bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducing the CO-to-H2 conversion factor in cosmological simulations of Milky-Way-mass galaxies
Authors: Keating Laura C , Richings Alexander J , Murray Norman , Faucher-Giguère Claude-André , Hopkins Philip F , Wetzel Andrew , Kereš Dušan , Benincasa Samantha , Feldmann Robert , Loebman Sarah , Orr Matthew E 
Published: September 2020

ABSTRACT
We present models of CO(1–0) emission from Milky-Way-mass galaxies at redshift zero in the FIRE-2 cosmological zoom-in simulations. We calculate the molecular abundances by post-processing the simulations with an equilibrium chemistry solver while accounting for the effects of local sources, and determine the emergent CO(1–0) emission using a line radiative transfer code. We find that the results depend strongly on the shielding length assumed, which, in our models, sets the attenuation of the incident UV radiation field. At the resolution of these simulations, commonly used choices for the shielding length, such as the Jeans length, result in CO abundances that are too high at a given H2 abundance. We find that a model with a distribution of shielding lengths, which has a median shielding length of ∼3 pc in cold gas (T &lt; 300 K) for both CO and H2, is able to reproduce both the observed CO(1–0) luminosity and inferred CO-to-H2 conversion factor at a given star formation rate compared with observations. We suggest that this short shielding length can be thought of as a subgrid model, which controls the amount of radiation that penetrates giant molecular clouds.
Fast algorithms to approximate the position-dependent point spread function responses in radio interferometric wide-field imaging
Authors: Atemkeng M , Smirnov O , Tasse C , Foster G , Makhathini S 
Published: September 2020

ABSTRACT
The desire for wide field of view, large fractional bandwidth, high sensitivity, high spectral and temporal resolution has driven radio interferometry to the point of big data revolution where the data are represented in at least three dimensions with an axis for spectral windows, baselines, sources, etc., where each axis has its own set of subdimensions. The cost associated with storing and handling these data is very large, and therefore several techniques to compress interferometric data and/or speed up processing have been investigated. Unfortunately, averaging-based methods for visibility data compression are detrimental to the data fidelity, since the point spread function (PSF) is position-dependent, that is, distorted and attenuated as a function of distance from the phase centre. The position dependence of the PSF becomes more severe, requiring more PSF computations for wide-field imaging. Deconvolution algorithms must take the distortion into account in the major and minor cycles to properly subtract the PSF and recover the fidelity of the image. This approach is expensive in computation since at each deconvolution iteration a distorted PSF must be computed. We present two algorithms that approximate these position-dependent PSFs with fewer computations. The first algorithm approximates the position-dependent PSFs in the uv-plane and the second algorithm approximates the position-dependent PSFs in the image plane. The proposed algorithms are validated using simulated data from the MeerKAT telescope.
Three- and two-point spatial correlations of IGM at z ∼ 2: cloud-based analysis using simulations
Authors: Maitra Soumak , Srianand Raghunathan , Gaikwad Prakash , Choudhury Tirthankar Roy , Paranjape Aseem , Petitjean Patrick 
Published: September 2020

ABSTRACT
Ly α forest absorption spectra decomposed into multiple Voigt profile components (clouds) allow us to study clustering of intergalactic medium (IGM) as a function of H i column density ($N_{\rm H\, \small{I}}$). Here, we explore the transverse three-point correlation (ζ) of Ly α clouds using mock triplet spectra from simulations at z ∼ 2 on scales of 1–5 h−1 cMpc. We find ζ to depend strongly on $N_{\rm H\, \small{I}}$ and scale and weakly on angle of the triplet configuration. We show that the ‘hierarchical ansatz’ is applicable for scales $\ge ~ 3\, h^{-1}$ cMpc, and obtain a median reduced three-point correlation (Q) in the range 0.2–0.7. We show, ζ is influenced strongly by the thermal and ionization state of the gas. As in the case of galaxies, the influence of physical parameters on Q is weaker compared to that on ζ. We show difference in ζ and Q between different simulations are minimized if we use appropriate $N_{\rm H\, \small{I}}$ cut-offs corresponding to a given baryon overdensity (Δ) using the $N_{\rm H\, \small{I}}~versus~\Delta$ relationship obtained from simulations. We study the effect of pressure broadening on ζ using a model with artificially boosted heating rates. However, for models with realistic thermal and ionization histories the effect of pressure broadening on ζ is subdominant compared to other local effects. We find the strong redshift evolution shown by ζ, mainly originating from the redshift evolution of thermal and ionization state of the IGM. We discuss the observational requirements for the detection of three-point correlation, specifically, in small intervals of configuration parameters and redshift.
High-resolution simulations of dark matter subhalo disruption in a Milky-Way-like tidal field
Authors: Webb Jeremy J , Bovy Jo 
Published: September 2020

