bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Finiteness of Quantum K-Theory of a Homogeneous Space
Authors: Anderson David , Chen Linda , Tseng Hsian-Hua
Published: April 2020

We show that the product in the quantum K-ring of a generalized flag manifold $G/P$ involves only finitely many powers of the Novikov variables. In contrast to previous approaches to this finiteness question, we exploit the finite difference module structure of quantum K-theory. At the core of the proof is a bound on the asymptotic growth of the $J$-function, which in turn comes from an analysis of the singularities of the zastava spaces studied in geometric representation theory. An appendix by H. Iritani establishes the equivalence between finiteness and a quadratic growth condition on certain shift operators.
Rapid Deployment of Inpatient Telemedicine In Response to COVID-19 Across Three Health Systems
Authors: Vilendrer Stacie , Patel Birju , Chadwick Whitney , Hwa Michael , Asch Steven , Pageler Natalie , Ramdeo Rajiv , Saliba-Gustafsson Erika A , Strong Philip , Sharp Christopher
Published: April 2020

Objective

To reduce pathogen exposure, conserve personal protective equipment, and facilitate health care personnel work participation in the setting of the COVID-19 pandemic, three affiliated institutions rapidly and independently deployed inpatient telemedicine programs during March 2020. We describe key features and early learnings of these programs in the hospital setting.

Methods

Relevant clinical and operational leadership from an academic medical center, pediatric teaching hospital, and safety net county health system met to share learnings shortly after deploying inpatient telemedicine. A summative analysis of their learnings was re-circulated for approval.

Results

All three institutions faced pressure to urgently standup new telemedicine systems while still maintaining secure information exchange. Differences across patient demographics and technological capabilities led to variation in solution design, though key technical considerations were similar. Rapid deployment in each system relied on readily available consumer-grade technology, given the existing familiarity to patients and clinicians and minimal infrastructure investment. Preliminary data from the academic medical center over one month suggested positive adoption with 631 inpatient video calls lasting an average (standard deviation) of 16.5 minutes (19.6) based on inclusion criteria.

Discussion

The threat of an imminent surge of COVID-19 patients drove three institutions to rapidly develop inpatient telemedicine solutions. Concurrently, federal and state regulators temporarily relaxed restrictions that would have previously limited these efforts. Strategic direction from executive leadership, leveraging off-the-shelf hardware, vendor engagement, and clinical workflow integration facilitated rapid deployment.

Conclusion

The rapid deployment of inpatient telemedicine is feasible across diverse settings as a response to the COVID-19 pandemic.
Multiplicity and Modifiers
Authors: Romoli Jacopo , Renans Agata
Published: April 2020

A sentence with an adverbial modifier under negation like Mike didn’t wash the window with soap gives rise to an inference that Mike did wash the window. A sentence with a plural noun like Mike washed windows gives rise to a so-called ‘multiplicity’ inference that Mike washed multiple windows. In this note, we focus on the interaction between these two inferences in sentences containing both an adverbial modifier and a plural noun under negation, like Mike didn’t wash windows with soap. We observe that this sentence has a reading conveying that Mike didn’t wash any window with soap but that he did wash multiple windows (albeit not with soap). As we discuss, this reading is not predicted by any version of the implicature approach to the multiplicity inference, in combination with the implicature treatment of the inference of adverbial modifiers. We sketch two solutions for this problem. The first keeps the implicature approach to adverbial modifiers but adopts a non-implicature approach to multiplicity based on homogeneity. The second solution holds on to the implicature approach to the multiplicity inference but accounts for the inference of adverbial modifiers as a presupposition. In addition, it adopts the idea that presuppositions can be strengthened via implicatures, as proposed recently in the literature. Either way, the interaction between multiplicity and the inference of adverbial modifiers suggests that we cannot treat both as implicatures: if we want to treat either one as an implicature, we need to do something different for the other. We end by comparing the case above to analogous cases involving different scalar inferences and showing that the ambiguity approach to the multiplicity inference does not provide a solution to our problem.
Inner-Space and Liquid Myths: J.G. Ballard as a Post-Secular Writer
Authors: Bowyer Andrew D
Published: April 2020

British novelist James Graham Ballard (1930–2009) was an inveterate mythmaker. In this article, I characterise him as a post-secular writer who saw the imagination as a means to confront trauma, probe memory, and salvage meaning in a secular age. Anchoring the argument in a selection of novels and works that constitute his ‘autobiographical turn’, I suggest that resonances with contemporary theology may be detected, particularly the disruptive, anti-fascist, postmodern, ‘tehomic’ theology of Catherine Keller.
A precise benchmark for cluster scaling relations: Fundamental Plane, Mass Plane, and IMF in the Coma cluster from dynamical models
Authors: Shetty Shravan , Cappellari Michele , McDermid Richard M , Krajnović Davor , de Zeeuw P T , Davies Roger L , Kobayashi Chiaki
Published: April 2020

