bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first comprehensive study of a giant nebula around a radio-quiet quasar in the z &lt; 1 Universe
Authors: Liu Zhuoqi , Johnson Sean D , Li Jennifer I-Hsiu , Rudie Gwen C , Schaye Joop , Chen Hsiao-Wen , Brinchmann Jarle , Cantalupo Sebastiano , Chen Mandy C , Kollatschny Wolfram , Maseda Michael V , Mishra Nishant , Muzahid Sowgat 
Published: November 2023

ABSTRACT
We present the first comprehensive study of a giant, ≈70 kpc-scale nebula around a radio-quiet quasar at z &lt; 1. The analysis is based on deep integral field spectroscopy with Multi-Unit Spectroscopic Explorer of the field of HE 0238−1904, a luminous quasar at z = 0.6282. The nebula emits strongly in [O ii], $\rm H \beta$, and [O iii], and the quasar resides in an unusually overdense environment for a radio-quiet system. The environment likely consists of two groups which may be merging, and in total have an estimated dynamical mass of Mdyn ≈ 4 × 1013 to 1014 M⊙. The nebula exhibits largely quiescent kinematics and irregular morphology. The nebula may arise primarily through interaction-related stripping of circumgalactic and interstellar medium (CGM/ISM) of group members, with some potential contributions from quasar outflows. The simultaneous presence of the giant nebula and a radio-quiet quasar in a rich environment suggests a correlation between such circum-quasar nebulae and environmental effects. This possibility can be tested with larger samples. The upper limits on the electron number density implied by the [O ii] doublet ratio range from $\log (n_{\rm e, [O\,{\small II}]} /\mathrm{cm}^{-3})&lt;1.2$ to 2.8. However, assuming a constant quasar luminosity and negligible projection effects, the densities implied from the measured line ratios between different ions (e.g. [O ii], [O iii], and [Ne v]) and photoionization simulations are often 10−400 times larger. This large discrepancy can be explained by quasar variability on a time-scale of ≈104−105 yr.
Free-form and hybrid lens models for SDSS J1004+4112: substructure and central image time delay constraints
Authors: Perera Derek , Williams Liliya L R , Liesenborgs Jori , Ghosh Agniva , Saha Prasenjit 
Published: November 2023

ABSTRACT
SDSS J1004+4112 is a well-studied gravitational lens with a recently measured time delay between its first and fourth arriving quasar images. Using this new constraint, we present updated free-form lens reconstructions using the lens inversion method grale, which only uses multiple image and time delay data as inputs. In addition, we obtain hybrid lens reconstructions by including a model of the brightest cluster galaxy as a Sersic lens. For both reconstructions, we use two sets of images as input: one with all identified images, and the other a revised set leaving out images that have been potentially misidentified. We also develop a source position optimization Markov chain Monte Carlo (MCMC) routine, performed on completed grale runs, that allows each model to better match observed image positions and time delays. All the reconstructions produce similar mass distributions, with the hybrid models finding a steeper profile in the centre. Similarly, all the mass distributions are fitted by the Navarro–Frenk–White profile, finding results consistent with previous parametric reconstructions and those derived from Chandra X-ray observations. We identify an ∼5 × 1011 M⊙ substructure apparently unaffiliated with any cluster member galaxy and present in all our models, and study its reality. Using our free-form and hybrid models, we predict a central quasar image time delay of ∼2980 ± 270 and ∼3280 ± 215 d, respectively. A potential future measurement of this time delay will, while being an observational challenge, further constrain the steepness of the central density profile.
A cool, magnetic white dwarf accreting planetary debris
Authors: Vennes Stéphane , Kawka Adela , Klein Beth L , Zuckerman B , Weinberger Alycia J , Melis Carl 
Published: November 2023

ABSTRACT
We present an analysis of spectroscopic data of the cool, highly magnetic, and polluted white dwarf 2MASS J0916−4215. The atmosphere of the white dwarf is dominated by hydrogen, but numerous spectral lines of magnesium, calcium, titanium, chromium, iron, and strontium, along with Li i, Na i, Al i, and K i lines, are found in the incomplete Paschen–Back regime, most visibly, in the case of Ca ii lines. Extensive new calculations of the Paschen–Back effect in several spectral lines are presented and results of the calculations are tabulated for the Ca ii H&K doublet. The abundance pattern shows a large lithium and strontium excess, which may be viewed as a signature of planetary debris akin to Earth’s continental crust accreted on to the star, although the scarcity of silicon indicates possible dilution in bulk Earth material. Accurate abundance measurements proved sensitive to the value of the broadening parameter due to collisions with neutral hydrogen ($\Gamma$H i), particularly in saturated lines such as the resonance lines of Ca i and Ca ii. We found that $\Gamma$H i if formulated with values from the literature could be overestimated by a factor of 10 in most resonance lines.
J-PLUS: galaxy-star-quasar classification for DR3
Authors: von Marttens R , Marra V , Quartin M , Casarini L , Baqui P O , Alvarez-Candal A , Galindo-Guil F J , Fernández-Ontiveros J A , del Pino Andrés , Díaz-García L A , López-Sanjuan C , Alcaniz J , Angulo R , Cenarro A J , Cristóbal-Hornillos D , Dupke R , Ederoclite A , Hernández-Monteagudo C , Marín-Franch A , Moles M , Sodré L , Varela J , Vázquez Ramió H 
Published: November 2023

