bluuebunny/crossref_metadata_2025_split huggingface dataset:
How the Distance Between Drag-Cloth Checks Affects the Estimate of Adult and Nymphal Ixodes scapularis (Acari: Ixodidae) Density
Authors: Borgmann-Winter Ben , Allen David 
Published: October 2019

Abstract
Drag-cloth sampling is the most commonly used method to sample for ticks. A cloth is dragged along the ground and checked for ticks at regular intervals to count ticks before they drop off. The distance between drag-cloth checks differs between studies, which could result in lower density estimates for studies with greater distances between checks. Here, we measured this effect by 1) calculating the rate at which nymphal and adult Ixodes scapularis Say ticks drop off the cloth per meter dragged and 2) measuring tick density by drag-cloth sampling with three different drag-cloth check interval distances. We found a higher drop-off rate for adult ticks, 0.083/m, than nymphal ticks, 0.047/m. The estimated density of ticks decreased with increasing check interval distance. Our results not only highlight the importance of accounting for check interval distance when estimating tick density, but also provide the first estimate of nymphal I. scapularis drop-off rate.
Stoichiometry of leaf carbon, nitrogen, and phosphorus along a geographic, climatic, and soil gradients in temperate desert of Hexi Corridor, northwest China
Authors: Zhang Ke , Li Mengmeng , Su Yongzhong , Yang Rong 
Published: October 2019

Abstract

Aims
Understanding the regional pattern of leaf stoichiometry and its contributing variables are of importance for predicting plant responses to global change and modelling the productivity and nutrient fluxes of ecosystems. In this study, we investigated leaf stoichiometry of plants that sampled from Hexi Corridor, a typical arid region in China, and tried to explore the contribution variables on leaf stoichiometry along the geographic, climatic, and soil gradients.

Methods
In August 2012, 70 sites in Hexi Corridor were investigated. Plant leaves and soils from five equivalent plots within each site were sampled. C, N, and P contents of leaf and soil were measured.

Important findings
Compared with leaf N and P contents in regional and global scales, leaf N content in Hexi Corridor was close to them with the value of 20.19 mg g-1, while leaf P content was lower than them with the value of 1.34 mg g-1. Overall, leaf N:P value in Hexi Corridor was 15.70. Individually, leaf N:P values of shrubs and herbs were 16.81 and 14.80, respectively. Scaling exponents for leaf N vs. P of overall and shrubs in Hexi Corridor were 1.29, higher than the scaling exponent of herbs (1.08). Leaf stoichiometry of shrubs and herbs did not show significant latitudinal and longitudinal patterns, meanwhile, it has no significant correlation with mean annual precipitation (MAP), mean annual temperature (MAT), and soil elements. However, only leaf stoichiometry of herbs has significant correlation with altitude and aridity degree. These results indicate that plants in Hexi Corridor are possibly co-limited by N and P, while shrubs are mainly limited by soil P and herbs are limited by soil N. Scaling relationship reveals that leaf N vs. P of herbs is isometric. With increasing altitude, the quadratic regression for leaf C and N contents and the linear regression for leaf P content of herbs reflect the difference responses of the three elements on the variation of MAT along the altitude and it could be explained by plant physiology hypothesis and biogeochemical hypotheses. With decreasing aridity, leaf N and N:P of herbs increased significantly, inferring that herbs growth would be limited by P increasingly and strengthening the increasing nitrogen availability with increasing precipitation. In conclusion, different altitude and aridity patterns for leaf stoichiometry of herbs and shrubs reveal the plastic survive strategies of different xerophytes in Hexi Corridor. Moreover, leaf stoichiometry of herbs in Hexi Corridor could be as indicator of the changing environment that caused by aridity.
Quantifying biological effects of radiation from high-energy linear accelerators on lymphocytes
Authors: Farkas Gyöngyi , Kocsis Zsuzsa S , Székely Gábor , Mihály Dalma , Pesznyák Csilla , Pócza Tamás , Major Tibor , Polgár Csaba , Jurányi Zsolt 
Published: October 2019

