bluuebunny/crossref_metadata_2025_split huggingface dataset:
Every Rule Has an Exception: a Cheater in the Community-Wide Mutualism in Antarctic Seaweed Forests
Authors: Heiser Sabrina , Amsler Charles D , McClintock James B , Shilling Andrew J , Baker Bill J 
Published: May 2020

Synopsis
Dense macroalgal forests on the Western Antarctic Peninsula serve important ecological roles both in terms of considerable biomass for primary production as well as in being ecosystem engineers. Their function within the Antarctic ecosystem has been described as a crucial member of a community-wide mutualism which benefits macroalgal species and dense assemblages of associated amphipod grazers. However, there is a cheater within the system that can feed on one of the most highly chemically defended macroalgal hosts. The amphipod Paradexamine fissicauda has been found to readily consume the finely branched red macroalga Plocamium cartilagineum. This amphipod grazer not only feeds on its host, but also appears to sequester its host’s chemical defenses for its own utilization. This review summarizes what we know about both of these exceptions to the community-wide mutualism.
Recommendations for Advancing Genome to Phenome Research in Non-Model Organisms
Authors: Burnett Karen G , Durica David S , Mykles Donald L , Stillman Jonathon H , Schmidt Carl 
Published: May 2020

Synopsis
The 2020 SICB Society-wide Symposium “Building Bridges from Genome to Phenome: Molecules, Methods and Models” brought together a diverse group of scientists to discuss recent progress in linking phenotype plasticity to changes at the level of the genome, epigenome, and proteome, while exploring the boundaries between variation and speciation. In a follow-up workshop, participants were asked to assess strengths and weaknesses of current approaches, to identify common barriers inhibiting their progress, and to outline the resources needed to overcome those barriers. Discussion groups generally recognized the absence of any overarching theoretical framework underlying current genome to phenome research and, therefore, called for a new emphasis on the development of conceptual models as well as the interdisciplinary collaborations needed to create and test those models. Participants also recognized a critical need for new and improved molecular and bioinformatic approaches to assist in describing function/phenotypes across phylogeny. Additionally, like all scientific endeavors, progress in genome to phenome research will be enhanced by improvements in science education and communication both within and among working groups.
A Novel Laboratory Assay to Monitor Unfractionated Heparin Dosing in Patients Taking Apixaban Prior to Hospital Admission
Authors: Strickland Sydney W , Palkimas Surabhi , Acker Mary , Bazydlo Lindsay A L 
Published: June 2020

Abstract

Introduction
When monitoring heparin, anti-Xa assays are susceptible to interference from apixaban taken before admission and can result in inappropriate dose adjustments that can negatively affect patient care.

Methods
We derived a novel assay, termed corrected heparin (CH), using quantified values from a chromogenic anti-Xa assay with heparin calibrators before and after heparinase treatment to eliminate any interference from apixaban within the patient sample. We retrospectively assessed 469 specimens from 72 patients at our institution who had their unfractionated heparin infusion monitored using the CH assay because of known apixaban use. These patients were included in the study if they had detectable apixaban levels (&gt;0.1 IU/mL by anti-Xa).

Results
The analytical performance of the assay was evaluated, and precision was found to be 8.8% within 1 day and 13.3% over multiple days, with acceptable linearity (R2 = 0.997). Evaluation of clinical performance was compared with the partial thromboplastin time (PTT), showing a lack of correlation similar to comparisons between the PTT and anti-Xa assay (Blood Coagul Fibrinolysis 1993;4:635–8). The mean time to a therapeutic result in this cohort was 10 hours and 10 minutes. The CH assay was used to determine how long the apixaban was detected by the anti-Xa assay. The majority of patients (80%) still had measurable anti-Xa assay interference from apixaban at 24 hours after the last apixaban dose.

Conclusions
We have developed and evaluated an assay capable of quantifying heparin in the presence of apixaban. This assay showed acceptable performance in both analytical and clinical performance.
Evaluate the Effect of Zinc Oxide and Silver Nanoparticles on Biofilm and icaA Gene Expression in Methicillin-Resistant Staphylococcus aureus Isolated From Burn Wound Infection
Authors: Shakerimoghaddam Ali , Razavi Delaramsadat , Rahvar Farzaneh , Khurshid Maria , Ostadkelayeh Shokoufeh Mogharabi , Esmaeili Seyed-Alireza , Khaledi Azad , Eshraghi Mohsen 
Published: June 2020