We study a sample of 148 early-type galaxies in the Coma cluster using SDSS photometry and spectra, and calibrate our results using detailed dynamical models for a subset of these galaxies, to create a precise benchmark for dynamical scaling relations in high-density environments. For these galaxies, we successfully measured global galaxy properties, modelled stellar populations, and created dynamical models, and support the results using detailed dynamical models of 16 galaxies, including the two most massive cluster galaxies, using data taken with the SAURON IFU. By design, the study provides minimal scatter in derived scaling relations due to the small uncertainty in the relative distances of galaxies compared to the cluster distance. Our results demonstrate low (≤55 per cent for 90th percentile) dark matter fractions in the inner 1Re of galaxies. Owing to the study design, we produce the tightest, to our knowledge, IMF–σe relation of galaxies, with a slope consistent with that seen in local galaxies. Leveraging our dynamical models, we transform the classical Fundamental Plane of the galaxies to the Mass Plane. We find that the coefficients of the Mass Plane are close to predictions from the virial theorem, and have significantly lower scatter compared to the Fundamental Plane. We show that Coma galaxies occupy similar locations in the (M*–Re) and (M*−σe) relations as local field galaxies but are older. This, and the fact we find only three slow rotators in the cluster, is consistent with the scenario of hierarchical galaxy formation and expectations of the kinematic morphology–density relation.
The onset of instability in resonant chains
Authors: Pichierri Gabriele , Morbidelli Alessandro
Published: April 2020

There is evidence that most chains of mean motion resonances of type k:k − 1 among exoplanets become unstable once the dissipative action from the gas is removed from the system, particularly for large N (the number of planets) and k (indicating how compact the chain is). We present a novel dynamical mechanism that can explain the origin of these instabilities and thus the dearth of resonant systems in the exoplanet sample. It relies on the emergence of secondary resonances between a fraction of the synodic frequency 2π(1/P1 − 1/P2) and the libration frequencies in the mean motion resonance. These secondary resonances excite the amplitudes of libration of the mean motion resonances, thus leading to an instability. We detail the emergence of these secondary resonances by carrying out an explicit perturbative scheme to second order in the planetary masses and isolating the harmonic terms that are associated with them. Focusing on the case of three planets in the 3:2–3:2 mean motion resonance as an example, a simple but general analytical model of one of these resonances is obtained, which describes the initial phase of the activation of one such secondary resonance. The dynamics of the excited system is also briefly described. Finally, a generalization of this dynamical mechanism is obtained for arbitrary N and k. This leads to an explanation of previous numerical experiments on the stability of resonant chains, showing why the critical planetary mass allowed for stability decreases with increasing N and k.
The impact of peculiar velocities on the estimation of the Hubble constant from gravitational wave standard sirens
Authors: Nicolaou Constantina , Lahav Ofer , Lemos Pablo , Hartley William , Braden Jonathan
Published: April 2020

In this work, we investigate the systematic uncertainties that arise from the calculation of the peculiar velocity when estimating the Hubble constant (H0) from gravitational wave standard sirens. We study the GW170817 event and the estimation of the peculiar velocity of its host galaxy, NGC 4993, when using Gaussian smoothing over nearby galaxies. NGC 4993 being a relatively nearby galaxy, at ∼40 Mpc away, is subject to a significant effect of peculiar velocities. We demonstrate a direct dependence of the estimated peculiar velocity value on the choice of smoothing scale. We show that when not accounting for this systematic, a bias of ${\sim }200~{\rm km\, s^{-1}}$ in the peculiar velocity incurs a bias of ${\sim }4~{\rm km\, s^{-1}\, Mpc^{-1}}$ on the Hubble constant. We formulate a Bayesian model that accounts for the dependence of the peculiar velocity on the smoothing scale and by marginalizing over this parameter we remove the need for a choice of smoothing scale. The proposed model yields $H_0 = 68.6 ^{+14.0} _{-8.5}~{\rm km\, s^{-1}\, Mpc^{-1}}$. We demonstrate that under this model a more robust unbiased estimate of the Hubble constant from nearby GW sources is obtained.
Revealing the tidal scars of the Small Magellanic Cloud
Authors: De Leo Michele , Carrera Ricardo , Noël Noelia E D , Read Justin I , Erkal Denis , Gallart Carme
Published: April 2020

