bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual role of PpV in Drosophila crystal cell proliferation and survival
Authors: Luo Wang , Zhang Fang , Zhao Fangzhen , Fang Yang , Zhao Long , Su Ying 
Published: July 2024

Abstract
Drosophila melanogaster crystal cells are a specialized type of blood cells for innate immune process upon injury. Under normal conditions, crystal cells rarely proliferate and constitute a small proportion of fly blood cells. Notch signaling has been known to guide the cell fate determination of crystal cells and maintain their survival. Here, we reported that protein phosphatase V (PpV), the unique catalytic subunit of protein phosphatase 6 in Drosophila, is a novel regulator of crystal cell proliferation and integrity. We found that PpV proteins highly accumulated in crystal cells in the larval hematopoietic organ termed the lymph gland. Silencing PpV using RNA interference led to increased crystal cell proliferation in a Notch-independent manner and induced crystal cell rupture dependent on Notch signaling. Moreover, additive PpV prevented the rupture of crystal cells in lymph glands upon a needle injury, suggesting the involvement of PpV in wound healing. Altogether, our results indicated that PpV plays a dual role in lymph glands, preventing crystal cell proliferation to limit the cell number, as well as inhibiting crystal cell rupture to maintain their survival.
Antibacterial mechanism of the methanol extract of Thamnolia subuliformis (Ehrh.) W. Culb against Staphylococcus aureus
Authors: Liu Menglong , Tian Hongqiao , Zhu Jiana , Ding Haiyan 
Published: July 2024

Abstract
Thamnolia subuliformis (Ehrh.) W. Culb is a species of lichen with edible and medicinal applications in China. Our previous studies demonstrated that the methanol extract of Thamnolia subuliformis (METS) exhibits broad antibacterial activity and stability against foodborne pathogens. This study aimed to investigate the antibacterial mechanism of METS against Staphylococcus aureus using nontargeted metabolomics, focusing on cell wall and membrane damage. The results revealed that the minimum inhibitory concentration (MIC) was 0.625 mg ml−1 and that METS had good biosafety at this concentration. METS caused significant damage to the cell wall and membrane integrity, based on both morphological observation by electron microscopy and the leakage of alkaline phosphatase, protein, and nucleic acid in the cell cultures. Treatment with METS at the MIC disrupted the lipid metabolism of S. aureus, causing a decrease in the metabolism of various phospholipids and sphingolipids in the cell membrane and an increase in the ratio of saturated fatty acids to unsaturated fatty acids. Moreover, it influenced intracellular amino acid and energy metabolism. These results shed light on the antibacterial mechanism of METS against S. aureus while also serving as a reference for the further development of natural antibacterial compounds derived from Thamnolia subuliformis.
The XAI system for answer set programming xASP2
Authors: Alviano Mario , Ly Trieu Ly , Cao Son Tran , Balduccini Marcello 
Published: July 2024

Abstract
Explainable artificial intelligence (XAI) aims at addressing complex problems by coupling solutions with reasons that justify the provided answer. In the context of Answer Set Programming (ASP) the user may be interested in linking the presence or absence of an atom in an answer set to the logic rules involved in the inference of the atom. Such explanations can be given in terms of directed acyclic graphs (DAGs). This article reports on the advancements in the development of the XAI system xASP by revising the main foundational notions and by introducing new ASP encodings to compute minimal assumption sets, explanation sequences, and explanation DAGs. DAGs are shown to the user in an interactive form via the xASP navigator application, also introduced in this work.
Discovery of a split stellar stream in the periphery of the Small Magellanic Cloud
Authors: Nidever David L 
Published: July 2024

