bluuebunny/crossref_metadata_2025_split huggingface dataset:
REBOUNDx: a library for adding conservative and dissipative forces to otherwise symplectic N-body integrations
Authors: Tamayo Daniel , Rein Hanno , Shi Pengshuai , Hernandez David M 
Published: October 2019

ABSTRACT
Symplectic methods, in particular the Wisdom–Holman map, have revolutionized our ability to model the long-term, conservative dynamics of planetary systems. However, many astrophysically important effects are dissipative. The consequences of incorporating such forces into otherwise symplectic schemes are not always clear. We show that moving to a general framework of non-commutative operators (dissipative or not) clarifies many of these questions, and that several important properties of symplectic schemes carry over to the general case. In particular, we show that explicit splitting schemes generically exploit symmetries in the applied external forces, which often strongly suppress integration errors. Furthermore, we demonstrate that so-called ‘symplectic correctors’ (which reduce energy errors by orders of magnitude at fixed computational cost) apply equally well to weakly dissipative systems and can thus be more generally thought of as ‘weak splitting correctors’. Finally, we show that previously advocated approaches of incorporating additional forces into symplectic methods work well for dissipative forces, but give qualitatively wrong answers for conservative but velocity-dependent forces like post-Newtonian corrections. We release REBOUNDx, an open-source C library for incorporating additional effects into REBOUNDN-body integrations, together with a convenient python wrapper. All effects are machine independent and we provide a binary format that interfaces with the SimulationArchive class in REBOUND to enable the sharing and reproducibility of results. Users can add effects from a list of pre-implemented astrophysical forces, or contribute new ones.
Resolving accretion flows in nearby active galactic nuclei with the Event Horizon Telescope
Authors: Bandyopadhyay Bidisha , Xie Fu-Guo , Nagar Neil M , Schleicher Dominik R G , Ramakrishnan Venkatessh , Arévalo Patricia , López Elena , Diaz Yaherlyn 
Published: October 2019

ABSTRACTThe Event Horizon Telescope (EHT), now with its first ever image of the photon ring around the supermassive black hole of M87, provides a unique opportunity to probe the physics of supermassive black holes through Very Long Baseline Interferometry (VLBI), such as the existence of the event horizon, the accretion processes as well as jet formation in low-luminosity AGNs (LLAGNs). We build a theoretical model that includes an advection dominated accretion flow (ADAF) with emission from thermal and non-thermal electrons in the flow and a simple radio jet outflow. The predicted spectral energy distribution (SED) of this model is compared to sub-arcsec resolution observations to get the best estimates of the model parameters. The model-predicted radial emission profiles at different frequency bands are used to predict whether the inflow can be resolved by the EHT or with telescopes such as the Global 3-mm VLBI array (GMVA). In this work the model is initially tested with high-resolution SED data of M87 and then applied to our sample of five galaxies (Cen A, M84, NGC 4594, NGC 3998, and NGC 4278). The model then allows us to predict if one can detect and resolve the inflow for any of these galaxies using the EHT or GMVA within an 8 h integration time.
A multidimensional implementation of the Advanced Spectral neutrino Leakage scheme
Authors: Gizzi D , O’Connor E , Rosswog S , Perego A , Cabezón R M , Nativi L 
Published: October 2019

