julilili42/papers huggingface dataset:
Hard X-ray view on intermediate polars in theGaiaera
2018-11-02

The hardness of the X-ray spectra of intermediate polars (IPs) is determined\\nmainly by the white dwarf (WD) compactness (mass-radius ratio, M/R) and, thus,\\nhard X-ray spectra can be used to constrain the WD mass. An accurate mass\\nestimate requires the finite size of the WD magnetosphere R_m to be taken into\\nthe account. We suggested to derive it either directly from the observed break\\nfrequency in power spectrum of X-ray or optical lightcurves of a polar, or\\nassuming the corotation. Here we apply this method to all IPs observed by\\nNuSTAR (10 objects) and Swift/BAT (35 objects). For the dwarf nova GK Per we\\nalso observe a change of the break frequency with flux, which allows to\\nconstrain the dependence of the magnetosphere radius on the mass-accretion\\nrate. For our analysis we calculated an additional grid of two-parameter (M and\\nR_m/R) model spectra assuming a fixed, tall height of the accretion column\\nH_sh/R=0.25, which is appropriate to determine WD masses in low mass-accretion\\nIPs like EX\\\\,Hya. Using the Gaia Data Release 2 we obtain for the first time\\nreliable estimates of the mass-accretion rate and the magnetic field strength\\nat the WD surface for a large fraction of objects in our sample. We find that\\nmost IPs accrete at rate of ~10^{-9} M_Sun/yr, and have magnetic fields in the\\nrange 1--10 MG. The resulting WD mass average of our sample is 0.79 +/- 0.16\\nM_Sun, which is consistent with earlier estimates.\\n
Identifying Respiration-Related Aliasing Artifacts in the Rodent Resting-State fMRI
2018-11-02

Resting-state functional magnetic resonance imaging (rs-fMRI) combined with optogenetics and electrophysiological/calcium recordings in animal models is becoming a popular platform to investigate brain dynamics under specific neurological states. Physiological noise originating from the cardiac and respiration signal is the dominant interference in human rs-fMRI and extensive efforts have been made to reduce these artifacts from the human data. In animal fMRI studies, physiological noise sources including the respiratory and cardiorespiratory artifacts to the rs-fMRI signal fluctuation have typically been less investigated. In this article, we demonstrate evidence of aliasing effects into the low-frequency rs-fMRI signal fluctuation mainly due to respiration-induced B0 offsets in anesthetized rats. This aliased signal was examined by systematically altering the fMRI sampling rate, i.e., the time of repetition (TR), in free-breathing conditions and by adjusting the rate of ventilation. Anesthetized rats under ventilation showed a significantly narrower frequency bandwidth of the aliasing effect than free-breathing animals. It was found that the aliasing effect could be further reduced in ventilated animals with a muscle relaxant. This work elucidates the respiration-related aliasing effects on the rs-fMRI signal fluctuation from anesthetized rats, indicating non-negligible physiological noise needed to be taken care of in both awake and anesthetized animal rs-fMRI studies.
Affectedness in international institutions: promises and pitfalls of involving the most affected
2018-11-02

Persons and groups affected by the choices and actions of international institutions increasingly claim to have a say in their making. They challenge governments, international bureaucrats, and classic NGOs for lacking legitimacy and acting in ways that disregard too many people's legitimate concerns. To study these recent developments, this collection brings together political science and international law scholars. Based on their observations, the introduction makes three major contributions: First, it conceptualises the rising involvement of affected persons' organisations (APOs) in global governance as a turn to affectedness-participation. As the contributions to this collection demonstrate, affected persons and groups by now participate in many areas of global rule- and law-making. Second, the introduction shows that their participation addresses current legitimacy problems of international public policy making and transnational (self-)governance. APOs often make innovative policy demands, articulate marginalised normative understandings and call for radical political change. However, third, this introduction also finds that pitfalls remain: conceptualising and identifying affected persons and their legitimate representatives is difficult, APOs often face serious capacity constraints and powerful international actors threaten to co-opt the newcomers. Nevertheless, the greater involvement of affected persons is a promising development in the journey towards more inclusive and legitimate global politics.
Extreme aridity prior to lake expansion deciphered from facies evolution in the Miocene Ili Basin, south‐east Kazakhstan
2018-11-02