ABSTRACT
I report the discovery of a stellar stream (Sutlej) using Gaia DR3 (third data release) proper motions and XP metallicities located $\sim$15° north of the Small Magellanic Cloud (SMC). The stream is composed of two parallel linear components (‘branches’) approximately $\sim$8° × 0.6° in size and separated by 2.5°. The stars have a mean proper motion of ($\mu _{\rm RA},\mu _{\rm Dec.}$) = (+0.08 mas yr−1, −1.41 mas yr−1), which is quite similar to the proper motion of stars on the western side of the SMC. The colour–magnitude diagram of the stream stars has a clear red giant branch, horizontal branch, and main-sequence turn-off that are well matched by a parsec isochrone of 10 Gyr, [Fe/H] = −1.8 at 32 kpc, and a total stellar mass of $\sim$33 000 M$_{\odot }$. The stream is spread out over an area of 9.6 deg2 and has a surface brightness of 32.5 mag arcsec−2. The metallicity of the stream stars from Gaia XP spectra extends over $-2.5$$\le$ [M/H] $\le$$-1.0$ with a median of [M/H] = −1.8. The tangential velocity of the stream stars is 214 km s−1 compared to the values of 448 km s−1 for the Large Magellanic Cloud and 428 km s−1 for the SMC. While the radial velocity of the stream is not yet known, a comparison of the space velocities using a range of assumed radial velocities shows that the stream is unlikely to be associated with the Magellanic Clouds. The tangential velocity vector is misaligned with the stream by nearly 90°, which might indicate an important gravitational influence from the nearby Magellanic Clouds.
Two distinct molecular cloud populations detected in massive galaxies
Authors: Rose Tom , McNamara B R , Combes F , Edge A C , McDonald M , O’Sullivan Ewan , Russell H , Fabian A C , Ferland G , Salomé P , Tremblay G 
Published: July 2024

ABSTRACT
We present new ALMA observations of CO, CN, CS, HCN, and HCO$^{+}$ absorption seen against the bright and compact radio continuum sources of eight galaxies. Combined with archival observations, they reveal two distinct populations of molecular clouds, which we identify by combining CO emission and absorption profiles to unambiguously reveal each cloud’s direction of motion and likely location. In galaxy discs, we see clouds with low velocity dispersions, low line-of-sight velocities, and a lack of any systemic inflow or outflow. In galactic cores, we find high velocity dispersion clouds inflowing at up to 550 km s−1. This provides observational evidence in favour of cold accretion on to galactic centres, which likely contributes to the fuelling of active galactic nuclei. We also see a wide range in the CO(2-1)/CO(1-0) ratios of the absorption lines. This is likely the combined effect of hierarchical substructure within the molecular clouds and continuum sources which vary in size with frequency.
Signatures of gas flows – I. Connecting the kinematics of the H i circumgalactic medium to galaxy rotation
Authors: Nateghi Hasti , Kacprzak Glenn G , Nielsen Nikole M , Murphy Michael T , Churchill Christopher W , Muzahid Sowgat , Sameer  , Charlton Jane C 
Published: July 2024

ABSTRACT
The circumgalactic medium (CGM) hosts many physical processes with different kinematic signatures that affect galaxy evolution. We address the CGM–galaxy kinematic connection by quantifying the fraction of H i that is aligned with galaxy rotation with the equivalent width co-rotation fraction, $f_{\rm EWcorot}$. Using 70 quasar sightlines having Hubble Space Telescope/Cosmic Origins Spectrograph H i absorption (${12\lt \log (N(\rm{{\rm H}\,{\small I}})/{\rm cm}^{-2})\lt 20}$) within $5R_{\rm vir}$ of $z\lt 0.6$ galaxies we find that $f_{\rm EWcorot}$ increases with increasing H i column density. $f_{\rm EWcorot}$ is flat at $\sim 0.6$ within $R_{\rm vir}$ and decreases beyond $R_{\rm vir}$ to $f_{\rm EWcorot}$$\sim 0.35$. $f_{\rm EWcorot}$ also has a flat distribution with azimuthal and inclination angles within $R_{\rm vir}$, but decreases by a factor of two outside of $R_{\rm vir}$ for minor axis gas and by a factor of 2 for edge-on galaxies. Inside $R_{\rm vir}$, co-rotation dominated H i is located within $\sim 20$ deg of the major and minor axes. We surprisingly find equal amounts of H i absorption consistent with co-rotation along both major and minor axes within $R_{\rm vir}$. However, this co-rotation disappears along the minor axis beyond $R_{\rm vir}$, suggesting that if this gas is from outflows, then it is bound to galaxies. $f_{\rm EWcorot}$ is constant over two decades of halo mass, with no decrease for log(M$_{\rm h}/{\rm M}_{\odot })\gt 12$ as expected from simulations. Our results suggest that co-rotating gas flows are best found by searching for higher column density gas within $R_{\rm vir}$ and near the major and minor axes.
P-based referencing for correcting tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry imaging of cancer samples
Authors: Kronenberg Katharina , Hoffmann Emily , Hiddeßen Lena , Maus Bastian , Gerwing Mirjam , Faber Cornelius , Sperling Michael , Wildgruber Moritz , Karst Uwe 
Published: July 2024