ABSTRACT
The aim of this study was to investigate the radiobiological effects of flattening filter (FF) and flattening filter-free (FFF) modes of linear electron accelerators and to understand whether there is any difference between the effects of these modes. We evaluated the number of chromosome aberrations following irradiation of lymphocytes from healthy volunteers with X-ray photons at two energy levels, 6 and 10 MV; the dose rate ranged between 5.50 and 23.08 Gy/min and absorbed doses ranged between 0.5 and 8 Gy. A 60Co curve was employed for comparison. Metaphases from the lymphocyte cultures were prepared using standard cytogenetic techniques and chromosome analysis was performed. Our results allow the performance of biodosimetry at higher energies and doses than the currently used reference dosimetry. We observed significant differences in aberration frequencies when different irradiation techniques were used. FFF mode has a higher radiobiological effect than the FF mode. Linear-quadratic dose response calibration curves were constructed and relative biological effectiveness (RBE) values were calculated. Average RBE values using 6 MV (5.50 Gy/min) as a reference radiation were 1.28 for 60Co γ irradiation, 1.11 for 6 FFF and 0.79–0.92 for 10 FFF. Since there are compelling differences between radiation modalities in cases of hypofractionation, these results may be even more important in a therapeutic situation. In case of an accidental overdose of a patient, use of the appropriate calibration curves for biodosimetry are also essential for quantifying the overdose.
Deletion of bem46 retards spore germination and may be related to the polar growth of Aspergillus fumigatus
Authors: Ma Yan , Ji Ying , Yang Jing , Li Wen , Li Jiajuan , Cen Wen , Wang Yan , Feng Wenli 
Published: October 2019

Abstract
Bud emergence 46 (BEM46), a member of the α/β hydrolase superfamily, has been reported to be essential for polarized growth in Neurospora crassa. However, the role of BEM46 in aspergillus fumigatus (A. fumigatus) remains unclear. In this study, we constructed an A. fumigatus strain expressing BEM46 fused with enhanced green fluorescent protein, and a Δbem46 mutant, to explore the localization and the role of growth of BEM46 in A. fumigatus, respectively. Confocal laser scanning microscopy revealed that BEM46 was dominantly expressed in the sites where hyphae germinated from conidia in A. fumigatus. When compared with the control strain, the Δbem46 mutant exhibited insignificant morphological changes but delayed germination. No significant changes were found regarding the radial growth of both strains in response to various antifungal agents. These results suggest that BEM46 plays an essential role in timely germination in A. fumigatus. From the observation of fluorescence localization, we infer that that BEM46 might be involved in polarized growth in A. fumigatus.
What information can we derive from historical Far Eastern guest stars for modern research on novae and cataclysmic variables?
Authors: Hoffmann Susanne M 
Published: October 2019

ABSTRACTRecently, there have been several studies on the evolution of binary systems using historical data that are treated as facts in the chain of argument. This paper discusses six case studies of modern dwarf novae with suggested historical counterparts from the historical point of view, as well as the derived consequences for the physics of close binary systems (the dwarf novae Z Cam and AT Cnc, the nebula in M22, and the possible Nova 101, Nova 483 and Nova 1437). I consider the historical Far Eastern reports and, after a careful re-reading of the text, map the given information on to the sky. In some cases, the positions given in modern lists of classical nova–guest star pairs turn out to be wrong, or they have to be considered highly approximate: the historical position should, in most cases, be transformed into areas of the celestial sphere and not into point coordinates. Based on the correct information, I consider the consequences concerning the evolution of close binary systems. The result is that none of the cases of cataclysmic variables suggested to have a historical counterpart can be (fully) supported. Because the identification of the historical record of observation with the cataclysmic variables known today turns out to be always uncertain, a potential historical observation alone cannot be relied on to draw conclusions on the evolution of binaries. Evolution scenarios should be derived from astrophysical observations and modelling only.
Scale-invariance of black hole accretion: modelling emission from a black hole X-ray binary with relativistic accretion flow simulations
Authors: Mościbrodzka M 
Published: October 2019

ABSTRACT
We model the non-thermal emission spectrum of the extremely sub-Eddington X-ray binary system A0620-00. It is believed that this non-thermal emission is produced by radiatively inefficient ‘quiescent’ accretion on to a stellar-mass black hole present in the system. We post-process general relativistic magnetohydrodynamics (GRMHD) simulations with multiwavelength, fully polarized, relativistic radiative transfer calculations to predict broad-band spectra and emission polarization levels for a range of electron models and accretion rates. We find that a model with strong coupling of electrons and ions in the accretion disc and accretion rate of only $\dot{M}=3\times 10^{-13} \, \rm [M_\odot \, yr^{-1}]$ is able to recover the observed X-ray spectral slope, as well as the excess of linear polarization detected in the source in the near-infrared (NIR)/optical bands. Our models constrain the spectral properties of a putative relativistic jet produced in this system. In addition, we show that the magnetized winds from our hot accretion flow carry away a small fraction of the orbital angular momentum of the binary, which is unable to explain the observed rapid orbital decay of the system. GRMHD simulations similar to the present ones are often used to explain emission from sub-Eddington supermassive black holes in Sgr A* or M87; the present simulations allow us to test whether some aspects of quiescent black hole accretion are scale-invariant.
Black hole accretion in scalar–tensor–vector gravity
Authors: John Anslyn J 
Published: October 2019

