bluuebunny/crossref_metadata_2025 huggingface dataset:
HiPERCAM: a quintuple-beam, high-speed optical imager on the 10.4-m Gran Telescopio Canarias
Authors: Dhillon V S , Bezawada N , Black M , Dixon S D , Gamble T , Gao X , Henry D M , Kerry P , Littlefair S P , Lunney D W , Marsh T R , Miller C , Parsons S G , Ashley R P , Breedt E , Brown A , Dyer M J , Green M J , Pelisoli I , Sahman D I , Wild J , Ives D J , Mehrgan L , Stegmeier J , Dubbeldam C M , Morris T J , Osborn J , Wilson R W , Casares J , Muñoz-Darias T , Pallé E , Rodríguez-Gil P , Shahbaz T , Torres M A P , de Ugarte Postigo A , Cabrera-Lavers A , Corradi R L M , Domínguez R D , García-Alvarez D
Published: July 2021

HiPERCAM is a portable, quintuple-beam optical imager that saw first light on the 10.4-m Gran Telescopio Canarias (GTC) in 2018. The instrument uses re-imaging optics and four dichroic beamsplitters to record $u_{\rm s}\, g_{\rm s}\, r_{\rm s}\, i_{\rm s}\, z_{\rm s}$ (320–1060 nm) images simultaneously on its five CCD cameras, each of 3.1-arcmin (diagonal) field of view. The detectors in HiPERCAM are frame-transfer devices cooled thermo-electrically to 183 K, thereby allowing both long-exposure, deep imaging of faint targets, as well as high-speed (over 1000 windowed frames per second) imaging of rapidly varying targets. A comparison-star pick-off system in the telescope focal plane increases the effective field of view to 6.7 arcmin for differential photometry. Combining HiPERCAM with the world’s largest optical telescope enables the detection of astronomical sources to gs ∼ 23 in 1 s and gs ∼ 28 in 1 h. In this paper, we describe the scientific motivation behind HiPERCAM, present its design, report on its measured performance, and outline some planned enhancements.
Hybrid deep convolutional neural network with one-versus-one approach for solar flare prediction
Authors: Zheng Yanfang , Li Xuebao , Si Yingzhen , Qin Weishu , Tian Huifeng
Published: July 2021

We propose a novel hybrid Convolutional Neural Network (CNN) model with one-versus-one approach to forecast solar flare occurrence with the outputs of four classes (No-flare, C, M, and X) within 24 h. We train and test our model using the same data sets as in Zheng, Li & Wang, and then compare our results with previous models using the true skill statistic (TSS) as primary metric. The main results are as follows. (1) This is the first time that the CNN model in conjunction with one-versus-one approach is used in solar physics to make multiclass flare prediction. (2) In the four-class flare prediction, our model achieves quite high mean scores of TSS = 0.703, 0.489, 0.432, and 0.436 for No-flare, C, M, and X class, respectively, which are much better than or comparable to those of previous studies. In addition, our model obtains TSS scores of 0.703 ± 0.070 for ≥C-class and 0.739 ± 0.109 for ≥M-class predictions. (3) This is the first attempt to open the black-box CNN model to study the visualization of feature maps for interpreting the prediction model. Furthermore, the visualization results indicate that our model pays attention to the regions with strong gradient, strong intensity, high total intensity, and large range of the intensity in high-level feature maps. The median gradient and intensity, the total intensity, and the range of the intensity for high-level feature maps increase approximately with the increase of flare level.
Simulating a stellar contact binary merger – I. Stellar models
Authors: Hatfull Roger W M , Ivanova Natalia , Lombardi James C
Published: July 2021

We study the initial conditions of a common envelope (CE) event resulting in a stellar merger. A merger’s dynamics could be understood through its light curve, but no synthetic light curve has yet been created for the full evolution. Using the smoothed particle hydrodynamics (SPH) code StarSmasher, we have created three-dimensional (3D) models of a 1.52 M⊙ star that is a plausible donor in the V1309 Sco progenitor. The integrated total energy profiles of our 3D models match their initial one-dimensional (1D) models to within a 0.1 per cent difference in the top 0.1 M⊙ of their envelopes. We have introduced a new method for obtaining radiative flux by linking intrinsically optically thick SPH particles to a single stellar envelope solution from a set of unique solutions. For the first time, we calculated our 3D models’ effective temperatures to within a few per cent of the initial 1D models, and found a corresponding improvement in luminosity by a factor of ≳106 compared to ray tracing. We let our highest resolution 3D model undergo Roche lobe overflow with a 0.16 M⊙ point-mass accretor (P ≃ 1.6 d) and found a bolometric magnitude variability amplitude of ∼0.3 – comparable to that of the V1309 Sco progenitor. Our 3D models are, in the top 0.1 M⊙ of the envelope and in terms of total energy, the most accurate models so far of the V1309 Sco donor star. A dynamical simulation that uses the initial conditions we presented in this paper can be used to create the first ever synthetic CE evolution light curve.
Discovery of multiple p-mode pulsation frequencies in the roAp star, HD 86181
Authors: Shi Fangfei , Kurtz Donald W , Holdsworth Daniel L , Saio Hideyuki , Cunha Margarida S , Zhang Huawei , Fu Jianning , Handler G
Published: July 2021