Due to their close proximity, the Large and Small Magellanic Clouds (LMC/SMC) provide natural laboratories for understanding how galaxies form and evolve. With the goal of determining the structure and dynamical state of the SMC, we present new spectroscopic data for ∼3000 SMC red giant branch stars observed using the AAOmega spectrograph at the Anglo-Australian Telescope. We complement our data with further spectroscopic measurements from previous studies that used the same instrumental configuration as well as proper motions from the Gaia Data Release 2 catalogue. Analysing the photometric and stellar kinematic data, we find that the SMC centre of mass presents a conspicuous offset from the velocity centre of its associated H i gas, suggesting that the SMC gas is likely to be far from dynamical equilibrium. Furthermore, we find evidence that the SMC is currently undergoing tidal disruption by the LMC within 2 kpc of the centre of the SMC, and possibly all the way into the very core. This is revealed by a net outward motion of stars from the SMC centre along the direction towards the LMC and an apparent tangential anisotropy at all radii. The latter is expected if the SMC is undergoing significant tidal stripping, as we demonstrate using a suite of N-body simulations of the SMC/LMC system disrupting around the Milky Way. Our results suggest that dynamical models for the SMC that assume a steady state will need to be revisited.
The unusual broad-band X-ray spectral variability of NGC 1313 X-1 seen with XMM–Newton, Chandra, and NuSTAR
Authors: Walton D J , Pinto C , Nowak M , Bachetti M , Sathyaprakash R , Kara E , Roberts T P , Soria R , Brightman M , Canizares C R , Earnshaw H P , Fürst F , Heida M , Middleton M J , Stern D , Tao L , Webb N , Alston W N , Barret D , Fabian A C , Harrison F A , Kosec P
Published: April 2020

We present results from the major coordinated X-ray observing programme on the ULX NGC 1313 X-1 performed in 2017, combining XMM–Newton, Chandra, and NuSTAR, focusing on the evolution of the broad-band (∼0.3–30.0 keV) continuum emission. Clear and unusual spectral variability is observed, but this is markedly suppressed above ∼10–15 keV, qualitatively similar to the ULX Holmberg IX X-1. We model the multi-epoch data with two-component accretion disc models designed to approximate super-Eddington accretion, allowing for both a black hole and a neutron star accretor. With regards to the hotter disc component, the data trace out two distinct tracks in the luminosity–temperature plane, with larger emitting radii and lower temperatures seen at higher observed fluxes. Despite this apparent anticorrelation, each of these tracks individually shows a positive luminosity–temperature relation. Both are broadly consistent with L ∝ T4, as expected for blackbody emission with a constant area, and also with L ∝ T2, as may be expected for an advection-dominated disc around a black hole. We consider a variety of possibilities for this unusual behaviour. Scenarios in which the innermost flow is suddenly blocked from view by outer regions of the super-Eddington disc/wind can explain the luminosity–temperature behaviour, but are difficult to reconcile with the lack of strong variability at higher energies, assuming this emission arises from the most compact regions. Instead, we may be seeing evidence for further radial stratification of the accretion flow than is included in the simple models considered, with a combination of winds and advection resulting in the suppressed high-energy variability.
Optical spectral characterization of the TeV extreme blazar 2WHSP J073326.7+515354
Authors: Becerra González J , Acosta-Pulido J A , Clavero R
Published: April 2020

The emission from the relativistic jets in blazars usually outshines their host galaxies, challenging the determination of their distances and the characterization of the stellar population. The situation becomes more favourable in the case of the extreme blazars (EHBLs), for which the bulk of the emission of the relativistic jets is emitted at higher energies, unveiling the optical emission from the host galaxy. The distance determination is fundamental for the study of the intrinsic characteristics of the blazars, especially to estimate the intrinsic gamma-ray spectra distorted due to the interaction with the extragalactic background light. In this work, we report on the properties of 2WHSP J073326.7+515354 host galaxy in the optical band, which is one of the few EHBLs detected at TeV energies. We present the first measurement of the distance of the source, z = 0.065 04 ± 0.000 02 (velocity dispersion $\sigma =237 \pm 9\, \mathrm{km s^{-1}}$). We also perform a detailed study of the stellar population of its host galaxy. We find that the mass-weighted mean stellar age is $11.72\pm 0.06\, \mathrm{Gyr}$ and the mean metallicity [M/H] = 0.159 ± 0.016. In addition, a morphological study of the host galaxy is also carried out. The surface brightness distribution is modelled by a composition of a dominant classical bulge (Re = 3.77 ± 1 arcsec or equivalently 4.74 kpc) plus an unresolved source which corresponds to the active nucleus. The black hole mass is estimated using both the mass relation with the velocity dispersion and the absolute magnitude from the bulge yielding comparable results: $(4.8\pm 0.9)\times 10^8$ and $(3.7\pm 1.0)\times 10^8\, \mathrm{ M}_{\odot }$, respectively.
Shot noise in multitracer constraints on fNL and relativistic projections: Power spectrum
Authors: Ginzburg Dimitry , Desjacques Vincent
Published: April 2020

