julilili42/papers huggingface dataset:
Accretion heated atmospheres of X-ray bursting neutron stars
2018-11-15

\\nSome thermonuclear (type I) X-ray bursts at the neutron star surfaces in low-mass X-ray binaries take place during hard persistent states of the systems. Spectral evolution of these bursts is well described by the atmosphere model of a passively cooling neutron star when the burst luminosity is high enough. The observed spectral evolution deviates from the model predictions when the burst luminosity drops below a critical value of 20–70% of the maximum luminosity. The amplitude of the deviations and the critical luminosity correlate with the persistent luminosity, which leads us to suggest that these deviations are induced by the additional heating of the accreted particles. We present a method for computation of the neutron star atmosphere models heated by accreted particles assuming that their energy is released via Coulomb interactions with electrons. We computed the temperature structures and the emergent spectra of the atmospheres of various chemical compositions and investigate the dependence of the results on the velocity of accreted particles, their temperature and the penetration angle. We show that the heated atmosphere develops two different regions. The upper one is the hot (20–100 keV) corona-like surface layer cooled by Compton scattering, and the deeper, almost isothermal optically thick region with a temperature of a few keV. The emergent spectra correspondingly have two components: a blackbody with the temperature close to that of the isothermal region and a hard Comptonized component (a power law with an exponential decay). Their relative contribution depends on the ratio of the energy dissipation rate of the accreted particles to the intrinsic flux from the neutron star surface. These spectra deviate strongly from those of undisturbed, passively cooling neutron star atmospheres, with the main differences being the presence of a high-energy tail and a strong excess in the low-energy part of the spectrum. They also lack the iron absorption edge, which is visible in the spectra of undisturbed low-luminosity atmospheres with solar chemical composition. Using the computed spectra, we obtained the dependences of the dilution and color-correction factors as functions of relative luminosities for pure helium and solar abundance atmospheres. We show that the helium model atmosphere heated by accretion corresponding to 5% of the Eddington luminosity describes well the late stages of the X-ray bursts in 4U 1820−30.\\n
A taxonomic reassessment of Piramys auffenbergi, a neglected turtle from the late Miocene of Piram Island, Gujarat, India
2018-11-15

Background Piramys auffenbergi was described as an emydine turtle based on a well-preserved skull retrieved from late Miocene deposits exposed on Piram Island, India. The description and figures provided in the original publication are vague and do not support assignment to Emydinae. This taxon has mostly been ignored by subsequent authors. Material and Methods We reexamine the holotype specimen, provide an extensive description and diagnosis for Piramys auffenbergi , and include this taxon in a global character-taxon matrix for Pleurodira. Results The presence of a processus trochlearis pterygoidei conclusively shows pleurodiran affinities for Piramys auffenbergi . Inclusion of this taxon in a phylogenetic analysis retrieves it within Stereogenyini closely related to the Asian taxa Shweboemys pilgrimi and Brontochelys gaffneyi . Discussion Our reexamination of the holotype of Piramys auffenbergi confidently rejects the original assessment of this taxon as an emydine testudinoid and conclusively shows affinities with the pleurodiran clade Stereogenyini instead. Even though most taxa from this lineage are thought to be coastal turtles, all Asian stereogenyines were collected from continental deposits, suggesting a more diverse paleoecology for the group.
Glycans Controlling Virus Infections: Meeting Report on the 1st International Symposium on Glycovirology Schöntal, Germany, 02–04 May 2018
2018-11-15

Glycans are, with nucleic acids, proteins and lipids, one of the four founding structures of cellular life. Due to their non-template synthesis, they are inherently heterogeneous and difficult to study with regards to their structure and function. Since 2016, the research group ViroCarb, funded by the German Research Foundation, has investigated the role of glycans in non-enveloped virus infections with a highly interdisciplinary approach. The core idea was to bring together scientists and students from various disciplines such as structural biology, cell biology, virology and chemistry to advance research by an interdisciplinary means. In 2018, ViroCarb hosted the 1st International Symposium on Glycovirology in Schöntal, Germany, with a similar aim. Scientists from various disciplines gathered to discuss their area of study, present recent findings, establish or strengthen collaborations, and mentor the next generation of glycovirologists through formal presentations and informal discussions. The secluded meeting at the monastery of Schöntal gave ample time for in-depth discussions. On behalf of ViroCarb, this report summarizes the reports and highlights advances in the field.
Pion distribution amplitude from Euclidean correlation functions: Exploring universality and higher-twist effects
2018-11-16