Abstract Central Asia witnessed progressive aridification during the Miocene, commonly related to mountain uplift, the Paratethys retreat and global climate cooling. However, the formation of Miocene lakes in Central Asia seems to oppose drier conditions, suggesting that the precise timing, extent and forcing of the aridification is still not well constrained. This study presents a facies model for the alluvial–lacustrine part of the Middle to Late Miocene of the Ili Basin, obtained from two successions. The model enables the semi‐quantitative assessment of regional water level and salinity, and characterizes the control of water level on evaporite formation and diagenesis. Both the proximal Kendyrlisai and the distal Aktau successions show an overall increase in water availability from dry mudflat deposits to lacustrine sedimentation with a transitional playa phase. Increasing evaporation rates outpaced the water supply and caused groundwater salinization. Subsequent lake expansion coincided with a basin‐wide desalinization and required a shift to a positive water budget. A climatic control of the hydrological evolution is inferred due to abrupt salinization and a minor tectonic influence. The long‐term water accumulation is probably related to the hydrological closure of the basin in the early Middle Miocene (15·3 Ma). Starting at 14·3 Ma, the step‐wise salinization occurred simultaneously with the global cooling of the Miocene Climate Transition. The Miocene Climate Transition led to extreme aridity in the Ili Basin, highlighted by the early diagenetic formation of displacive anhydrite in the basin centre. The expansion of the freshwater lake (12·7 to 11·5 Ma) was possibly promoted by lower evaporation rates due to decreasing air temperatures in the Ili Basin after the Miocene Climate Transition. The extreme aridity in the Ili Basin is interpreted as a continental counterpart to the Badenian Salinity Crisis in the Central Paratethys. This emphasizes the role of atmospheric forcing on evaporite sedimentation across Eurasia during the Middle Miocene.
The first record ofAnancus(Mammalia, Proboscidea) in the late Miocene of Greece and reappraisal of the primitive anancines from Europe
2018-11-02

In this article, we present the proboscideans from the late Miocene (Turolian) locality Chomateri, Greece, near the classical locality Pikermi. The material consists of juvenile teeth, whose morphological features, such as the dislocation of the half-loph(id)s and the resultant alternate arrangement of the successive loph(id)s (anancoidy), permit assignment to the tetralophodont gomphothere Anancus. However, the anancoidy is rather weak and the occlusal morphology simple, both regarded as primitive features within anancines. Reexamination of the late Miocene anancines from Europe reveals that they all share primitive molar features (weak anancoidy, simple morphology, thick enamel) with the material from Hohenwarth, Austria, showing further primitive skull features, such as the longer mandibular symphysis compared with other anancines. The proper name to refer to the late Miocene anancines from Europe is Anancus lehmanni (Gaziry, 1997), with type locality Dorn-Dürkheim 1 (Turolian; Germany). The presence of Anancus in Chomateri constitutes the first late Miocene record of the genus in Greece, and the first faunal element that clearly indicates that Chomateri postdates the classical Pikermi. Finally, we discuss the biostratigraphy and the biogeography of the late Miocene anancines of the Old World. Anancus originated possibly at ∼9.0–8.5 Ma in Asia and entered Europe during the second half of the Turolian, at ∼7.2 Ma (Tortonian-Messinian boundary). The arrival of Anancus in Europe coincides with a faunal turnover in both the eastern and western sectors of the European Mediterranean region, and in the southern Balkans in particular, with the decline of the 'Pikermian' large-mammal fauna.
Shifting the paradigm: a typology of affected persons’ participation in international institutions
2018-11-02

International law and politics are made first and foremost by states, either independently or through their exclusive membership in international organisations. Nevertheless, civil society has had access to intergovernmental decision-making arenas for several decades, mostly through NGOs. Based on Article 71 UN Charter, NGOs have been granted observer status at many international organisations to advocate for public interest issues like the protection of human rights or the environment. This public interest paradigm, however, is increasingly being challenged by the affectedness paradigm. The latter refers to the increasing participation of people who are affected by issues subject to international regulation. So far, legal scholars have largely overlooked this shift. To address this research gap, this paper examines how the affectedness paradigm has become institutionalised at different international organisations and proposes a typology of affected persons’ participation. The paper argues that affected-led advocacy has not replaced public-interest advocacy, but that the affectedness paradigm has been institutionalised in at least three different ways: the subordination, parity, and priority models. They can be placed on a scale with the priority model giving the strongest role to affected population groups.
Variable Wavefront Curvature Phase Retrieval Compared to Off-Axis Holography and Its Useful Application to Support Intraoperative Tissue Discrimination
2018-11-03