Multiple tracers of the same surveyed volume can enhance the signal-to-noise on a measurement of local primordial non-Gaussianity and the relativistic projections. Increasing the number of tracers comparably increases the number of shot noise terms required to describe the stochasticity of the data. Although the shot noise is white on large scales, it is desirable to investigate the extent to which it can degrade constraints on the parameters of interest. In a multitracer analysis of the power spectrum, a marginalization over shot noise does not degrade the constraints on fNL by more than ∼30 per cent so long as haloes of mass $M\lesssim 10^{12}\, \mathrm{M}_\odot$ are resolved. However, ignoring cross shot noise terms induces large systematics on a measurement of fNL at redshift z < 1 when small mass haloes are resolved. These effects are less severe for the relativistic projections, especially for the dipole term. In the case of a low and high mass tracer, the optimal sample division maximizes the signal-to-noise on fNL and the projection effects simultaneously, reducing the errors to the level of ∼10 consecutive mass bins of equal number density. We also emphasize that the non-Poissonian noise corrections that arise from small-scale clustering effects cannot be measured with random dilutions of the data. Therefore, they must either be properly modelled or marginalized over.
Magnetohydrodynamic modelling of star–planet interaction and associated auroral radio emission
Authors: Turnpenney Sam , Nichols J D , Wynn G A , Jia X
Published: April 2020

We present calculations of auroral radio powers of magnetized hot Jupiters orbiting Sun-like stars, computed using global magnetohydrodynamic (MHD) modelling of the magnetospheric and ionospheric convection arising from the interaction between the magnetosphere and the stellar wind. Exoplanetary auroral radio powers are traditionally estimated using empirical or analytically derived relations, such as the radiometric Bode’s law (RBL), which relates radio power to the magnetic or kinetic energy dissipated in the stellar wind–planet interaction. Such methods risk an oversimplification of the magnetospheric electrodynamics giving rise to radio emission. As the next step towards a self-consistent picture, we model the stellar wind–magnetosphere–ionosphere coupling currents using a 3D MHD model. We compute electron-cyclotron maser instability-driven emission from the calculated ionospheric field-aligned current density. We show that the auroral radio power is highly sensitive to interplanetary magnetic field (IMF) strength, and that the emission is saturated for plausible hot Jupiter Pedersen conductances, indicating that radio power may be largely independent of ionospheric conductance. We estimate peak radio powers of 1014 W from a planet exposed to an IMF strength of 103 nT, implying flux densities at a distance of 15 pc from Earth potentially detectable with current and future radio telescopes. We also find a relation between radio power and planetary orbital distance that is broadly consistent with results from previous analytic models of magnetosphere–ionosphere coupling at hot Jupiters, and indicates that the RBL likely overestimates the radio powers by up to two orders of magnitude in the hot Jupiter regime.
Model-Based Detection of Whole-Genome Duplications in a Phylogeny
Authors: Zwaenepoel Arthur , Van de Peer Yves
Published: April 2020

Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the “background” gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set of a priori selected WGD hypotheses and cannot be used to discover WGDs in a phylogeny. In this study, we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth–death model that includes WGD in a flexible hierarchical Bayesian approach and use reversible-jump Markov chain Monte Carlo to perform Bayesian inference of branch-specific duplication, loss, and WGD retention rates across the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants, and discuss the statistical intricacies of model-based WGD inference.
CoCoCoNet: conserved and comparative co-expression across a diverse set of species
Authors: Lee John , Shah Manthan , Ballouz Sara , Crow Megan , Gillis Jesse
Published: April 2020

Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data.
Extraforaminal Thoracic and Lumbar Spinal Nerve Ultrasound-Guided Percutaneous Peripheral Nerve Stimulation
Authors: Gargya Akshat , Singh Harmandeep , Lin Tiffany , Gulati Amitabh
Published: April 2020

Objective

Peripheral nerve stimulation provides targeted stimulation and pain relief within a specific nerve distribution. This technical case report provides a method to perform selective nerve root stimulation of thoracic and lumbar spinal nerves using ultrasonography.

Methods

Ultrasound-guided peripheral nerve stimulation of thoracic and lumbar spinal nerves allows better visualization of soft tissue anatomy and planning of needle trajectory.

