bluuebunny/crossref_metadata_2025_split huggingface dataset:
rescuer: cosmological K-corrections for star clusters
Authors: Reina-Campos Marta , Harris William E 
Published: June 2024

ABSTRACT
The advent of JWST now allows entire star cluster populations to be imaged in galaxies at cosmologically significant redshifts, bringing with it the need to apply K-corrections to their magnitudes and colour indices. Since the stellar populations within star clusters can be well approximated by a single age and metallicity, their spectral energy distributions are very different from those of galaxies or supernovae, and their K-corrections behave differently. We derive the photometric K-corrections versus redshift for model star clusters that cover a wide range of ages and metallicities, illustrating the results particularly for the broad-band filters on the Hubble Space Telescope/Advanced Camera for Surveys and the JWST/Near-Infrared Camera that are most commonly being used for imaging of populations of star clusters in distant galaxies. In an appendix, we introduce a webtool called rescuer (REdshifted Star ClUstERs) that can generate K-values and their uncertainties for any user-defined combination of cluster properties.
AuriDESI: mock catalogues for the DESI Milky Way Survey
Authors: Kizhuprakkat Namitha , Cooper Andrew P , Riley Alexander H , Koposov Sergey E , Aguilar Jessica Nicole , Ahlen Steven , Allende Prieto Carlos , Brooks David , Claybaugh Todd , Dawson Kyle , de la Macorra Axel , Doel Peter , Forero-Romero Jaime E , Frenk Carlos , Gaztañaga Enrique , Gnedin Oleg Y , Grand Robert J J , Gontcho A Gontcho Satya , Honscheid Klaus , Kehoe Robert , Landriau Martin , Manera Marc , Meisner Aaron , Miquel Ramon , Nie Jundan , Prada Francisco , Rezaie Mehdi , Rossi Graziano , Sanchez Eusebio , Schubnell Michael , Seo Hee-Jong , Tarlé Gregory , Valluri Monica , Zhou Zhimin 
Published: June 2024

ABSTRACT
The Dark Energy Spectroscopic Instrument Milky Way Survey (DESI MWS) will explore the assembly history of the Milky Way by characterizing remnants of ancient dwarf galaxy accretion events and improving constraints on the distribution of dark matter in the outer halo. We present mock catalogues that reproduce the selection criteria of MWS and the format of the final MWS data set. These catalogues can be used to test methods for quantifying the properties of stellar halo substructure and reconstructing the Milky Way’s accretion history with the MWS data, including the effects of halo-to-halo variance. The mock catalogues are based on a phase-space kernel expansion technique applied to star particles in the Auriga suite of six high-resolution lambda-cold dark matter magnetohydrodynamic zoom-in simulations. They include photometric properties (and associated errors) used in DESI target selection and the outputs of the MWS spectral analysis pipeline (radial velocity, metallicity, surface gravity, and temperature). They also include information from the underlying simulation, such as the total gravitational potential and information on the progenitors of accreted halo stars. We discuss how the subset of halo stars observable by MWS in these simulations corresponds to their true content and properties. These mock Milky Ways have rich accretion histories, resulting in a large number of substructures that span the whole stellar halo out to large distances and have substantial overlap in the space of orbital energy and angular momentum.
Revisiting the accretion disc spectra of dwarf novae and nova-like variables: implications for the standard disc model
Authors: Zsidi Gabriella , Nixon C J , Naylor T , Pringle J E 
Published: June 2024