Building upon our recent study arXiv:1709.04325, we investigate the\\nfeasibility of calculating the pion distribution amplitude from suitably chosen\\nEuclidean correlation functions at large momentum. We demonstrate in this work\\nthe advantage of analyzing several correlation functions simultaneously and\\nextracting the pion distribution amplitude from a global fit. This approach\\nalso allows us to study higher-twist corrections, which are a major source of\\nsystematic error. Our result for the higher-twist parameter is\\nin good agreement with estimates from QCD sum rules. Another novel element is\\nthe use of all-to-all propagators, calculated using stochastic estimators,\\nwhich enables an additional volume average of the correlation functions,\\nthereby reducing statistical errors.\\n
Can Google Trends data improve forecasting of Lyme disease incidence?
2018-11-16

Abstract Background Online activity‐based epidemiological surveillance and forecasting is getting more and more attention. To date, Google search volumes have not been assessed for forecasting of tick‐borne diseases. Thus, we performed an analysis of forecasting of the Lyme disease incidence based on the traditional data extended with Google Trends. Methods Data on the weekly incidence of Lyme disease in Germany from 16 June 2013 to 27 May 2018 were obtained from the database of the Robert Koch Institute. Data of Internet searches were obtained from Google Trends searching “Borreliose” in Germany for the “last 5 years” as a timespan category. Data were split into the training (from 16 June 2013 to 11 June 2017) and validation (from 12 June 2017, to 27 May 2018) data sets. A seasonal autoregressive moving average model, SARIMA (0,1,1) (0,1,1) [52] model was selected to describe the time series of the weekly Lyme incidence. After this, we added the Google Trends data as an external regressor and identified the SARIMA (0,1,1) (0,1,1) [52] model as optimal. We made predictions for the validation interval using these two models and compared predictions with the values of the validation data set. Results Forecasting for the validation timespan resulted in similar values for the models. Comparing the forecasted values with the reported ones resulted in an residual mean squared error (RMSE) of 0.3763; the mean absolute percentage error (MAPE) was 8.233 for the model without Google searches with an RMSE of 0.3732; and the MAPE was 8.17495 for the Google Trends values‐expanded model. The difference between the predictive performances was insignificant (Diebold‐Mariano Test, p ‐value = 0.4152). Conclusion Google Trends data are a good correlate of the reported incidence of Lyme disease in Germany, but it failed to significantly improve the forecasting accuracy in models based on traditional data.
Distributed corporeality: Anatomy, knowledge and the technological reconfiguration of bodies in ballet
2018-11-16

Various specialist cultures configure bodies as complex technological devices. We know little about how exactly this is done. I focus on one of these cultures, classical ballet, to praxeologically reconstruct the conceptual, situational and material configuration of bodies as particular instruments. The technologization of the body is closely intertwined with the scientification of the practice – its ladenness with scientific knowledge about the body and an elaborate apparatus for the production of bodies. When anatomical knowledge and didactics intertwine in ballet class, this facilitates an opening of the black box ‘body’ for technical improvement. ‘A body’ becomes a plurality of (in this case, anatomically distinguished) actants. This distributed corporeality suggests that ‘the body’ is an assemblage that becomes apparent as such in moments of its modification. The empirical case as well as the analytical approach here give reason to reconsider the distinction between humans and non-humans that still prevails in actor-network theory and elsewhere.
Branching of center vortices in SU(3) lattice gauge theory
2018-11-16