Abstract
Methicillin-resistant Staphylococcus aureus is the cause of nosocomial and community-acquired infections. This study aimed to evaluate the effect of zinc oxide and silver nanoparticles (ZnO-Ag NPs) on biofilms formation and icaA gene expression in methicillin-resistant S. aureus (MRSA). In this study, three standard strains (ATCC 43300, 25923, and 29913) and a clinical isolate are included. The minimum inhibitory concentration (MIC) of nanoparticles was determined by microdilution broth method. The antibacterial effects of ZnO-Ag NPs either alone or in combination with each other were compared with vancomycin (as the control group). The effect of MIC and sub-MIC concentrations of ZnO-Ag NPs on biofilm formation was determined by the microtiter plate method. The expression level of the icaA gene was assessed by real-time PCR LightCycler® 96 software (Version 1.1.0.1320, Roche, Germany). technique. All experiments were repeated three times. Data were analyzed using SPSS software through ANOVA and t-test. The P-value of less than .05 was considered as statistically significant. The average MICs of ZnO, Ag, and ZnO-Ag NPs compounds were 393.2, 179.8, and 60.8 μg/ml, respectively. The compound of ZnO-Ag NPs had a synergistic effect against all isolates. ZnO-Ag NPs decreased the biofilm formation rate at MIC and sub-MIC concentrations (P &lt; .001). Sub-MIC ZnO-Ag NPs concentration significantly reduced the icaA gene expression in S. aureus strains (P &lt; .03). The sub-MIC concentration of ZnO-Ag NPs reduced biofilm formation rate and icaA gene expression in Staphylococcus aureus strains compared with vancomycin. It can be used to cover medical devices after examining more clinical isolates to prevent bacterial colonization.
Distribution characteristics of the advance abutment pressure in a deep stope
Authors: Zhang Pingsong , Sun Binyang 
Published: June 2020

Abstract
The advance abutment pressure on the coal mining face of a deep stope plays a decisive role in the surrounding rock instability, rock burst and coal-gas outburst. Based on distributed optical fiber sensing technology and theoretical analysis of the stress state, the distribution characteristics of the advance abutment pressure were tested. Taking the 61103 coal mining face of a mine in Inner Mongolia as an example, downhole measurement research was carried out. Based on the monitoring data, a two-dimensional (2D) geological model for the distribution of the advance abutment pressure during the mining process was developed. To verify the validity of the model, a verification borehole was located on the 61201 coal mining face of the same mining area, the two borehole datasets were comprehensively analysed and the model was corrected. The modified model shows that the influence scope of the advance abutment pressure is 0–26.5 m, the position of the peak stress is 5.1–6.4 m in front of the coal mining face and the peak stress can reach 21.98–23.98 MPa. The stress concentration coefficient is 1.22–1.91 and the vertical influence depth is 13–14 m. Moreover, the advance abutment pressure exhibits obvious zoning in the transverse direction, and the stress at the same position in front of the coal mining face will undergo a process of steady-slow increase-significant increase-peak-decrease. The technical parameters obtained from this study can be used for other coal mining faces in the area. In addition, the testing result of the abutment pressure from the distributed optical fiber sensors is effective and can provide a new research method for mine safety monitoring.
The complexity of definability by open first-order formulas
Authors: Areces Carlos , Campercholi Miguel , Penazzi Daniel , Ventura Pablo 
Published: May 2020

Abstract
In this article, we formally define and investigate the computational complexity of the definability problem for open first-order formulas (i.e. quantifier free first-order formulas) with equality. Given a logic $\boldsymbol{\mathcal{L}}$, the $\boldsymbol{\mathcal{L}}$-definability problem for finite structures takes as an input a finite structure $\boldsymbol{A}$ and a target relation $T$ over the domain of $\boldsymbol{A}$ and determines whether there is a formula of $\boldsymbol{\mathcal{L}}$ whose interpretation in $\boldsymbol{A}$ coincides with $T$. We show that the complexity of this problem for open first-order formulas (open definability, for short) is coNP-complete. We also investigate the parametric complexity of the problem and prove that if the size and the arity of the target relation $T$ are taken as parameters, then open definability is $\textrm{coW}[1]$-complete for every vocabulary $\tau $ with at least one, at least binary, relation.
Estimating COVID-19 outbreak risk through air travel
Authors: Daon Yair , Thompson Robin N , Obolski Uri 
Published: June 2020

