bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole plastomes are not enough: phylogenomic and morphometric exploration at multiple demographic levels of the bee orchid clade Ophrys sect. Sphegodes
Authors: Bateman Richard M , Rudall Paula J , Murphy Alexander R M , Cowan Robyn S , Devey Dion S , Peréz-Escobar Oscar A 
Published: December 2020

Abstract
Plastid sequences have long dominated phylogeny reconstruction at all time depths, predicated on a usually untested assumption that they accurately represent the evolutionary histories of phenotypically circumscribed species. We combined detailed in situ morphometrics (124 plants) and whole-plastome sequencing through genome skimming (71 plants) in order to better understand species-level diversity and speciation in arguably the most challenging monophyletic group within the taxonomically controversial, pseudo-copulatory bee orchid genus Ophrys. Using trees and ordinations, we interpreted the data at four nested demographic levels—macrospecies, mesospecies, microspecies, and local population—seeking the optimal level for bona fide species. Neither morphological nor molecular discontinuities are evident at any level below macrospecies, the observed overlap among taxa suggesting that both mesospecies and microspecies reflect arbitrary division of a continuum of variation. Plastomes represent geographic location more strongly than taxonomic assignment and correlate poorly with morphology, suggesting widespread plastid capture and possibly post-glacial expansion from multiple southern refugia. As they are rarely directly involved in the speciation process, plastomes depend on extinction of intermediate lineages to provide phylogenetic signal and so cannot adequately document evolutionary radiations. The popular ‘ethological’ evolutionary model recognizes as numerous ‘ecological species’ (microspecies) lineages perceived as actively diverging as a result of density-dependent selection on very few features that immediately dictate extreme pollinator specificity. However, it is assumed rather than demonstrated that the many microspecies are genuinely diverging. We conversely envisage a complex four-dimensional reticulate network of lineages, generated locally and transiently through a wide spectrum of mechanisms, but each unlikely to maintain an independent evolutionary trajectory long enough to genuinely speciate by escaping ongoing gene flow. The frequent but localized microevolution that characterizes the Ophrys sphegodes complex is often convergent and rarely leads to macroevolution. Choosing between the contrasting ‘discontinuity’ and ‘ethology’ models will require next-generation sequencing of nuclear genomes plus ordination of corresponding morphometric matrices, seeking the crucial distinction between retained ancestral polymorphism—consistent with lineage divergence—and polymorphisms reflecting gene flow through ‘hybridization’—more consistent with lineage convergence.
An application of data visualization technique in Arabic literature and linguistics
Authors: Yi Fan , Mahmoudi Mohammad Reza , S Band Shahab 
Published: December 2020

AbstractIn this work, we intended to study and compare the traits of God in the Medinan and Meccan Qur'an’s Suras, based on statistics and data visualization. The entire verses of Qur’an were considered and the count of each beauty and divine glory trait was calculated, separately in Medinan and Meccan Suras. The frequencies of the divine glory, the beauty and total traits in Meccan, Medinan and total Suras were studied and compared using data visualization technique. The results indicated that for Medinan Suras, in divine glory traits, Hakem and Aziz, in beauty traits, Alim and Rahim, and totally, Alim, Rahim, and Hakem had the most uses; for Meccan Suras, in divine glory traits, Aziz and Hakim, in beauty traits, Rahman and Rahim, and totally, Rahman and Rahim had the most uses; and for total Suras, in divine glory traits, Hakem and Aziz, in beauty traits, Rahim, Rahman, and Alim, and totally, Rahim, Rahman, and Alim had the most uses. Moreover, the rates of using divine glory traits in Medinan and Meccan Suras (16.1% and 17.6%) and the rates of using beauty traits in Medinan and Meccan Suras (83.9% and 82.4%) significantly did not differ.
Feedback-limited accretion: variable luminosity from growing planets
Authors: Gárate M , Cuadra J , Montesinos M , Arévalo P 
Published: December 2020

