bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protoclusters as drivers of stellar mass growth in the early Universe, a case study: Taralay – a massive protocluster at z ∼ 4.57
Authors: Staab Priti , Lemaux Brian C , Forrest Ben , Shah Ekta , Cucciati Olga , Lubin Lori , Gal Roy R , Hung Denise , Shen Lu , Giddings Finn , Khusanova Yana , Zamorani Giovanni , Bardelli Sandro , Cassara Letizia Pasqua , Cassata Paolo , Chiang Yi-Kuan , Fudamoto Yoshinobu , Fukushima Shuma , Garilli Bianca , Giavalisco Mauro , Gruppioni Carlotta , Guaita Lucia , Gururajan Gayathri , Hathi Nimish , Kashino Daichi , Scoville Nick , Talia Margherita , Vergani Daniela , Zucca Elena 
Published: February 2024

ABSTRACT
Simulations predict that the galaxy populations inhabiting protoclusters may contribute considerably to the total amount of stellar mass growth of galaxies in the early universe. In this study, we test these predictions observationally, using the Taralay protocluster (formerly PCl J1001+0220) at z ∼ 4.57 in the COSMOS field. With the Charting Cluster Construction with VUDS and ORELSE (C3VO) survey, we spectroscopically confirmed 44 galaxies within the adopted redshift range of the protocluster (4.48 &lt; z &lt; 4.64) and incorporate an additional 18 galaxies from ancillary spectroscopic surveys. Using a density mapping technique, we estimate the total mass of Taralay to be ∼1.7 × 1015 M⊙, sufficient to form a massive cluster by the present day. By comparing the star formation rate density (SFRD) within the protocluster (SFRDpc) to that of the coeval field (SFRDfield), we find that SFRDpc surpasses the SFRDfield by Δlog (SFRD/M⊙yr−1 Mpc−3) = 1.08 ± 0.32 (or ∼12 ×). The observed contribution fraction of protoclusters to the cosmic SFRD adopting Taralay as a proxy for typical protoclusters is $33.5~{{\ \rm per\ cent}}^{+8.0~{{\ \rm per\ cent}}}_{-4.3~{{\ \rm per\ cent}}}$, a value ∼2σ higher than the predictions from simulations. Taralay contains three peaks that are 5σ above the average density at these redshifts. Their SFRD is ∼0.5 dex higher than the value derived for the overall protocluster. We show that 68 per cent of all star formation in the protocluster takes place within these peaks, and that the innermost regions of the peaks encase $\sim 50~{{\ \rm per\ cent}}$ of the total star formation in the protocluster. This study strongly suggests that protoclusters drive stellar mass growth in the early universe and that this growth may proceed in an inside-out manner.
Dust-to-neutral gas ratio of the intermediate- and high-velocity H i clouds derived based on the sub-mm dust emission for the whole sky
Authors: Hayakawa Takahiro , Fukui Yasuo 
Published: February 2024

ABSTRACT
We derived the dust-to-H i ratio of the intermediate-velocity clouds (IVCs), the high-velocity clouds (HVCs), and the local H i gas, by carrying out a multiple-regression analysis of the 21 cm H i emission combined with the sub-mm dust optical depth. The method covers over 80 per cent of the sky contiguously at a resolution of 47 arcmin and is distinguished from the absorption-line measurements toward bright galaxies and stars covering a tiny fraction of the sky. Major results include that the ratio of the IVCs is in a range of 0.1–1.5 with a mode at 0.6 (relative to the solar-neighbourhood value, likewise below) and that a significant fraction, ∼20 per cent, of the IVCs include dust-poor gas with a ratio of &lt;0.5. It is confirmed that 50 per cent of the HVC Complex C has a ratio of &lt;0.3, and that the Magellanic Stream has the lowest ratio with a mode at ∼0.1. The results prove that some IVCs have low metallicity gas, contrary to the previous absorption-line measurements. Considering that the recent works show that the IVCs are interacting and exchanging momentum with the high-metallicity Galactic halo gas, we argue that the high-metallicity gas contaminates a significant fraction of the IVCs. Accordingly, we argue that the IVCs include a significant fraction of the low-metallicity gas supplied from outside the Galaxy as an alternative to the Galactic-fountain model.
Rotation plays a role in the generation of magnetic fields in single white dwarfs
Authors: Hernandez Mercedes S , Schreiber Matthias R , Landstreet John D , Bagnulo Stefano , Parsons Steven G , Chavarria Martin , Toloza Odette , Bell Keaton J 
Published: February 2024