ABSTRACT
Accretion discs are fundamental to much of astronomy. They can occur around stars, both young and old, around compact objects they provide a window into the extremes of physics, and around supermassive black holes in galaxy centres, they generate spectacular luminosities that can outshine the entire galaxy. However, our understanding of the inner workings of accretion discs remains far from complete. Here, we revisit a conundrum in the observations of some of the simplest accreting systems: the cataclysmic variables (CVs). The high-accretion-rate states of (non-magnetic) CVs can be divided into the short-lived outbursts (∼a week), typical of dwarf novae (DNe), and the long-lived (and sometimes perpetual) high states of nova-like (NL) CVs. Since both sorts of high-state occur in approximately steady-state accretion discs with similar properties and accretors, we would expect them to display similar spectral energy distributions. However, previous analyses based on UV spectra from the International Ultraviolet Explorer have shown that their spectral energy distributions are different. We perform a re-analysis of the data using up to date calibrations and distance (and thus dereddening) estimates to test whether this difference persists and whether it is statistically significant over the sample. We find that it does persist, and it is statistically significant. We propose routes to investigating this discrepancy further and discuss the implications this has for other accreting systems, such as X-ray binaries, active galactic nuclei, and protoplanetary discs.
A mock redshift catalogue of the dusty star-forming galaxy population with intrinsic clustering and lensing for deep millimetre surveys
Authors: Nava-Moreno Norma Araceli , Montaña Alfredo , Aretxaga Itziar , Rodríguez-Puebla Aldo , Avila-Reese Vladimir , Peralta Edgar 
Published: June 2024

ABSTRACT
We present a new cosmologically motivated mock redshift survey of the dusty star-forming galaxy population. Our mock survey is based on the Bolshoi–Planck dark matter halo simulation and covers an area of 5.3 deg2. Using a semi-empirical approach, we generate a light-cone and populate the dark matter haloes with galaxies. Infrared properties are assigned to the galaxies based on theoretical and empirical relations from the literature. Additionally, background galaxies are gravitationally lensed by dark matter haloes along the line of sight assuming a point-mass model approximation. We characterize the mock survey by measuring the star formation rate density, integrated number counts, redshift distribution, and infrared luminosity function. When compared with single-dish and interferometric observations, the predictions from our mock survey closely follow the compiled results from the literature. We have also directed this study towards characterizing one of the extragalactic legacy surveys to be observed with the TolTEC camera at the Large Millimeter Telescope: the 0.8 sq. degree Ultra Deep Survey, with expected depths of 0.025, 0.018, and 0.012 mJy beam−1 at 1.1, 1.4, and 2.0 mm. Exploiting the clustering information in our mock survey, we investigate its impact on the effect of flux boosting by the fainter population of dusty galaxies, finding that clustering can increase the median boosting by 0.5  per cent at 1.1 mm, 0.8  per cent at 1.4 mm, and 2.0  per cent at 2.0 mm, and with higher dispersion.
Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes
Authors: Moldovan John B , Kopera Huira C , Liu Ying , Garcia-Canadas Marta , Catalina Purificacion , Leone Paola E , Sanchez Laura , Kitzman Jacob O , Kidd Jeffrey M , Garcia-Perez Jose Luis , Moran John V 
Published: June 2024

Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing mRNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINEs use strategies to ‘hijack′ L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.
Principles of miRNA/miRNA* function in plant MIRNA processing
Authors: Rosatti Santiago , Rojas Arantxa M L , Moro Belén , Suarez Irina P , Bologna Nicolas G , Chorostecki Uciel , Palatnik Javier F 
Published: June 2024

Abstract
MicroRNAs (miRNAs) are essential regulators of gene expression, defined by their unique biogenesis, which requires the precise excision of the small RNA from an imperfect fold-back precursor. Unlike their animal counterparts, plant miRNA precursors exhibit variations in sizes and shapes. Plant MIRNAs can undergo processing in a base-to-loop or loop-to-base direction, with DICER-LIKE1 (DCL1) releasing the miRNA after two cuts (two-step MIRNAs) or more (sequential MIRNAs). In this study, we demonstrate the critical role of the miRNA/miRNA* duplex region in the processing of miRNA precursors. We observed that endogenous MIRNAs frequently experience suboptimal processing in vivo due to mismatches in the miRNA/miRNA* duplex, a key region that fine-tunes miRNA levels. Enhancing the interaction energy of the miRNA/miRNA* duplex in two-step MIRNAs results in a substantial increase in miRNA levels. Conversely, sequential MIRNAs display distinct and specific requirements for the miRNA/miRNA* duplexes along their foldback structure. Our work establishes a connection between the miRNA/miRNA* structure and precursor processing mechanisms. Furthermore, we reveal a link between the biological function of miRNAs and the processing mechanism of their precursors with the evolution of plant miRNA/miRNA* duplex structures.
Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA
Authors: Unlu Irem , Maguire Sean , Guan Shengxi , Sun Zhiyi 
Published: June 2024