ABSTRACT
The Javalambre Photometric Local Universe Survey (J-PLUS) is a 12-band photometric survey using the 83-cm JAST telescope. Data Release 3 includes 47.4 million sources. J-PLUS DR3 only provides star-galaxy classification so that quasars are not identified from the other sources. Given the size of the data set, machine learning methods could provide a valid alternative classification and a solution to the classification of quasars. Our objective is to classify J-PLUS DR3 sources into galaxies, stars, and quasars, outperforming the available classifiers in each class. We use an automated machine learning tool called TPOT to find an optimized pipeline to perform the classification. The supervised machine learning algorithms are trained on the crossmatch with SDSS DR18, LAMOST DR8, and Gaia. We checked that the training set of about 660 thousand galaxies, 1.2 million stars, and 270 thousand quasars is both representative and contain a minimal presence of contaminants (less than 1 per cent). We considered 37 features: the 12 photometric bands with respective errors, 6 colours, 4 morphological parameters, galactic extinction with its error, and the PSF relative to the corresponding pointing. With TPOT genetic algorithm, we found that XGBoost provides the best performance: the AUC for galaxies, stars, and quasars is above 0.99 and the average precision is above 0.99 for galaxies and stars and 0.96 for quasars. XGBoost outperforms the classifiers already provided in J-PLUS DR3 and also classifies quasars.
Fisher forecast for the BAO measurements from the CSST spectroscopic and photometric galaxy clustering
Authors: Ding Zhejie , Yu Yu , Zhang Pengjie 
Published: November 2023

ABSTRACT
The China Space Station Telescope (CSST) is a forthcoming Stage IV galaxy survey. It will simultaneously undertake the photometric redshift (photo-z) and slitless spectroscopic redshift (spec-z) surveys mainly for weak lensing and galaxy clustering studies. The two surveys cover the same sky area and overlap on the redshift range. At z &gt; 1, due to the sparse number density of the spec-z sample, it limits the constraints on the scale of baryon acoustic oscillations (BAO). By cross-correlating the spec-z sample with the high density photo-z sample, we can effectively enhance the constraints on the angular diameter distances DA(z) from the BAO measurement. Based on the Fisher matrix, we forecast a &gt;30 per cent improvement on constraining DA(z) from the joint analysis of the spec-z and cross galaxy power spectra at 1.0 &lt; z &lt; 1.2. Such improvement is generally robust against different systematic effects including the systematic noise and the redshift success rate of the spec-z survey, as well as the photo-z error. We also show the BAO constraints from other Stage-IV spectroscopic surveys for the comparison with CSST. Our study can be a reference for the future BAO analysis on real CSST data. The methodology can be applied to other surveys with spec-z and photo-z data in the same survey volume.
MOG as symmetry breaking in scalar–vector–tensor gravity
Authors: Rouhani Shahin , Rahvar Sohrab 
Published: November 2023

ABSTRACT
The Modified Gravity Model (MOG) has been proposed as a solution to the dark matter problem, but it does not meet the gauge invariant condition. The aim of this work is to propose a gauge-invariant theory, which suggests that symmetry can break at a low temperature in the Universe, leading to the MOG theory. This theory has the potential to alter the dynamics of the early and late Universe and naturally produce cosmological inflation.
Mitonuclear Sex Determination? Empirical Evidence from Bivalves
Authors: Smith Chase H , Mejia-Trujillo Raquel , Breton Sophie , Pinto Brendan J , Kirkpatrick Mark , Havird Justin C 
Published: November 2023

Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
Authors: Varadi Mihaly , Bertoni Damian , Magana Paulyna , Paramval Urmila , Pidruchna Ivanna , Radhakrishnan Malarvizhi , Tsenkov Maxim , Nair Sreenath , Mirdita Milot , Yeo Jingi , Kovalevskiy Oleg , Tunyasuvunakool Kathryn , Laydon Agata , Žídek Augustin , Tomlinson Hamish , Hariharan Dhavanthi , Abrahamson Josh , Green Tim , Jumper John , Birney Ewan , Steinegger Martin , Hassabis Demis , Velankar Sameer 
Published: November 2023