Abstract
A referencing strategy based on the element P is presented to compensate for cryosectioning tissue artifacts in laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) data. The study examines how the gadolinium-based contrast agent Gadofosveset is distributed in murine cancer tissue, and illustrates how referenced images can compensate for tissue artifacts like folds, overlaps, and density variations. Compared to non-referenced images that provide information on the absolute distribution of the analyte, referenced images allow for the representation of the analyte distribution relative to the amount of material introduced into the instrument, which in this case is correlated to the P signal. Tissue artifacts were corrected in referenced images for both Gadofosveset and endogenous elements, such as Fe and Zn. Additionally, the referencing approach provides valuable information on the Gd uptake relative to the tissue density in necrotic compared to vital tumor areas, which is not obtained from in vivo magnetic resonance imaging (MRI) data. However, validation of in vivo MRI and ex vivo LA-ICP-MS methods was possible by establishing a mean ratio of necrotic to vital tumor areas in the T1-weighted image post Gadofosveset injection and the non-referenced LA-ICP-MS image of Gd. In summary, P-based correction of LA-ICP-MS imaging data allows for a more accurate spatial representation of certain elements, including endogenous and exogenous elements such as injected contrast agents.
Solution structures and effects of a platinum compound successively bound MYC G-quadruplex
Authors: Liu Wenting , Zhu Bo-Chen , Liu Liu-Yi , Xia Xiao- Yu , Jang Jinho , Dickerhoff Jonathan , Yang Danzhou , Mao Zong-Wan 
Published: July 2024

Abstract
G-quadruplex (G4) structures play integral roles in modulating biological functions and can be regulated by small molecules. The MYC gene is critical during tumor initiation and malignant progression, in which G4 acts as an important modulation motif. Herein, we reported the MYC promoter G4 recognized by a platinum(II) compound Pt-phen. Two Pt-phen–MYC G4 complex structures in 5 mM K+ were determined by NMR. The Pt-phen first strongly binds the 3′-end of MYC G4 to form a 1:1 3′-end binding complex and then binds 5′-end to form a 2:1 complex with more Pt-phen. In the complexes, the Pt-phen molecules are well-defined and stack over four bases at the G-tetrad for a highly extensive π–π interaction, with the Pt atom aligning with the center of the G-tetrad. The flanking residues were observed to rearrange and cover on top of Pt-phen to stabilize the whole complex. We further demonstrated that Pt-phen targets G4 DNA in living cells and represses MYC gene expression in cancer cells. Our work elucidated the structural basis of ligand binding to MYC promoter G4. The platinum compound bound G4 includes multiple complexes formation, providing insights into the design of metal ligands targeting oncogene G4 DNA.
Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0
Authors: Assa Guy , Kalter Nechama , Rosenberg Michael , Beck Avigail , Markovich Oshry , Gontmakher Tanya , Hendel Ayal , Yakhini Zohar 
Published: July 2024

AbstractOff-target effects present a significant impediment to the safe and efficient use of CRISPR-Cas genome editing. Since off-target activity is influenced by the genomic sequence, the presence of sequence variants leads to varying on- and off-target profiles among different alleles or individuals. However, a reliable tool that quantifies genome editing activity in an allelic context is not available. Here, we introduce CRISPECTOR2.0, an extended version of our previously published software tool CRISPECTOR, with an allele-specific editing activity quantification option. CRISPECTOR2.0 enables reference-free, allele-aware, precise quantification of on- and off-target activity, by using de novo sample-specific single nucleotide variant (SNV) detection and statistical-based allele-calling algorithms. We demonstrate CRISPECTOR2.0 efficacy in analyzing samples containing multiple alleles and quantifying allele-specific editing activity, using data from diverse cell types, including primary human cells, plants, and an original extensive human cell line database. We identified instances where an SNV induced changes in the protospacer adjacent motif sequence, resulting in allele-specific editing. Intriguingly, differential allelic editing was also observed in regions carrying distal SNVs, hinting at the involvement of additional epigenetic factors. Our findings highlight the importance of allele-specific editing measurement as a milestone in the adaptation of efficient, accurate, and safe personalized genome editing.
Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor
Authors: Becker Nicole A , Peters Justin P , Lewis Elizabeth , Daby Camden L , Clark Karl , Maher L James 
Published: July 2024