Abstract
Circular RNA (circRNA) has recently gained attention for its emerging biological activities, relevance to disease, potential as biomarkers, and promising an alternative modality for RNA vaccines. Nevertheless, sequencing circRNAs has presented challenges. In this context, we introduce a novel circRNA sequencing method called Induro-RT mediated circRNA-sequencing (IMCR-seq), which relies on a group II intron reverse transcriptase with robust rolling circle reverse transcription activity. The IMCR-seq protocol eliminates the need for conventional circRNA enrichment methods such as rRNA depletion and RNaseR digestion yet achieved the highest circRNA enrichment and detected 6–1000 times more circRNAs for the benchmarked human samples compared to other methods. IMCR-seq is applicable to any organism, capable of detecting circRNAs of longer than 7000 nucleotides, and is effective on samples as small as 10 ng of total RNA. These enhancements render IMCR-seq suitable for clinical samples, including disease tissues and liquid biopsies. We demonstrated the clinical relevance of IMCR-seq by detecting cancer-specific circRNAs as potential biomarkers from IMCR-seq results on lung tumor tissues together with blood plasma samples from both a healthy individual and a lung cancer patient. In summary, IMCR-seq presents an efficient and versatile circRNA sequencing method with high potential for research and clinical applications.
iSuRe-HadCre is an essential tool for effective conditional genetics
Authors: Garcia-Gonzalez Irene , Rocha Susana F , Hamidi Anahita , Garcia-Ortega Lourdes , Regano Alvaro , Sanchez-Muñoz Maria S , Lytvyn Mariya , Garcia-Cabero Aroa , Roig-Soucase Sergi , Schoofs Hans , Castro Marco , Sabata Helena , Potente Michael , Graupera Mariona , Makinen Taija , Benedito Rui 
Published: June 2024

Abstract
Methods for modifying gene function at high spatiotemporal resolution in mice have revolutionized biomedical research, with Cre-loxP being the most widely used technology. However, the Cre-loxP technology has several drawbacks, including weak activity, leakiness, toxicity, and low reliability of existing Cre-reporters. This is mainly because different genes flanked by loxP sites (floxed) vary widely in their sensitivity to Cre-mediated recombination. Here, we report the generation, validation, and utility of iSuRe-HadCre, a new dual Cre-reporter and deleter mouse line that avoids these drawbacks. iSuRe-HadCre achieves this through a novel inducible dual-recombinase genetic cascade that ensures that cells expressing a fluorescent reporter had only transient Cre activity, that is nonetheless sufficient to effectively delete floxed genes. iSuRe-HadCre worked reliably in all cell types and for the 13 floxed genes tested. This new tool will enable the precise, efficient, and trustworthy analysis of gene function in entire mouse tissues or in single cells.
The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition
Authors: Garate Ximena , Gómez-García Pablo Aurelio , Merino Manuel Fernández , Angles Marta Cadevall , Zhu Chenggan , Castells-García Alvaro , Ed-daoui Ilyas , Martin Laura , Ochiai Hiroshi , Neguembor Maria Victoria , Cosma Maria Pia 
Published: June 2024