ABSTRACT
Planets form in discs of gas and dust around stars, and continue to grow by accretion of disc material while available. Massive planets clear a gap in their protoplanetary disc, but can still accrete gas through a circumplanetary disc. For high enough accretion rates, the planet should be detectable at infrared wavelengths. As the energy of the gas accreted on to the planet is released, the planet surroundings heat up in a feedback process. We aim to test how this planet feedback affects the gas in the coorbital region and the accretion rate itself. We modified the 2D code FARGO-AD to include a prescription for the accretion and feedback luminosity of the planet and use it to model giant planets on 10 au circular and eccentric orbits around a solar mass star. We find that this feedback reduces but does not halt the accretion on to the planet, although this result might depend on the near-coincident radial ranges where both recipes are implemented. Our simulations also show that the planet heating gives the accretion rate a stochastic variability with an amplitude $\Delta \dot{M}_p \sim 0.1 \dot{M}_p$. A planet on an eccentric orbit (e = 0.1) presents a similar variability amplitude, but concentrated on a well-defined periodicity of half the orbital period and weaker broad-band noise, potentially allowing observations to discriminate between both cases. Finally, we find that the heating of the co-orbital region by the planet feedback alters the gas dynamics, reducing the difference between its orbital velocity and the Keplerian motion at the edge of the gap, which can have important consequences for the formation of dust rings.
An ALMA/NOEMA survey of the molecular gas properties of high-redshift star-forming galaxies
Authors: Birkin Jack E , Weiss Axel , Wardlow J L , Smail Ian , Swinbank A M , Dudzevičiūtė U , An Fang Xia , Ao Y , Chapman S C , Chen Chian-Chou , da Cunha E , Dannerbauer H , Gullberg B , Hodge J A , Ikarashi S , Ivison R J , Matsuda Y , Stach S M , Walter F , Wang W-H , van der Werf P 
Published: December 2020

ABSTRACT
We have used ALMA and NOEMA to study the molecular gas reservoirs in 61 ALMA-identified submillimetre galaxies (SMGs) in the COSMOS, UDS, and ECDFS fields. We detect 12CO ($J_{\rm up} =$ 2–5) emission lines in 50 sources, and [C i](3P1 − 3P0) emission in eight, at $z =$ 1.2–4.8 and with a median redshift of 2.9 ± 0.2. By supplementing our data with literature sources, we construct a statistical CO spectral line energy distribution and find that the 12CO line luminosities in SMGs peak at Jup ∼ 6, consistent with similar studies. We also test the correlations of the CO, [C i], and dust as tracers of the gas mass, finding the three to correlate well, although the CO and dust mass as estimated from the 3-mm continuum are preferable. We estimate that SMGs lie mostly on or just above the star-forming main sequence, with a median gas depletion timescale, tdep = Mgas/SFR, of 210 ± 40 Myr for our sample. Additionally, tdep declines with redshift across z ∼ 1–5, while the molecular gas fraction, μgas = Mgas/M*, increases across the same redshift range. Finally, we demonstrate that the distribution of total baryonic mass and dynamical line width, Mbaryon–σ, for our SMGs is consistent with that followed by early-type galaxies in the Coma cluster, providing strong support to the suggestion that SMGs are progenitors of massive local spheroidal galaxies. On the basis of this, we suggest that the SMG populations above and below an 870-μm flux limit of S870 ∼ 5 mJy may correspond to the division between slow and fast rotators seen in local early-type galaxies.
The Swift bulge survey: motivation, strategy, and first X-ray results
Authors: Bahramian A , Heinke C O , Kennea J A , Maccarone T J , Evans P A , Wijnands R , Degenaar N , in’t Zand J J M , Shaw A W , Rivera Sandoval L E , McClure S , Tetarenko A J , Strader J , Kuulkers E , Sivakoff G R 
Published: December 2020

ABSTRACT
Very faint X-ray transients (VFXTs) are X-ray transients with peak X-ray luminosities (LX) of L$_X \lesssim 10^{36}$ erg s−1, which are not well understood. We carried out a survey of 16 deg2 of the Galactic Bulge with the Swift Observatory, using short (60 s) exposures, and returning every 2 weeks for 19 epochs in 2017–18 (with a gap from 2017 November to 2018 February, when the Bulge was in sun-constraint). Our main goal was to detect and study VFXT behaviour in the Galactic Bulge across various classes of X-ray sources. In this work, we explain the observing strategy of the survey, compare our results with the expected number of source detections per class, and discuss the constraints from our survey on the Galactic VFXT population. We detected 91 X-ray sources, 25 of which have clearly varied by a factor of at least 10. In total, 45 of these X-ray sources have known counterparts: 17 chromospherically active stars, 12 X-ray binaries, 5 cataclysmic variables (and 4 candidates), 3 symbiotic systems, 2 radio pulsars, 1 active galactic nuclei, and a young star cluster. The other 46 are of previously undetermined nature. We utilize X-ray hardness ratios, searches for optical/infrared counterparts in published catalogues, and flux ratios from quiescence to outburst to constrain the nature of the unknown sources. Of these 46, 7 are newly discovered hard transients, which are likely VFXT X-ray binaries. Furthermore, we find strong new evidence for a symbiotic nature of four sources in our full sample, and new evidence for accretion power in six X-ray sources with optical counterparts. Our findings indicate that a large subset of VXFTs is likely made up of symbiotic systems.
Multiwavelength analysis of low surface brightness galaxies to study possible dark matter signature
Authors: Bhattacharjee Pooja , Majumdar Pratik , Das Mousumi , Das Subinoy , Joarder Partha S , Biswas Sayan 
Published: December 2020