We report the frequency analysis of a known roAp star, HD 86181 (TIC 469246567), with new inferences from Transiting Exoplanet Survey Satellite (TESS) data. We derive the rotation frequency to be νrot = 0.48753 ± 0.00001 d−1. The pulsation frequency spectrum is rich, consisting of two doublets and one quintuplet, which we interpret to be oblique pulsation multiplets from consecutive, high-overtone dipole, quadrupole, and dipole modes. The central frequency of the quintuplet is 232.7701 d−1 (2.694 mHz). The phases of the sidelobes, the pulsation phase modulation, and a spherical harmonic decomposition all show that the quadrupole mode is distorted. Following the oblique pulsator model, we calculate the rotation inclination, i, and magnetic obliquity, β, of this star, which provide detailed information about the pulsation geometry. The i and β derived from the best fit of the pulsation amplitude and phase modulation to a theoretical model, including the magnetic field effect, slightly differ from those calculated for a pure quadrupole, indicating the contributions from ℓ = 4, 6, 8,... are small. Non-adiabatic models with different envelope convection conditions and physics configurations were considered for this star. It is shown that models with envelope convection almost fully suppressed can explain the excitation at the observed pulsation frequencies.
A study of superluminous stars with the Fermi-Large Area Telescope
Authors: de Menezes Raniere , Orlando Elena , Di Mauro Mattia , Strong Andrew
Published: July 2021

The γ-ray emission from stars is induced by the interaction of cosmic rays with stellar atmospheres and photon fields. This emission is expected to come in two components: a stellar disc emission, where γ-rays are mainly produced in atmospheric showers generated by hadronic cosmic rays, and an extended halo emission, where the high density of soft photons in the surroundings of stars create a suitable environment for γ-ray production via inverse Compton (IC) scattering by cosmic ray electrons. Besides the Sun, no other disc or halo from single stars has ever been detected in γ-rays. However, by assuming a cosmic ray spectrum similar to that observed on Earth, the predicted γ-ray emission of superluminous stars, e.g. Betelgeuse and Rigel, could be high enough to be detected by the Fermi Large Area Telescope (LAT) after its first decade of operations. In this work, we use 12 yr of Fermi-LAT observations along with IC models to study nine superluminous nearby stars, both individually and via stacking analysis. Our results show no significant γ-ray emission, but allow us to restrict the stellar γ-ray fluxes to be on average <3.3 × 10−11 ph cm−2 s−1 at a 3σ confidence level, which translates to an average local density of electrons in the surroundings of our targets to be less than twice of that observed for the Solar system.
The impact of the spin–orbit misalignment and of the spin of B on the Lense–Thirring orbital precessions of the double pulsar PSR J0737–3039A/B
Authors: Iorio Lorenzo
Published: July 2021

In the double pulsar, the Lense–Thirring periastron precession $\dot{\omega }^\mathrm{LT}$ could be used to measure/constrain the moment of inertia $\mathcal {I}_\mathrm{A}$ of A. Conversely, if $\mathcal {I}_\mathrm{A}$ will be independently determined with sufficient accuracy by other means, tests of the Lense–Thirring effect could be performed. Such findings rely upon a formula for $\dot{\omega }^\mathrm{LT,\, A}$ induced by the spin angular momentum ${\boldsymbol{S}}^\mathrm{A}$ of A, valid if the orbital angular momentum $\boldsymbol{L}$ and ${\boldsymbol{S}}^\mathrm{A}$ are aligned, and neglecting $\dot{\omega }^\mathrm{LT,\, B}$ because of the smallness of ${\boldsymbol{S}}^\mathrm{B}$. The impact on $\dot{\omega }^\mathrm{LT,\, A}$ of the departures of the ${\boldsymbol{S}}^\mathrm{A}$–$\boldsymbol{L}$ geometry from the ideal alignment is calculated. With the current upper bound on the misalignment angle δA between them, the angles $\lambda _\mathrm{A},\ \eta _\mathrm{A}$ of ${\boldsymbol{S}}^\mathrm{A}$ are constrained within $85^\circ \lesssim \lambda _\mathrm{A}\lesssim 92^\circ ,\ 266^\circ \lesssim \eta _\mathrm{A} \lesssim 274^\circ$. In units of the first-order post-Newtonian mass-dependent periastron precession $\dot{\omega }^\mathrm{GR}=16{_{.}^{\circ}}89 \, \mathrm{yr}^{-1}$, a range variation $\Delta \dot{\omega }^\mathrm{LT,\, A}\doteq \dot{\omega }^\mathrm{LT,\, A}_\mathrm{max} - \dot{\omega }^\mathrm{LT,\, A}_\mathrm{min} = 8\times 10^{-8}\, \omega ^\mathrm{GR}$ is implied. The experimental uncertainty $\sigma _{\dot{\omega }_\mathrm{obs}}$ in measuring the periastron rate should become smaller by 2028–2030. Then, the spatial orientation of ${\boldsymbol{S}}^\mathrm{B}$ is constrained from the existing bounds on the misalignment angle δB, and $\dot{\omega }^\mathrm{LT,\, B}\simeq 2\times 10^{-7}\, \dot{\omega }^\mathrm{GR}$ is correspondingly calculated. The error $\sigma _{\dot{\omega }_\mathrm{obs}}$ should become smaller around 2025. The Lense–Thirring inclination and node precessions $\dot{I}^\mathrm{LT},\ \dot{\Omega }^\mathrm{LT}$ are predicted to be ${\lesssim} 0.05\, \mathrm{arcsec\, yr^{-1}}$, far below the current experimental accuracies $\sigma _{I_\mathrm{obs}}=0{_{.}^{\circ}}5 , \ \sigma _{\Omega _\mathrm{obs}}=2^\circ$ in measuring $I,\ \Omega$ over 1.5 yr with the scintillation technique. The Lense–Thirring rate $\dot{x}_\mathrm{A}^\mathrm{LT}$ of the projected semimajor axis xA of PSR J0737−3039A is ${\lesssim} 2\times 10^{-16}\, \mathrm{s\, s}^{-1}$, just two orders of magnitude smaller than a putative experimental uncertainty $\sigma _{\dot{x}^\mathrm{obs}_\mathrm{A}}\simeq 10^{-14}\, \mathrm{s\, s}^{-1}$ guessed from 2006 data.
Anisotropic neutrinos and gravitational waves from black hole neutrino-dominated accretion flows in fallback core-collapse supernovae
Authors: Wei Yun-Feng , Liu Tong , Xue Li
Published: July 2021

