bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatility of Volatility Estimation: Central Limit Theorems for the Fourier Transform Estimator and Empirical Study of the Daily Time Series Stylized Facts
Authors: Toscano Giacomo , Livieri Giulia , Mancino Maria Elvira , Marmi Stefano 
Published: November 2022

Abstract
We study the asymptotic normality of two feasible estimators of the integrated volatility of volatility based on the Fourier methodology, which does not require the pre-estimation of the spot volatility. We show that the bias-corrected estimator reaches the optimal rate n1/4, while the estimator without bias-correction has a slower convergence rate and a smaller asymptotic variance. Additionally, we provide simulation results that support the theoretical asymptotic distribution of the rate-efficient estimator and show the accuracy of the latter in comparison with a rate-optimal estimator based on the pre-estimation of the spot volatility. Finally, using the rate-optimal Fourier estimator, we reconstruct the series of the daily volatility of volatility of the S&P500 and EUROSTOXX50 indices over long samples and provide novel insight into the existence of stylized facts about the volatility of volatility dynamics.
Hybrid mode atomic force microscopy of phase modulation and frequency modulation
Authors: Yamamoto Tatsuya , Miyazaki Masato , Nomura Hikaru , Li Yan Jun , Sugawara Yasuhiro 
Published: November 2022

Abstract
We propose hybrid phase modulation (PM)/frequency modulation (FM) atomic force microscopy (AFM) to increase the imaging speed of AFM in high-Q environments. We derive the relationship between the phase shift, the frequency shift and the tip–sample interaction force from the equation of motion for the cantilever in high-Q environments. The tip–sample conservative force is approximately given by the sum of the conservative force with respect to the phase shift in the PM mode and that with respect to the frequency shift in the FM mode. We preliminarily demonstrate that the hybrid PM/FM-AFM is a new and very promising AFM operation mode that can increase imaging speed.
Cis-regulatory variation expands the colour palette of the Brassicaceae
Authors: Fattorini Róisín , Ó’Maoiléidigh Diarmuid S 
Published: November 2022

This article comments on:
Ye S, Hua S, Ma T, Ma X, Chen Y, Wu L, Zhao L, Yi B, Ma C, Tu J, Shen J, Fu T, Wen J. 2022. Genetic and multi-omics analyses reveal BnaA07.PAP2In-184-317 as the key gene conferring anthocyanin-based color in Brassica napus flowers. Journal of Experimental Botany 73,6630–6645.
In situcontrol of root–bacteria interactions using optical trapping in transparent soil
Authors: Ge Sisi , Dong Xingshui , Liu Yangminghao , Wright Kathryn M , Humphris Sonia N , Dupuy Lionel X , MacDonald Michael P 
Published: November 2022

AbstractBacterial attachment on root surfaces is an important step preceding the colonization or internalization and subsequent infection of plants by pathogens. Unfortunately, bacterial attachment is not well understood because the phenomenon is difficult to observe. Here we assessed whether this limitation could be overcome using optical trapping approaches. We have developed a system based on counter-propagating beams and studied its ability to guide Pectobacterium atrosepticum (Pba) cells to different root cell types within the interstices of transparent soils. Bacterial cells were successfully trapped and guided to root hair cells, epidermal cells, border cells, and tissues damaged by laser ablation. Finally, we used the system to quantify the bacterial cell detachment rate of Pba cells on root surfaces following reversible attachment. Optical trapping techniques could greatly enhance our ability to deterministically characterize mechanisms linked to attachment and formation of biofilms in the rhizosphere.
r-process nucleosynthesis and kilonovae from hypermassive neutron star post-merger remnants
Authors: Curtis Sanjana , Mösta Philipp , Wu Zhenyu , Radice David , Roberts Luke , Ricigliano Giacomo , Perego Albino 
Published: November 2022