Abstract
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released in 2021. Enabled by the groundbreaking AlphaFold2 artificial intelligence (AI) system, the predictions archived in AlphaFold DB have been integrated into primary data resources such as PDB, UniProt, Ensembl, InterPro and MobiDB. Our manuscript details subsequent enhancements in data archiving, covering successive releases encompassing model organisms, global health proteomes, Swiss-Prot integration, and a host of curated protein datasets. We detail the data access mechanisms of AlphaFold DB, from direct file access via FTP to advanced queries using Google Cloud Public Datasets and the programmatic access endpoints of the database. We also discuss the improvements and services added since its initial release, including enhancements to the Predicted Aligned Error viewer, customisation options for the 3D viewer, and improvements in the search engine of AlphaFold DB.
Human Ageing Genomic Resources: updates on key databases in ageing research
Authors: de Magalhães João Pedro , Abidi Zoya , dos Santos Gabriel Arantes , Avelar Roberto A , Barardo Diogo , Chatsirisupachai Kasit , Clark Peter , De-Souza Evandro A , Johnson Emily J , Lopes Inês , Novoa Guy , Senez Ludovic , Talay Angelo , Thornton Daniel , To Paul Ka Po 
Published: November 2023

Abstract
Ageing is a complex and multifactorial process. For two decades, the Human Ageing Genomic Resources (HAGR) have aided researchers in the study of various aspects of ageing and its manipulation. Here, we present the key features and recent enhancements of these resources, focusing on its six main databases. One database, GenAge, focuses on genes related to ageing, featuring 307 genes linked to human ageing and 2205 genes associated with longevity and ageing in model organisms. AnAge focuses on ageing, longevity, and life-history across animal species, containing data on 4645 species. DrugAge includes information about 1097 longevity drugs and compounds in model organisms such as mice, rats, flies, worms and yeast. GenDR provides a list of 214 genes associated with the life-extending benefits of dietary restriction in model organisms. CellAge contains a catalogue of 866 genes associated with cellular senescence. The LongevityMap serves as a repository for genetic variants associated with human longevity, encompassing 3144 variants pertaining to 884 genes. Additionally, HAGR provides various tools as well as gene expression signatures of ageing, dietary restriction, and replicative senescence based on meta-analyses. Our databases are integrated, regularly updated, and manually curated by experts. HAGR is freely available online (https://genomics.senescence.info/).
Human lysyl-tRNA synthetase phosphorylation promotes HIV-1 proviral DNA transcription
Authors: Tang Yingke , Behrens Ryan T , St Gelais Corine , Wu Siqi , Vivekanandan Saravanan , Razin Ehud , Fang Pengfei , Wu Li , Sherer Nathan , Musier-Forsyth Karin 
Published: November 2023

Abstract
Human lysyl-tRNA synthetase (LysRS) was previously shown to be re-localized from its normal cytoplasmic location in a multi-aminoacyl-tRNA synthetase complex (MSC) to the nucleus of HIV-1 infected cells. Nuclear localization depends on S207 phosphorylation but the nuclear function of pS207-LysRS in the HIV-1 lifecycle is unknown. Here, we show that HIV-1 replication was severely reduced in a S207A-LysRS knock-in cell line generated by CRISPR/Cas9; this effect was rescued by S207D-LysRS. LysRS phosphorylation up-regulated HIV-1 transcription, as did direct transfection of Ap4A, an upstream transcription factor 2 (USF2) activator that is synthesized by pS207-LysRS. Overexpressing an MSC-derived peptide known to stabilize LysRS MSC binding inhibited HIV-1 replication. Transcription of HIV-1 proviral DNA and other USF2 target genes was reduced in peptide-expressing cells. We propose that nuclear pS207-LysRS generates Ap4A, leading to activation of HIV-1 transcription. Our results suggest a new role for nuclear LysRS in facilitating HIV-1 replication and new avenues for antiviral therapy.
Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase
Authors: Fu Iwen , Geacintov Nicholas E , Broyde Suse 
Published: November 2023

Abstract
Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6−4 pyrimidone (6−4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6–4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6−4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6−4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6−4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6−4PP.
To let go or not to let go: how ParA can impact the release of the chromosomal anchoring in Caulobacter crescentus
Authors: Puentes-Rodriguez Stephanie G , Norcross John D , Mera Paola E 
Published: November 2023