AbstractBackgroundSubstantial limitations have been imposed on passenger air travel to reduce transmission of severe acute respiratory syndrome coronavirus 2 between regions and countries. However, as case numbers decrease, air travel will gradually resume. We considered a future scenario in which case numbers are low and air travel returns to normal. Under that scenario, there will be a risk of outbreaks in locations worldwide due to imported cases. We estimated the risk of different locations acting as sources of future coronavirus disease 2019 outbreaks elsewhere.MethodsWe use modelled global air travel data and population density estimates from locations worldwide to analyse the risk that 1364 airports are sources of future coronavirus disease 2019 outbreaks. We use a probabilistic, branching-process-based approach that considers the volume of air travelers between airports and the reproduction number at each location, accounting for local population density.ResultsUnder the scenario we model, we identify airports in East Asia as having the highest risk of acting as sources of future outbreaks. Moreover, we investigate the locations most likely to cause outbreaks due to air travel in regions that are large and potentially vulnerable to outbreaks: India, Brazil and Africa. We find that outbreaks in India and Brazil are most likely to be seeded by individuals travelling from within those regions. We find that this is also true for less vulnerable regions, such as the United States, Europe and China. However, outbreaks in Africa due to imported cases are instead most likely to be initiated by passengers travelling from outside the continent.ConclusionsVariation in flight volumes and destination population densities creates a non-uniform distribution of the risk that different airports pose of acting as the source of an outbreak. Accurate quantification of the spatial distribution of outbreak risk can therefore facilitate optimal allocation of resources for effective targeting of public health interventions.
Cannabinoid Hyperemesis Syndrome: An Unexpected Problem in an Unusual Setting—A Case Report
Authors: Stuart Rory , Richards John Ray 
Published: May 2020

Abstract
Cannabinoid hyperemesis syndrome presents with abdominal pain, nausea, and intractable vomiting caused by phytogenic and synthetic cannabinoid use. Complications associated with this disorder range from severe dehydration to acute kidney injury and rhabdomyolysis. This syndrome mimics many acute surgical and emergency medical conditions and can present several diagnostic and treatment challenges. While this syndrome is increasingly recognized as a common clinical entity in civilian emergency departments, there is little data concerning experience at military hospitals. We present a case of cannabinoid hyperemesis syndrome that was diagnosed and treated in a combat-zone US military emergency department in Southwest Asia.
Stellar population models based on the SDSS-IV MaStar library of stellar spectra – I. Intermediate-age/old models
Authors: Maraston C , Hill L , Thomas D , Yan R , Chen Y , Lian J , Parikh T , Neumann J , Meneses-Goytia S , Bershady M , Drory N , Bizyaev D , Concas A , Brownstein J , Lazarz D , Stringfellow G , Stassun K 
Published: June 2020

ABSTRACT
We use the first release of the SDSS/MaStar stellar library comprising ∼9000, high S/N spectra, to calculate integrated spectra of stellar population models. The models extend over the wavelength range 0.36–1.03 µm and share the same spectral resolution ($R\sim 1800$) and flux calibration as the SDSS-IV/MaNGA galaxy data. The parameter space covered by the stellar spectra collected thus far allows the calculation of models with ages and chemical composition in the range $\rm {\mathit{ t}\gt 200 \,Myr, -2 \lt = [Z/H] \lt = + 0.35}$, which will be extended as MaStar proceeds. Notably, the models include spectra for dwarf main-sequence stars close to the core H-burning limit, as well as spectra for cold, metal-rich giants. Both stellar types are crucial for modelling λ &gt; 0.7 µm absorption spectra. Moreover, a better parameter coverage at low metallicity allows the calculation of models as young as 500 Myr and the full account of the blue horizontal branch phase of old populations. We present models adopting two independent sets of stellar parameters (Teff, log g, [Z/H]). In a novel approach, their reliability is tested ‘on the fly’ using the stellar population models themselves. We perform tests with Milky Way and Magellanic Clouds globular clusters, finding that the new models recover their ages and metallicities remarkably well, with systematics as low as a few per cent for homogeneous calibration sets. We also fit a MaNGA galaxy spectrum, finding residuals of the order of a few per cent comparable to the state-of-art models, but now over a wider wavelength range.
Lyman α absorption beyond the disc of simulated spiral galaxies
Authors: Röttgers Bernhard , Naab Thorsten , Cernetic Miha , Davé Romeel , Kauffmann Guinevere , Borthakur Sanchayeeta , Foidl Horst 
Published: June 2020

