bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring M31 globular cluster ages and metallicities using both photometry and spectroscopy
Authors: Usher Christopher , Caldwell Nelson , Cabrera-Ziri Ivan 
Published: January 2024

ABSTRACT
The ages and metallicities of globular clusters play an important role not just in testing models for their formation and evolution but also in understanding the assembly history of their host galaxies. Here, we use a combination of imaging and spectroscopy to measure the ages and metallicities of globular clusters in M31, the closest massive galaxy to our own. We use the strength of the near-infrared calcium triplet spectral feature to provide a relatively age-insensitive prior on the metallicity when fitting stellar population models to the observed photometry. While the age–extinction degeneracy is an issue for globular clusters projected on to the disc of M31, we find generally old ages for globular clusters in the halo of M31 and in its satellite galaxy NGC 205 in line with previous studies. We measure ages for a number of outer halo globular clusters for the first time, finding that globular clusters associated with halo substructure extend to younger ages and higher metallicities than those associated with the smooth halo. This is in line with the expectation that the smooth halo was accreted earlier than the substructured halo.
Joint gravitational wave-short GRB detection of binary neutron star mergers with existing and future facilities
Authors: Bhattacharjee Soumyadeep , Banerjee Smaranika , Bhalerao Varun , Beniamini Paz , Bose Sukanta , Hotokezaka Kenta , Pai Archana , Saleem Muhammed , Waratkar Gaurav 
Published: January 2024

ABSTRACT
We explore the joint detection prospects of short gamma-ray bursts (sGRBs) and their gravitational wave (GW) counterparts by the current and upcoming high-energy GRB and GW facilities from binary neutron star (BNS) mergers. We consider two GW detector networks: (1) a four-detector network comprising LIGO Hanford, Livingston, Virgo, and Kagra (IGWN4) and (2) a future five-detector network including the same four detectors and LIGO India (IGWN5). For the sGRB detection, we consider existing satellites Fermi and Swift and the proposed all-sky satellite Daksha. Most of the events for the joint detection will be off-axis, hence, we consider a broad range of sGRB jet models predicting the off-axis emission. Also, to test the effect of the assumed sGRB luminosity function, we consider two different functions for one of the emission models. We find that for the different jet models, the joint sGRB and GW detection rates for Fermi and Swift with IGWN4 (IGWN5) lie within 0.07–0.62  yr−1 0.8–4.0 yr−1) and 0.02–0.14 yr−1 (0.15–1.0 yr−1), respectively, when the BNS merger rate is taken to be 320 Gpc−3 yr−1. With Daksha, the rates increase to 0.2–1.3 yr−1 (1.3–8.3 yr−1), which is 2–9 times higher than the existing satellites. We show that such a mission with higher sensitivity will be ideal for detecting a higher number of fainter events observed off-axis or at a larger distance. Thus, Daksha will boost the joint detections of sGRB and GW, especially for the off-axis events. Finally, we find that our detection rates with optimal SNRs are conservative, and noise in GW detectors can increase the rates further.
Origin of reduced dynamical friction by dark matter haloes with net prograde rotation
Authors: Chiba Rimpei , Kataria Sandeep Kumar 
Published: January 2024

ABSTRACT
We provide an explanation for the reduced dynamical friction on galactic bars in spinning dark matter haloes. Earlier work based on linear theory predicted an increase in dynamical friction when dark haloes have a net forward rotation because prograde orbits couple to bars with greater strength than retrograde orbits. Subsequent numerical studies, however, found the opposite trend: dynamical friction weakens with increasing spin of the halo. We revisit this problem and demonstrate that linear theory in fact correctly predicts a reduced torque in forward-rotating haloes. We show that shifting the halo mass from retrograde to prograde phase space generates a positive gradient in the distribution function near the origin of the z-angular momentum (Lz = 0), which results in a resonant transfer of Lz to the bar, making the net dynamical friction weaker. While this effect is subdominant for the major resonances, including the corotation resonance, it leads to a significant positive torque on the bar for the series of direct radial resonances as these resonances are strongest at Lz = 0. The overall dynamical friction from spinning haloes is shown to decrease with the halo’s spin in agreement with the secular behaviour of N-body simulations. We validate our linear calculation by computing the non-linear torque from individual resonances using the angle-averaged Hamiltonian.
Multiple mechanisms activate GCN2 eIF2 kinase in response to diverse stress conditions
Authors: Misra Jagannath , Carlson Kenneth R , Spandau Dan F , Wek Ronald C 
Published: January 2024