Fallback in core-collapse supernovae (CCSNe) plays an important role in determining the properties of the central compact remnants, which might produce a black hole (BH) hyperaccretion system in the centre of a massive CCSN. When the accretion rate is extremely high and neutrino cooling is dominant, the hyperaccretion should be in the phase of the neutrino-dominated accretion flows (NDAFs), and thus a large number of anisotropic MeV neutrinos will be launched from the disc along with the strong gravitational waves (GWs). In this paper, we perform a series of one-dimensional CCSN simulations with the initial explosion energy in the range of 2−8 B (1 B = 1051 erg) to investigate the fallback processes. By considering the evolution of the central BH mass and spin in the fallback accretion, we present the effects of the initial explosion energies, masses, and metallicities of the massive progenitor stars on the spectra of anisotropic MeV neutrinos and the waveform of GWs from NDAFs. These neutrino or GW signals might be detected by operational or future detectors, and the multimessenger joint detections could constrain the properties of CCSNe and progenitor stars.
COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man
Authors: Edmonds Katherine A , Jordan Matthew R , Giedroc David P
Published: July 2021

Transition metal homeostasis ensures that cells and organisms obtain sufficient metal to meet cellular demand while dispensing with any excess so as to avoid toxicity. In bacteria, zinc restriction induces the expression of one or more Zur (zinc-uptake repressor)-regulated Cluster of Orthologous Groups (COG) COG0523 proteins. COG0523 proteins encompass a poorly understood sub-family of G3E P-loop small GTPases, others of which are known to function as metallochaperones in the maturation of cobalamin (CoII) and NiII cofactor-containing metalloenzymes. Here, we use genomic enzymology tools to functionally analyse over 80 000 sequences that are evolutionarily related to Acinetobacter baumannii ZigA (Zur-inducible GTPase), a COG0523 protein and candidate zinc metallochaperone. These sequences segregate into distinct sequence similarity network (SSN) clusters, exemplified by the ZnII-Zur-regulated and FeIII-nitrile hydratase activator CxCC (C, Cys; X, any amino acid)-containing COG0523 proteins (SSN cluster 1), NiII-UreG (clusters 2, 8), CoII-CobW (cluster 4), and NiII-HypB (cluster 5). A total of five large clusters that comprise ≈ 25% of all sequences, including cluster 3 which harbors the only structurally characterized COG0523 protein, Escherichia coli YjiA, and many uncharacterized eukaryotic COG0523 proteins. We also establish that mycobacterial-specific protein Y (Mpy) recruitment factor (Mrf), which promotes ribosome hibernation in actinomycetes under conditions of ZnII starvation, segregates into a fifth SSN cluster (cluster 17). Mrf is a COG0523 paralog that lacks all GTP-binding determinants as well as the ZnII-coordinating Cys found in CxCC-containing COG0523 proteins. On the basis of this analysis, we discuss new perspectives on the COG0523 proteins as cellular reporters of widespread nutrient stress induced by ZnII limitation.
Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo
Authors: Kamagata Kiyoto , Itoh Yuji , Tan Cheng , Mano Eriko , Wu Yining , Mandali Sridhar , Takada Shoji , Johnson Reid C
Published: July 2021

Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
Antisense ribosomal siRNAs inhibit RNA polymerase I-directed transcription inC. elegans
Authors: Liao Shimiao , Chen Xiangyang , Xu Ting , Jin Qile , Xu Zongxiu , Xu Demin , Zhou Xufei , Zhu Chengming , Guang Shouhong , Feng Xuezhu
Published: July 2021

Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed the association of NRDE proteins with pre-rRNAs and the silencing of pre-rRNAs. In the presence of risiRNAs, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNAs inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the RNAi-targeted site. Meanwhile, exosomes mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results established a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.
A novel cell-cycle-regulated interaction of the Bloom syndrome helicase BLM with Mcm6 controls replication-linked processes
Authors: Shastri Vivek M , Subramanian Veena , Schmidt Kristina H
Published: July 2021