ABSTRACT
We present an analysis of the origin and properties of the circumgalactic medium (CGM) in a suite of 11 cosmological zoom simulations resembling present-day spiral galaxies. On average the galaxies retain about 50 per cent of the cosmic fraction in baryons, almost equally divided into disc (interstellar medium) gas, cool CGM gas and warm-hot CGM gas. At radii smaller than 50 kpc the CGM is dominated by recycled warm-hot gas injected from the central galaxy, while at larger radii it is dominated by cool gas accreted on to the halo. The recycled gas typically accounts for one-third of the CGM mass. We introduce the novel publicly available analysis tool pygad to compute ion abundances and mock absorption spectra. For Lyman α absorption, we find good agreement of the simulated equivalent width (EW) distribution and observations out to large radii. Disc galaxies with quiescent assembly histories show significantly more absorption along the disc major axis. By comparing the EW and H i column densities, we find that CGM Lyman α absorbers are best represented by an effective line width b ≈ 50–70 km s−1 that increases mildly with halo mass, larger than typically assumed.
ATOMS: ALMA three-millimeter observations of massive star-forming regions – II. Compact objects in ACA observations and star formation scaling relations
Authors: Liu Tie , Evans Neal J , Kim Kee-Tae , Goldsmith Paul F , Liu Sheng-Yuan , Zhang Qizhou , Tatematsu Ken’ichi , Wang Ke , Juvela Mika , Bronfman Leonardo , Cunningham Maria R , Garay Guido , Hirota Tomoya , Lee Jeong-Eun , Kang Sung-Ju , Li Di , Li Pak-Shing , Mardones Diego , Qin Sheng-Li , Ristorcelli Isabelle , Tej Anandmayee , Toth L Viktor , Wu Jing-Wen , Wu Yue-Fang , Yi Hee-weon , Yun Hyeong-Sik , Liu Hong-Li , Peng Ya-Ping , Li Juan , Li Shang Huo , Lee Chang Won , Shen Zhi-Qiang , Baug Tapas , Wang Jun-Zhi , Zhang Yong , Issac Namitha , Zhu Feng-Yao , Luo Qiu-Yi , Liu Xun-Chuan , Xu Feng-Wei , Wang Yu , Zhang Chao , Ren Zhiyuan , Zhang Chao 
Published: May 2020

ABSTRACT
We report studies of the relationships between the total bolometric luminosity (Lbol or LTIR) and the molecular line luminosities of J = 1 − 0 transitions of H13CN, H13CO+, HCN, and HCO+ with data obtained from ACA observations in the ‘ATOMS’ survey of 146 active Galactic star-forming regions. The correlations between Lbol and molecular line luminosities $L^{\prime }_{\rm mol}$ of the four transitions all appear to be approximately linear. Line emission of isotopologues shows as large scatters in Lbol–$L^{\prime }_{\rm mol}$ relations as their main line emission. The log(Lbol/$L^{\prime }_{\rm mol}$) for different molecular line tracers have similar distributions. The Lbol-to-$L^{\prime }_{\rm mol}$ ratios do not change with galactocentric distances (RGC) and clump masses (Mclump). The molecular line luminosity ratios (HCN-to-HCO+, H13CN-to-H13CO+, HCN-to-H13CN, and HCO+-to-H13CO+) all appear constant against Lbol, dust temperature (Td), Mclump, and RGC. Our studies suggest that both the main lines and isotopologue lines are good tracers of the total masses of dense gas in Galactic molecular clumps. The large optical depths of main lines do not affect the interpretation of the slopes in star formation relations. We find that the mean star formation efficiency (SFE) of massive Galactic clumps in the ‘ATOMS’ survey is reasonably consistent with other measures of the SFE for dense gas, even those using very different tracers or examining very different spatial scales.
Extended X-ray emission from the classic nova DQ Her – on the possible presence of a magnetized jet
Authors: Toalá J A , Guerrero M A , Santamaría E , Ramos-Larios G , Sabin L 
Published: June 2020