Quantitative phase imaging can reveal morphological features without having to stain the biological sample. This property has important implications for intraoperative applications since the time spent during histopathology can be reduced from a few minutes to a few seconds. However, most common quantitative phase imaging techniques are based on the interferometric principle, which makes them more prone to disturbing environmental influences, such as temperature drift and air turbulence. In the last decade, with the advance of computing power, many different iterative quantitative phase imaging techniques, which only require the recording of the diffracted wavefield, and therefore offer increased robustness towards environmental disturbances, have been proposed. These are particularly well-suited for the application outside the well-controlled lab environment such as an operating theatre. The optical performance of our developed iterative phase retrieval method based on variable wavefront curvature will be evaluated by reference to off-axis digital holography and applied for intraoperative discrimination of tissue.
Supplemental material for going beyond convergence in Bayesian estimation: Why precision matters too and how to assess It (published in Structural Equation Modeling)
2018-11-03

The following tables provide detailed results from the simulation studies. Tables S1 and S2 show comparisons of the estimates of the regression coefficient in the macro-micro design (Study 1) for the default in Mplus (i.e, PSR &lt; 1:05 for models with only one parameter, and PSR &lt; 1:10 for models with many parameters) with the ESS criteria (e.g., ESS &gt; 400) with respect to the relative bias and the relative RMSE. Table S3 compares the coverage rates of Mplus’ default criterion with those of the ESS criteria in Study 1. The remaining tables present the detailed results from Study 2 (micro-macro design) as well as those from the additional study.
Supplemental material for Going Beyond Convergence in Bayesian Estimation: Why Precision Matters too and How to Assess It (published in Structural Equation Modeling)
2018-11-03

The following tables provide detailed results from the simulation studies. Tables S1 and S2 show comparisons of the estimates of the regression coefficient in the macro-micro design (Study 1) for the default in Mplus (i.e, PSR &lt; 1:05 for models with only one parameter, and PSR &lt; 1:10 for models with many parameters) with the ESS criteria (e.g., ESS &gt; 400) with respect to the relative bias and the relative RMSE. Table S3 compares the coverage rates of Mplus’ default criterion with those of the ESS criteria in Study 1. The remaining tables present the detailed results from Study 2 (micro-macro design) as well as those from the additional study.
Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites
2018-11-05

Abstract Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6–11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13–16% of each genome). In addition, the compound enhygrolide A, known from E . salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.
The Impact of Visualization Format and Navigational Options on Laypeople’s Perception and Preference of Surgery Information Videos: Randomized Controlled Trial and Online Survey
2018-11-05

Deutsches Register Klinischer Studien DRKS00016003; https://www.drks.de/drks_web/ navigate.do?navigationId= trial.HTML&TRIAL_ID=DRKS00016003 (Archived by WebCite at http://www.webcitation.org/746ASSAhN).
Power behind the curtain: the Eurogroup’s role in the crisis and the value of informality in economic governance
2018-11-05

During the crisis, the Eurogroup underwent a significant expansion of competences in the field of loan provision, fiscal surveillance and structural reform. Still, to that day, it remains an informal institution, largely avoiding codification and public sanctioning. Against this background, this paper asks how the Eurogroup works internally and which value its informal character has for its modus operandi. For this, institutions are conceptualised as structures which distribute institutional power between members. Using data of expert interviews and official documents, the conflict over the Greek reform programme in 2015 is analysed. It shows that selective communication and immediate interaction, both particular qualities of informality, had a significant impact on the solutions produced within the group. The northern European countries were able to pull outcomes closer to their preferred austerity-political course by using these qualities to divert and focus external pressure and react adaptably to resistance. The findings indicate that, at least in the case of strong conflict, the consensus logic of informal environments such as the Eurogroup makes way for the use of institutional power.
Impact of Brain Fatty Acid Signaling on Peripheral Insulin Action in Mice
2018-11-05