ABSTRACT
We investigate r-process nucleosynthesis and kilonova emission resulting from binary neutron star (BNS) mergers based on a three-dimensional (3D) general-relativistic magnetohydrodynamic (GRMHD) simulation of a hypermassive neutron star (HMNS) remnant. The simulation includes a microphysical finite-temperature equation of state (EOS) and neutrino emission and absorption effects via a leakage scheme. We track the thermodynamic properties of the ejecta using Lagrangian tracer particles and determine its composition using the nuclear reaction network SkyNet. We investigate the impact of neutrinos on the nucleosynthetic yields by varying the neutrino luminosities during post-processing. The ejecta show a broad distribution with respect to their electron fraction Ye, peaking between ∼0.25–0.4 depending on the neutrino luminosity employed. We find that the resulting r-process abundance patterns differ from solar, with no significant production of material beyond the second r-process peak when using luminosities recorded by the tracer particles. We also map the HMNS outflows to the radiation hydrodynamics code SNEC and predict the evolution of the bolometric luminosity as well as broadband light curves of the kilonova. The bolometric light curve peaks on the timescale of a day and the brightest emission is seen in the infrared bands. This is the first direct calculation of the r-process yields and kilonova signal expected from HMNS winds based on 3D GRMHD simulations. For longer-lived remnants, these winds may be the dominant ejecta component producing the kilonova emission.
ALMACAL VIII: a pilot survey for untargeted extragalactic CO emission lines in deep ALMA calibration data
Authors: Hamanowicz Aleksandra , Zwaan Martin A , Péroux Céline , Lagos Claudia del P , Klitsch Anne , Ivison Rob J , Biggs Andrew D , Szakacs Roland , Fresco Alejandra 
Published: November 2022

ABSTRACT
We present a pilot, untargeted extragalactic carbon monoxide (CO) emission-line survey using ALMACAL, a project utilizing ALMA calibration data for scientific purposes. In 33 deep (Texp &gt; 40 min) ALMACAL fields, we report six CO emission-line detections above S/N &gt; 4, one-third confirmed by MUSE observations. With this pilot survey, we probe a cosmologically significant volume of ∼105 cMpc3, widely distributed over many pointings in the southern sky, making the survey largely insusceptible to the effects of cosmic variance. We derive the redshift probability of the CO detections using probability functions from the Shark semi-analytical model of galaxy formation. By assuming typical CO excitations for the detections, we put constraints on the cosmic molecular gas mass density evolution over the redshift range 0 &lt; z &lt; 1.5. The results of our pilot survey are consistent with the findings of other untargeted emission-line surveys and the theoretical model predictions and currently cannot rule out a non-evolving molecular gas mass density. Our study demonstrates the potential of using ALMA calibrator fields as a multi-sightline untargeted CO emission-line survey. Applying this approach to the full ALMACAL database will provide an accurate, free of cosmic variance, measurement of the molecular luminosity function as a function of redshift.
Unveiling polarized emission from interstellar dust of the Large Magellanic Cloud with Planck
Authors: Alina D , Bernard J-Ph , Yuen K H , Lazarian A , Hughes A , Iskakova M , Akimkhan A , Mukanova A 
Published: November 2022

ABSTRACT
Polarization of interstellar dust emission is a powerful probe of dust properties and magnetic field structure. Yet studies of external galaxies are hampered by foreground dust contribution. The study aims at separating the polarized signal from the Large Magellanic Cloud (LMC) from that of the Milky Way (MW) to construct a wide-field, spatially complete map of dust polarization using the Planck 353 GHz data. To estimate the foreground polarization direction, we used velocity gradients in H i spectral line data and assessed the performance of the output by comparing to starlight extinction polarization. We estimate the foreground intensity using the dust-to-gas correlation and the average intensity around the LMC and we assume the foreground polarization to be uniform and equal to the average of the MW around the galaxy to derive foreground I, Q, and U parameters. After foreground removal, the geometry of the plane-of-the-sky magnetic field tends to follow the structure of the atomic gas. This is notably the case along the molecular ridges extending south and south-east of the 30 Doradus star-forming complex and along the more diffuse southern arm extending towards the Small Magellanic Cloud. There is also an alignment between the magnetic field and the outer arm in the western part. The median polarization fraction in the LMC is slightly lower than that observed for the MW as well as the anticorrelation between the polarization angle dispersion function and the polarization fraction. Overall, polarization fraction distribution is similar to that observed in the MW.
The effects of stellar rotation along the main sequence of the 100-Myr-old massive cluster NGC 1850
Authors: Kamann S , Saracino S , Bastian N , Gossage S , Usher C , Baade D , Cabrera-Ziri I , de Mink S E , Ekstrom S , Georgy C , Hilker M , Larsen S S , Mackey D , Niederhofer F , Platais I , Yong D 
Published: November 2022