ABSTRACT
Recent surveys of close white dwarf binaries as well as single white dwarfs have provided evidence for the late appearance of magnetic fields in white dwarfs, and a possible generation mechanism, a crystallization and rotation-driven dynamo has been suggested. A key prediction of this dynamo is that magnetic white dwarfs rotate, at least on average, faster than their non-magnetic counterparts and/or that the magnetic field strength increases with rotation. Here we present rotation periods of ten white dwarfs within 40 pc measured using photometric variations. Eight of the light curves come from TESS observations and are thus not biased towards short periods, in contrast to most period estimates that have been reported previously in the literature. These TESS spin periods are indeed systematically shorter than those of non-magnetic white dwarfs. This means that the crystallization and rotation-driven dynamo could be responsible for a fraction of the magnetic fields in white dwarfs. However, the full sample of magnetic white dwarfs also contains slowly rotating strongly magnetic white dwarfs which indicates that another mechanism that leads to the late appearance of magnetic white dwarfs might be at work, either in addition to or instead of the dynamo. The fast-spinning and massive magnetic white dwarfs that appear in the literature form a small fraction of magnetic white dwarfs, and probably result from a channel related to white dwarf mergers.
Differentiable stochastic halo occupation distribution
Authors: Horowitz Benjamin , Hahn ChangHoon , Lanusse Francois , Modi Chirag , Ferraro Simone 
Published: February 2024

ABSTRACT
In this work, we demonstrate how differentiable stochastic sampling techniques developed in the context of deep reinforcement learning can be used to perform efficient parameter inference over stochastic, simulation-based, forward models. As a particular example, we focus on the problem of estimating parameters of halo occupation distribution (HOD) models that are used to connect galaxies with their dark matter haloes. Using a combination of continuous relaxation and gradient re-parametrization techniques, we can obtain well-defined gradients with respect to HOD parameters through discrete galaxy catalogue realizations. Having access to these gradients allows us to leverage efficient sampling schemes, such as Hamiltonian Monte Carlo, and greatly speed up parameter inference. We demonstrate our technique on a mock galaxy catalogue generated from the Bolshoi simulation using a standard HOD model and find near-identical posteriors as standard Markov chain Monte Carlo techniques with an increase of ∼8× in convergence efficiency. Our differentiable HOD model also has broad applications in full forward model approaches to cosmic structure and cosmological analysis.
Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes
Authors: Mihalič Filip , Arcila Dahiana , Pettersson Mats E , Farkhondehkish Pouria , Andersson Eva , Andersson Leif , Betancur-R Ricardo , Jemth Per 
Published: February 2024

Abstract
The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 μM). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of “functional affinity” in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein–protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.
Long-term suboptimal dietary trace element supply does not affect trace element homeostasis in murine cerebellum
Authors: Friese Sharleen , Ranzini Giovanna , Tuchtenhagen Max , Lossow Kristina , Hertel Barbara , Pohl Gabriele , Ebert Franziska , Bornhorst Julia , Kipp Anna Patricia , Schwerdtle Tanja 
Published: February 2024

