade Segmentation Using Auto-Context
2017-04-24

This paper introduces a fast and efficient segmentation technique for 2D images and 3D point clouds of building facades. Facades of buildings are highly structured and consequently most methods that have been proposed for this problem aim to make use of this strong prior information. Contrary to most prior work, we are describing a system that is almost domain independent and consists of standard segmentation methods. We train a sequence of boosted decision trees using auto-context features. This is learned using stacked generalization. We find that this technique performs better, or comparable with all previous published methods and present empirical results on all available 2D and 3D facade benchmark datasets. The proposed method is simple to implement, easy to extend, and very efficient at test-time inference.
Luminescent Ni0 Diisocyanide Chelates as Analogues of CuI Diimine Complexes
2017-04-24

Abstract Invited for the cover of this issue is the group of Oliver S. Wenger at the University Basel. The image depicts a homoleptic Ni 0 diisocyanide complex that displays photoluminescence at low temperatures. Read the full text of the article at 10.1002/chem.201700103 .
Legitimacy and protest under authoritarianism: explaining student mobilization in Egypt and Morocco during the Arab uprisings
2017-04-25

ABSTRACT Political protests constitute a major concern to authoritarian regimes. Existing research has argued that they indicate a lack of regime legitimacy. However, empirical evidence on the relationship between legitimacy and protest participation remains rare. Based on new survey data from Morocco and Egypt, this study investigates whether legitimacy played a significant role in student mobilization during the 2011 uprisings. In doing so, we first develop a context-sensitive concept of legitimacy. This allows us to differentiate the ruler's legitimacy claims and the citizens' legitimacy beliefs. Furthermore, we distinguish between two different objects of legitimacy: the broader political community and specific regime institutions. Our empirical analysis suggests that legitimacy had an independent and significant impact on students' protest participation, yet in more nuanced ways than generally assumed. While protest participation was driven by nationalist sentiments in Egypt, it was motivated by dissatisfaction with the political performance of specific regime institutions in Morocco.
Low-Valent Lead Hydride and Its Extreme Low-Field 1H NMR Chemical Shift
2017-04-25

Although hydrides of the group 14 elements are well-known as versatile starting materials in many chemical transformations, a hydride of lead in oxidation state II is so far unknown. In this work, we finally complete the jigsaw puzzle by reporting the isolation of the first low valent organolead hydride. The thermolabile dimeric organolead hydride was synthesized at low temperature and features a hydride <sup>1</sup>H NMR signal (in solution 35.61 ppm; in the solid state 31.1 ppm) at the lowest field observed so far for a diamagnetic compound in agreement with quantum chemical predictions.
Gamma-Glutamylpolyamine Synthetase GlnA3 Is Involved in the First Step of Polyamine Degradation Pathway in Streptomyces coelicolor M145
2017-04-25

<i>Streptomyces coelicolor</i> M145 was shown to be able to grow in the presence of high concentrations of polyamines, such as putrescine, cadaverine, spermidine, or spermine, as a sole nitrogen source. However, hardly anything is known about polyamine utilization and its regulation in streptomycetes. In this study, we demonstrated that only one of the three proteins annotated as glutamine synthetase-like protein, GlnA3 (SCO6962), was involved in the catabolism of polyamines. Transcriptional analysis revealed that the expression of <i>glnA3</i> was strongly induced by exogenous polyamines and repressed in the presence of ammonium. The Δ<i>glnA3</i> mutant was shown to be unable to grow on defined Evans agar supplemented with putrescine, cadaverine, spermidine, and spermine as sole nitrogen source. HPLC analysis demonstrated that the Δ<i>glnA3</i> mutant accumulated polyamines intracellularly, but was unable to degrade them. In a rich complex medium supplemented with a mixture of the four different polyamines, the Δ<i>glnA3</i> mutant grew poorly showing abnormal mycelium morphology and decreased life span in comparison to the parental strain. These observations indicated that the accumulation of polyamines was toxic for the cell. An <i>in silico</i> analysis of the GlnA3 protein model suggested that it might act as a gamma-glutamylpolyamine synthetase catalyzing the first step of polyamine degradation. GlnA3-catalyzed glutamylation of putrescine was confirmed in an enzymatic <i>in vitro</i> assay and the GlnA3 reaction product, gamma-glutamylputrescine, was detected by HPLC/ESI-MS. In this work, the first step of polyamine utilization in <i>S. coelicolor</i> has been elucidated and the putative polyamine utilization pathway has been deduced based on the sequence similarity and transcriptional analysis of homologous genes expressed in the presence of polyamines.
Systematic search for very-high-energy gamma-rayemission from bow shocks of runaway stars
2017-04-25