We analyze the branching of center vortices in Yang-Mills theory in\\nmaximal center gauge. When properly normalized, we can define a branching\\nprobability that turns out to be independent of the lattice spacing (in the\\nlimited scaling window studied here). The branching probability shows a rapid\\nchange at the deconfinement phase transition which is much more pronounced in\\nspace slices of the lattice as compared to time slices. Though not a strict\\norder parameter (in the sense that it vanishes in one phase) the branching\\nprobability is thus found to be a reliable indicator for both the location of\\nthe critical temperature and the geometric re-arrangement of vortex matter\\nacross the deconfinement phase transition.\\n
Recovery of the Peptidoglycan Turnover Product Released by the Autolysin Atl in Staphylococcus aureus Involves the Phosphotransferase System Transporter MurP and the Novel 6-phospho-N-acetylmuramidase MupG
2018-11-16

The peptidoglycan of the bacterial cell wall undergoes a permanent turnover during cell growth and differentiation. In the Gram-positive pathogen <i>Staphylococcus aureus</i>, the major peptidoglycan hydrolase Atl is required for accurate cell division, daughter cell separation and autolysis. Atl is a bifunctional <i>N</i>-acetylmuramoyl-L-alanine amidase/endo-β-<i>N</i>-acetylglucosaminidase that releases peptides and the disaccharide <i>N</i>-acetylmuramic acid-β-1,4-<i>N</i>-acetylglucosamine (MurNAc-GlcNAc) from the peptido-glycan. Here we revealed the recycling pathway of the cell wall turnover product MurNAc-GlcNAc in <i>S. aureus</i>. The latter disaccharide is internalized and concomitantly phosphorylated by the phosphotransferase system (PTS) transporter MurP, which had been implicated previously in the uptake and phosphorylation of MurNAc. Since MurP mutant cells accumulate MurNAc-GlcNAc and not MurNAc in the culture medium during growth, the disaccharide represents the physiological substrate of the PTS transporter. We further identified and characterized a novel 6-phospho-<i>N</i>-acetylmuramidase, named MupG, which intracellularly hydrolyses MurNAc 6-phosphate-GlcNAc, the product of MurP-uptake and phosphorylation, yielding MurNAc 6-phosphate and GlcNAc. MupG is the first characterized representative of a novel family of glycosidases containing domain of unknown function 871 (DUF871). The corresponding gene <i>mupG</i> (<i>SAUSA300_0192</i>) of <i>S. aureus</i> strain USA300 is the first gene within a putative operon that also includes genes encoding the MurNAc 6-phosphate etherase MurQ, MurP, and the putative transcriptional regulator MurR. Using mass spectrometry, we observed cytoplasmic accumulation of MurNAc 6-phosphate-GlcNAc in Δ<i>mupG</i> and Δ<i>mupGmurQ</i> markerless non-polar deletion mutants, but not in the wild type or in the complemented Δ<i>mupG</i> strain. MurNAc 6-phosphate-GlcNAc levels in the mutants increased during stationary phase, in accordance with previous observations regarding peptidoglycan recycling in <i>S. aureus</i>.
The effect of the optical design of multifocal contact lenses on choroidal thickness
2018-11-16

Studies have found reduced myopia progression with multifocal contact lenses, albeit with an unclear mechanism behind their protective effect. It is hypothesized that the induced myopic defocus of the addition zones of the multifocal contact lenses leads to choroidal thickening and therefore inhibits eye growth. In the current study, the effect of the optical design of multifocal contact lenses on choroidal thickness was investigated. Eighteen myopic participants wore four different contact lenses ((1) single-vision lenses corrected for distance, (2) single-vision lenses with +2.50 D full-field defocus, (3) Multifocal center-distance design, (4) Multifocal center-near design, both with addition power +2.50 D) for 30 min each on their right eye. Automated analysis of the macular choroidal thickness and vitreous chamber depth were performed before and after the wear of each of the contact lenses. Peripheral refraction profiles in primary gaze were obtained using eccentric photorefraction prior to contact lens wear. Choroidal thickness and vitreous chamber depth showed no significant differences to baseline with any of the contact lenses (all p > 0.05). Choroidal thickness increased by +2.1 ± 11.1 μm with the Multifocal center-distance design, by +2.0 ± 11.1 μm with the full-field defocus lens, followed by the Multifocal center-near design with +1.6 ± 11.3 μm and the single-vision contact lens correcting for distance with +0.9 ± 11.2 μm. Multifocal contact lenses have no significant influence on choroidal thickness after short-term wear. Therefore, changes in choroidal thickness might not be the main contributor to the protective effect of multifocal contact lenses in myopia control.
The Gigahertz and Terahertz spectrum of monodeutero-oxirane (c-C2H3DO)
2018-11-16