Abstract
During early development, gene expression is tightly regulated. However, how genome organization controls gene expression during the transition from naïve embryonic stem cells to epiblast stem cells is still poorly understood. Using single-molecule microscopy approaches to reach nanoscale resolution, we show that genome remodeling affects gene transcription during pluripotency transition. Specifically, after exit from the naïve pluripotency state, chromatin becomes less compacted, and the OCT4 transcription factor has lower mobility and is more bound to its cognate sites. In epiblast cells, the active transcription hallmark, H3K9ac, decreases within the Oct4 locus, correlating with reduced accessibility of OCT4 and, in turn, with reduced expression of Oct4 nascent RNAs. Despite the high variability in the distances between active pluripotency genes, distances between Nodal and Oct4 decrease during epiblast specification. In particular, highly expressed Oct4 alleles are closer to nuclear speckles during all stages of the pluripotency transition, while only a distinct group of highly expressed Nodal alleles are in close proximity to Oct4 when associated with a nuclear speckle in epiblast cells. Overall, our results provide new insights into the role of the spatiotemporal genome remodeling during mouse pluripotency transition and its correlation with the expression of key pluripotency genes.
CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics
Authors: Zhao Yan , Kohl Clemens , Rosebrock Daniel , Hu Qinan , Hu Yuhui , Vingron Martin 
Published: June 2024

Abstract
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsible for the clustering are only inferred in a subsequent step. Clustering cells and genes together would be the remit of biclustering algorithms, which are often bogged down by the size of single-cell data. Here we present ‘Correspondence Analysis based Biclustering on Networks’ (CAbiNet) for joint clustering and visualization of single-cell RNA-sequencing data. CAbiNet performs efficient co-clustering of cells and their respective marker genes and jointly visualizes the biclusters in a non-linear embedding for easy and interactive visual exploration of the data.
KDM6A–SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance
Authors: Wu Jian , Jiang Yixin , Zhang Qin , Mao Xiaobing , Wu Tong , Hao Mengqiu , Zhang Su , Meng Yang , Wan Xiaowen , Qiu Lei , Han Junhong 
Published: June 2024

Abstract
Genomic instability is one of the hallmarks of cancer. While loss of histone demethylase KDM6A increases the risk of tumorigenesis, its specific role in maintaining genomic stability remains poorly understood. Here, we propose a mechanism in which KDM6A maintains genomic stability independently on its demethylase activity. This occurs through its interaction with SND1, resulting in the establishment of a protective chromatin state that prevents replication fork collapse by recruiting of RPA and Ku70 to nascent DNA strand. Notably, KDM6A–SND1 interaction is up-regulated by KDM6A SUMOylation, while KDM6AK90A mutation almost abolish the interaction. Loss of KDM6A or SND1 leads to increased enrichment of H3K9ac and H4K8ac but attenuates the enrichment of Ku70 and H3K4me3 at nascent DNA strand. This subsequently results in enhanced cellular sensitivity to genotoxins and genomic instability. Consistent with these findings, knockdown of KDM6A and SND1 in esophageal squamous cell carcinoma (ESCC) cells increases genotoxin sensitivity. Intriguingly, KDM6A H101D & P110S, N1156T and D1216N mutations identified in ESCC patients promote genotoxin resistance via increased SND1 association. Our finding provides novel insights into the pivotal role of KDM6A–SND1 in genomic stability and chemoresistance, implying that targeting KDM6A and/or its interaction with SND1 may be a promising strategy to overcome the chemoresistance.
Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs
Authors: Gadgil Rujuta Yashodhan , Rider S Dean , Shrestha Resha , Alhawach Venicia , Hitch David C , Leffak Michael 
Published: June 2024

Abstract
Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. We used inverse PCR of non-B microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures integrated at a common ectopic chromosomal site to show that these non-B DNAs generate highly mutagenized eccDNAs by replication-dependent mechanisms. Mutagenesis occurs within the non-B DNAs and extends several kilobases bidirectionally into flanking and nonallelic DNA. Each non-B DNA exhibits a different pattern of mutagenesis, while sister clones containing the same non-B DNA also display distinct patterns of recombination, microhomology-mediated template switching and base substitutions. Mutations include mismatches, short duplications, long nontemplated insertions, large deletions and template switches to sister chromatids and nonallelic chromosomes. Drug-induced replication stress or the depletion of DNA repair factors Rad51, the COPS2 signalosome subunit or POLη change the pattern of template switching and alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA double strand breaks to account for the generation and circularization of mutagenized eccDNAs and the appearance of genomic homologous recombination deficiency (HRD) scars. These results may help to explain the appearance of tumor eccDNAS and their roles in neoantigen production, oncogenesis and resistance to chemotherapy.
Improved selection of canonical proteins for reference proteomes
Authors: Insana Giuseppe , Martin Maria J , Pearson William R 
Published: June 2024