ABSTRACT
Young star clusters enable us to study the effects of stellar rotation on an ensemble of stars of the same age and across a wide range in stellar mass and are therefore ideal targets for understanding the consequences of rotation on stellar evolution. We combine MUSE spectroscopy with HST photometry to measure the projected rotational velocities (Vsin i) of 2184 stars along the split main sequence and on the main sequence turn-off (MSTO) of the 100 Myr-old massive ($10^5\, {\rm M_{\odot }}$) star cluster NGC 1850 in the Large Magellanic Cloud. At fixed magnitude, we observe a clear correlation between Vsin i and colour, in the sense that fast rotators appear redder. The average Vsin i values for stars on the blue and red branches of the split main sequence are $\sim \! 100\, {\rm km\, s^{-1}}$ and $\sim \! 200\, {\rm km\, s^{-1}}$, respectively. The values correspond to about $25-30{{\ \rm per\ cent}}$ and $50-60{{\ \rm per\ cent}}$ of the critical rotation velocity and imply that rotation rates comparable to those observed in field stars of similar masses can explain the split main sequence. Our spectroscopic sample contains a rich population of ∼200 fast rotating Be stars. The presence of shell features suggests that 23 per cent of them are observed through their decretion discs, corresponding to a disc opening angle of 15 degrees. These shell stars can significantly alter the shape of the MSTO, hence care should be taken when interpreting this photometric feature. Overall, our findings impact our understanding of the evolution of young massive clusters and provide new observational constraints for testing stellar evolutionary models.
Constraints on electron acceleration in gamma-ray bursts afterglows from radio peaks
Authors: Duncan Ruby A , van der Horst Alexander J , Beniamini Paz 
Published: November 2022

ABSTRACT
Studies of gamma-ray bursts (GRBs) and their multiwavelength afterglows have led to insights in electron acceleration and emission properties from relativistic, high-energy astrophysical sources. Broad-band modelling across the electromagnetic spectrum has been the primary means of investigating the physics behind these sources, although independent diagnostic tools have been developed to inform and corroborate assumptions made in particle acceleration simulations and broad-band studies. We present a methodology to constrain three physical parameters related to electron acceleration in GRB blast waves: the fraction of shock energy in electrons, ϵe; the fraction of electrons that gets accelerated into a power-law distribution of energies, ξe; and the minimum Lorentz factor of the accelerated electrons, γm. These parameters are constrained by observations of the peaks in radio afterglow light curves and spectral energy distributions. From a sample of 49 radio afterglows, we are able to find narrow distributions for these parameters, hinting at possible universality of the blast wave microphysics, although observational bias could play a role in this. Using radio peaks and considerations related to the prompt gamma-ray emission efficiency, we constrain the allowed parameter ranges for both ϵe and ξe to within about one order of magnitude, 0.01 ≲ ϵe ≲ 0.2 and 0.1 ≲ ξe ≲ 1. Such stringent constraints are inaccessible for ξe from broad-band studies due to model degeneracies.
Chemical evolution of fluorine in the Milky Way
Authors: Womack Kate A , Vincenzo Fiorenzo , Gibson Brad K , Côté Benoit , Pignatari Marco , Brinkman Hannah E , Ventura Paolo , Karakas Amanda 
Published: November 2022

