bluuebunny/crossref_metadata_2025_split huggingface dataset:
More from less: Genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans
Authors: Tan Mun Hua , Gan Han Ming , Bracken-Grissom Heather , Chan Tin-Yam , Grandjean Frederic , Austin Christopher M 
Published: March 2021

AbstractLow coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for crustacean phylogenomics. The recovery of high-copy-number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach based on our research with freshwater crayfishes (Astacidea). We explored the potential of genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects using decapod crustaceans. Using an in silico-baited approach, we recovered three additional core histone genes (H2A, H2B, and H4) from our low-coverage decapod dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses using various combinations of mitochondrial and nuclear genes for the entire decapod dataset and a subset of 40 species of crayfishes showed that the evolutionary rates for different classes of genes varied widely. A very high level of congruence was nevertheless found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high-copy-number genes across the decapod dataset, and recovery of NaK, PEPCK, and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.
Gender Differences in Second Language Proficiency—Evidence from Recent Humanitarian Migrants in Germany
Authors: Bernhard Sarah , Bernhard Stefan 
Published: March 2021

Abstract
In this paper, we address gender differences in the host language proficiency of humanitarian migrants. Prior research has produced inconclusive results with regard to women’s host language proficiency relative to that of men: sometimes women’s proficiency exceeds that of men, sometimes women lag behind men, and sometimes there are no substantial differences. Using data on recent humanitarian migrants in Germany, we investigate factors contributing to similarities and differences in men’s and women’s language proficiency. We consider gender differences with respect to the family-related factors: marital status, children’s ages and children’s childcare situations are important for women but not for men. These findings point to the continued relevance of a gendered division of work. It also becomes clear that gendered role expectations are particularly consequential for mothers and wives. Moreover, we find evidence that women are more efficient learners than men are, while they have fewer learning opportunities than men.
A Dynamic Survival Modeling Approach to the Prediction of Web Survey Breakoff
Authors: Mittereder Felicitas , West Brady T 
Published: March 2021

Abstract
Respondents who break off from a web survey prior to completing it are a prevalent problem in data collection. To prevent breakoff bias, it is crucial to keep as many diverse respondents in a web survey as possible. As a first step of preventing breakoffs, this study aims to understand breakoff and the associated response behavior. We analyze data from an annual online survey using dynamic survival models and ROC analyses. We find that breakoff risks between respondents using mobile devices versus PCs do not differ at the beginning of the questionnaire, but the risk for mobile device users increases as the survey progresses. Very fast respondents as well as respondents with changing response times both have a higher risk of quitting the questionnaire, compared to respondents with slower and steady response times. We conclude with a discussion of the implications of these findings for future practice and research in web survey methodology.
Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed
Authors: Qian Mingchao , Fan Yonghai , Li Yanhua , Liu Miao , Sun Wei , Duan Huichun , Yu Mengna , Chang Wei , Niu Yue , Li Xiaodong , Liang Ying , Qu Cunmin , Li Jiana , Lu Kun 
Published: March 2021

Abstract
Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 signiﬁcant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants.
Information entropy in cosmological inference problems
Authors: Pinho Ana Marta , Reischke Robert , Teich Marie , Schäfer Björn Malte 
Published: March 2021

ABSTRACT
The subject of this paper is a quantification of the information content of cosmological probes of the large-scale structures, specifically of temperature and polarization anisotropies in the cosmic microwave background (CMB), CMB-lensing, weak cosmic shear and galaxy clustering, in terms of information theory measures like entropies. We aim to establish relationships between conventional measures of statistical uncertainties and information entropies for Gaussian likelihoods, which are described by the Fisher-formalism. Furthermore, we extend these studies to the computation of (Bayesian) evidences and the power of measurement to distinguish between competing models. We investigate in detail how cosmological data decrease information entropy by reducing statistical errors and by breaking degeneracies. In addition, we work out how tensions between data sets increase information entropy and quantify this effect in three examples: the discrepancy in Ωm and σ8 between the CMB and weak lensing, the role of intrinsic alignments in weak lensing data when attempting the dark energy equation of state parameters, and the famous H0-tension between Cepheids in the Hubble keystone project and the CMB as observed by Planck.
Towards a larger sample of radio jets from quiescent black hole X-ray binaries
Authors: Plotkin R M , Bahramian A , Miller-Jones J C A , Reynolds M T , Atri P , Maccarone T J , Shaw A W , Gandhi P 
Published: March 2021