ABSTRACT
We present a new, multidimensional implementation of the Advanced Spectral Leakage (ASL) scheme with the purpose of modelling neutrino–matter interactions in neutron star mergers. A major challenge is the neutrino absorption in the semitransparent regime, which is responsible for driving winds from the merger remnant. The composition of such winds is crucial in the understanding of the electromagnetic emission in the recently observed macronova following GW170817. Compared to the original version, we introduce an optical-depth-dependent flux factor to model the average angle of neutrino propagation, and a modulation that accounts for flux anisotropies in non-spherical geometries. We scrutinize our approach by first comparing the new scheme against the original one for a spherically symmetric core-collapse supernova snapshot, both in 1D and in 3D, and additionally against a two-moment (M1) scheme as implemented in 1D into the code GR1D. The luminosities and mean energies agree to a few per cents in most tests. Finally, for the case of a binary merger remnant snapshot we compare the new ASL scheme with the M1 scheme that is implemented in the Eulerian adaptive mesh refinement code flash. We find that the neutrino absorption distribution in the semitransparent regime is overall well reproduced. Both approaches agree to within $\lesssim 15{{\ \rm per\ cent}}$ for the average energies and to better than $\sim 35 {{\ \rm per\ cent}}$ in the total luminosities.
Inclined jets inside a common envelope of a triple stellar system
Authors: Schreier Ron , Hillel Shlomi , Soker Noam 
Published: October 2019

Abstract
We conduct a three-dimensional hydrodynamical simulation to study the interaction of two opposite inclined jets inside the envelope of a giant star, and find that the jets induce many vortexes inside the envelope and that they efficiently remove mass from the envelope and form a very clumpy outflow. We assume that this very rare type of interaction occurs when a tight binary system enters the envelope of a giant star, and that the orbital plane of the tight binary system and that of the triple stellar system are inclined to each other. We further assume that one of the stars of the tight binary system accretes mass and launches two opposite jets and that the jets’ axis is inclined to the angular momentum axis of the triple stellar system. The many vortexes that the jets induce along the orbit of the tight binary system inside the giant envelope might play an important role in the common envelope evolution (CEE) by distributing energy in the envelope. The density fluctuations that accompany the vortexes lead to an outflow with many clumps that might facilitate the formation of dust. This outflow lacks any clear symmetry, and it might account for very rare types of ‘messy’ planetary nebulae and ‘messy’ nebulae around massive stars. On a broader scope, our study adds to the notion that jets can play important roles in the CEE, and that they can form a rich variety of shapes of nebulae around evolved stars.
Cosmological constraints from galaxy–lensing cross-correlations using BOSS galaxies with SDSS and CMB lensing
Authors: Singh Sukhdeep , Mandelbaum Rachel , Seljak Uroš , Rodríguez-Torres Sergio , Slosar Anže 
Published: October 2019

ABSTRACT
We present cosmological parameter constraints based on a joint modelling of galaxy–lensing cross-correlations and galaxy clustering measurements in the SDSS, marginalizing over small-scale modelling uncertainties using mock galaxy catalogues, without explicit modelling of galaxy bias. We show that our modelling method is robust to the impact of different choices for how galaxies occupy dark matter haloes and to the impact of baryonic physics (at the $\sim 2{{\ \rm per\ cent}}$ level in cosmological parameters) and test for the impact of covariance on the likelihood analysis and of the survey window function on the theory computations. Applying our results to the measurements using galaxy samples from BOSS and lensing measurements using shear from SDSS galaxies and CMB lensing from Planck, with conservative scale cuts, we obtain $S_8\equiv \left(\frac{\sigma _8}{0.8228}\right)^{0.8}\left(\frac{\Omega _\mathrm{ m}}{0.307}\right)^{0.6}=0.85\pm 0.05$ (stat.) using LOWZ × SDSS galaxy lensing, and S8 = 0.91 ± 0.1 (stat.) using combination of LOWZ and CMASS × Planck CMB lensing. We estimate the systematic uncertainty in the galaxy–galaxy lensing measurements to be $\sim 6{{\ \rm per\ cent}}$ (dominated by photometric redshift uncertainties) and in the galaxy–CMB lensing measurements to be $\sim 3{{\ \rm per\ cent}}$, from small-scale modelling uncertainties including baryonic physics.
Parameter inference and model comparison using theoretical predictions from noisy simulations
Authors: Jeffrey Niall , Abdalla Filipe B 
Published: October 2019

