bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACT
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

ABSTRACT
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

Abstract
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

Abstract
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

AbstractEukaryotic 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT

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

Abstract

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

AbstractSignaling 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

AbstractThe 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.