The rotational spectrum of monodeutero-oxirane was analysed as measured using the Zurich Gigahertz (GHz) spectrometer and our highest resolution Fourier Transform Infrared (FTIR) spectrometer system coupled to synchrotron radiation at the Swiss Light Source (SLS).
Synthesis and Ring Strain of a Benzoborirene‐N‐Heterocyclic Carbene Adduct
2018-11-16

Abstract The reduction of an N ‐heterocyclic carbene (1,3‐diisopropyl‐4,5‐dimethylimidazolin‐2‐ylidene, I i Pr ) adduct of dichloro( ortho ‐bromophenyl)borane by tert ‐butyl lithium at low temperature yields the I i Pr adduct A of parent benzoborirene, a highly strained boron‐containing bicyclic compound. A is unstable at room temperature and dimerizes at low temperature to the bis‐I i Pr adduct of 9,10‐dihydro‐9,10‐diboraanthracene, characterized by single‐crystal X‐ray crystallography.
Clinical Pharmacogenetics Implementation Consortium Guideline for Thiopurine Dosing Based on TPMT and NUDT15 Genotypes: 2018 Update
2018-11-17

Thiopurine methyltransferase (TPMT) activity exhibits a monogenic codominant inheritance and catabolizes thiopurines. TPMT variant alleles are associated with low enzyme activity and pronounced pharmacologic effects of thiopurines. Loss‐of‐function alleles in the NUDT15 gene are common in Asians and Hispanics and reduce the degradation of active thiopurine nucleotide metabolites, also predisposing to myelosuppression. We provide recommendations for adjusting starting doses of azathioprine, mercaptopurine, and thioguanine based on TPMT and NUDT15 genotypes (updates on www.cpicpgx.org ).
Jets and outflows of massive protostars
2018-11-17

Context. Massive stars live short but intense lives. While less numerous than low-mass stars, they enormously impact their surroundings by several feedback mechanisms. They form in opaque and far-away regions of the galaxy, such that one of these feedback mechanisms also becomes a record of their evolution: their bright large-scale jets and outflows. Aims. In a comprehensive convergence study, we investigate the computational conditions necessary to resolve (pseudo-) disk formation and jet-launching processes, and analyze possible caveats. We explore the magneto-hydrodynamic (MHD) processes of the collapse of massive prestellar cores in detail, including an analysis of the forces involved and their temporal evolution for up to two free-fall times. Methods. We conduct MHD simulations using the state-of-the-art code PLUTO, combining nonideal MHD, self-gravity, and very high resolutions as they have never been achieved before. Our setup includes a 100 M ⊙ cloud core that collapses under its own self-gravity to self-consistently form a dense disk structure and launch tightly collimated magneto-centrifugal jets and wide-angle tower flows. Results. We show a comprehensive evolutionary picture of the collapse of a massive prestellar core with a detailed analysis of the physical processes involved and our high-resolution simulations can resolve a magneto-centrifugal jet and a magnetic pressure-driven outflow, separately. The nature of the outflows depends critically on spatial resolution. Only high-resolution simulations are able to differentiate a magneto-centrifugally launched, highly collimated jet from a slow wide-angle magnetic-pressure-driven tower flow. Of these two outflow components, the tower flow dominates angular-momentum transport. The mass outflow rate is dominated by the entrained material from the interaction of the jet with the stellar environment and only part of the ejected medium is directly launched from the accretion disk. A tower flow can only develop to its full extent when much of the original envelope has already dispersed. Taking into account both the mass launched from the surface of the disk and the entrained material from the envelope, we find an ejection-to-accretion efficiency of 10%. Nonideal MHD is required to form centrifugally supported accretion disks and the disk size is strongly dependent on spatial resolution. A converged result for disk and both outflow components requires a spatial resolution of Δ x ≤ 0.17 au at 1 au and sink-cell sizes ≤3.1 au. Conclusions. Massive stars not only possess slow wide-angle tower flows, but also produce magneto-centrifugal jets, just as their low-mass counterparts. The actual difference between low-mass and high-mass star formation lies in the “embeddedness” of the high-mass star which implies that the jet and tower flow interact with the infalling large-scale stellar environment, potentially resulting in entrainment.
The Mechanism behind Bacterial Lipoprotein Release: Phenol-Soluble Modulins Mediate Toll-Like Receptor 2 Activation via Extracellular Vesicle Release from Staphylococcus aureus
2018-11-19