Abstract
Chromosomal maintenance is vital for the survival of bacteria. In Caulobacter crescentus, chromosome replication initiates at ori and segregation is delayed until the nearby centromere-like region parS is replicated. Our understanding of how this sequence of events is regulated remains limited. The segregation of parS has been shown to involve multiple steps including polar release from anchoring protein PopZ, slow movement and fast ParA-dependent movement to the opposite cell pole. In this study, we demonstrate that ParA’s competing attractions from PopZ and from DNA are critical for segregation of parS. Interfering with this balance of attractions—by expressing a variant ParA-R195E unable to bind DNA and thus favoring interactions exclusively between ParA-PopZ—results in cell death. Our data revealed that ParA-R195E’s sole interactions with PopZ obstruct PopZ’s ability to release the polar anchoring of parS, resulting in cells with multiple parS loci fixed at one cell pole. We show that the inability to separate and segregate multiple parS loci from the pole is specifically dependent on the interaction between ParA and PopZ. Collectively, our results reveal that the initial steps in chromosome segregation are highly regulated.
DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options
Authors: Basu Sushmita , Zhao Bi , Biró Bálint , Faraggi Eshel , Gsponer Jörg , Hu Gang , Kloczkowski Andrzej , Malhis Nawar , Mirdita Milot , Söding Johannes , Steinegger Martin , Wang Duolin , Wang Kui , Xu Dong , Zhang Jian , Kurgan Lukasz 
Published: November 2023

Abstract
The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
The forkhead DNA-binding domain binds specific G2-rich RNA sequences
Authors: Zutterling Caroline , Todeschini Anne-Laure , Fourmy Deborah , Busso Didier , Veaute Xavier , Ducongé Frédéric , Veitia Reiner A 
Published: November 2023

Abstract
Transcription factors contain a DNA-binding domain ensuring specific recognition of DNA target sequences. The family of forkhead (FOX) transcription factors is composed of dozens of paralogs in mammals. The forkhead domain (FHD) is a segment of about 100 amino acids that binds an A-rich DNA sequence. Using DNA and RNA PCR-SELEX, we show that recombinant FOXL2 proteins, either wild-type or carrying the oncogenic variant C134W, recognize similar DNA-binding sites. This suggests that the oncogenic variant does not alter the intrinsic sequence-specificity of FOXL2. Most importantly, we show that FOXL2 binds G2-rich RNA sequences whereas it virtually fails to bind similar sequences in DNA chemistry. Interestingly, a statistically significant subset of genes responding to the knock-down of FOXL2/Foxl2 harbor such G2-rich sequences and are involved in crucial signaling pathways and cellular processes. In addition, we show that FOXA1, FOXO3a and chimeric FOXL2 proteins containing the FHD of the former are also able to interact with some of the preferred FOXL2-binding sequences. Our results point to an unexpected and novel characteristic of the forkhead domain, the biological relevance of which remains to be explored.
The Neurogenome study: Comprehensive molecular profiling to optimize treatment for Danish glioblastoma patients
Authors: Nørøxe Dorte Schou , Maarup Simone , Fougner Vincent , Muhic Aida , Møller Søren , Urup Thomas , Lü Maya Jeje Schuang , Weischenfeldt Joachim , Hansen Adam Espe , Skovgaard Poulsen Hans , Lassen Ulrik , Hasselbalch Benedikte 
Published: November 2023

Abstract

Background
Glioblastoma is an aggressive brain cancer with no possibility for cure. Treatment and survival have only improved slightly since 2005 when the current regime was implemented. The limited improvements in the treatment of glioblastoma may reflect our poor understanding of the disease. We hypothesize that systematically collected translational data will improve knowledge and hereby treatment.

Methods
We have been performing whole exome sequencing in glioblastoma tumor tissue since 2016 and whole genome sequencing (WGS) since 2020 with the aim of offering experimental treatment.

Results
We have sequenced 400+ GBM patients and from these 100+ are paired tumor samples from relapse surgery. To develop genomic profiling and to increase the information on each patient´s contribution, we have initiated the Neurogenome study as of June 2022. The Neurogenome protocol is a national, comprehensive, translational, and omic protocol. It is a continuation of 2 previous protocols from 2016 and forth in our department, but with more substudies added, focusing on the translational and clinical utility. We collect and analyze data from an out-patient clinic in a systematic approach to a number of subprojects ranging from basic science to applied clinical science, including clinical trials.

Conclusions
The protocol will act as a backbone for future projects in the national research center, Danish Comprehensive Cancer Center—Brain Tumor Center with the overall aim to select eligible patients for experimental treatment based upon genomic alterations. The article will present the Neurogenome setup and a presentation of selected projects that are based upon inclusion.