ABSTRACT
We present an analysis of archival Chandra and XMM–Newton observations of the magnetically active cataclysmic variable DQ Her and the shell around it ejected in a nova event in 1934. A careful revision of the Chandra observations confirms previous claims on the presence of extended X-ray emission around DQ Her and reveals that it actually corresponds to a bipolar jet-like structure extending ≃32 arcsec along a direction from north-east to south-west. Therefore, this X-ray emission extends beyond the optical nova shell and is perpendicular to its major axis. The XMM–Newton observations confirm the presence of the extended X-ray emission detected by Chandra, suggesting the additional presence of a diffuse X-ray emission from a hot bubble filling the nova shell. This hot bubble was very likely produced by the explosion that created the nebular shell detected in optical images. The bipolar feature can be modelled by the combination of an optically thin plasma emission component with temperature T ≈ 2 × 106 K and a power-law component with a photon index of Γ = 1.1 ± 0.9. Its X-ray luminosity in the 0.3–5 keV energy range is LX = (2.1 ± 1.3) × 1029 erg s−1, for an electron density ne ≈ 2 cm−3 and a mass mX ≈ 3 × 10−6 M⊙. We suggest that the X-ray bipolar structure in DQ Her is a jet and interpret its non-thermal X-ray emission in terms of a magnetized jet.
The early growth of supermassive black holes in cosmological hydrodynamic simulations with constrained Gaussian realizations
Authors: Huang Kuan-Wei , Ni Yueying , Feng Yu , Di Matteo Tiziana 
Published: May 2020

ABSTRACT
The paper examines the early growth of supermassive black holes (SMBHs) in cosmological hydrodynamic simulations with different BH seeding scenarios. Employing the constrained Gaussian realization, we reconstruct the initial conditions in the large-volume bluetides simulation and run them to z = 6 to cross-validate that the method reproduces the first quasars and their environments. Our constrained simulations in a volume of $(15 \, h^{-1} {\rm Mpc})^3$ successfully recover the evolution of large-scale structure and the stellar and BH masses in the vicinity of a ${\sim}10^{12} \, M_{\odot }$ halo which we identified in bluetides at z ∼ 7 hosting a ${\sim}10^9 \, M_{\odot }$ SMBH. Among our constrained simulations, only the ones with a low-tidal field and high-density peak in the initial conditions induce the fastest BH growth required to explain the z &gt; 6 quasars. We run two sets of simulations with different BH seed masses of 5 × 103, 5 × 104, and $5 \times 10^5 \, h^{-1} M_{\odot }$, (i) with the same ratio of halo to BH seed mass and (ii) with the same halo threshold mass. At z = 6, all the SMBHs converge in mass to ${\sim}10^9 \, M_{\odot }$ except for the one with the smallest seed in (ii) undergoing critical BH growth and reaching 108 – $10^9 \, M_{\odot }$, albeit with most of the growth in (ii) delayed compared to set (i). The finding of eight BH mergers in the small-seed scenario (four with masses 104 – $10^6 \, M_{\odot }$ at z &gt; 12), six in the intermediate-seed scenario, and zero in the large-seed scenario suggests that the vast BHs in the small-seed scenario merge frequently during the early phases of the growth of SMBHs. The increased BH merger rate for the low-mass BH seed and halo threshold scenario provides an exciting prospect for discriminating BH formation mechanisms with the advent of multimessenger astrophysics and next-generation gravitational wave facilities.
Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks
Authors: Szlachta Karol , Manukyan Arkadi , Raimer Heather M , Singh Sandeep , Salamon Anita , Guo Wenying , Lobachev Kirill S , Wang Yuh-Hwa 
Published: June 2020

AbstractDNA double-stranded breaks (DSBs) trigger human genome instability, therefore identifying what factors contribute to DSB induction is critical for our understanding of human disease etiology. Using an unbiased, genome-wide approach, we found that genomic regions with the ability to form highly stable DNA secondary structures are enriched for endogenous DSBs in human cells. Human genomic regions predicted to form non-B-form DNA induced gross chromosomal rearrangements in yeast and displayed high indel frequency in human genomes. The extent of instability in both analyses is in concordance with the structure forming ability of these regions. We also observed an enrichment of DNA secondary structure-prone sites overlapping transcription start sites (TSSs) and CCCTC-binding factor (CTCF) binding sites, and uncovered an increase in DSBs at highly stable DNA secondary structure regions, in response to etoposide, an inhibitor of topoisomerase II (TOP2) re-ligation activity. Importantly, we found that TOP2 deficiency in both yeast and human leads to a significant reduction in DSBs at structure-prone loci, and that sites of TOP2 cleavage have a greater ability to form highly stable DNA secondary structures. This study reveals a direct role for TOP2 in generating secondary structure-mediated DNA fragility, advancing our understanding of mechanisms underlying human genome instability.