ABSTRACT
Fluorine has many different potential sites and channels of production, making narrowing down a dominant site of fluorine production particularly challenging. In this work, we investigate which sources are the dominant contributors to the galactic fluorine by comparing chemical evolution models to observations of fluorine abundances in Milky Way stars covering a metallicity range of −2 &lt; [Fe/H] &lt; 0.4 and upper limits in the range of −3.4 &lt; [Fe/H] &lt; −2.3. In our models, we use a variety of stellar yield sets in order to explore the impact of varying both asymptotic giant branch (AGB) and massive star yields on the chemical evolution of fluorine. In particular, we investigate different prescriptions for initial rotational velocity in massive stars as well as a metallicity-dependent mix of rotational velocities. We find that the observed [F/O] and [F/Fe] abundance ratios at low metallicity and the increasing trend of [F/Ba] at [Fe/H] ≳ −1 can only be reproduced by chemical evolution models assuming, at all metallicities, a contribution from rapidly rotating massive stars with initial rotational velocities as high as 300 km s−1. A mix of rotational velocities may provide a more physical solution than the sole use of massive stars with vrot  =  300 km s−1, which are predicted to overestimate the fluorine and average s-process elemental abundances at [Fe/H] ≳ −1. The contribution from AGB stars is predicted to start at [Fe/H] ≈ −1 and becomes increasingly important at high metallicity, being strictly coupled to the evolution of the nitrogen abundance. Finally, by using modern yield sets, we investigate the fluorine abundances of Wolf–Rayet winds, ruling them out as dominant contributors to the galactic fluorine.
Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus)
Authors: Hempel Elisabeth , Bibi Faysal , Faith J Tyler , Koepfli Klaus-Peter , Klittich Achim M , Duchêne David A , Brink James S , Kalthoff Daniela C , Dalén Love , Hofreiter Michael , Westbury Michael V 
Published: November 2022

AbstractThe blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
Rapid single-molecule characterisation of enzymes involved in nucleic-acid metabolism
Authors: Mueller Stefan H , Fitschen Lucy J , Shirbini Afnan , Hamdan Samir M , Spenkelink Lisanne M , van Oijen Antoine M 
Published: November 2022

Abstract
The activity of enzymes is traditionally characterised through bulk-phase biochemical methods that only report on population averages. Single-molecule methods are advantageous in elucidating kinetic and population heterogeneity but are often complicated, time consuming, and lack statistical power. We present a highly-generalisable and high-throughput single-molecule assay to rapidly characterise proteins involved in DNA metabolism. The assay exclusively relies on changes in total fluorescence intensity of surface-immobilised DNA templates as a result of DNA synthesis, unwinding or digestion. Combined with an automated data-analysis pipeline, our method provides enzymatic activity data of thousands of molecules in less than an hour. We demonstrate our method by characterising three fundamentally different enzyme activities: digestion by the phage λ exonuclease, synthesis by the phage Phi29 polymerase, and unwinding by the E. coli UvrD helicase. We observe the previously unknown activity of the UvrD helicase to remove neutravidin bound to 5′-, but not 3′-ends of biotinylated DNA.
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment
Authors: Han Ya , Wang Yuting , Dong Xin , Sun Dongqing , Liu Zhaoyang , Yue Jiali , Wang Haiyun , Li Taiwen , Wang Chenfei 
Published: November 2022