ABSTRACTLow surface brightness (LSB) galaxies have very diffuse, low surface density stellar discs that appear faint in optical images. They are very rich in neutral hydrogen (H i) gas, which extends well beyond the stellar discs. Their extended H i rotation curves and stellar discs indicate that they have very massive dark matter (DM) haloes compared to normal bright galaxies. Hence, LSB galaxies may represent valuable laboratories for the indirect detection of DM. In this paper, we search for weakly interacting massive particle annihilation signatures in four LSB galaxies and present an analysis of nearly 9 yr of data from the Fermi Large Area Telescope (Fermi-LAT). Above 500 MeV, no excess emission was detected from the LSB galaxies. We obtain constraints on the DM cross-section for different annihilation channels, for both individual and stacked targets. In addition to this, we use radio data from the Very Large Array radio telescope in order to derive DM constraints, following a multiwavelength approach. The constraints obtained from the four considered LSB galaxies are nearly three orders of magnitude weaker than the predicted limits for the thermal relic abundances and the combined limits achieved from Fermi-LAT observations of dwarf spheroidal galaxies. Finally, we discuss the possibility of detecting emission from LSB galaxies using the upcoming ground-based γ-ray and radio observatories, namely the Cherenkov Telescope Array and the Square Kilometre Array.
The Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the BAO and growth rate of structure of the emission line galaxy sample from the anisotropic power spectrum between redshift 0.6 and 1.1
Authors: de Mattia Arnaud , Ruhlmann-Kleider Vanina , Raichoor Anand , Ross Ashley J , Tamone Amélie , Zhao Cheng , Alam Shadab , Avila Santiago , Burtin Etienne , Bautista Julian , Beutler Florian , Brinkmann Jonathan , Brownstein Joel R , Chapman Michael J , Chuang Chia-Hsun , Comparat Johan , Bourboux Hélion du Mas des , Dawson Kyle S , de la Macorra Axel , Gil-Marín Héctor , Gonzalez-Perez Violeta , Gorgoni Claudio , Hou Jiamin , Kong Hui , Lin Sicheng , Nadathur Seshadri , Newman Jeffrey A , Mueller Eva-Maria , Percival Will J , Rezaie Mehdi , Rossi Graziano , Schneider Donald P , Tiwari Prabhakar , Vivek M , Wang Yuting , Zhao Gong-Bo 
Published: December 2020

Abstract
We analyse the large-scale clustering in Fourier space of emission line galaxies (ELG) from the Data Release 16 of the Sloan Digital Sky Survey IV extended Baryon Oscillation Spectroscopic Survey. The ELG sample contains 173,736 galaxies covering 1,170 square degrees in the redshift range 0.6 &lt; z &lt; 1.1. We perform a BAO measurement from the post-reconstruction power spectrum monopole, and study redshift space distortions (RSD) in the first three even multipoles. Photometric variations yield fluctuations of both the angular and radial survey selection functions. Those are directly inferred from data, imposing integral constraints which we model consistently. The full data set has only a weak preference for a BAO feature (1.4σ). At the effective redshift zeff = 0.845 we measure $D_{\rm V}(z_{\rm eff})/r_{\rm drag} = 18.33_{-0.62}^{+0.57}$, with DV the volume-averaged distance and rdrag the comoving sound horizon at the drag epoch. In combination with the RSD measurement, at zeff = 0.85 we find $f\sigma _8(z_{\rm eff}) = 0.289_{-0.096}^{+0.085}$, with f the growth rate of structure and σ8 the normalisation of the linear power spectrum, $D_{\rm H}(z_{\rm eff})/r_{\rm drag} = 20.0_{-2.2}^{+2.4}$ and DM(zeff)/rdrag = 19.17 ± 0.99 with DH and DM the Hubble and comoving angular distances, respectively. These results are in agreement with those obtained in configuration space, thus allowing a consensus measurement of fσ8(zeff) = 0.315 ± 0.095, $D_{\rm H}(z_{\rm eff})/r_{\rm drag} = 19.6_{-2.1}^{+2.2}$ and DM(zeff)/rdrag = 19.5 ± 1.0. This measurement is consistent with a flat ΛCDM model with Planck parameters.
Crystal structure of a tick-borne flavivirus RNA-dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses
Authors: Yang Jieyu , Jing Xuping , Yi Wenfu , Li Xiao-Dan , Yao Chen , Zhang Bo , Zheng Zhenhua , Wang Hanzhong , Gong Peng 
Published: December 2020