Our study highlights the roles of surfactant-like molecules in bacterial inflammation with important implications for the prevention and therapy of inflammatory disorders. It describes a potential pathway for the transfer of hydrophobic bacterial lipoproteins, the major TLR2 agonists, from the cytoplasmic membrane of Gram-positive bacteria to the TLR2 receptor at the surface of host cells. Moreover, our study reveals a molecular mechanism that explains how cytoplasmic and membrane-embedded bacterial proteins can be released by bacterial cells without using any of the typical protein secretion routes, thereby contributing to our understanding of the processes used by bacteria to communicate with host organisms and the environment.
Lefschetz (1,1)-theorem in tropical geometry
2018-11-19

For a tropical manifold of dimension n we show that the tropical homology classes of degree (n-1, n-1) which arise as fundamental classes of tropical cycles are precisely those in the kernel of the eigenwave map. To prove this we establish a tropical version of the Lefschetz (1, 1)-theorem for rational polyhedral spaces that relates tropical line bundles to the kernel of the wave homomorphism on cohomology. Our result for tropical manifolds then follows by combining this with Poincar\\'e duality for integral tropical homology. Comment: 27 pages, 6 figures, published version
Review of the therapeutic neurofeedback method using electroencephalography: EEG Neurofeedback
2018-11-20

Electroencephalographic neurofeedback (EEG-NFB) represents a broadly used method that involves a real-time EEG signal measurement, immediate data processing with the extraction of the parameter(s) of interest, and feedback to the individual in a real-time. Using such a feedback loop, the individual may gain better control over the neurophysiological parameters, by inducing changes in brain functioning and, consequently, behavior. It is used as a complementary treatment for a variety of neuropsychological disorders and improvement of cognitive capabilities, creativity or relaxation in healthy subjects. In this review, various types of EEG-NFB training are described, including training of slow cortical potentials (SCPs) and frequency and coherence training, with their main results and potential limitations. Furthermore, some general concerns about EEG-NFB methodology are presented, which still need to be addressed by the NFB community. Due to the heterogeneity of research designs in EEG-NFB protocols, clear conclusions on the effectiveness of this method are difficult to draw. Despite that, there seems to be a well-defined path for the EEG-NFB research in the future, opening up possibilities for improvement.
Regulation ofFUSCA3Expression During Seed Development in Arabidopsis
2018-11-20

FUSCA3 (FUS3) is a master regulator of seed development important in establishing and maintaining embryonic identity whose expression is tightly regulated at genetic and epigenetic levels. Despite this prominent role, the control of FUS3 expression remains poorly understood. Promoter and functional complementation analyses provided insight into the regulation of FUS3. W-boxes present in the promoter proximal to the start of transcription are recognized by WRKY type-1 factors which are necessary for the activation of FUS3 expression. The RY motif, the binding site of B3 factors, is important for the activation of FUS3 in the embryo proper but not in the suspensor. The loss of a negative regulatory sequence (NRS) leads to preferential expression of FUS3 in the vasculature of vegetative tissues. Since the NRS includes the RY motif, mechanisms of activation and repression target adjacent or overlapping regions. These findings discriminate the regulation of FUS3 from that of LEAFY COTYLEDON2 by the control exerted by WRKY factors and by the presence of the RY motif, yet also confirm conservation of certain regulatory elements, thereby implicating potential regulation by BASIC PENTACYSTEINE (BPC) factors and POLYCOMB REPRESSIVE COMPLEX2 (PRC2).