The Bloom syndrome DNA helicase BLM contributes to chromosome stability through its roles in double-strand break repair by homologous recombination and DNA replication fork restart during the replication stress response. Loss of BLM activity leads to Bloom syndrome, which is characterized by extraordinary cancer risk and small stature. Here, we have analyzed the composition of the BLM complex during unperturbed S-phase and identified a direct physical interaction with the Mcm6 subunit of the minichromosome maintenance (MCM) complex. Using distinct binding sites, BLM interacts with the N-terminal domain of Mcm6 in G1 phase and switches to the C-terminal Cdt1-binding domain of Mcm6 in S-phase, with a third site playing a role for Mcm6 binding after DNA damage. Disruption of Mcm6-binding to BLM in S-phase leads to supra-normal DNA replication speed in unperturbed cells, and the helicase activity of BLM is required for this increased replication speed. Upon disruption of BLM/Mcm6 interaction, repair of replication-dependent DNA double-strand breaks is delayed and cells become hypersensitive to DNA damage and replication stress. Our findings reveal that BLM not only plays a role in the response to DNA damage and replication stress, but that its physical interaction with Mcm6 is required in unperturbed cells, most notably in S-phase as a negative regulator of replication speed.
Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides
Authors: Padmanabhan Prasad Kottayil , Ferreira Gabriel Reis , Zghidi-Abouzid Ouafa , Oliveira Camila , Dumas Carole , Mariz Filipe Colaço , Papadopoulou Barbara
Published: July 2021

DDX3 is a multifaceted RNA helicase of the DEAD-box family that plays central roles in all aspects of RNA metabolism including translation initiation. Here, we provide evidence that the Leishmania DDX3 ortholog functions in post-initiation steps of translation. We show that genetic depletion of DDX3 slows down ribosome movement resulting in elongation-stalled ribosomes, impaired translation elongation and decreased de novo protein synthesis. We also demonstrate that the essential ribosome recycling factor Rli1/ABCE1 and termination factors eRF3 and GTPBP1 are less recruited to ribosomes upon DDX3 loss, suggesting that arrested ribosomes may be inefficiently dissociated and recycled. Furthermore, we show that prolonged ribosome stalling triggers co-translational ubiquitination of nascent polypeptide chains and a higher recruitment of E3 ubiquitin ligases and proteasome components to ribosomes of DDX3 knockout cells, which further supports that ribosomes are not elongating optimally. Impaired elongation of translating ribosomes also results in the accumulation of cytoplasmic protein aggregates, which implies that defects in translation overwhelm the normal quality controls. The partial recovery of translation by overexpressing Hsp70 supports this possibility. Collectively, these results suggest an important novel contribution of DDX3 to optimal elongation of translating ribosomes by preventing prolonged translation stalls and stimulating recycling of arrested ribosomes.
EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles
Authors: Liu Chun-Jie , Xie Gui-Yan , Miao Ya-Ru , Xia Mengxuan , Wang Yi , Lei Qian , Zhang Qiong , Guo An-Yuan
Published: July 2021

Extracellular vesicles (EVs) packing various molecules play vital roles in intercellular communication. Non-coding RNAs (ncRNAs) are important functional molecules and biomarkers in EVs. A comprehensive investigation of ncRNAs expression in EVs under different conditions is a fundamental step for functional discovery and application of EVs. Here, we curated 2030 small RNA-seq datasets for human EVs (1506 sEV and 524 lEV) in 24 conditions and over 40 diseases. We performed a unified reads dynamic assignment algorithm (RDAA) considering mismatch and multi-mapping reads to quantify the expression profiles of seven ncRNA types (miRNA, snoRNA, piRNA, snRNA, rRNA, tRNA and Y RNA). We constructed EVAtlas (http://bioinfo.life.hust.edu.cn/EVAtlas), a comprehensive database for ncRNA expression in EVs with four functional modules: (i) browse and compare the distribution of ncRNAs in EVs from 24 conditions and eight sources (plasma, serum, saliva, urine, sperm, breast milk, primary cell and cell line); (ii) prioritize candidate ncRNAs in condition related tissues based on their expression; (iii) explore the specifically expressed ncRNAs in EVs from 24 conditions; (iv) investigate ncRNA functions, related drugs, target genes and EVs isolation methods. EVAtlas contains the most comprehensive ncRNA expression in EVs and will be a key resource in this field.
Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14
Authors: Zheng Shuangping , Bi Yucong , Chen Haining , Gong Bo , Jia Shunji , Li Haitao
Published: July 2021

Histone recognition constitutes a key epigenetic mechanism in gene regulation and cell fate decision. PHF14 is a conserved multi-PHD finger protein that has been implicated in organ development, tissue homeostasis, and tumorigenesis. Here we show that PHF14 reads unmodified histone H3(1–34) through an integrated PHD1-ZnK-PHD2 cassette (PHF14PZP). Our binding, structural and HDX-MS analyses revealed a feature of bipartite recognition, in which PHF14PZP utilizes two distinct surfaces for concurrent yet separable engagement of segments H3-Nter (e.g. 1–15) and H3-middle (e.g. 14–34) of H3(1–34). Structural studies revealed a novel histone H3 binding mode by PHD1 of PHF14PZP, in which a PHF14-unique insertion loop but not the core β-strands of a PHD finger dominates H3K4 readout. Binding studies showed that H3-PHF14PZP engagement is sensitive to modifications occurring to H3 R2, T3, K4, R8 and K23 but not K9 and K27, suggesting multiple layers of modification switch. Collectively, our work calls attention to PHF14 as a ‘ground’ state (unmodified) H3(1–34) reader that can be negatively regulated by active marks, thus providing molecular insights into a repressive function of PHF14 and its derepression.
Diffusion kurtosis imaging as an imaging biomarker for predicting prognosis in chronic kidney disease patients
Authors: Liu Yan , Zhang Gu-Mu-Yang , Peng Xiaoyan , Li Xuemei , Sun Hao , Chen Limeng
Published: July 2021

Background

Renal fibrosis is the strongest prognostic predictor of end-stage renal disease (ESRD) in chronic kidney disease (CKD). Diffusion kurtosis imaging (DKI) is a promising method of magnetic resonance imaging successfully used to assess renal fibrosis in immunoglobulin A nephropathy. This study aimed to be the first to evaluate the long-term prognostic value of DKI in CKD patients.