ABSTRACT
Quiescent black hole X-ray binaries (X-ray luminosities ${\lesssim} 10^{34}\,{\rm erg}\, {\rm s}^{-1}$) are believed to be fed by hot accretion flows that launch compact, relativistic jets. However, due to their low luminosities, quiescent jets have been detected in the radio waveband from only five systems so far. Here, we present radio observations of two quiescent black hole X-ray binaries with the Australia Telescope Compact Array. One system, GS 1124-684, was not detected. The other system, BW Cir, was detected over two different epochs in 2018 and 2020, for which we also obtained quasi-simultaneous X-ray detections with Chandra and Swift. BW Cir is now the sixth quiescent X-ray binary with a confirmed radio jet. However, the distance to BW Cir is uncertain, and we find that BW Cir shows different behaviour in the radio/X-ray luminosity plane depending on the correct distance. Estimates based on its G-type subgiant donor star place BW Cir at &gt;25 kpc, while initial optical astrometric measurements from Gaia Data Release 2 suggested likely distances of just a few kpc. Here, we use the most recent measurements from Gaia Early Data Release 3 and find a distance $d=7.1^{+4.8}_{-3.9}$ kpc and a potential kick velocity PKV = $165^{+81}_{-17}$ km s−1, with distances up to ≈20 kpc possible based on its parallax and proper motion. Even though there is now less tension between the parallax and donor-star based distance measurements, it remains an unresolved matter, and we conclude with suggestions on how to reconcile the two measurements.
Implications of an improved water equation of state for water-rich planets
Authors: Huang(黄辰亮) Chenliang , Rice David R , Grande Zachary M , Smith Dean , Smith Jesse S , Boisvert John H , Tschauner Oliver , Salamat Ashkan , Steffen Jason H 
Published: March 2021

ABSTRACT
Water (H2O), in all forms, is an important constituent in planetary bodies, controlling habitability and influencing geological activity. Under conditions found in the interior of many planets, as the pressure increases, the H-bonds in water gradually weaken and are replaced by ionic bonds. Recent experimental measurements of the water equation of state (EOS) showed both a new phase of H-bonded water ice, ice-VIIt, and a relatively low transition pressure just above 30 GPa to ionic bonded ice-X, which has a bulk modulus 2.5 times larger. The higher bulk modulus of ice-X produces larger planets for a given mass, thereby either reducing the atmospheric contribution to the volume of many exoplanets or limiting their water content. We investigate the impact of the new EOS measurements on the planetary mass–radius relation and interior structure for water-rich planets. We find that the change in the planet mass–radius relation caused by the systematic differences between previous and new experimental EOS measurements is comparable to the observational uncertainties in some planet sizes – an issue that will become more important as observations continue to improve.
A unified calibration framework for 21 cm cosmology
Authors: Byrne Ruby , Morales Miguel F , Hazelton Bryna J , Wilensky Michael 
Published: March 2021

ABSTRACT
Calibration precision is currently a limiting systematic in 21 cm cosmology experiments. While there are innumerable calibration approaches, most can be categorized as either ‘sky-based,’ relying on an extremely accurate model of astronomical foreground emission, or ‘redundant,’ requiring a precisely regular array with near-identical antenna response patterns. Both of these classes of calibration are inflexible to the realities of interferometric measurement. In practice, errors in the foreground model, antenna position offsets, and beam response inhomogeneities degrade calibration performance and contaminate the cosmological signal. Here, we show that sky-based and redundant calibration can be unified into a highly general and physically motivated calibration framework based on a Bayesian statistical formalism. Our new framework includes sky-based and redundant calibration as special cases but can additionally support relaxing the rigid assumptions implicit in those approaches. We present simulation results demonstrating that, in a simple case, working in an intermediate regime between sky-based and redundant calibration improves calibration performance. Our framework is highly general and encompasses novel calibration approaches including techniques for calibrating compact non-redundant arrays, calibrating to incomplete sky models, and constraining calibration solutions across frequency.
On the alignment of haloes, filaments and magnetic fields in the simulated cosmic web
Authors: Banfi S , Vazza F , Gheller C 
Published: March 2021