Abstract
The ‘canonical’ protein sets distributed by UniProt are widely used for similarity searching, and functional and structural annotation. For many investigators, canonical sequences are the only version of a protein examined. However, higher eukaryotes often encode multiple isoforms of a protein from a single gene. For unreviewed (UniProtKB/TrEMBL) protein sequences, the longest sequence in a Gene-Centric group is chosen as canonical. This choice can create inconsistencies, selecting &gt;95% identical orthologs with dramatically different lengths, which is biologically unlikely. We describe the ortho2tree pipeline, which examines Reference Proteome canonical and isoform sequences from sets of orthologous proteins, builds multiple alignments, constructs gap-distance trees, and identifies low-cost clades of isoforms with similar lengths. After examining 140 000 proteins from eight mammals in UniProtKB release 2022_05, ortho2tree proposed 7804 canonical changes for release 2023_01, while confirming 53 434 canonicals. Gap distributions for isoforms selected by ortho2tree are similar to those in bacterial and yeast alignments, organisms unaffected by isoform selection, suggesting ortho2tree canonicals more accurately reflect genuine biological variation. 82% of ortho2tree proposed-changes agreed with MANE; for confirmed canonicals, 92% agreed with MANE. Ortho2tree can improve canonical assignment among orthologous sequences that are &gt;60% identical, a group that includes vertebrates and higher plants.
Evidence for inflammation in normal-appearing brain regions in patients with growing sporadic vestibular schwannoma: A PET study
Authors: Alfaifi Bandar , Hinz Rainer , Jackson Alan , Wadeson Andrea , Pathmanaban Omar N , Hammerbeck-Ward Charlotte , Rutherford Scott A , King Andrew T , Lewis Daniel , Coope David J 
Published: June 2024

Abstract

Background
Nonauditory symptoms can be a prominent feature in patients with sporadic vestibular schwannoma (VS), but the cause of these symptoms is unknown. Inflammation is hypothesized to play a key role in the growth and symptomatic presentation of sporadic VS, and in this study, we investigated through translocator protein (TSPO) positron emission tomography (PET) whether inflammation occurred within the “normal appearing” brain of such patients and its association with tumor growth.

Methods
Dynamic PET datasets from 15 patients with sporadic VS (8 static and 7 growing) who had been previously imaged using the TSPO tracer [11C](R)-PK11195 were included. Parametric images of [11C](R)-PK11195 binding potential (BPND) and the distribution volume ratio (DVR) were derived and compared across VS growth groups within both contralateral and ipsilateral gray (GM) and white matter (WM) regions. Voxel-wise cluster analysis was additionally performed to identify anatomical regions of increased [11C](R)-PK11195 binding.

Results
Compared with static tumors, growing VS demonstrated significantly higher cortical (GM, 1.070 vs. 1.031, P = .03) and whole brain (GM & WM, 1.045 vs. 1.006, P = .03) [11C](R)-PK11195 DVR values. The voxel-wise analysis supported the region-based analysis and revealed clusters of high TSPO binding within the precentral, postcentral, and prefrontal cortex in patients with growing VS.

Conclusions
We present the first in vivo evidence of increased TSPO expression and inflammation within the brains of patients with growing sporadic VS. These results provide a potential mechanistic insight into the development of nonauditory symptoms in these patients and highlight the need for further studies interrogating the role of neuroinflammation in driving VS symptomatology.