Abstract Aims and Methods Glucose homeostasis and energy balance are under control by peripheral and brain processes. Especially insulin signaling in the brain seems to impact whole body glucose homeostasis and interacts with fatty acid signaling. In humans circulating saturated fatty acids are negatively associated with brain insulin action while animal studies suggest both positive and negative interactions of fatty acids and insulin brain action. This apparent discrepancy might reflect a difference between acute and chronic fatty acid signaling. To address this question we investigated the acute effect of an intracerebroventricular palmitic acid administration on peripheral glucose homeostasis. We developed and implemented a method for simultaneous monitoring of brain activity and peripheral insulin action in freely moving mice by combining radiotelemetry electrocorticography (ECoG) and euglycemic-hyperinsulinemic clamps. This method allowed gaining insight in the early kinetics of brain fatty acid signaling and its contemporaneous effect on liver function in vivo, which, to our knowledge, has not been assessed so far in mice. Results Insulin-induced brain activity in the theta and beta band was decreased by acute intracerebroventricular application of palmitic acid. Peripherally it amplified insulin action as demonstrated by a significant inhibition of endogenous glucose production and increased glucose infusion rate. Moreover, our results further revealed that the brain effect of peripheral insulin is modulated by palmitic acid load in the brain. Conclusion These findings suggest that insulin action is amplified in the periphery and attenuated in the brain by acute palmitic acid application. Thus, our results indicate that acute palmitic acid signaling in the brain may be different from chronic effects.
Structure and function of a bacterial gap junction analog
2018-11-05

Summary Multicellular lifestyle requires cell-cell connections. In multicellular cyanobacteria, septal junctions enable molecular exchange between sister cells and are required for cellular differentiation. The structure of septal junctions is poorly understood and it is unknown whether they regulate intercellular communication. Here we resolved the in situ architecture of septal junctions by electron cryotomography of cryo-focused ion beam-milled cyanobacteria. Septal junctions consisted of a tube traversing the septal peptidoglycan. Each tube end comprised a plug that was covered by a cytoplasmic cap. Fluorescence recovery after photobleaching showed that intercellular communication was blocked upon stress. This gating was accompanied by a conformational change of the septal junctions, mediated by the proteins FraC/D. We provide the mechanistic framework for a cell junction that predates eukaryotic gap junctions by a billion years. The conservation of a gated dynamic mechanism across different domains of life emphasizes the importance of controlling molecular exchange, e.g. upon injury.
TAPBPR mediates peptide dissociation from MHC class I using a leucine lever
2018-11-05

Abstract Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules, however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics in combination with novel cell-based assays that assess TAPBPR-mediate peptide exchange, we reveal a critical role for the K22-D35 loop of TAPBPR in mediating peptide exchange on MHC I. We identify a specific leucine within this loop that enables TAPBPR to facilitate peptide dissociation from MHC I. Moreover, we delineate the molecular features of the MHC I F pocket required for TAPBPR to promote peptide dissociation in a loop-dependent manner. These data reveal that chaperone-mediated peptide editing of MHC I can occur by different mechanisms dependent on the C-terminal residue that the MHC I accommodates in its F pocket and provide novel insights that may inform the therapeutic potential of TAPBPR manipulation to increase tumour immunogenicity. Impact Statement This work demonstrates for the first time that the K22-D35 loop of TAPBPR is the essential region for mediating peptide exchange and peptide selection on major histocompatibility complex class I molecules.
Tamagawa numbers of polarized algebraic varieties
2018-11-06

Let L = (L, ‖ · ‖v) be an ample metrized invertible sheaf on a smooth quasi-projective algebraic variety V over a number field F . Denote by N(V,L, B) the number of rational points in V having Lheight ≤ B. In this paper we consider the problem of a geometric and arithmetic interpretation of the asymptotic for N(V,L, B) as B → ∞ in connection with recent conjectures of Fujita concerning the Minimal Model Program for polarized algebraic varieties. We introduce the notions of L-primitive varieties and L-primitive fibrations. For L-primitive varieties V over F we propose a method to define an adelic Tamagawa number τL(V ) which is a generalization of the Tamagawa number τ(V ) introduced by Peyre for smooth Fano varieties. Our method allows us to construct Tamagawa numbers for Q-Fano varieties with at worst canonical singularities. In a series of examples of smooth polarized varieties and singular Fano varieties we show that our Tamagawa numbers express the dependence of the asymptotic of N(V,L, B) on the choice of v-adic metrics on L.
Harmonizing semantic annotations for computational models in biology
2018-11-06

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.