ABSTRACT
We compare the results of high-resolution simulations of individual dark matter subhaloes evolving in external tidal fields with and without baryonic bulge and disc components, where the average dark matter particle mass is three orders of magnitude smaller than cosmological zoom-in simulations of galaxy formation. The Via Lactea II simulation is used to setup our initial conditions and provides a basis for our simulations of subhaloes in a dark-matter-only tidal field, while an observationally motivated model for the Milky-Way is used for the tidal field that is comprised of a dark matter halo, a stellar disc, and a stellar bulge. Our simulations indicate that including stellar components in the tidal field results in the number of subhaloes in Milky-Way-like galaxies being only $65{{\ \rm per\ cent}}$ of what is predicted by Λ cold dark matter (ΛCDM). For subhaloes with small pericentres (rp ≲ 25 kpc), the subhalo abundance is reduced further to $40{{\ \rm per\ cent}}$, with the surviving subhaloes being less dense and having a tangentially anisotropic orbital distribution. Conversely, subhaloes with larger pericentres are minimally affected by the inclusion of a stellar component in the tidal field, with the total number of outer subhaloes $\approx 75{{\ \rm per\ cent}}$ of the ΛCDM prediction. The densities of outer subhaloes are comparable to predictions from ΛCDM, with the subhaloes having an isotropic distribution of orbits. These ratios are higher than those found in previous studies that include the effects baryonic matter, which are affected by spurious disruption caused by low resolution.
Recovery of 21-cm intensity maps with sparse component separation
Authors: Carucci Isabella P , Irfan Melis O , Bobin Jérôme 
Published: September 2020

ABSTRACT
21-cm intensity mapping has emerged as a promising technique to map the large-scale structure of the Universe. However, the presence of foregrounds with amplitudes orders of magnitude larger than the cosmological signal constitutes a critical challenge. Here, we test the sparsity-based algorithm generalized morphological component analysis (GMCA) as a blind component separation technique for this class of experiments. We test the GMCA performance against realistic full-sky mock temperature maps that include, besides astrophysical foregrounds, also a fraction of the polarized part of the signal leaked into the unpolarized one, a very troublesome foreground to subtract, usually referred to as polarization leakage. To our knowledge, this is the first time the removal of such component is performed with no prior assumption. We assess the success of the cleaning by comparing the true and recovered power spectra, in the angular and radial directions. In the best scenario looked at, GMCA is able to recover the input angular (radial) power spectrum with an average bias of ${\sim} 5{{\ \rm per\ cent}}$ for ℓ &gt; 25 ($20\!-\!30 {{\ \rm per\ cent}}$ for $k_{\parallel } \gtrsim 0.02 \, h^{-1}$ Mpc), in the presence of polarization leakage. Our results are robust also when up to $40{{\ \rm per\ cent}}$ of channels are missing, mimicking a radio-frequency interference (RFI) flagging of the data. Having quantified the notable effect of polarization leakage on our results, in perspective we advocate the use of more realistic simulations when testing 21-cm intensity mapping capabilities.
Radiolysis of NH3:CO ice mixtures – implications for Solar system and interstellar ices
Authors: de Barros A L F , Bergantini A , Domaracka A , Rothard H , Boduch P , da Silveira E F 
Published: September 2020

ABSTRACT
Experimental results on the processing of NH3:CO ice mixtures of astrophysical relevance by energetic (538 MeV 64Ni24+) projectiles are presented. NH3 and CO are two molecules relatively common in interstellar medium and Solar system; they may be precursors of amino acids. 64Ni ions may be considered as representative of heavy cosmic ray analogues. Laboratory data were collected using mid-infrared Fourier transform spectroscopy and revealed the formation of ammonium cation (NH$_4^+$), cyanate (OCN−), molecular nitrogen (N2), and CO2. Tentative assignments of carbamic acid (NH2COOH), formate ion (HCOO−), zwitterionic glycine (NH$_3^+$CH2COO−), and ammonium carbamate (NH$_4^+$NH2COO−) are proposed. Despite the confirmation on the synthesis of several complex species bearing C, H, O, and N atoms, no N–O-bearing species was detected. Moreover, parameters relevant for computational astrophysics, such as destruction and formation cross-sections, are determined for the precursor and the main detected species. Those values scale with the electronic stopping power (Se) roughly as σ ∼ a S$_\mathrm{ e}^n$, where n ∼ 3/2. The power law is helpful for predicting the CO and NH3 dissociation and CO2 formation cross-sections for other ions and energies; these predictions allow estimating the effects of the entire cosmic ray radiation field.
Power spectrum response of large-scale structure in 1D and in 3D: tests of prescriptions for post-collapse dynamics
Authors: Halle Anaëlle , Nishimichi Takahiro , Taruya Atsushi , Colombi Stéphane , Bernardeau Francis 
Published: September 2020