ABSTRACTWhen inferring unknown parameters or comparing different models, data must be compared to underlying theory. Even if a model has no closed-form solution to derive summary statistics, it is often still possible to simulate mock data in order to generate theoretical predictions. For realistic simulations of noisy data, this is identical to drawing realizations of the data from a likelihood distribution. Though the estimated summary statistic from simulated data vectors may be unbiased, the estimator has variance that should be accounted for. We show how to correct the likelihood in the presence of an estimated summary statistic by marginalizing over the true summary statistic in the framework of a Bayesian hierarchical model. For Gaussian likelihoods where the covariance must also be estimated from simulations, we present an alteration to the Sellentin–Heavens corrected likelihood. We show that excluding the proposed correction leads to an incorrect estimate of the Bayesian evidence with Joint Light-Curve Analysis data. The correction is highly relevant for cosmological inference that relies on simulated data for theory (e.g. weak lensing peak statistics and simulated power spectra) and can reduce the number of simulations required.
Lynx canadensis (Carnivora: Felidae)
Authors: Lavoie Maxime , Renard Aurélie , Larivière Serge 
Published: October 2019

Abstract Lynx canadensis Kerr, 1792, commonly called the Canada lynx, is a medium size felid and is the second largest of the four species in the genus Lynx. It is distributed throughout the boreal forest of most of Canada and Alaska and across portions of the northern United States. It prefers dense, regenerating coniferous forests with moderate canopy and understory cover. L. canadensis is a snowshoe hare specialist, and its ecology, morphology, and behavior closely reflect that of its main prey. It is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources, is on Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, and its population size trend is considered stable. However, the status of United States subpopulations, being largely peripheral to the Canadian population, is more tenuous and the species is protected.
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Authors: Fornes Oriol , Castro-Mondragon Jaime A , Khan Aziz , van der Lee Robin , Zhang Xi , Richmond Phillip A , Modi Bhavi P , Correard Solenne , Gheorghe Marius , Baranašić Damir , Santana-Garcia Walter , Tan Ge , Chèneby Jeanne , Ballester Benoit , Parcy François , Sandelin Albin , Lenhard Boris , Wasserman Wyeth W , Mathelier Anthony 
Published: October 2019

AbstractJASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.
Intrathecal liposomal cytarabine plus systemic therapy versus systemic chemotherapy alone for newly diagnosed leptomeningeal metastasis from breast cancer
Authors: Le Rhun Emilie , Wallet Jennifer , Mailliez Audrey , Le Deley Marie Cecile , Rodrigues Isabelle , Boulanger Thomas , Lorgis Veronique , Barrière Jerome , Robin Yves Marie , Weller Michael , Bonneterre Jacques 
Published: October 2019

Abstract

Background
DEPOSEIN (NCT01645839) was a randomized open-label phase III study to explore the role of intrathecal chemotherapy in patients with newly diagnosed leptomeningeal metastasis (LM), a common manifestation of breast cancer.

Methods
Patients with newly diagnosed LM defined by tumor cells in the cerebrospinal fluid or combination of clinical and neuroimaging signs of LM were randomized to receive systemic therapy alone (control group) or systemic therapy plus intrathecal liposomal cytarabine (experimental group). Progression-free survival related to LM (LM-PFS) was the primary endpoint.

Results
Thirty-seven and 36 patients were assigned to the control and the experimental groups. Median number of liposomal cytarabine injections in the experimental group was 5 (range 1–20). Focal radiotherapy was performed in 6 (16%) and 3 (8%) patients in the control and experimental groups. In the intent-to-treat population, median LM-PFS was 2.2 months (95% CI: 1.3–3.1) in the control versus 3.8 months (95% CI: 2.3–6.8) in the experimental group (hazard ratio 0.61, 95% CI: 0.38–0.98) (P = 0.04). Seventy-one patients have died. Median overall survival was 4.0 months (95% CI: 2.2–6.3) in the control versus 7.3 months (95% CI: 3.9–9.6) in the experimental group (hazard ratio 0.85, 95% CI: 0.53–1.36) (P = 0.51). Serious adverse events were reported in 22 and 30 patients, respectively. Quality of life until progression did not differ between groups.