Abstract
The ageing process is associated with alterations of systemic trace element (TE) homeostasis increasing the risk, e.g. neurodegenerative diseases. Here, the impact of long-term modulation of dietary intake of copper, iron, selenium, and zinc was investigated in murine cerebellum. Four- and 40-wk-old mice of both sexes were supplied with different amounts of those TEs for 26 wk. In an adequate supply group, TE concentrations were in accordance with recommendations for laboratory mice while suboptimally supplied animals received only limited amounts of copper, iron, selenium, and zinc. An additional age-adjusted group was fed selenium and zinc in amounts exceeding recommendations. Cerebellar TE concentrations were measured by inductively coupled plasma–tandem mass spectrometry. Furthermore, the expression of genes involved in TE transport, DNA damage response, and DNA repair as well as selected markers of genomic stability [8-oxoguanine, incision efficiency toward 8-oxoguanine, 5-hydroxyuracil, and apurinic/apyrimidinic sites and global DNA (hydroxy)methylation] were analysed. Ageing resulted in a mild increase of iron and copper concentrations in the cerebellum, which was most pronounced in the suboptimally supplied groups. Thus, TE changes in the cerebellum were predominantly driven by age and less by nutritional intervention. Interestingly, deviation from adequate TE supply resulted in higher manganese concentrations of female mice even though the manganese supply itself was not modulated. Parameters of genomic stability were neither affected by age, sex, nor diet. Overall, this study revealed that suboptimal dietary TE supply does not substantially affect TE homeostasis in the murine cerebellum.
Uptake and accumulation mechanisms of hexachloroplatinate(IV) ions in the unicellular alga, Pseudococcomyxa simplex
Authors: Tokoro Masato , Imamura Yu , Kumagai Kazuhiro , Hokura Akiko 
Published: February 2024

Abstract
Platinum uptake was examined by adding hexachloroplatinate(IV) solution to the unicellular alga Pseudococcomyxa simplex. After the addition of platinum solution ([Pt] = 100 mg/kg, pH 3.2–3.4) for a certain time, the cells were quickly frozen and subjected to μ-XRF (X-ray fluorescence) analysis using synchrotron X-rays. The beam size of approximately 1 micrometer allowed visualization of the platinum distribution within a single cell. On the other hand, we examined platinum uptake in enzyme-treated protoplasts and lyophilized cells and found that the platinum uptake concentrations in these samples were higher than in living in-vivo cells. Cell wall and cell metabolism were presumed to interfere with the uptake of hexachloroplatinate(IV) ions. All platinum ions taken up by the cells were reduced to divalent form. The effect of light on platinum addition was also investigated. When platinum was added under light conditions, some samples showed higher platinum accumulation than under shade conditions.
Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework
Authors: Liu Jiayi , Ashuach Tal , Inoue Fumitaka , Ahituv Nadav , Yosef Nir , Kreimer Anat 
Published: February 2024

Abstract
The advent of perturbation-based massively parallel reporter assays (MPRAs) technique has facilitated the delineation of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate and establish guidelines for sequence design strategies for perturbation MPRAs. In this study, we propose a framework for evaluating and comparing various perturbation strategies for MPRA experiments. Within this framework, we benchmark three different perturbation approaches from the perspectives of alteration in motif-based profiles, consistency of MPRA outputs, and robustness of models that predict the activities of putative regulatory motifs. While our analyses show very similar results across multiple benchmarking metrics, the predictive modeling for the approach involving random nucleotide shuffling shows significant robustness compared with the other two approaches. Thus, we recommend designing sequences by randomly shuffling the nucleotides of the perturbed site in perturbation-MPRA, followed by a coherence check to prevent the introduction of other variations of the target motifs. In summary, our evaluation framework and the benchmarking findings create a resource of computational pipelines and highlight the potential of perturbation-MPRA in predicting non-coding regulatory activities.
RAVER1 hinders lethal EMT and modulates miR/RISC activity by the control of alternative splicing
Authors: Wedler Alice , Bley Nadine , Glaß Markus , Müller Simon , Rausch Alexander , Lederer Marcell , Urbainski Julia , Schian Laura , Obika Kingsley-Benjamin , Simon Theresa , Peters Lara Meret , Misiak Claudia , Fuchs Tommy , Köhn Marcel , Jacob Roland , Gutschner Tony , Ihling Christian , Sinz Andrea , Hüttelmaier Stefan 
Published: February 2024