Conclusions

Ultrasound-guided peripheral nerve stimulation procedures may provide a safer method for neurostimulation lead placement when compared with fluoroscopic-guided techniques.
On Grounds, Anchors, and Diseases: A Reply to Glackin
Authors: Miller Tate Alex James , Davies Thomas
Published: April 2020

Shane Glackin's 2019 Philosophical Quarterly article aims to (a) offer a framework for understanding the philosophical debate about the nature of disease and (b) utilise this framework to reply to several standard objections to normativist (particularly social constructivist) theories of disease. Specifically, Glackin claims his model avoids three central challenges to normativism, which we term the ‘Flippancy Problem’ (which charges that normativism implies diseases can be cured by adjusting our attitudes towards them), ‘Repugnancy Problem’ (which charges that normativism implies we must endorse repugnant historical views regarding ‘conditions’ like Drapetomania as ‘genuine diseases in their day’), and the ‘Explanatory Problem’ (which charges that normativism cannot explain why diseases warrant certain kinds of medical intervention without lapsing into vicious circularity). Although we find Glackin's framework helpful in clarifying the terrain of the debate, we argue these three challenges continue to afflict his preferred construal of the normativist/social constructivist position.
Mortality, causes of death and influence of medication use in patients with systemic lupus erythematosus vs matched controls
Authors: Bultink Irene E M , de Vries Frank , van Vollenhoven Ronald F , Lalmohamed Arief
Published: April 2020

Objectives

We wanted to estimate the magnitude of the risk from all-cause, cause-specific and sex-specific mortality in patients with SLE and relative risks compared with matched controls and to evaluate the influence of exposure to medication on risk of mortality in SLE.

Methods

We conducted a population-based cohort study using the Clinical Practice Research Datalink, Hospital Episode Statistics and national death certificates (from 1987 to 2012). Each SLE patient (n = 4343) was matched with up to six controls (n = 21 780) by age and sex. Cox proportional hazards models were used to estimate overall and cause-specific mortality rate ratios.

Results

Patients with SLE had a 1.8-fold increased mortality rate for all-cause mortality compared with age- and sex-matched subjects [adjusted hazard ratio (HR) = 1.80, 95% CI: 1.57, 2.08]. The HR was highest in patients aged 18–39 years (adjusted HR = 4.87, 95% CI: 1.93, 12.3). Mortality rates were not significantly different between male and female patients. Cumulative glucocorticoid use raised the mortality rate, whereas the HR was reduced by 45% with cumulative low-dose HCQ use. Patients with SLE had increased cause-specific mortality rates for cardiovascular disease, infections, non-infectious respiratory disease and for death attributable to accidents or suicide, whereas the mortality rate for cancer was reduced in comparison to controls.

Conclusion

British patients with SLE had a 1.8-fold increased mortality rate compared with the general population. Glucocorticoid use and being diagnosed at a younger age were associated with an increased risk of mortality. HCQ use significantly reduced the mortality rate, but this association was found only in the lowest cumulative dosage exposure group.
Impact of storage conditions and premix type on phytase stability
Authors: Saensukjaroenphon Marut , Evans Caitlin E , Paulk Chad B , Gebhardt Jordan T , Woodworth Jason C , Stark Charles R , Bergstrom Jon R , Jones Cassandra K
Published: April 2020

Potential use of medium-chain fatty acids (MCFA), increased temperatures and exposure time may be implemented to mitigate biological hazards in premixes and feed ingredients. However, there are no data on how these strategies influence phytase stability. For Exp. 1, there were no four- and three-way interactions among premix type (PT), oil type (OT), storage condition (SC), and storage time (ST) for phytase stability (P > 0.111). There were two-way interactions for PT × SC (P < 0.001) and SC × ST (P < 0.001). The OT did not affect phytase stability when premixes-containing phytase were added as either mineral oil (MO) or MCFA (P = 0.382). For Exp. 2, there was no interaction between PT and OT (P = 0.121). There were also no differences for phytase stability between vitamin premix (VP)- and vitamin trace mineral (VTM) premix-containing phytase were heated at 60 °C (P = 0.141) and between premixes-containing phytase were mixed with 1% MO added and 1% MCFA (P = 0.957). Therefore, the phytase was stable when mixed with both VP and VTM premix and stored at 22 °C with 28.4% relative humidity (RH). The phytase stability was dramatically decreased when the phytase was mixed with premixes and stored at 39.5 °C with 78.8% RH. Also, MCFA did not influence phytase degradation during storage up to 90 d and in the heat pulse process. The phytase activity was decreased by 20% after the premixes containing the phytase was heated at 60 °C for approximately 9.5 h. If both MCFA and heat pulse treatment have similar efficiency at neutralizing or reducing the target pathogen, the process of chemical treatment could become a more practical practice.
MawuAP1 promotes flowering and fruit development in the basal angiosperm Magnolia wufengensis (Magnoliaceae)
Authors: Li Cunjie , Chen Liyuan , Fan Xiaoning , Qi Wenjuan , Ma Jiang , Tian Tian , Zhou Tao , Ma Luyi , Chen Faju
Published: April 2020