Methods

Forty-two patients with CKD were prospectively enrolled, and underwent DKI on a clinical 3T MR scanner. We excluded patients with comorbidities that could affect the volume or the components of the kidney. DKI parameters, including mean Kurtosis (K), mean diffusivity and apparent diffusion coefficient (ADC) of kidney cortex were obtained by region-of-interest measurement. We followed up these patients for a median of 43 months and investigated the correlations between each DKI parameter and overall renal prognosis.

Results

Both K and ADC values were correlated well with the estimated glomerular filtration rate (eGFR) on recruitment and the eGFR of the last visit in follow-up (P ˂ 0.001). K and ADC values were also well associated with the eGFR slopes in CKD patients, both with the first–last time point slope (P = 0.011 and P ˂ 0.001, respectively) and with the regression slope (P = 0.010 and P ˂ 0.001, respectively). Cox proportional hazard regression indicated that lower eGFR and ADC values independently predicted eGFR loss of ˃30% and ESRD. The receiver operating characteristic analysis showed that K and ADC values were predictable for renal prognosis, and ADC displayed better capabilities for both ESRD [area under the curve (AUC) 0.936, sensitivity 92.31%, specificity 82.76%] and the composite endpoint (eGFR loss ˃30% or ESRD) (AUC 0.881, sensitivity 66.67%, specificity 96.3%).

Conclusions

Renal ADC values obtained from DKI showed significant predictive value for the prognosis of CKD patients, which could be a promising noninvasive technique in follow-up.
Trends in the Number and Type of Tobacco Product Retailers, United States, 2000–2017
Authors: Golden Shelley D , Baggett Christopher D , Kuo Tzy-Mey , Kong Amanda Y , Delamater Paul L , Tao Vivian Qingzi , Ribisl Kurt M
Published: July 2021

Introduction

Tobacco product retailers provide access to tobacco products and exposure to tobacco marketing. Without a national tobacco retailer licensing system in the United States, there are no estimates of national trends in tobacco retailer numbers and store type over time.

Methods

We developed a protocol to identify likely tobacco retailers across the United States between 2000 and 2017 using industry codes and retailer names in the annual National Establishment Time Series (NETS) database. We calculated annual counts of tobacco retailers in seven store-type categories and annual numbers of tobacco retailers that opened and closed.

Results

We estimate that there were 317 492 tobacco product retailers in 2000; the number grew to 412 536 in 2009 before falling to 356 074 in 2017, for a net 12% increase overall. Gas/convenience stores and grocery stores accounted for more than two thirds of all retailers. On average, new openings accounted for 8.0% of the total retailers, whereas 7.3% of retailers closed or stopped selling tobacco each year, with stronger market volatility following the Great Recession. Since 2011, there was a disproportionate reduction in tobacco-selling pharmacies and an increase in both tobacco-specialty shops and tobacco-selling discount stores.

Conclusions

During two decades when smoking declined, tobacco retailer availability increased in the United States. The economic climate, corporate and public policies, and new tobacco products may all contribute to trends in tobacco retailer availability. State and local jurisdictions considering tobacco retailer policies may find retailer trend information useful for forecasting or evaluating potential policy impacts.

Implications

This study provides historic data tracking tobacco retailers in the United States between 2000 and 2017, documenting trends that unfolded as the general economic market contracted and grew, with greater regulation of the tobacco retailer environment. These data provide a context for better understanding future changes in the tobacco retailer market. In addition, the protocol established in this study could be applied in any US-based location without tobacco retailer licensing to allow identification of stores and tracking of trends.
Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling
Authors: Karanam Aravind , He David , Hsu Po-Kai , Schulze Sebastian , Dubeaux Guillaume , Karmakar Richa , Schroeder Julian I , Rappel Wouter-Jan
Published: July 2021

Signaling networks are at the heart of almost all biological processes. Most of these networks contain large number of components, and often either the connections between these components are not known or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to detailed mathematical models that contain rate constants and other parameters. Therefore, open-source platforms of Boolean models for community use are desirable. Here, we present Boolink, a freely available graphical user interface that allows users to easily construct and analyze existing Boolean networks. Boolink can be applied to any Boolean network. We demonstrate its application using a previously published network for abscisic acid (ABA)-driven stomatal closure in Arabidopsis spp. (Arabidopsis thaliana). We also show how Boolink can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested, and the model was iteratively modified based on experiments showing that ABA effectively closes Arabidopsis stomata at near-zero CO2 concentrations (1.5-ppm CO2). Thus, Boolink enables public generation and the use of existing Boolean models, including the prior developed ABA signaling model with added CO2 signaling components.
Designs, applications, and limitations of genetically encoded fluorescent sensors to explore plant biology
Authors: Sadoine Mayuri , Ishikawa Yuuma , Kleist Thomas J. , Wudick Michael M. , Nakamura Masayoshi , Grossmann Guido , Frommer Wolf B. , Ho Cheng-Hsun
Published: July 2021