Context. Runaway stars form bow shocks by ploughing through the interstellar medium at supersonic speeds and are promising sources of non-thermal emission of photons. One of these objects has been found to emit non-thermal radiation in the radio band. This triggered the development of theoretical models predicting non-thermal photons from radio up to very-high-energy (VHE, E ≥ 0.1 TeV) gamma rays. Subsequently, one bow shock was also detected in X-ray observations. However, the data did not allow discrimination between a hot thermal and a non-thermal origin. Further observations of different candidates at X-ray energies showed no evidence for emission at the position of the bow shocks either. A systematic search in the Fermi -LAT energy regime resulted in flux upper limits for 27 candidates listed in the E-BOSS catalogue. Aim. Here we perform the first systematic search for VHE gamma-ray emission from bow shocks of runaway stars. Methods. Using all available archival H.E.S.S. data we search for very-high-energy gamma-ray emission at the positions of bow shock candidates listed in the second E-BOSS catalogue release. Out of the 73 bow shock candidates in this catalogue, 32 have been observed with H.E.S.S. Results. None of the observed 32 bow shock candidates in this population study show significant emission in the H.E.S.S. energy range. Therefore, flux upper limits are calculated in five energy bins and the fraction of the kinetic wind power that is converted into VHE gamma rays is constrained. Conclusions. Emission from stellar bow shocks is not detected in the energy range between 0.14 and 18 TeV.The resulting upper limits constrain the level of VHE gamma-ray emission from these objects down to 0.1–1% of the kinetic wind energy.
Ecological plant epigenetics: Evidence from model and non-model species, and the way forward
2017-04-25

Abstract Growing evidence makes a strong case that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology from dissecting developmental processes to understanding aspects of human health and disease. In ecology, recent studies have merged ecological experimental design with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress response, adaptation to habitat, or species range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, many studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which allow for a more mechanistic understanding but have limited ecological realism. To understand the true significance of epigenetics for plant ecology and evolution, we must combine both approaches transferring knowledge and methods from model-species research to genomes of evolutionarily divergent species, and examining responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration between molecular epigeneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.
The LXR Ligand T0901317 Acutely Inhibits Insulin Secretion by Affecting Mitochondrial Metabolism
2017-04-25

Abstract The role of liver X receptor (LXR) in pancreatic β-cell physiology and pathophysiology is still unclear. It has been postulated that chronic LXR activation in β-cells induces lipotoxicity, a key step in the development of β-cell dysfunction, which accompanies type 2 diabetes mellitus. In most of these studies, the LXR ligand T0901317 has been administered chronically in the micromolar range to study the significance of LXR activation. In the current study, we have evaluated acute effects of T0901317 on stimulus-secretion coupling of β-cells. We found that 10 μM T0901317 completely suppressed oscillations of the cytosolic Ca2+ concentration induced by 15 mM glucose. Obviously, this effect was due to inhibition of mitochondrial metabolism. T0901317 markedly depolarized the mitochondrial membrane potential, thus inhibiting adenosine triphosphate (ATP) production and reducing the cytosolic ATP concentration. This led in turn to a huge increase in KATP current and hyperpolarization of the cell membrane potential. Eventually, T0901317 inhibited glucose-induced insulin secretion. These effects were rapid in on-set and not compatible with the activation of a nuclear receptor. In vivo, T0901317 acutely increased the blood glucose concentration after intraperitoneal application. In summary, these data clearly demonstrate that T0901317 exerts acute effects on stimulus-secretion coupling. This observation questions the chronic use of T0901317 and limits the interpretation of results obtained under these experimental conditions.
Biologically meaningful scents: a framework for understanding predator–prey research across disciplines
2017-04-26

ABSTRACT Fear of predation is a universal motivator. Because predators hunt using stealth and surprise, there is a widespread ability among prey to assess risk from chemical information – scents – in their environment. Consequently, scents often act as particularly strong modulators of memory and emotions. Recent advances in ecological research and analytical technology are leading to novel ways to use this chemical information to create effective attractants, repellents and anti‐anxiolytic compounds for wildlife managers, conservation biologists and health practitioners. However, there is extensive variation in the design, results, and interpretation of studies of olfactory‐based risk discrimination. To understand the highly variable literature in this area, we adopt a multi‐disciplinary approach and synthesize the latest findings from neurobiology, chemical ecology, and ethology to propose a contemporary framework that accounts for such disparate factors as the time‐limited stability of chemicals, highly canalized mechanisms that influence prey responses, and the context within which these scents are detected (e.g. availability of alternative resources, perceived shelter, and ambient physical parameters). This framework helps to account for the wide range of reported responses by prey to predator scents, and explains, paradoxically, how the same individual predator scent can be interpreted as either safe or dangerous to a prey animal depending on how, when and where the cue was deposited. We provide a hypothetical example to illustrate the most common factors that influence how a predator scent (from dingoes, Canis dingo ) may both attract and repel the same target organism (kangaroos, Macropus spp. ). This framework identifies the catalysts that enable dynamic scents, odours or odorants to be used as attractants as well as deterrents. Because effective scent tools often relate to traumatic memories (fear and/or anxiety) that cause future avoidance, this information may also guide the development of appeasement, enrichment and anti‐anxiolytic compounds, and help explain the observed variation in post‐traumatic‐related behaviours (including post‐traumatic stress disorder, PTSD ) among diverse terrestrial taxa, including humans.