The APETALA1/SQUAMOSA (AP1/SQUA)-like genes of flowering plants play crucial roles in the development processes of floral meristems, sepals, petals and fruits. Although many of the AP1/SQUA-like genes have been characterized in angiosperms, few have been identified in basal angiosperm taxa. Therefore, the functional evolution of the AP1/SQUA subfamily is still unclear. We characterized an AP1 homolog, MawuAP1, from Magnolia wufengensis that is an ornamental woody plant belonging to the basal angiosperms. Gene sequence and phylogenetic analyses suggested that MawuAP1 was clustered with the FUL-like homologous genes of basal angiosperms and had FUL motif and paleoAP1 motif domain, but it did not have the euAP1 motif domain of core eudicots. Expression pattern analysis showed that MawuAP1 was highly expressed in vegetative and floral organs, particularly in the early stage of flower bud development and pre-anthesis. Protein–protein interaction pattern analysis revealed that MawuAP1 has interaction with an A-class gene (MawuAP1), C-class gene (MawuAG-1) and E-class gene (MawuAGL9) of the MADS-box family genes. Ectopic expression in Arabidopsis thaliana indicated that MawuAP1 could significantly promote flowering and fruit development, but it could not restore the sepal and petal formation of ap1 mutants. These results demonstrated that there are functional differences in the specification of sepal and petal floral organs and development of fruits among the AP1/SQUA-like genes, and functional conservation in the regulation of floral meristem. These findings provide strong evidence for the important functions of MawuAP1 in floral meristem determination, promoting flowering and fruit development, and further highlight the importance of AP1/SQUA subfamily in biological evolution and diversity.
Prediction and Characterization of RXLR Effectors in Pythium Species
Authors: Ai Gan , Yang Kun , Ye Wenwu , Tian Yuee , Du Yaxin , Zhu Hai , Li Tianli , Xia Qingyue , Shen Danyu , Peng Hao , Jing Maofeng , Xia Ai , Dou Daolong
Published: April 2020

RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.
Fungi Associated with Damage Observed on Branches of Juglans nigra in Indiana, Missouri, and Tennessee
Authors: McDermott-Kubeczko Margaret E. , Juzwik Jennifer , Reed Sharon E. , Klingeman William E.
Published: April 2020

Branch and stem cankers caused by Geosmithia morbida associated with mass attack by its primary insect vector (Pityophthorus juglandis) result in thousand cankers disease (TCD) on Juglans and Pterocarya species. Because other fungi and insects can cause visible damage to Juglans nigra, a baseline assessment was performed to document damage types present and to characterize fungi associated with each type. Two branches were collected from trees with visually healthy crowns in TCD-free locations (Indiana and Missouri) and two branches from trees with and without crown symptoms characteristic of TCD within the disease range in Tennessee. In most cases, one of the two branches was girdled at the base 3 to 4 months prior to harvest. Outer bark was peeled from branch subsamples, observed damage characterized, and isolation of fungi from each damage type attempted. Three known pathogens of J. nigra were obtained from different damage types: G. morbida, in Tennessee only; Botryosphaeria dothidea, in Indiana and Tennessee; and Fusarium solani (= members of F. solani species complex), in all three states. The latter two fungi may exacerbate branch dieback and mortality of TCD-affected trees. These results will be of value to plant health specialists monitoring J. nigra in the field and laboratory diagnosticians processing survey samples.
Performance of Fabrics for Home-Made Masks Against the Spread of Respiratory Infections Through Droplets: A Quantitative Mechanistic Study
Authors: Aydin Onur , Emon Bashar , Cheng Shyuan , Hong Liu , Chamorro Leonardo P. , Saif M. Taher A.
Published: April 2020

Respiratory infections may spread through droplets and aerosols released by infected individuals coughing, sneezing, or speaking. In the case of Coronavirus Disease 2019 (COVID-19), spread can occur from symptomatic, pre-symptomatic, and asymptomatic persons. Given the limited supply of professional face masks and respirators, the U.S. Centers for Disease Control and Prevention (CDC) has recommended home-made cloth face coverings for use by the general public in areas of significant community-based transmission. There is, however, little information on the effectiveness of cloth face coverings in reducing droplet dissemination. Here, we ascertained the performance of 11 household fabrics at blocking high-velocity droplets, using a commercial medical mask as a benchmark. We also assessed their breathability (air permeability), texture, fiber composition, and water absorption properties. We found that droplet blocking efficiency anti-correlates with breathability; less breathable fabrics being more effective in blocking. However, materials with high breathability are desirable for comfort and to reduce airflow through gaps between the mask and face. Our measurements indicate that 2 or 3 layers of highly permeable fabric, such as T-shirt cloth, may block droplets with an efficacy similar to that of medical masks, while still maintaining comparable breathability. Overall, our study suggests that cloth face coverings, especially with multiple layers, may help reduce droplet transmission of respiratory infections. Furthermore, face coverings made from biodegradable fabrics such as cotton allow washing and reusing, and can help reduce the adverse environmental effects of widespread use of commercial disposable and non-biodegradable facemasks.
Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays
Authors: Crawford Katharine H.D. , Eguia Rachel , Dingens Adam S. , Loes Andrea N. , Malone Keara D. , Wolf Caitlin R. , Chu Helen Y. , Tortorici M. Alejandra , Veesler David , Murphy Michael , Pettie Deleah , King Neil P. , Balazs Alejandro B. , Bloom Jesse D.
Published: April 2020

SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.
Association of mitochondrial DNA copy number with cardiometabolic diseases in a large cross-sectional study of multiple ancestries
Authors: Liu Xue , Longchamps Ryan J. , Wiggins Kerri , Raffield Laura M. , Bielak Lawrence F. , Zhao Wei , Pitsillides Achilleas , Blackwell Thomas , Yao Jie , Guo Xiuqing , Kurniansyah Nuzulul , Thyagarajan Bharat , Pankratz Nathan , Rich Stephen S. , Taylor Kent D. , Peyser Patricia A. , Heckbert Susan R. , Seshadri Sudha , Cupples L Adrienne , Boerwinkle Eric , Grove Megan L. , Larson Nicholas , Smith Jennifer A. , Vasan Ramachandran S , Sofer Tamar , Fitzpatrick Annette L , Fornage Myriam , Ding Jun , Correa Adolfo , Abecasis Goncalo , Psaty Bruce M. , Wilson James G. , Levy Daniel , Rotter Jerome I. , Bis Joshua C. , Satizabal Claudia L , Arking Dan E. , Liu Chunyu
Published: April 2020

Aims

We tested the hypothesis that mitochondrial DNA copy number (CN) is associated with cardiometabolic disease (CMD) traits.

Methods and results

We determined the cross-sectional association of mtDNA CN measured in whole blood with several CMD traits in 65,996 individuals (mean age 60, 54% women, and 79% European descent). Cohort- and ancestry/ethnicity-specific association analysis was performed adjusting for trait- and cohort-specific covariates. Age was slightly positively associated with age (0.03 s.d. / 10 years (95% CI=0.01, 0.05)) before 65 years, while every 10 years older age was associated with 0.14 s.d. lower level of mtDNA CN after 65 years (95% CI= -0.18, -0.10). In meta-analysis without adjustment for white blood cell (WBC) and differential count in participants of European descent (N=52,491), low mtDNA CN was associated with increased odds of obesity (OR with 95% CI=1.13 (1.11, 1.16), P=3.3e-30) and hypertension (OR=1.05 (1.03, 1.08), P=4.0e-07). Further adjusting for WBC and differential count in the same participants of European descent (N=44,035), associations became non-significant (P>0.05) for hypertension, attenuated for obesity (ORwithout cell count=1.15 (1.12, 1.18) versus ORcell count=1.06 (1.03, 1.08)) but strengthened for hyperlipidemia (ORwithout cell counts=1.03 (1.00, 1.06) versus ORcell counts=1.06 (1.03, 1.09)). The magnitude and directionality of most associations were consistent between participants of European descent and other ethnicity/ancestry origins.

Conclusion

Low levels of mtDNA CN in peripheral blood were associated with an increased risk of CMD diseases.
A phased approach to unlocking during the COVID-19 pandemic – Lessons from trend analysis
Authors: Stedman Mike , Davies Mark , Lunt Mark , Verma Arpana , Anderson Simon G. , Heald Adrian H
Published: April 2020

With the COVID-19 pandemic leading to radical political control of social behaviour, including restricted movement outsides homes. Can more detailed analysis of the published confirmed local case data from the pandemic in England using infection ratio and comparing local level data provide a deeper understanding of the wider community infection and inform the future unlocking process.

The historic daily published 78,842 confirmed cases in England up to 13/4/2020 in each of 149 Upper Tier Local Authority (UTLA) were converted to Average Daily Infection Rate (RADIR), an R-value - the number of further people infected by one infected person after their 5-day incubation and during their 5-day infectious phase, and the associated Rate of Change of Infection Rate (ΔIR) also calculated. Results compared to look for significant variances between regions. Stepwise regression was carried out to see what local factors could be linked to the difference in local infection rates.

The peak of COVID-19 infection has passed. The current RADIR is now below 1. The rate of decline is such that within 14 days it may be below 0.5. There are significant variations in the current RADIR and ΔIR between the UTLAs, suggesting that the disease locally may be at different stages.

Regression analysis across UTLAs found that the only factor that could be related to the fall in RADIR was an increase in the number of confirmed infection/1,000 population. Extrapolation of these results showed that based on assuming a link to increased immunity, unreported community infection may be over 200 times higher than the reported confirmed cases providing evidence that by the end of the second week in April 26% of the population may already have had the disease and so now have increased immunity. Linking these increased estimated infected numbers to recorded deaths indicates a possible mortality rate of 0.14%.