The understanding of signaling and metabolic processes in multicellular organisms requires knowledge of the spatial dynamics of small molecules and the activities of enzymes, transporters, and other proteins in vivo, as well as biophysical parameters inside cells and across tissues. The cellular distribution of receptors, ligands, and activation state must be integrated with information about the cellular distribution of metabolites in relation to metabolic fluxes and signaling dynamics in order to achieve the promise of in vivo biochemistry. Genetically encoded sensors are engineered fluorescent proteins that have been developed for a wide range of small molecules, such as ions and metabolites, or to report biophysical processes, such as transmembrane voltage or tension. First steps have been taken to monitor the activity of transporters in vivo. Advancements in imaging technologies and specimen handling and stimulation have enabled researchers in plant sciences to implement sensor technologies in intact plants. Here, we provide a brief history of the development of genetically encoded sensors and an overview of the types of sensors available for quantifying and visualizing ion and metabolite distribution and dynamics. We further discuss the pros and cons of specific sensor designs, imaging systems, and sample manipulations, provide advice on the choice of technology, and give an outlook into future developments.
Efficacy of diammonium glycyrrhizinate combined with vitamin C for treating hospitalized COVID-19 patients: a retrospective, observational study
Authors: Tan R , Xiang X , Chen W , Yang Z , Hu W , Qu H , Liu J
Published: July 2021

Background

The current global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown limited responses to medical treatments.

Aims

To observe the effect of combination treatment of giammonium glycyrrhizinate and vitamin C (DV) on the prognoses of patients with COVID-19.

Methods

This retrospective observational study recruited 207 COVID-19 patients from Tongji Hospital, patients were assigned to DV and non-DV groups on the basis of the DV treatment. To make the results more credible, a propensity score matching (PSM) approach was adopted at a 1:3 ratio to determine the participants. Logistic analysis was used to assess the effect of DV therapy in the progress of COVID-19.

Results

In the DV group, the new-onset incidence rate of acute respiratory distress syndrome (ARDS) after admission was clearly lower than that in the non-DV group (DV vs. non-DV groups, 15.2% vs. 35.7%; P = 0.002). Compared with the non-DV group, the DV group showed fewer new onset of complications (such as ARDS, acute liver injury and acute myocardial injury) (DV vs. non-DV groups, 19.6% vs. 46.1%; P = 0.000). Moreover, DG+VC may help to recover the count of NK cells and decrease the level of sIL-2R.

Conclusions

DG+VC might be a promising candidate for preventing the deterioration of COVID-19 patients, which is worthy to be studied in large and perspective cohort.
Long-term effects of early pulse methylprednisolone and intravenous immunoglobulin in patients with dermatomyositis and polymyositis
Authors: Hoff Leonardo S , de Souza Fernando H C , Miossi Renata , Shinjo Samuel K
Published: July 2021

Objective

To evaluate the long-term effects of pulse i.v. methylprednisolone (IVMP) or IVIG administered during the first year of diagnosis in DM and PM patients.

Methods

This is a retrospective single-centre cohort study of patients with PM/DM followed for up to 4 years from 2001 to 2017. We used Cox regression models to estimate hazard ratios (HRs) and assess the effects of early pulse IVMP or IVIG on three outcomes: complete clinical response, CS discontinuation, and survival. Analysis was adjusted for clinical, laboratory and treatment covariates.

Results

A total of 204 patients were included and categorized into four initial treatment groups: pulse IVMP (n = 46), pulse IVMP + IVIG (n = 55), IVIG (n = 10), and without IVMP or IVIG (n = 93). The groups of early pulse IVMP and pulse IVMP + IVIG had a higher HR for complete clinical response in the multivariate models (HR = 1.56, 95% CI: 1.05, 2.33, P = 0.029; and HR = 1.58, 95% CI: 1.02, 2.45, P = 0.041, respectively). Only the group of pulse IVMP + IVIG had a significant association with CS discontinuation in the multivariate analysis (HR = 1.65, 95% CI: 1.02, 2.68, P = 0.043). Early pulse IVMP or IVIG had no impact on mortality.

Conclusion

Despite having a more severe disease profile, patients with PM/DM submitted to pulse IVMP or pulse IVMP + IVIG during the first year of diagnosis had a higher HR for complete clinical response, whereas the combination of pulse IVMP + IVIG had an association with CS discontinuation. Prospective long-term studies are warranted to confirm these benefits of early pulse IVMP and IVIG on patients with PM/DM.
Outcomes linked to eligibility for stem cell transplantation trials in diffuse cutaneous systemic sclerosis
Authors: Spierings Julia , Nihtyanova Svetlana I , Derrett-Smith Emma , Clark Kristina E N , van Laar Jacob M , Ong Voon , Denton Christopher P
Published: July 2021

Objectives

The aim of this study was to explore outcomes in a cohort of dcSSc patients fulfilling eligibility criteria for stem cell transplantation (SCT) studies but receiving standard immunosuppression.

Methods

From a large single-centre dcSSc cohort (n = 636), patients were identified using the published SCT trials’ inclusion criteria. Patients meeting the trials’ exclusion criteria were excluded.