Abstract
Diverse environmental insults induce the integrated stress response (ISR), which features eIF2 phosphorylation and translational control that serves to restore protein homeostasis. The eIF2 kinase GCN2 is a first responder in the ISR that is activated by amino acid depletion and other stresses not directly related to nutrients. Two mechanisms are suggested to trigger an ordered process of GCN2 activation during stress: GCN2 monitoring stress via accumulating uncharged tRNAs or by stalled and colliding ribosomes. Our results suggest that while ribosomal collisions are indeed essential for GCN2 activation in response to translational elongation inhibitors, conditions that trigger deacylation of tRNAs activate GCN2 via its direct association with affected tRNAs. Both mechanisms require the GCN2 regulatory domain related to histidyl tRNA synthetases. GCN2 activation by UV irradiation features lowered amino acids and increased uncharged tRNAs and UV-induced ribosome collisions are suggested to be dispensable. We conclude that there are multiple mechanisms that activate GCN2 during diverse stresses.
Smoother: on-the-fly processing of interactome data using prefix sums
Authors: Schmidt Markus R , Barcons-Simon Anna , Rabuffo Claudia , Siegel T Nicolai 
Published: January 2024

Abstract
Nucleic acid interactome data, such as chromosome conformation capture data and RNA–DNA interactome data, are currently analyzed via pipelines that must be rerun for each new parameter set. A more dynamic approach is desirable since the optimal parameter set is commonly unknown ahead of time and rerunning pipelines is a time-consuming process. We have developed an approach fast enough to process interactome data on-the-fly using a sparse prefix sum index. With this index, we created Smoother, a flexible, multifeatured visualization and analysis tool that allows interactive filtering, e.g. by mapping quality, almost instant comparisons between different normalization approaches, e.g. iterative correction, and ploidy correction. Further, Smoother can overlay other sequencing data or genomic annotations, compare different samples, and perform virtual 4C analysis. Smoother permits a novel way to interact with and explore interactome data, fostering comprehensive, high-quality data analysis. Smoother is available at https://github.com/Siegel-Lab/BioSmoother under the MIT license.
Decoding the universal human chromatin landscape through teratoma-based profiling
Authors: Kidder Benjamin L 
Published: January 2024

Abstract
Teratoma formation is key for evaluating differentiation of human pluripotent stem cells into embryonic germ layers and serves as a model for understanding stem cell differentiation and developmental processes. Its potential for insights into epigenome and transcriptome profiling is significant. This study integrates the analysis of the epigenome and transcriptome of hESC-generated teratomas, comparing transcriptomes between hESCs and teratomas. It employs cell type-specific expression patterns from single-cell data to deconvolve RNA-Seq data and identify cell types within teratomas. Our results provide a catalog of activating and repressive histone modifications, while also elucidating distinctive features of chromatin states. Construction of an epigenetic signature matrix enabled the quantification of diverse cell populations in teratomas and enhanced the ability to unravel the epigenetic landscape in heterogeneous tissue contexts. This study also includes a single cell multiome atlas of expression (scRNA-Seq) and chromatin accessibility (scATAC-Seq) of human teratomas, further revealing the complexity of these tissues. A histology-based digital staining tool further complemented the annotation of cell types in teratomas, enhancing our understanding of their cellular composition. This research is a valuable resource for examining teratoma epigenomic and transcriptomic landscapes and serves as a model for epigenetic data comparison.
Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4
Authors: Saotome Mika , Poduval Deepak B , Grimm Sara A , Nagornyuk Aerica , Gunarathna Sakuntha , Shimbo Takashi , Wade Paul A , Takaku Motoki 
Published: January 2024

Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here, we determine the roles of CHD4 in enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During cellular reprogramming induced by the pioneer factor GATA3, CHD4 activity is necessary to prevent inappropriate chromatin opening. Mechanistically, CHD4 promotes nucleosome positioning over GATA3 binding motifs to compete with transcription factor–DNA interaction. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors.
NMR measurements of transient low-populated tautomeric and anionic Watson–Crick-like G·T/U in RNA:DNA hybrids: implications for the fidelity of transcription and CRISPR/Cas9 gene editing
Authors: Szekely Or , Rangadurai Atul Kaushik , Gu Stephanie , Manghrani Akanksha , Guseva Serafima , Al-Hashimi Hashim M 
Published: January 2024