ABSTRACT
The continuous flow of gas and dark matter across scales in the cosmic web can generate correlated dynamical properties of haloes and filaments (and the magnetic fields they contain). With this work, we study the halo spin properties and orientation with respect to filaments, and the morphology of the magnetic field around these objects, for haloes with masses in the range ∼108–1014 M⊙ and filaments up to ∼8 Mpc long. Furthermore, we study how these properties vary in presence, or lack thereof, of different (astro)physical processes and with different magnetic initial conditions. We perform cosmological magnetohydrodynamical simulations with the Eulerian code Enzo and we develop a simple and robust algorithm to study the filamentary connectivity of haloes in three dimensions. We investigate the morphological and magnetic properties and focus on the alignment of the magnetic field along filaments: our analysis suggests that the degree of this alignment is partially dependent on the physical processes involved, as well as on magnetic initial conditions. We discuss the contribution of this effect on a potential attempt to detect the magnetic field surrounding these objects: we find that it introduces a bias in the estimation of the magnetic field from Faraday rotation measure techniques. Specifically, given the strong tendency we find for extragalactic magnetic fields to align with the filaments axis, the value of the magnetic field can be underestimated by a factor ∼3, because this effect contributes to making the line-of-sight magnetic field (for filaments in the plane of the sky) much smaller than the total one.
Constraining neutron star radii in black hole–neutron star mergers from their electromagnetic counterparts
Authors: Fragione Giacomo , Loeb Abraham 
Published: March 2021

ABSTRACT
Mergers of black hole (BH) and neutron star (NS) binaries are of interest since the emission of gravitational waves (GWs) can be followed by an electromagnetic (EM) counterpart, which could power short gamma-ray bursts. Until now, LIGO/Virgo has only observed a candidate BH–NS event, GW190426_152155, which was not followed by any EM counterpart. We discuss how the presence (absence) of a remnant disc, which powers the EM counterpart, can be used along with spin measurements by LIGO/Virgo to derive a lower (upper) limit on the radius of the NS. For the case of GW190426_152155, large measurement errors on the spin and mass ratio prevent from placing an upper limit on the NS radius. Our proposed method works best when the aligned component of the BH spin (with respect to the orbital angular momentum) is the largest, and can be used to complement the information that can be extracted from the GW signal to derive valuable information on the NS equation of state.
On the zero point constant of the bolometric correction scale
Authors: Eker Z , Bakış V , Soydugan F , Bilir S 
Published: March 2021

ABSTRACT
Arbitrariness attributed to the zero-point constant of the V-band bolometric corrections (BCV) and its relation to ‘bolometric magnitude of a star ought to be brighter than its visual magnitude’ and ‘bolometric corrections must always be negative’ was investigated. The falsehood of the second assertion became noticeable to us after IAU 2015 General Assembly Resolution B2, where the zero-point constant of bolometric magnitude scale was decided to have a definite value CBol(W) = 71.197 425 ... . Since the zero-point constant of the BCV scale could be written as C2 = CBol − CV, where CV is the zero-point constant of the visual magnitudes in the basic definition BCV = MBol − MV = mbol − mV, and CBol &gt; CV, the zero-point constant (C2) of the BCV scale cannot be arbitrary anymore; rather, it must be a definite positive number obtained from the two definite positive numbers. The two conditions C2 &gt; 0 and 0 &lt; BCV &lt; C2 are also sufficient for LV &lt; L, a similar case to negative BCV numbers, which means that ‘bolometric corrections are not always negative’. In sum it becomes apparent that the first assertion is misleading causing one to understand bolometric corrections must always be negative, which is not necessarily true.
Revisiting the Kepler field with TESS: Improved ephemerides using TESS 2 min data
Authors: Battley Matthew P , Kunimoto Michelle , Armstrong David J , Pollacco Don 
Published: March 2021

ABSTRACT
Up to date planet ephemerides are becoming increasingly important as exoplanet science moves from detecting exoplanets to characterizing their architectures and atmospheres in depth. In this work, ephemerides are updated for 22 Kepler planets and 4 Kepler planet candidates, constituting all Kepler planets and candidates with sufficient signal to noise in the TESS 2 min data set. A purely photometric method is utilized here to allow ephemeris updates for planets even when they do not posses significant radial velocity data. The obtained ephemerides are of very high precision and at least seven years ‘fresher’ than archival ephemerides. In particular, significantly reduced period uncertainties for Kepler-411d, Kepler-538b, and the candidates K00075.01/K00076.01 are reported. O–C diagrams were generated for all objects, with the most interesting ones discussed here. Updated TTV fits of five known multiplanet systems with significant TTVs were also attempted (Kepler-18, Kepler-25, Kepler-51, Kepler-89, and Kepler-396), however these suffered from the comparative scarcity and dimness of these systems in TESS. Despite these difficulties, TESS has once again shown itself to be an incredibly powerful follow-up instrument as well as a planet-finder in its own right. Extension of the methods used in this paper to the 30 min-cadence TESS data and TESS extended mission has the potential to yield updated ephemerides of hundreds more systems in the future.
Genetic and epigenetic changes in the eutopic endometrium of women with endometriosis: association with decreased endometrial αvβ3 integrin expression
Authors: Joshi Niraj R , Kohan-Ghadr Hamid-Reza , Roqueiro Damian S , Yoo Jung Yoon , Fru Karenne , Hestermann Eli , Yuan Lingwen , Ho Shuk-Mei , Jeong Jae-Wook , Young Steven L , Lessey Bruce A , Fazleabas Asgerally T 
Published: March 2021