Results

Of the 227 eligible patients, 214 met the inclusion criteria for ASTIS (Autologous Stem Cell Transplantation International Scleroderma), 82 for SCOT (Scleroderma: Cyclophosphamide Or Transplantation) and 185 for the UPSIDE (UPfront autologous haematopoietic Stem cell transplantation vs Immunosuppressive medication in early DiffusE cutaneous systemic sclerosis) trial, and 66 were excluded based on age >65 years, low diffusing capacity of the lungs for carbon monoxide (DLco), pulmonary hypertension or creatinine clearance <40 ml/min. The mean follow-up time was 12 years (s.d. 7). Among the eligible patients, 103 (45.4%) died. Survival was 96% at 2 years, 88% at 5 years, 73% at 10 years and 43% at 20 years. Compared with this ‘SCT-eligible’ cohort, those patients who would have been excluded from SCT trials had a worse long-term survival (97% at 2 years, 77% at 5 years, 52% at 10 years and 15% at 20 years, log rank P < 0.001). Excluded patients also had a significantly worse long-term event-free survival. Hazard of death was higher in patients with higher age at onset [hazard ratio (HR) 1.05, P < 0.001], higher ESR at baseline (HR 1.01, P = 0.025) and males (HR 2.12, P = 0.008).

Conclusion

SCT inclusion criteria identify patients with poor outcome despite current best practice treatment. Patients meeting the inclusion criteria for SCT but who would have been excluded from the trials because of age, pulmonary hypertension, poor kidney function or DLco <40% had worse outcomes.
Hub-and-Spoke Regulation and Bank Leverage
Authors: Gopalan Yadav , Kalda Ankit , Manela Asaf
Published: July 2021

Regulators often delegate monitoring to local supervisors, which can improve information collection, but can also lead to agency problems and capture. We document that following the closure of a US bank regulator’s field offices, the banks they previously supervised actively increased their risk of failure by distributing cash, increasing leverage, and lending more than similar banks at the same time and place. Supervisor proximity is a channel through which these effects operate. Our findings suggest that local supervision is an important part of regulation, as it facilitates collection of information imperfectly reflected in reported measures, and that switching from onsite to offsite supervision can increase bank risk.
SURFACE DOSE ESTIMATION BY A KAP METER FOR KILOVOLTAGE X-RAY BEAMS
Authors: Araki F , Umeno S
Published: July 2021

This study aims to estimate the entrance surface dose (ESD) of a water phantom for kilovoltage x-ray beams using an air kerma area product meter (KAP meter) equipped in an x-ray unit. The KAP meter was calibrated in terms of the ESD determined by a plane-parallel ionization chamber based on a 60Co absorbed dose-to-water calibration coefficient, ${N}_{D,w}^{{}^{60}\mathrm{C}\mathrm{o}}$. The ESD measured using the KAP meter was verified by comparing it with that estimated by the air kerma calibration coefficient, NK, for x-ray beam qualities. The ratio of ESDs based on ${N}_{D,w}^{{}^{60}\mathrm{C}\mathrm{o}}$ and NK was 1.003 on average and independent of the beam quality. The ESD by the KAP meter was an agreement within ±1.5% with that measured using the plane-parallel chamber for 10 × 10–30 × 30 cm2 fields with a source-surface distance of 75–150 cm. It was possible to estimate the ESD directly in a water phantom for x-ray beams without correction factors compared to the existing air kerma calibration, using a KAP meter calibrated based on ${N}_{D,w}^{{}^{60}\mathrm{C}\mathrm{o}}$.
Promoting the ICT Industry for the future with fears from the past
Authors: Kim Jongheon
Published: July 2021

Unlike other developed countries, the Fourth Industrial Revolution (4IR) discourse has become the central element within technology governance in Korea. This paper examines the reasons for the discourse’s success and its political and social implications. Based on the analysis of policy documents and the media coverage, I argue that political and economic elites have actively introduced the 4IR discourse to create novel momentum for promoting Information and Communications Technology (ICT) and to justify deregulatory measures while re-enacting the developmentalist imaginary. I also highlight that the 4IR discourse’s promoters have drawn upon the dialectics between the desirable future and the nation’s shared fear to urge the Korean society to accept the measures privileging the industry as the means of making the nation a developed country and avoiding being colonized again.
The role of integrated programs in the prevention of COVID-19 in a humanitarian setting
Authors: Ali Yousif , Ahmed Ayman , Siddig Emmanuel Edwar , Mohamed Nouh S
Published: July 2021

The COVID-19 pandemic has caused a severe depletion to health systems worldwide. In the South Kordofan state, a war-torn humanitarian region in Sudan, the United Nations High Commissioner for Refugees and the WHO Emergencies Programme have led the development of integrated programs for health, peace and rehabilitation by training rapid response teams to strengthen both surveillance system and response capacities, engaging the communities at risk with health education and promotion activities, as well as following proper infection, prevention and control measures during case investigation. Also, Early Help Assessment coordinators met with health services managers and recruited 14 teams who were trained to ensure a rapid response to COVID-19. Also, the implementation of water, sanitation and hygiene services was upscaled. Although the local community of South Kordofan is fragile and at high risk of infectious diseases, the limited numbers of detected cases of COVID-19 and COVID-19 deaths could be attributed to the early preparation and integration of programs that helped to prevent the local spread of COVID-19. This lesson needs to be thoroughly investigated to estimate whether it is cost-effective and to determine the feasibility of it being successfully implemented in other humanitarian settings.
A Diagnostic Guide for Phytophthora capsici Infecting Vegetable Crops
Authors: Parada-Rojas Camilo H. , Granke Leah L. , Naegele Rachel P. , Hansen Zachariah , Hausbeck Mary K. , Kousik Chandrasekar S. , McGrath Margaret T. , D. Smart Christine , Quesada-Ocampo Lina M.
Published: July 2021