Abstract
Many biochemical processes use the Watson–Crick geometry to distinguish correct from incorrect base pairing. However, on rare occasions, mismatches such as G·T/U can transiently adopt Watson–Crick-like conformations through tautomerization or ionization of the bases, giving rise to replicative and translational errors. The propensities to form Watson–Crick-like mismatches in RNA:DNA hybrids remain unknown, making it unclear whether they can also contribute to errors during processes such as transcription and CRISPR/Cas editing. Here, using NMR R1ρ experiments, we show that dG·rU and dT·rG mismatches in two RNA:DNA hybrids transiently form tautomeric (Genol·T/U $ \mathbin{\lower.3ex\hbox{$\buildrel\textstyle\rightarrow\over {\smash{\leftarrow}\vphantom{_{\vbox to.5ex{\vss}}}}$}}$ G·Tenol/Uenol) and anionic (G·T−/U−) Watson–Crick-like conformations. The tautomerization dynamics were like those measured in A-RNA and B-DNA duplexes. However, anionic dG·rU− formed with a ten-fold higher propensity relative to dT−·rG and dG·dT− and this could be attributed to the lower pKa (ΔpKa ∼0.4–0.9) of U versus T. Our findings suggest plausible roles for Watson–Crick-like G·T/U mismatches in transcriptional errors and CRISPR/Cas9 off-target gene editing, uncover a crucial difference between the chemical dynamics of G·U versus G·T, and indicate that anionic Watson–Crick-like G·U− could play a significant role evading Watson–Crick fidelity checkpoints in RNA:DNA hybrids and RNA duplexes.
MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops
Authors: Tang Li , Liao Jiaqi , Hill Matthew C , Hu Jiaxin , Zhao Yichao , Ellinor Patrick T , Li Min 
Published: January 2024

Abstract
Protein-specific Chromatin Conformation Capture (3C)-based technologies have become essential for identifying distal genomic interactions with critical roles in gene regulation. The standard techniques include Chromatin Interaction Analysis by Paired-End Tag (ChIA-PET), in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) also known as PLAC-seq. To identify chromatin interactions from these data, a variety of computational methods have emerged. Although these state-of-art methods address many issues with loop calling, only few methods can fit different data types simultaneously, and the accuracy as well as the efficiency these approaches remains limited. Here we have generated a pipeline, MMCT-Loop, which ensures the accurate identification of strong loops as well as dynamic or weak loops through a mixed model. MMCT-Loop outperforms existing methods in accuracy, and the detected loops show higher activation functionality. To highlight the utility of MMCT-Loop, we applied it to conformational data derived from neural stem cell (NSCs) and uncovered several previously unidentified regulatory regions for key master regulators of stem cell identity. MMCT-Loop is an accurate and efficient loop caller for targeted conformation capture data, which supports raw data or pre-processed valid pairs as input, the output interactions are formatted and easily uploaded to a genome browser for visualization.
Rat1 promotes premature transcription termination at R-loops
Authors: Mérida-Cerro José Antonio , Maraver-Cárdenas Pablo , Rondón Ana G , Aguilera Andrés 
Published: January 2024

Abstract
Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.
Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human
Authors: Ren Guiping , Gu Xiaoqian , Zhang Lu , Gong Shimin , Song Shuang , Chen Shunkai , Chen Zhenjing , Wang Xiaoyan , Li Zhanbiao , Zhou Yingshui , Li Longxi , Yang Jiao , Lai Fan , Dang Yunkun 
Published: January 2024

Abstract
Ribosomal frameshifting refers to the process that ribosomes slip into +1 or −1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats, which may expand the coding capacity of mRNA and diversify the regulation in human.
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells
Authors: Aydin Jens , Gabel Alexander , Zielinski Sebastian , Ganskih Sabina , Schmidt Nora , Hartigan Christina R , Schenone Monica , Carr Steven A , Munschauer Mathias 
Published: January 2024

Abstract
RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5′ and 3′-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.
EquiPNAS: improved protein–nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks
Authors: Roche Rahmatullah , Moussad Bernard , Shuvo Md Hossain , Tarafder Sumit , Bhattacharya Debswapna 
Published: January 2024