Abstract
The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By solving the RdRP crystal structure of the tick-borne encephalitis virus (TBEV), a tick-borne flavivirus, and comparing the structural and sequence features with mosquito-borne flavivirus RdRPs, we found that a region between RdRP catalytic motifs B and C, namely region B-C, clearly bears host-related diversity. Inter-virus substitutions of region B-C sequence were designed in both TBEV and mosquito-borne Japanese encephalitis virus backbones. While region B-C substitutions only had little or moderate effect on RdRP catalytic activities, virus proliferation was not supported by these substitutions in both virus systems. Importantly, a TBEV replicon-derived viral RNA replication was significantly reduced but not abolished by the substitution, suggesting the involvement of region B-C in viral and/or host processes beyond RdRP catalysis. A systematic structural analysis of region B-C in viral RdRPs further emphasizes its high level of structure and length diversity, providing a basis to further refine its relevance in RNA virus-host interactions in a general context.
Whole-brain radiotherapy with and without concurrent erlotinib in NSCLC with brain metastases: a multicenter, open-label, randomized, controlled phase III trial
Authors: Yang Zhenzhou , Zhang Yan , Li Rongqing , Yisikandaer Abulimiti , Ren Biyong , Sun Jianguo , Li Jianjun , Chen Long , Zhao Ren , Zhang Juying , Xia Xuefeng , Liao Zhongxing , Carbone David P 
Published: December 2020

Abstract

Background
Erlotinib combined with whole-brain radiotherapy (WBRT) demonstrated a favorable objective response rate in a phase II single-arm trial of non–small cell lung cancer (NSCLC) patients with brain metastases. We assessed whether concurrent erlotinib with WBRT is safe and benefits patients in a phase III, randomized trial.

Methods
NSCLC patients with two or more brain metastases were enrolled and randomly assigned (1:1) to WBRT (n = 115) or WBRT combined with erlotinib arms (n = 109). The primary endpoint was intracranial progression-free survival (iPFS) and cognitive function (CF) was assessed by the Mini-Mental State Examination (MMSE).

Results
A total of 224 patients from 10 centers across China were randomized to treatments. Median follow-up was 11.2 months. Median iPFS for WBRT concurrent erlotinib was 11.2 months vs 9.2 months for WBRT-alone (P = .601). Median PFS and overall survival (OS) of combination group were 5.3 vs 4.0 months (P = .825) and 12.9 vs 10.0 months (P = .545), respectively, compared with WBRT-alone. In EGFR-mutant patients, iPFS (14.6 vs 12.8 months; P = .164), PFS (8.8 vs 6.4 months; P = .702), and OS (17.5 vs 16.9 months; P = .221) were not significantly improved in combination group over WBRT-alone. Moreover, there were no significant differences in patients experiencing MMSE score change between the treatments.

Conclusion
Concurrent erlotinib with WBRT didn’t improve iPFS and excessive CF detriment either in the intent-to-treat (ITT) population or in EGFR-mutant patients compared with WBRT-alone, suggesting that while safe for patients already taking the drug, there is no justification for adding concurrent EGFR-TKI with WBRT for the treatment of brain metastases.
Trial registration: Clinical trials.gov identifier: NCT01887795
Poststudy Point-of-Care Oral Fluid Testing in Human Immunodeficiency Virus-1 Vaccinees
Authors: Oganezova Karina , Fontana-Martinez Elvin J , Gothing Jon A , Pandit Alisha , Kwara Esther , Yanosick Katherine , Dragavon Joan , Goecker Erin A , Maenza Janine , Espy Nicole , Tomaka Frank , Lavreys Ludo , Allen Mary , D’Souza Patricia , Hural John , Coombs Robert W , Dolin Raphael , Seaman Michael S , Walsh Stephen R , Baden Lindsey R 
Published: December 2020

Abstract

Background
Experimental human immunodeficiency virus (HIV)-1 vaccines frequently elicit antibodies against HIV-1 that may react with commonly used HIV diagnostic tests, a phenomenon known as vaccine-induced seropositivity/seroreactivity (VISP/VISR). We sought to determine, under clinic conditions, whether a patient-controlled HIV test, OraQuick ADVANCE Rapid HIV-1/2 Antibody Test, detected HIV-1 vaccine-induced antibodies.