Conclusion
The addition of intrathecal liposomal cytarabine to systemic treatment improves LM-related PFS. Confirmatory trials with optimized patient selection criteria and more active drugs may be required to demonstrate a survival benefit from intrathecal pharmacotherapy.
Incorporating New Technology Into a Surgical Technique: The Learning Curve of a Single Surgeon's Stereo-Electroencephalography Experience
Authors: McGovern Robert A , Butler Robert S , Bena James , Gonzalez-Martinez Jorge 
Published: October 2019

Abstract

BACKGROUND
Technological improvements frequently outpace the publication of randomized, controlled trials in surgical patients. This makes the application of new surgical techniques difficult as surgeons solely use clinical experience to guide changes in their practice.

OBJECTIVE
To quantitatively examine the learning curve of incorporating new technology into a surgical technique and discuss the clinical significance of incorporating this new technology into daily practice. To identify areas of improvement for operative efficiency and safety.

METHODS
A retrospective observational study examining quantitative measures of operative efficiency and safety from 2009 to 2017 in 454 consecutive patients undergoing stereo-electroencephalography depth electrode implantations.

RESULTS
The transition to a new robotic technique significantly improved operative times (196 min [95% CI 173-219] vs 115 min [95% CI 111-118], P < .0001). Cumulative sum (CUSUM) analysis demonstrated that mastery of the robotic technique took much longer than the frame-based technique (operative time peak at case 75 vs case 25, plateau of 150 vs 10 cases). Although hemorrhage rates using different vascular imaging techniques did not appear to differ using traditional statistical analysis (magnetic resonance imaging, MRI 22.3%, computed tomography angiography, CTA 17.9%, angiogram 18.1%, likelihood ratio χ2 = 4.84, P = .30), CUSUM analysis suggested MRI as the vascular imaging modality leading to higher hemorrhage and symptomatic hemorrhage rates at our center.

CONCLUSION
This experience demonstrates an improvement in operative efficiency through a series of changes made using clinical experience and intuition while transitioning to a completely new paradigm. CUSUM analysis identified potential areas for improvement in both operative efficiency and safety if used in a prospective manner.
ASSESSMENT OF DOSE DUE TO AMBIENT Rn222/Rn220 PROGENY IN DIFFERENT DWELLINGS OF JAMMU AND KASHMIR STATE, INDIA
Authors: Sharma S , Kumar A , Mehra R , Mishra R 
Published: October 2019

Abstract
The un-attached part of radon (222Rn) progeny is one of the imperative variables for the definitive evaluation of the effective dose from the radon exposure perspective, and it might fluctuate enormously in various ecological conditions. Therefore, estimate dispersion of 222Rn/220Rn progeny, un-attached part and aerosol concentration was estimated in an indoor domain of Jammu and Kashmir State, India utilizing progeny deposition based sensors. Distinctive sorts of residence were picked up for this exploratory examination and maximum 222Rn and thoron (220Rn) descendants concentration was found in working environments or workplaces when contrasted from other abodes because of low ventilation rate. The average evaluated portions of an unattached for 222Rn and 220Rn are 0.29 and 0.26 and in addition, observed to be most extreme in work environments. The age-dependent dose has furthermore been determined utilizing attached and un-attached 222Rn/220Rn progeny concentrations. The dose to trachea-bronchial region and aerosol concentrations has additionally been estimated.
Effects of amino acid biomass or feed-grade amino acids on growth performance of growing swine and poultry12
Authors: Wensley Madie R , Woodworth Jason C , Derouchey Joel M , Dritz Steve S , Tokach Mike D , Goodband Robert D , Walters Hunter G , Leopold Bryce A , Coufal Craig D , Haydon Keith D , Lee Jason T 
Published: October 2019