Analysis of the current reported local case data using the infectious ratio does provide greater insight into the current levels of community infection and can be used to make better-informed decisions about the future management of restricted social behaviour and movement
COVID-19 pandemic: examining the faces of spatial differences in the morbidity and mortality in sub-Saharan Africa, Europe and USA
Authors: Otitoloju Adebayo A. , Okafor Ifeoma P. , Fasona Mayowa , Bawa-Allah Kafilat A. , Isanbor Chukwuemeka , Chukwudozie Onyeka S. , Folarin Olawale S. , Adubi Taiwo O. , Sogbanmu Temitope O. , Ogbeibu Anthony E.
Published: April 2020

Background

COVID-19, the disease associated with the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently a global pandemic with several thousands of confirmed cases of infection and death. However, the death rate across affected countries shows variation deserving of critical evaluation.

Methods

In this study, we evaluated differentials in COVID-19 confirmed cases of infection and associated deaths of selected countries in Sub-Sahara Africa (Nigeria and Ghana), South Africa, Europe (Italy, Spain, Sweden and UK) and USA. Data acquired for various standard databases on mutational shift of the SARS-CoV-2 virus based on geographical location, BCG vaccination policy, malaria endemicity, climatic conditions (temperature), differential healthcare approaches were evaluated over a period of 45 days from the date of reporting the index case.

Results

The number of confirmed cases of infection and associated deaths in Sub-Sahara Africa were found to be very low compared to the very high values in Europe and USA over the same period. Recovery rate from COVID-19 is not correlated with the mutational attributes of the virus with the sequenced strain from Nigeria having no significant difference (p>0.05) from other geographical regions. Significantly higher (p<0.05) infection rate and mortality from COVID-19 were observed in countries (Europe and USA) without a current universal BCG vaccination policy compared to those with one (Sub-Sahara African countries). Countries with high malaria burden had significantly lower (p<0.05) cases of COVID-19 than those with low malaria burden. A strong negative correlation (−0.595) between mean annual temperature and COVID-19 infection and death was observed with 14.8% variances between temperature and COVID-19 occurrence among the countries. A clear distinction was observed in the COVID-19 disease management between the developed countries (Europe and USA) and Sub-Sahara Africa.

Conclusions

The study established that the wide variation in the outcome of the COVID-19 disease burden in the selected countries are attributable largely to climatic condition (temperature) and differential healthcare approaches to management of the disease. We recommend consideration and mainstreaming of these findings for urgent intervention and management of COVID-19 across these continents.
Estimating the undetected infections in the Covid-19 outbreak by harnessing capture-recapture methods
Authors: Böhning Dankmar , Rocchetti Irene , Maruotti Antonello , Holling Heinz
Published: April 2020

A major open question, affecting the policy makers decisions, is the estimation of the true size of COVID-19 infections. Most of them are undetected, because of a large number of asymptomatic cases. We provide an efficient, easy to compute and robust lower bound estimator for the number of undetected cases. A “modified” version of the Chao estimator is proposed, based on the cumulative time-series distribution of cases and deaths. Heterogeneity has been accounted for by assuming a geometrical distribution underlying the data generation process. An (approximated) analytical variance formula has been properly derived to compute reliable confidence intervals at 95%. An application to Austrian situation is provided and results from other European Countries are mentioned in the discussion.
A cell phone data driven time use analysis of the COVID-19 epidemic
Authors: Fenichel Eli P. , Berry Kevin , Bayham Jude , Gonsalves Gregg
Published: April 2020

Transmission of the SAR-COV-2 virus that causes COVID-19 is largely driven by human behavior and person-to-person contact. By staying home, people reduce the probability of contacting an infectious individual, becoming infected, and passing on the virus. One of the most promising sources of data on time use is smartphone location data. We develop a time use driven proportional mixing SEIR model that naturally incorporates time spent at home measured using smartphone location data and allows people of different health statuses to behave differently. We simulate epidemics in almost every county in the United States. The model suggests that Americans’ behavioral shifts have reduced cases in 55%-86% of counties and for 71%-91% of the population, depending on modeling assumptions. Resuming pre-epidemic behavior would lead to a rapid rise in cases in most counties. Spatial patterns of bending and flattening the curve are robust to modeling assumptions. Depending on epidemic history, county demographics, and behavior within a county, returning those with acquired immunity (assuming it exists) to regular schedules generally helps reduce cumulative COVID-19 cases. The model robustly identifies which counties would experience the greatest share of case reduction relative to continued distancing behavior. The model occasionally mischaracterizes epidemic patterns in counties tightly connected to larger counties that are experiencing large epidemics. Understanding these patterns is critical for prioritizing testing resources and back-to-work planning for the United States.