ABSTRACT
The power spectrum response function of the large-scale structure of the Universe describes how the evolved power spectrum is modified by a small change in initial power through non-linear mode coupling of gravitational evolution. It was previously found that the response function for the coupling from small to large scales is strongly suppressed in amplitude, especially at late times, compared to predictions from perturbation theory (PT) based on the single-stream approximation. One obvious explanation for this is that PT fails to describe the dynamics beyond shell crossing. We test this idea by comparing measurements in N-body simulations to prescriptions based on PT but augmented with adaptive smoothing to account for the formation of non-linear structures of various sizes in the multistream regime. We first start with one-dimensional (1D) cosmology, where the Zel’dovich approximation provides the exact solution in the single-stream regime. Similarly to the three-dimensional (3D) case, the response function of the large-scale modes exhibits a strong suppression in amplitude at small scales that cannot be explained by the Zel’dovich solution alone. However, by performing adaptive smoothing of initial conditions to identify haloes of different sizes and solving approximately post-collapse dynamics in the three-stream regime, agreement between theory and simulations drastically improves. We extend our analyses to the 3D case using the pinocchio algorithm, in which similar adaptive smoothing is implemented on the Lagrangian PT fields to identify haloes and is combined with a spherical halo prescription to account for post-collapse dynamics. Again, a suppression is found in the coupling between small- and large-scale modes and the agreement with simulations is improved.
MAMMOTH: confirmation of two massive galaxy overdensities at z = 2.24 with Hα emitters
Authors: Zheng Xian Zhong , Cai Zheng , An Fang Xia , Fan Xiaohui , Shi Dong Dong 
Published: September 2020

ABSTRACT
Massive galaxy overdensities at the peak epoch of cosmic star formation provide ideal testbeds for the formation theories of galaxies and large-scale structure. We report the confirmation of two massive galaxy overdensities at z = 2.24, BOSS1244 and BOSS1542, selected from the Mapping the Most Massive Overdensities Through Hydrogen (MAMMOTH) project using Lyα absorption from the intergalactic medium over the scales of 15−30 h−1 Mpc imprinted on the quasar spectra. We use Hα emitters (HAEs) as the density tracer and identify them using deep narrow-band H2S(1) and broad-band Ks imaging data obtained with the wide-field infrared camera (WIRCam) at the Canada–France–Hawaii Telescope. In total, 244 and 223 line emitters are detected in these two fields, and 196 ± 2 and 175 ± 2 are expected to be HAEs with an Hα flux of &gt;2.5 × 10−17 erg s−1 cm−2 (corresponding to a star formation rate of &gt;5 M⊙ yr−1). The detection rate of HAE candidates suggests an overdensity factor of δgal = 5.6 ± 0.3 and 4.9 ± 0.3 over the volume of 54 × 32 × 32 co-moving Mpc3. The overdensity factor increases two to three times when focusing on the high-density regions of scales 10–15  co-moving Mpc. Interestingly, the HAE density maps reveal that BOSS1244 contains a dominant structure, while BOSS1542 manifests as a giant filamentary structure. We measure the Hα luminosity functions (HLFs), finding that BOSS1244’s HLF is nearly identical to that of the general field at the same epoch, while BOSS1542 shows an excess of HAEs with high Hα luminosity, indicating the presence of enhanced star formation or active galactic nuclei activity. We conclude that the two massive MAMMOTH overdensities are undergoing a rapid galaxy mass assembly.
Two-dimensional multifibre spectral image correction based on machine learning techniques
Authors: Xu Jiali , Yin Qian , Guo Ping , Zheng Xin 
Published: September 2020