Abstract
Three experiments were conducted to determine the effect of three fermented amino acids (AA) with their respective biomass compared to crystalline AA on the growth performance of swine and poultry. In experiment 1, 315 barrows (DNA 200 × 400, initially 11.3 ± 0.69 kg) were allotted to 1 of 4 dietary treatments with 5 pigs per pen and 15 or 16 pens per treatment. Dietary treatments included a negative control (16% standardized ileal digestible [SID] Tryptophan:lysine [Trp:Lys] ratio), positive control (21% SID Trp:Lys ratio from crystalline Trp), or diets containing Trp with biomass to provide 21 or 23.5% SID Trp:Lys ratios, respectively. Pigs fed the positive control or low Trp with biomass diet had increased (P &lt; 0.05) ADG compared to pigs fed the negative control diet, with pigs fed the high Trp with biomass diet intermediate. Pigs fed the low Trp with biomass diet had increased (P &lt; 0.05) G:F compared to the negative control diet, with others intermediate. In experiment 2, 1,320 1-d-old male broilers (Cobb 500, initially 45.2 g) were allotted to one of four dietary treatments with 33 birds per pen and 10 pens per treatment. Dietary treatments included a negative control (58/58% Threonine:lysine [Thr:Lys] ratio), positive control (65/66% Thr:Lys ratio from crystalline Thr), or diets containing Thr with biomass to provide 65/66 or 69/70% Thr:Lys ratios in starter and grower diets, respectively. Broilers fed the positive control or Thr with biomass diets had increased (P &lt; 0.05) ADG compared to broilers fed the negative control diet. Broilers fed the positive control or the low Thr with biomass diet had increased (P &lt; 0.05) G:F compared to the negative control and high Thr with biomass treatments. In experiment 3, 2,100 one-day-old male broilers (Cobb 500, initially 39.4 g) were allotted to one of four dietary treatments with 35 birds per pen and 15 pens per treatment. Dietary treatments included a negative control (59/63% Valine:lysine [Val:Lys] ratio), positive control (75/76% Val:Lys ratio from crystalline Val), or diets containing Val with biomass to provide 75/76 or 84/83% Val:Lys ratios in starter and grower diets, respectively. Broilers fed the positive control or Val with biomass diets had increased (P &lt; 0.05) ADG, ADFI, and G:F compared to those fed the negative control diet. In conclusion, Trp, Thr, or Val with their respective biomass appear to be equally bioavailable and a suitable alternative to crystalline AA in swine and poultry diets.
Development of a Generic Physiologically Based Kinetic Model to Predict In Vivo Uterotrophic Responses Induced by Estrogenic Chemicals in Rats Based on In Vitro Bioassays
Authors: Zhang Mengying , van Ravenzwaay Bennard , Rietjens Ivonne M C M 
Published: October 2019

Abstract
The present study assessed the potential of a generic physiologically based kinetic (PBK) model to convert in vitro data for estrogenicity to predict the in vivo uterotrophic response in rats for diethylstibestrol (DES), ethinylestradiol (EE2), genistein (GEN), coumestrol (COU), and methoxychlor (MXC). PBK models were developed using a generic approach and in vitro concentration-response data from the MCF-7 proliferation assay and the yeast estrogen screening assay were translated into in vivo dose-response data. Benchmark dose analysis was performed on the predicted data and available in vivo uterotrophic data to evaluate the model predictions. The results reveal that the developed generic PBK model adequate defines the in vivo kinetics of the estrogens. The predicted dose-response data of DES, EE2, GEN, COU, and MXC matched the reported in vivo uterus weight response in a qualitative way, whereas the quantitative comparison was somewhat hampered by the variability in both in vitro and in vivo data. From a safety perspective, the predictions based on the MCF-7 proliferation assay would best guarantee a safe point of departure for further risk assessment although it may be conservative. The current study indicates the feasibility of using a combination of in vitro toxicity data and a generic PBK model to predict the relative in vivo uterotrophic response for estrogenic chemicals.