Abstract
Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wide range of predictive modeling tasks, but their power has not yet been harnessed for predicting protein–nucleic acid binding sites, critical for characterizing the interactions between proteins and nucleic acids. Here, we present EquiPNAS, a new pLM-informed E(3) equivariant deep graph neural network framework for improved protein–nucleic acid binding site prediction. By combining the strengths of pLM and symmetry-aware deep graph learning, EquiPNAS consistently outperforms the state-of-the-art methods for both protein–DNA and protein–RNA binding site prediction on multiple datasets across a diverse set of predictive modeling scenarios ranging from using experimental input to AlphaFold2 predictions. Our ablation study reveals that the pLM embeddings used in EquiPNAS are sufficiently powerful to dramatically reduce the dependence on the availability of evolutionary information without compromising on accuracy, and that the symmetry-aware nature of the E(3) equivariant graph-based neural architecture offers remarkable robustness and performance resilience. EquiPNAS is freely available at https://github.com/Bhattacharya-Lab/EquiPNAS.
Ultrafast micro/nano-manufacturing of metastable materials for energy
Authors: Cui Xiaoya , Liu Yanchang , Chen Yanan 
Published: January 2024

ABSTRACT
The structural engineering of metastable nanomaterials with abundant defects has attracted much attention in energy-related fields. The high-temperature shock (HTS) technique, as a rapidly developing and advanced synthesis strategy, offers significant potential for the rational design and fabrication of high-quality nanocatalysts in an ultrafast, scalable, controllable and eco-friendly way. In this review, we provide an overview of various metastable micro- and nanomaterials synthesized via HTS, including single metallic and bimetallic nanostructures, high entropy alloys, metal compounds (e.g. metal oxides) and carbon nanomaterials. Note that HTS provides a new research dimension for nanostructures, i.e. kinetic modulation. Furthermore, we summarize the application of HTS—as supporting films for transmission electron microscopy grids—in the structural engineering of 2D materials, which is vital for the direct imaging of metastable materials. Finally, we discuss the potential future applications of high-throughput and liquid-phase HTS strategies for non-equilibrium micro/nano-manufacturing beyond energy-related fields. It is believed that this emerging research field will bring new opportunities to the development of nanoscience and nanotechnology in both fundamental and practical aspects.
Anisotropic microtopography surface of chitosan scaffold regulating skin precursor-derived Schwann cells towards repair phenotype promotes neural regeneration
Authors: Cong Meng , Wu Xia , Zhu Lingjie , Gu Guohao , Ding Fei , Li Guicai , Shi Haiyan 
Published: January 2024

Abstract
For repairing peripheral nerve and spinal cord defects, biomaterial scaffold-based cell-therapy was emerged as an effective strategy, requiring the positive response of seed cells to biomaterial substrate and environment signals. Previous work highlighted that the imposed surface properties of scaffold could provide important guidance cues to adhered cells for polarization. However, the insufficiency of native Schwann cells and unclear cellular response mechanisms remained to be addressed. Given that, this study aimed to illuminate the micropatterned chitosan-film action on the rat skin precursor-derived Schwann cells (SKP-SCs). Chitosan-film with different ridge/groove size was fabricated and applied for the SKP-SCs induction. Results indicated that SKP-SCs cultured on 30 μm size microgroove surface showed better oriented alignment phenotype. Induced SKP-SCs presented similar genic phenotype as repair Schwann cells, increasing expression of c-Jun, neural cell adhesion molecule, and neurotrophic receptor p75. Moreover, SKP-SC-secretome was subjected to cytokine array GS67 assay, data indicated the regulation of paracrine phenotype, a panel of cytokines was verified up-regulated at secreted level and gene expression level in induced SKP-SCs. These up-regulated cytokines exhibit a series of promotive neural regeneration functions, including cell survival, cell migration, cell proliferation, angiogenesis, axon growth, and cellular organization etc. through bioinformatics analysis. Furthermore, the effectively polarized SKP-SCs-sourced secretome, promoted the proliferation and migration capacity of the primarily cultured native rat Schwann cells, and augmented neurites growth of the cultured motoneurons, as well as boosted axonal regrowth of the axotomy-injured motoneurons. Taken together, SKP-SCs obtained pro-neuroregeneration phenotype in adaptive response to the anisotropic topography surface of chitosan-film, displayed the oriented parallel growth, the transition towards repair Schwann cell genic phenotype, and the enhanced paracrine effect on neural regeneration. This study provided novel insights into the potency of anisotropic microtopography surface to Schwann-like cells phenotype regulation, that facilitating to provide promising engineered cell-scaffold in neural injury therapies.