Phytophthora capsici is an oomycete pathogen causing economically important diseases in a wide range of hosts worldwide including cucurbitaceous, solanaceous, and fabaceous crops. All plant parts, crown and roots, or only the fruit may be affected depending on the host, and symptoms can range from wilting to rot and plant death. Considered a hemibiotroph, P. capsici can be cultured in artificial media and maintained in long-term storage. In this diagnostic guide, we describe methods to identify P. capsici infection based on disease symptoms and pathogen signs. We also outline methods for molecular identification, pathogen isolation, storage of single-sporangium cultures, and pathogenicity testing.
Fascia Iliaca Blocks Performed in the Emergency Department Decrease Opioid Consumption and Length of Stay in Patients with Hip Fracture
Authors: Kolodychuk Nicholas , Krebs John Collin , Stenberg Robert , Talmage Lance , Meehan Anita , DiNicola Nicholas
Published: July 2021

Objectives:

To examine the impact of fascia iliaca (FI) blocks performed in the emergency department on patients with hip fracture on opioid consumption, length of stay, and readmission rate.

Design:

Prospective cohort study.

Setting:

Community-based Level 1 trauma center.

Patients/Participants:

Ninety-eight patients with isolated femoral neck, intertrochanteric, and subtrochanteric femur fractures (OTA/AO 31-A and 31-B) presenting from January 1, 2020, to June 30, 2020.

Intervention:

Ultrasound-guided FI compartment block using 40 mL of 0.25% bupivacaine.

Main Outcome Measurements:

Opioid consumption, length of stay, discharge disposition, and 30-day readmission rate.

Results:

Thirty-three patients had contraindication to FI block. Thirty-nine of 65 patients (60%) without contraindications to undergoing FIB received FI block. Mean age, body mass index, fracture type, and surgical procedure were similar between patients undergoing FIB and not receiving FIB. The FIB group had significantly lower opioid consumption preoperatively [17.4 vs. 32.0 morphine milliequivalents (MMEs)], postoperatively (37.1 vs. 85.5 MMEs), over total hospital stay (54.5 vs. 117.5 MMEs), and mean opioid consumption per day of hospital stay (13.3 vs. 24.0 MMEs). Patients in the FIB group had shorter length of stay compared with the control group (4.3 vs. 5.2 days). There was no significant difference in discharge disposition destination between groups. No patients reported complications of FI block.

Conclusions:

Undergoing FI block in the emergency department was associated with decreased opioid consumption, decreased length of stay, and decreased hospital readmission within 30 days of hip fracture.

Level of Evidence:

Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
The Prevalence of Bullying Among Pediatric Orthopaedic Patients
Authors: Carrillo Laura A. , Sabatini Coleen S. , Brar Ravinder K. , Jagodzinski Jason E. , Sabharwal Sanjeev , Delgado Eliana , Livingston Kristin S.
Published: July 2021

Background:

Bullying is destructive and pervasive. Although the literature suggests children with chronic health conditions are at higher risk of being bullied, there is minimal research regarding the prevalence of bullying among children with orthopaedic conditions. Our study aimed to assess the prevalence of bullying among pediatric orthopaedic outpatients and evaluate the association of orthopaedic conditions and use of orthopaedic devices with perceptions of bullying.

Methods:

Patients in outpatient pediatric orthopaedic clinics, ages 10 to 17 and their parents were surveyed using the Child-Adolescent Bullying Scale-9. Basic demographic, information about the child’s orthopaedic condition, and parent’s perception of their child being subject to bullying were also collected. Children were asked if they had used any orthopaedic devices in the last 3 months, whether they were bullied because of their device, and if bullying affected their compliance with device use. The analysis utilized a t test or analysis of variance to compare mean Child-Adolescent Bullying Scale-9 scores across different groups.

Results:

Among the 198 patients surveyed, 61% (N=121) perceived no-to-minimal exposure to bullying, 36% (N=72) moderate exposure, and 3% (N=5) severe exposure. Children ages 10 to 13 (N=100) and children ages 14 to 17 (N=98) reported similar rates of bullying (P=0.97). Higher rates of moderate to severe bullying were reported by patients with foot deformity (80%), multiple orthopaedic diagnoses (55%), chronic pain (39%), fracture/acute injury (37%), and scoliosis (33%). Moderate to severe bullying was reported by 37% of patients who wore a cast, 40% who wore a brace/orthotic, and 52% who used multiple orthopaedic devices. Parental concern that their child was being bullied was highly correlated with their child’s bullying score (P=0.0002).

Conclusions:

More than one third of our pediatric orthopaedic outpatients (39%) experience moderate to severe levels of bullying, which is higher than the general population’s reported rates of 20% to 35%. Exposure to bullying may be higher in certain diagnoses or with use of certain orthopaedic devices. Further research is needed to delineate who is at highest risk.

Level of Evidence:

Level IV.