AbstractAbout 40% of women with infertility and 70% of women with pelvic pain suffer from endometriosis. The pregnancy rate in women undergoing IVF with low endometrial integrin αvβ3 (LEI) expression is significantly lower compared to the women with high endometrial integrin αvβ3 (HEI). Mid-secretory eutopic endometrial biopsies were obtained from healthy controls (C; n=3), and women with HEI (n=4) and LEI (n=4) and endometriosis. Changes in gene expression were assessed using human gene arrays and DNA methylation data were derived using 385 K Two-Array Promoter Arrays. Transcriptional analysis revealed that LEI and C groups clustered separately with 396 differentially expressed genes (DEGs) (P&lt;0.01: 275 up and 121 down) demonstrating that transcriptional and epigenetic changes are distinct in the LEI eutopic endometrium compared to the C and HEI group. In contrast, HEI vs C and HEI vs LEI comparisons only identified 83 and 45 DEGs, respectively. The methylation promoter array identified 1304 differentially methylated regions in the LEI vs C comparison. The overlap of gene and methylation array data identified 14 epigenetically dysregulated genes and quantitative RT–PCR analysis validated the transcriptomic findings. The analysis also revealed that aryl hydrocarbon receptor (AHR) was hypomethylated and significantly overexpressed in LEI samples compared to C. Further analysis validated that AHR transcript and protein expression are significantly (P&lt;0.05) increased in LEI women compared to C. The increase in AHR, together with the altered methylation status of the 14 additional genes, may provide a diagnostic tool to identify the subset of women who have endometriosis-associated infertility.
Origin and Use of Hydrogen Peroxide in Neurosurgery
Authors: Bailey David , Rizk Elias B 
Published: March 2021

Abstract
Hydrogen peroxide (H2O2) is a chemical with a wide range of applications. This includes its use in the medical field, in which its use has been ubiquitous but is most useful as an antiseptic and in achieving hemostasis. Neurosurgeons have been using H2O2 for well over a century, primarily for its hemostatic and antiseptic effects. This is in spite of the fact that the actual effectiveness of H2O2 as an antiseptic is questionable, and its use, in general, may be more dangerous than it appears. We review the application of H2O2 in medicine generally and, more specifically, in neurosurgery. This review outlines the reasoning behind the use of H2O2 as an antiseptic and details why it may not be as effective as one might think. We also detail its use as a hemostatic agent in neurosurgery, reviewing a number of techniques in which it has been useful in this role. Finally, we review the documented cases of complications associated with the use of H2O2 in neurosurgery. Ultimately, we conclude that the use of H2O2 in neurosurgery be reconsidered because of its lack of effectiveness as an antiseptic and potentially fatal complications.
Diagnosing axial spondyloarthritis: estimation of the disease probability in patients witha prioridifferent likelihoods of the diagnosis
Authors: Poddubnyy Denis , Proft Fabian , Spiller Laura , Protopopov Mikhail , Rios Rodriguez Valeria , Muche Burkhard , Rademacher Judith , Torgutalp Murat , Vahldiek Janis Lucas , Sieper Joachim , Redeker Imke 
Published: March 2021

AbstractObjectiveTo evaluate the diagnostic value of SpA parameters and their combination for the diagnosis of axial SpA in patients with an a priori different probability of the diagnosis.MethodsA total of 361 patients with chronic back pain and suspicion of axial SpA (181 referred by primary care physicians or orthopaedists, 180 recruited via an online screening tool) received a structured rheumatologic examination, which resulted into a diagnosis or exclusion of axial SpA. The prevalence of axial SpA indicating the pre-test probability was 40% in the physician-referred subgroup and 20% in the online screening subgroup. Sensitivities, specificities and likelihood ratios for SpA features were determined in both subgroups and the respective post-test probabilities of axial SpA were calculated.ResultsThe relative diagnostic value of single SpA features varied substantially between the groups with different referral pathways. For instance, HLA-B27 positivity increased the probability of the presence of axial SpA by 35% to 55% in online-screened patients and by 22% to 62% in physician-referred patients. The absence of HLA-B27 resulted in a sharp decrease in the probability of the presence of axial SpA in physician-referred patients (from 40% to 6%). This decrease was less sharp in the online screening group (from 20% to 10%). These differences were especially relevant in patients with a small number (one to two) of positive SpA features.ConclusionThe diagnostic value of SpA features varies in different patient populations, which should be considered in the diagnostic approach.