ABSTRACT
Owing to the limited size and imperfections of the optical components in a spectrometer, aberrations inevitably make their way into 2D multifibre spectral images in the Large Sky Area Multi-Object Fiber Spectroscopy Telescope (LAMOST), which leads to obvious spatial variation of the point spread functions (PSFs). However, if spatially variant PSFs are estimated directly, the large storage and intensive computational requirements result in the deconvolution spectrum extraction method becoming intractable. In this paper, we propose a novel method to solve the problem of spatial variation of the PSFs through image aberration correction. When CCD image aberrations are corrected, the convolution kernel can be approximated by only one spatially invariant PSF. Specifically, a novel method based on machine learning is proposed to calibrate the distorted spectral images. The method includes many techniques, such as total least squares (TLS) algorithm, self-supervised learning and multilayer feed-forward neural networksnetworks, and it makes use of a special training set sampling scheme combining 2D distortion features in a flat-field spectrum and calibration lamp spectrum. The calibration experiments on the LAMOST CCD images show that the proposed method is feasible. Furthermore, the spectrum extraction results before and after calibration are compared, and the experimental results show that the characteristics of the extracted 1D waveform are closer to those of an ideal optics system after image correction, and that the PSF of the corrected object spectrum estimated by the blind deconvolution method is nearly centrosymmetric, which indicates that our proposed method can significantly reduce the complexity of spectrum extraction and improve extraction accuracy.
LSD1 prevents aberrant heterochromatin formation in Neurospora crassa
Authors: Storck William K , Bicocca Vincent T , Rountree Michael R , Honda Shinji , Ormsby Tereza , Selker Eric U 
Published: September 2020

AbstractHeterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.
Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication
Authors: Obi Ikenna , Rentoft Matilda , Singh Vandana , Jamroskovic Jan , Chand Karam , Chorell Erik , Westerlund Fredrik , Sabouri Nasim 
Published: September 2020

Abstract
G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.
Interactions of replication initiator RctB with single- and double-stranded DNA in origin opening of Vibrio cholerae chromosome 2
Authors: Chatterjee Soniya , Jha Jyoti K , Ciaccia Peter , Venkova Tatiana , Chattoraj Dhruba K 
Published: September 2020

AbstractStudies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing an open structure, but how the initiator participates in this process and the contributions of the several binding sites remain unclear. Here, we show that the initiator protein of Vibrio cholerae specific to chromosome 2 (Chr2) also has single-strand binding activity in the AT-rich region of its origin. Binding is strand specific, depends on repeats of the sequence 5′ATCA and is greatly stabilized in vitro by specific double-stranded sites of the origin. The stability derives from the formation of ternary complexes of the initiator with the single- and double-stranded sites. An IHF site lies between these two kinds of sites in the Chr2 origin and an IHF-induced looping out of the intervening DNA mediates their interaction. Simultaneous binding to two kinds of sites in the origin appears to be a common mechanism by which bacterial replication initiators stabilize an open origin.
tRFtarget: a database for transfer RNA-derived fragment targets
Authors: Li Ningshan , Shan Nayang , Lu Lingeng , Wang Zuoheng 
Published: September 2020

AbstractTransfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID® web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.
Translation reprogramming by eIF3 linked to glioblastoma resistance
Authors: Bertorello Juliette , Sesen Julie , Gilhodes Julia , Evrard Solène , Courtade-Saïdi Monique , Augustus Meera , Uro-Coste Emmanuelle , Toulas Christine , Moyal Elizabeth Cohen-Jonathan , Seva Catherine , Dassi Erik , Cammas Anne , Skuli Nicolas , Millevoi Stefania 
Published: September 2020

Abstract
Intrinsic resistance to current therapies, leading to dismal clinical outcomes, is a hallmark of glioblastoma multiforme (GBM), the most common and aggressive brain tumor. Understanding the underlying mechanisms of such malignancy is, therefore, an urgent medical need. Deregulation of the protein translation machinery has been shown to contribute to cancer initiation and progression, in part by driving selective translational control of specific mRNA transcripts involved in distinct cancer cell behaviors. Here, we focus on eIF3, a multimeric complex with a known role in the initiation of translation and that is frequently deregulated in cancer. Our results show that the deregulated expression of eIF3e, the e subunit of eIF3, in specific GBM regions could impinge on selective protein synthesis impacting the GBM outcome. In particular, eIF3e restricts the expression of proteins involved in the response to cellular stress and increases the expression of key functional regulators of cell stemness. Such a translation program can therefore serve as a double-edged sword promoting GBM tumor growth and resistance to radiation.