ABSTRACTWe examine the accretion of matter on to a black hole in scalar–tensor–vector gravity (STVG) also known as modified gravity (MOG). The gravitational constant is G = GN(1 + α) where α is a parameter taken to be constant for static black holes in the theory. The MOG black hole is spherically symmetric and characterized by two event horizons. The matter falling into the black hole obeys the polytrope equation of state and passes through two critical points before entering the outer horizon. We obtain analytical expressions for the mass accretion rate as well as for the outer critical point, critical velocity, and critical sound speed. Our results complement existing strong field tests like lensing and orbital motion and could be used in conjunction to determine observational constraints on MOG.
Photometric flaring fraction of M dwarf stars from the SkyMapper Southern Survey
Authors: Chang Seo-Won , Wolf Christian , Onken Christopher A 
Published: October 2019

ABSTRACT
We present our search for flares from M dwarf stars in the SkyMapper Southern Survey DR1, which covers nearly the full Southern hemisphere with six-filter sequences that are repeatedly observed in the passbands uvgriz. This allows us to identify bona fide flares in single-epoch observations on time-scales of less than four minutes. Using a correlation-based outlier search algorithm we find 254 flare events in the amplitude range of Δu ∼ 0.1 to 5 mag. In agreement with previous work, we observe the flaring fraction of M dwarfs to increase from ∼30 to ∼1000 per million stars for spectral types M0 to M5. We also confirm the decrease in flare fraction with larger vertical distance from the Galactic plane which is expected from declining stellar activity with age. Based on precise distances from Gaia DR2, we find a steep decline in the flare fraction from the plane to 150 pc vertical distance and a significant flattening towards larger distances. We then reassess the strong type dependence in the flaring fraction with a volume-limited sample within a distance of 50 pc from the Sun: in this sample the trend disappears and we find instead a constant fraction of ∼1 650 per million stars for spectral types M1 to M5. Finally, large-amplitude flares with Δi > 1 mag are very rare with a fraction of ∼0.5 per million M dwarfs. Hence, we expect that M-dwarf flares will not confuse SkyMapper’s search for kilonovae from gravitational-wave events. proper references for those databases (or follow their guideline on citation).
Tidal flows with convection: frequency-dependence of the effective viscosity and evidence for anti-dissipation
Authors: Duguid Craig D , Barker Adrian J , Jones C A 
Published: October 2019

Abstract
Tidal interactions are important in driving spin and orbital evolution in planetary and stellar binary systems, but the fluid dynamical mechanisms responsible remain incompletely understood. One key mechanism is the interaction between tidal flows and convection. Turbulent convection is thought to act as an effective viscosity in damping large-scale tidal flows, but there is a long-standing controversy over the efficiency of this mechanism when the tidal frequency exceeds the turnover frequency of the dominant convective eddies. This high frequency regime is relevant for many applications, such as for tides in stars hosting hot Jupiters. We explore the interaction between tidal flows and convection using hydrodynamical simulations within a local Cartesian model of a small patch of a convection zone of a star or planet. We adopt the Boussinesq approximation and simulate Rayleigh-Bénard convection, modelling the tidal flow as a background oscillatory shear flow. We demonstrate that the effective viscosity of both laminar and turbulent convection is approximately frequency-independent for low frequencies. When the forcing frequency exceeds the dominant convective frequency, the effective viscosity scales inversely with the square of the tidal frequency. We also show that negative effective viscosities are possible, particularly for high frequency tidal forcing, suggesting the surprising possibility of tidal anti-dissipation. These results are supported by a complementary high-frequency asymptotic analysis that extends prior work by Ogilvie & Lesur. We discuss the implications of these results for interpreting the orbital decay of hot Jupiters, and for several other astrophysical problems.
GRB 171010A/SN 2017htp: a GRB-SN at z = 0.33
Authors: Melandri A , Malesani D B , Izzo L , Japelj J , Vergani S D , Schady P , Sagués Carracedo A , de Ugarte Postigo A , Anderson J P , Barbarino C , Bolmer J , Breeveld A , Calissendorff P , Campana S , Cano Z , Carini R , Covino S , D’Avanzo P , D’Elia V , della Valle M , De Pasquale M , Fynbo J P U , Gromadzki M , Hammer F , Hartmann D H , Heintz K E , Inserra C , Jakobsson P , Kann D A , Kotilainen J , Maguire K , Masetti N , Nicholl M , Olivares E F , Pugliese G , Rossi A , Salvaterra R , Sollerman J , Stone M B , Tagliaferri G , Tomasella L , Thöne C C , Xu D , Young D R 
Published: October 2019