Abstract
The Tumor Immune Single Cell Hub 2 (TISCH2) is a resource of single-cell RNA-seq (scRNA-seq) data from human and mouse tumors, which enables comprehensive characterization of gene expression in the tumor microenvironment (TME) across multiple cancer types. As an increasing number of datasets are generated in the public domain, in this update, TISCH2 has included 190 tumor scRNA-seq datasets covering 6 million cells in 50 cancer types, with 110 newly collected datasets and almost tripling the number of cells compared with the previous release. Furthermore, TISCH2 includes several new functions that allow users to better utilize the large-scale scRNA-seq datasets. First, in the Dataset module, TISCH2 provides the cell–cell communication results in each dataset, facilitating the analyses of interacted cell types and the discovery of significant ligand–receptor pairs between cell types. TISCH2 also includes the transcription factor analyses for each dataset and visualization of the top enriched transcription factors of each cell type. Second, in the Gene module, TISCH2 adds functions for identifying correlated genes and providing survival information for the input genes. In summary, TISCH2 is a user-friendly, up-to-date and well-maintained data resource for gene expression analyses in the TME. TISCH2 is freely available at http://tisch.comp-genomics.org/.
The nucleoplasmic phase of pre-40S formation prior to nuclear export
Authors: Cheng Jingdong , Lau Benjamin , Thoms Matthias , Ameismeier Michael , Berninghausen Otto , Hurt Ed , Beckmann Roland 
Published: November 2022

Abstract
Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23–TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
Structural insights into target DNA recognition and cleavage by the CRISPR-Cas12c1 system
Authors: Zhang Bo , Lin Jinying , Perčulija Vanja , Li Yu , Lu Qiuhua , Chen Jing , Ouyang Songying 
Published: November 2022

Abstract
Cas12c is the recently characterized dual RNA-guided DNase effector of type V-C CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein) systems. Due to minimal requirements for a protospacer adjacent motif (PAM), Cas12c is an attractive candidate for genome editing. Here we report the crystal structure of Cas12c1 in complex with single guide RNA (sgRNA) and target double-stranded DNA (dsDNA) containing the 5′-TG-3′ PAM. Supported by biochemical and mutation assays, this study reveals distinct structural features of Cas12c1 and the associated sgRNA, as well as the molecular basis for PAM recognition, target dsDNA unwinding, heteroduplex formation and recognition, and cleavage of non-target and target DNA strands. Cas12c1 recognizes the PAM through a mechanism that is interdependent on sequence identity and Cas12c1-induced conformational distortion of the PAM region. Another special feature of Cas12c1 is the cleavage of both non-target and target DNA strands at a single, uniform site with indistinguishable cleavage capacity and order. Location of the sgRNA seed region and minimal length of target DNA required for triggering Cas12c1 DNase activity were also determined. Our findings provide valuable information for developing the CRISPR-Cas12c1 system into an efficient, high-fidelity genome editing tool.
A forward genetic screen in C. elegans identifies conserved residues of spliceosomal proteins PRP8 and SNRNP200/BRR2 with a role in maintaining 5′ splice site identity
Authors: Cartwright-Acar Catiana H , Osterhoudt Kenneth , Suzuki Jessie M N G L , Gomez Destiny R , Katzman Sol , Zahler Alan M 
Published: November 2022

Abstract
The spliceosome undergoes extensive rearrangements as it assembles onto precursor messenger RNAs. In the earliest assembly step, U1snRNA identifies the 5′ splice site. However, U1snRNA leaves the spliceosome relatively early in assembly, and 5′ splice site identity is subsequently maintained through interactions with U6snRNA, protein factor PRP8, and other components during the rearrangements that build the catalytic site. Using a forward genetic screen in Caenorhabditis elegans, we have identified suppressors of a locomotion defect caused by a 5′ss mutation. Here we report three new suppressor alleles from this screen, two in PRP8 and one in SNRNP200/BRR2. mRNASeq studies of these suppressor strains indicate that they also affect specific native alternative 5′ss, especially for suppressor PRP8 D1549N. A strong suppressor at the unstructured N-terminus of SNRNP200, N18K, indicates a novel role for this region. By examining distinct changes in the splicing of native genes, examining double mutants between suppressors, comparing these new suppressors to previously identified splicing suppressors from yeast, and mapping conserved suppressor residues onto cryoEM structural models of assembling human spliceosomes, we conclude that there are multiple interactions at multiple stages in spliceosome assembly responsible for maintaining the initial 5′ss identified by U1snRNA for entry into the catalytic core.