Abstract
The RAVER1 protein serves as a co-factor in guiding the polypyrimidine tract-binding protein (PTBP)-dependent control of alternative splicing (AS). Whether RAVER1 solely acts in concert with PTBPs and how it affects cancer cell fate remained elusive. Here, we provide the first comprehensive investigation of RAVER1-controlled AS in cancer cell models. This reveals a pro-oncogenic role of RAVER1 in modulating tumor growth and epithelial-mesenchymal-transition (EMT). Splicing analyses and protein-association studies indicate that RAVER1 guides AS in association with other splicing regulators, including PTBPs and SRSFs. In cancer cells, one major function of RAVER1 is the stimulation of proliferation and restriction of apoptosis. This involves the modulation of AS events within the miR/RISC pathway. Disturbance of RAVER1 impairs miR/RISC activity resulting in severely deregulated gene expression, which promotes lethal TGFB-driven EMT. Among others, RAVER1-modulated splicing events affect the insertion of protein interaction modules in factors guiding miR/RISC-dependent gene silencing. Most prominently, in all three human TNRC6 proteins, RAVER1 controls AS of GW-enriched motifs, which are essential for AGO2-binding and the formation of active miR/RISC complexes. We propose, that RAVER1 is a key modulator of AS events in the miR/RISC pathway ensuring proper abundance and composition of miR/RISC effectors. This ensures balanced expression of TGFB signaling effectors and limits TGFB induced lethal EMT.
Mage transposon: a novel gene delivery system for mammalian cells
Authors: Tian Jinghan , Tong Doudou , Li Zhendong , Wang Erqiang , Yu Yifei , Lv Hangya , Hu Zhendan , Sun Fang , Wang Guoping , He Min , Xia Tian 
Published: February 2024

Abstract
Transposons, as non-viral integration vectors, provide a secure and efficient method for stable gene delivery. In this study, we have discovered Mage (MG), a novel member of the piggyBac(PB) family, which exhibits strong transposability in a variety of mammalian cells and primary T cells. The wild-type MG showed a weaker insertion preference for near genes, transcription start sites (TSS), CpG islands, and DNaseI hypersensitive sites in comparison to PB, approaching the random insertion pattern. Utilizing in silico virtual screening and feasible combinatorial mutagenesis in vitro, we effectively produced the hyperactive MG transposase (hyMagease). This variant boasts a transposition rate 60% greater than its native counterpart without significantly altering its insertion pattern. Furthermore, we applied the hyMagease to efficiently deliver chimeric antigen receptor (CAR) into T cells, leading to stable high-level expression and inducing significant anti-tumor effects both in vitro and in xenograft mice models. These findings provide a compelling tool for gene transfer research, emphasizing its potential and prospects in the domains of genetic engineering and gene therapy.
Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system
Authors: Murányi Gábor , Szabó Mónika , Acsai Károly , Kiss János 
Published: February 2024

Abstract
The SGI1 family integrative mobilizable elements, which are efficient agents in distribution of multidrug resistance in Gammaproteobacteria, have a complex, parasitic relationship with their IncC conjugative helper plasmids. Besides exploiting the transfer apparatus, SGI1 also hijacks IncC plasmid control mechanisms to time its own excision, replication and expression of self-encoded T4SS components, which provides advantages for SGI1 over its helpers in conjugal transfer and stable maintenance. Furthermore, SGI1 destabilizes its helpers in an unknown, replication-dependent way when they are concomitantly present in the same host. Here we report how SGI1 exploits the helper plasmid partitioning system to displace the plasmid and simultaneously increase its own stability. We show that SGI1 carries two copies of sequences mimicking the parS sites of IncC plasmids. These parS-like elements bind the ParB protein encoded by the plasmid and increase SGI1 stability by utilizing the parABS system of the plasmid for its own partitioning, through which SGI1 also destabilizes the helper plasmid. Furthermore, SGI1 expresses a small protein, Sci, which significantly strengthens this plasmid-destabilizing effect, as well as SGI1 maintenance. The plasmid-induced replication of SGI1 results in an increased copy-number of parS-like sequences and Sci expression leading to strong incompatibility with the helper plasmid.
CRUX, a platform for visualising, exploring and analysing cancer genome cohort data
Authors: El-Kamand Sam , Quinn Julian M W , Sareen Heena , Becker Therese M , Wong-Erasmus Marie , Cowley Mark J 
Published: February 2024