Methods
Plasma assessment of HIV-1 cross-reactivity was examined in end-of-study samples from 57 healthy, HIV-uninfected participants who received a candidate vaccine that has entered Phase 2B and 3 testing. We also screened 120 healthy, HIV-uninfected, unblinded HIV-1 vaccine participants with VISP/VISR for an assessment using saliva. These participants came from 21 different parent vaccine protocols representing 17 different vaccine regimens, all of which contained an HIV-1 envelope immunogen. OraQuick ADVANCE was compared with results from concurrent blood samples using a series of commercial HIV screening immunoassays.

Results
Fifty-seven unique participant plasma samples were assayed in vitro, and only 1 (1.8%) was reactive by OraQuick ADVANCE. None of the 120 clinic participants (0%; 95% confidence interval, 0% to 3.7%) tested positive by OraQuick ADVANCE, and all were confirmed to be uninfected by HIV-1 viral ribonucleic acid testing. One hundred eighteen of the 120 (98.3%) participants had a reactive HIV test for VISP/VISR: 77 (64%) had at least 1 reactive fourth-generation HIV-1 diagnostic test (P &lt; .0001 vs no reactive OraQuick ADVANCE results), and 41 (34%) only had a reactive test by the less specific third-generation Abbott Prism assay.

Conclusions
These data suggest that this widely available patient-controlled test has limited reactivity to HIV-1 antibodies elicited by these candidate HIV-1 vaccines.
Validation of N95 Filtering Facepiece Respirator Decontamination Methods Available at a Large University Hospital
Authors: Wigginton Krista R , Arts Peter J , Clack Herek L , Fitzsimmons William J , Gamba Mirko , Harrison Katherine R , LeBar William , Lauring Adam S , Li Lucinda , Roberts William W , Rockey Nicole C , Torreblanca Jania , Young Carol , Anderegg Loïc G , Cohn Amy M , Doyle John M , Meisenhelder Cole M , Raskin Lutgarde , Love Nancy G , Kaye Keith S 
Published: December 2020

Abstract

Background
Due to unprecedented shortages in N95 filtering facepiece respirators, healthcare systems have explored N95 reprocessing. No single, full-scale reprocessing publication has reported an evaluation including multiple viruses, bacteria, and fungi along with respirator filtration and fit.

Methods
We explored reprocessing methods using new 3M 1860 N95 respirators, including moist (50%–75% relative humidity [RH]) heat (80–82°C for 30 minutes), ethylene oxide (EtO), pulsed xenon UV-C (UV-PX), hydrogen peroxide gas plasma (HPGP), and hydrogen peroxide vapor (HPV). Respirator samples were analyzed using 4 viruses (MS2, phi6, influenza A virus [IAV], murine hepatitis virus [MHV)]), 3 bacteria (Escherichia coli, Staphylococcus aureus, Geobacillus stearothermophilus spores, and vegetative bacteria), and Aspergillus niger. Different application media were tested. Decontaminated respirators were evaluated for filtration integrity and fit.

Results
Heat with moderate RH most effectively inactivated virus, resulting in reductions of &gt;6.6-log10 MS2, &gt;6.7-log10 Phi6, &gt;2.7-log10 MHV, and &gt;3.9-log10 IAV and prokaryotes, except for G stearothermohphilus. Hydrogen peroxide vapor was moderately effective at inactivating tested viruses, resulting in 1.5- to &gt;4-log10 observable inactivation. Staphylococcus aureus inactivation by HPV was limited. Filtration efficiency and proper fit were maintained after 5 cycles of heat with moderate RH and HPV. Although it was effective at decontamination, HPGP resulted in decreased filtration efficiency, and EtO treatment raised toxicity concerns. Observed virus inactivation varied depending upon the application media used.

Conclusions
Both moist heat and HPV are scalable N95 reprocessing options because they achieve high levels of biological indicator inactivation while maintaining respirator fit and integrity.
Cybersecurity in Japan
Authors: Bartlett Benjamin 
Published: December 2020

Abstract
Two recent trends have been visible in Japanese politics: the increasing importance of politicians versus bureaucrats in policymaking, and the increasing willingness of the Japanese government to expand its authority and capability in dealing with national security. While these trends have affected Japanese cybersecurity policy as well, those effects have been limited. Much of the drafting of cybersecurity policy is done within a cabinet body primarily staffed with bureaucrats seconded from three ministries and one agency: METI, MIC, MOD, and NPA. And while the capabilities of the JSDF and the conditions under which it can operate have been expanded, as of yet there has been little sign that potential trade-offs between priorities are being resolved in favor of national security. The purpose of this chapter is to explain how bureaucratic politics and these trends in Japanese politics have shaped Japanese cybersecurity policy over time.