ABSTRACT
The number of supernovae known to be connected with long-duration gamma-ray bursts (GRBs) is increasing and the link between these events is no longer exclusively found at low redshift (z ≲ 0.3) but is well established also at larger distances. We present a new case of such a liaison at z = 0.33 between GRB 171010A and SN 2017htp. It is the second closest GRB with an associated supernova of only three events detected by Fermi-LAT. The supernova is one of the few higher redshift cases where spectroscopic observations were possible and shows spectral similarities with the well-studied SN 1998bw, having produced a similar Ni mass ($M_{\rm Ni}=0.33\pm 0.02 ~\rm {M_{\odot }}$) with slightly lower ejected mass ($M_{\rm ej}=4.1\pm 0.7~\rm {M_{\odot }}$) and kinetic energy ($E_{\rm K} = 8.1\pm 2.5 \times 10^{51} ~\rm {erg}$). The host-galaxy is bigger in size than typical GRB host galaxies, but the analysis of the region hosting the GRB revealed spectral properties typically observed in GRB hosts and showed that the progenitor of this event was located in a very bright H ii region of its face-on host galaxy, at a projected distance of ∼ 10 kpc from its galactic centre. The star-formation rate (SFRGRB ∼ 0.2 M⊙ yr−1) and metallicity (12 + log(O/H) ∼8.15 ± 0.10) of the GRB star-forming region are consistent with those of the host galaxies of previously studied GRB–SN systems.
ProteomicsDB: a multi-omics and multi-organism resource for life science research
Authors: Samaras Patroklos , Schmidt Tobias , Frejno Martin , Gessulat Siegfried , Reinecke Maria , Jarzab Anna , Zecha Jana , Mergner Julia , Giansanti Piero , Ehrlich Hans-Christian , Aiche Stephan , Rank Johannes , Kienegger Harald , Krcmar Helmut , Kuster Bernhard , Wilhelm Mathias 
Published: October 2019

AbstractProteomicsDB (https://www.ProteomicsDB.org) started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data. In this manuscript, we summarize new developments since the previous update that was published in Nucleic Acids Research in 2017. Over the past two years, we have enriched the data content by additional datasets and extended the platform to support protein turnover data. Another important new addition is that ProteomicsDB now supports the storage and visualization of data collected from other organisms, exemplified by Arabidopsis thaliana. Due to the generic design of ProteomicsDB, all analytical features available for the original human resource seamlessly transfer to other organisms. Furthermore, we introduce a new service in ProteomicsDB which allows users to upload their own expression datasets and analyze them alongside with data stored in ProteomicsDB. Initially, users will be able to make use of this feature in the interactive heat map functionality as well as the drug sensitivity prediction, but ultimately will be able to use all analytical features of ProteomicsDB in this way.
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems
Authors: Gumerov Vadim M , Ortega Davi R , Adebali Ogun , Ulrich Luke E , Zhulin Igor B 
Published: October 2019

Abstract
Bacteria and archaea employ dedicated signal transduction systems that modulate gene expression, second-messenger turnover, quorum sensing, biofilm formation, motility, host-pathogen and beneficial interactions. The updated MiST database provides a comprehensive classification of microbial signal transduction systems. This update is a result of a substantial scaling to accommodate constantly growing microbial genomic data. More than 125 000 genomes, 516 million genes and almost 100 million unique protein sequences are currently stored in the database. For each bacterial and archaeal genome, MiST 3.0 provides a complete signal transduction profile, thus facilitating theoretical and experimental studies on signal transduction and gene regulation. New software infrastructure and distributed pipeline implemented in MiST 3.0 enable regular genome updates based on the NCBI RefSeq database. A novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes. The data can be explored online or via RESTful API (freely available at https://mistdb.com).
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
Authors: Naithani Sushma , Gupta Parul , Preece Justin , D’Eustachio Peter , Elser Justin L , Garg Priyanka , Dikeman Daemon A , Kiff Jason , Cook Justin , Olson Andrew , Wei Sharon , Tello-Ruiz Marcela K , Mundo Antonio Fabregat , Munoz-Pomer Alfonso , Mohammed Suhaib , Cheng Tiejun , Bolton Evan , Papatheodorou Irene , Stein Lincoln , Ware Doreen , Jaiswal Pankaj 
Published: October 2019

Abstract
Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model and framework. It currently hosts 298 reference pathways, including metabolic and transport pathways, transcriptional networks, hormone signaling pathways, and plant developmental processes. In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway knowledge. The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials. The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).