Abstract
To better understand how tumours develop, identify prognostic biomarkers and find new treatments, researchers have generated vast catalogues of cancer genome data. However, these datasets are complex, so interpreting their important features requires specialized computational skills and analytical tools, which presents a significant technical challenge. To address this, we developed CRUX, a platform for exploring genomic data from cancer cohorts. CRUX enables researchers to perform common analyses including cohort comparisons, biomarker discovery, survival analysis, and to create visualisations including oncoplots and lollipop charts. CRUX simplifies cancer genome analysis in several ways: (i) it has an easy-to-use graphical interface; (ii) it enables users to create custom cohorts, as well as analyse precompiled public and private user-created datasets; (iii) it allows analyses to be run locally to address data privacy concerns (though an online version is also available) and (iv) it makes it easy to use additional specialized tools by exporting data in the correct formats. We showcase CRUX’s capabilities with case studies employing different types of cancer genome analysis, demonstrating how it can be used flexibly to generate valuable insights into cancer biology. CRUX is freely available at https://github.com/CCICB/CRUX and https://ccicb.shinyapps.io/crux (DOI: 10.5281/zenodo.8015714).
Functional domain annotation by structural similarity
Authors: Borujeni Poorya Mirzavand , Salavati Reza 
Published: February 2024

Abstract
Traditional automated in silico functional annotation uses tools like Pfam that rely on sequence similarities for domain annotation. However, structural conservation often exceeds sequence conservation, suggesting an untapped potential for improved annotation through structural similarity. This approach was previously overlooked before the AlphaFold2 introduction due to the need for more high-quality protein structures. Leveraging structural information especially holds significant promise to enhance accurate annotation in diverse proteins across phylogenetic distances. In our study, we evaluated the feasibility of annotating Pfam domains based on structural similarity. To this end, we created a database from segmented full-length protein structures at their domain boundaries, representing the structure of Pfam seeds. We used Trypanosoma brucei, a phylogenetically distant protozoan parasite as our model organism. Its structome was aligned with our database using Foldseek, the ultra-fast structural alignment tool, and the top non-overlapping hits were annotated as domains. Our method identified over 400 new domains in the T. brucei proteome, surpassing the benchmark set by sequence-based tools, Pfam and Pfam-N, with some predictions validated manually. We have also addressed limitations and suggested avenues for further enhancing structure-based domain annotation.
First report of the rare tintinnid genus Stelidiella Kofoid and Campbell 1929 in the Indian Ocean
Authors: Sarun T P , Patil Jagadish S 
Published: February 2024

Abstract
This study provides detailed information on the morphometry and distribution of some rare tintinnids species found in the Indian Ocean. The morphological features (scabbard-shaped with a fenestrated collar) reported here resemble those of the genus Stelidiella. Here, lorica morphology (fenestra arrangement and oral margin (OM) pattern) was the sole criteria for Stelidiella species identification. The dimensions and morphology (presence of two layers of fenestrae rings with smooth OMs) resemble the original description of Stelidiella fenestrata, a warm-water species. We found both small (260 μm long) and large S. fenestrata (309 μm long) with smaller and larger bowls in the former and latter, respectively. In the Indian Ocean, S. fenestrata was more abundant (i) between 12oN and 18oS (particularly, central Indian Ocean) similar to that reported in the Pacific Ocean; (ii) in the mesopelagic zone (100–1000 m) than the epipelagic zone (0–100 m) and (iii) in the winter season of December 2021–January 2022 than in spring inter-monsoon of March–May 2021. The S. fenestrata, despite being in low abundance (2–26 individuals 10 m−3), is widespread in the region, and their role in the ecosystem merits further investigation.