Abstract
Natural prokaryotic gene repression systems often exploit DNA looping to increase the local concentration of gene repressor proteins at a regulated promoter via contributions from repressor proteins bound at distant sites. Using principles from the Escherichia coli lac operon we design analogous repression systems based on target sequence-programmable Transcription Activator-Like Effector dimer (TALED) proteins. Such engineered switches may be valuable for synthetic biology and therapeutic applications. Previous TALEDs with inducible non-covalent dimerization showed detectable, but limited, DNA loop-based repression due to the repressor protein dimerization equilibrium. Here, we show robust DNA loop-dependent bacterial promoter repression by covalent TALEDs and verify that DNA looping dramatically enhances promoter repression in E. coli. We characterize repression using a thermodynamic model that quantitates this favorable contribution of DNA looping. This analysis unequivocally and quantitatively demonstrates that optimized TALED proteins can drive loop-dependent promoter repression in E. coli comparable to the natural LacI repressor system. This work elucidates key design principles that set the stage for wide application of TALED-dependent DNA loop-based repression of target genes.
The cullin Rtt101 promotes ubiquitin-dependent DNA−protein crosslink repair across the cell cycle
Authors: Noireterre Audrey , Soudet Julien , Bagdiul Ivona , Stutz Françoise 
Published: July 2024

Abstract
DNA−protein crosslinks (DPCs) challenge faithful DNA replication and smooth passage of genomic information. Our study unveils the cullin E3 ubiquitin ligase Rtt101 as a DPC repair factor. Genetic analyses demonstrate that Rtt101 is essential for resistance to a wide range of DPC types including topoisomerase 1 crosslinks, in the same pathway as the ubiquitin-dependent aspartic protease Ddi1. Using an in vivo inducible Top1-mimicking DPC system, we reveal the significant impact of Rtt101 ubiquitination on DPC removal across different cell cycle phases. High-throughput methods coupled with next-generation sequencing specifically highlight the association of Rtt101 with replisomes as well as colocalization with DPCs. Our findings establish Rtt101 as a main contributor to DPC repair throughout the yeast cell cycle.
The complete pathway for co-transcriptional mRNA maturation within a large protein of a non-segmented negative-strand RNA virus
Authors: Ogino Minako , Green Todd J , Ogino Tomoaki 
Published: July 2024

Abstract
Non-segmented negative-strand (NNS) RNA viruses, such as rabies, Nipah and Ebola, produce 5′-capped and 3′-polyadenylated mRNAs resembling higher eukaryotic mRNAs. Here, we developed a transcription elongation-coupled pre-mRNA capping system for vesicular stomatitis virus (VSV, a prototypic NNS RNA virus). Using this system, we demonstrate that the single-polypeptide RNA-dependent RNA polymerase (RdRp) large protein (L) catalyzes all pre-mRNA modifications co-transcriptionally in the following order: (i) 5′-capping (polyribonucleotidylation of GDP) to form a GpppA cap core structure, (ii) 2′-O-methylation of GpppA into GpppAm, (iii) guanine-N7-methylation of GpppAm into m7GpppAm (cap 1), (iv) 3′-polyadenylation to yield a poly(A) tail. The GDP polyribonucleotidyltransferase (PRNTase) domain of L generated capped pre-mRNAs of 18 nucleotides or longer via the formation of covalent enzyme–pre-mRNA intermediates. The single methyltransferase domain of L sequentially methylated the cap structure only when pre-mRNAs of 40 nucleotides or longer were associated with elongation complexes. These results suggest that the formation of pre-mRNA closed loop structures in elongation complexes via the RdRp and PRNTase domains followed by the RdRp and MTase domains on the same polypeptide is required for the cap 1 formation during transcription. Taken together, our findings indicate that NNS RNA virus L acts as an all-in-one viral mRNA assembly machinery.
A phased small interfering RNA-derived pathway mediates lead stress tolerance in maize
Authors: Li Zhaoling , Jiang Li , Long Ping , Wang Chen , Liu Peng , Hou Fengxia , Zhang Minyan , Zou Chaoying , Huang Yongcai , Ma Langlang , Shen Yaou 
Published: July 2024

Abstract
Phased small interfering RNAs (phasiRNAs) are a distinct class of endogenous small interfering RNAs, which regulate plant growth, development, and environmental stress response. To determine the effect of phasiRNAs on maize (Zea mays L.) tolerance to lead (Pb) stress, the roots of 305 maize lines under Pb treatment were subjected to generation of individual databases of small RNAs. We identified 55 high-confidence phasiRNAs derived from 13 PHAS genes (genes producing phasiRNAs) in this maize panel, of which 41 derived from 9 PHAS loci were negatively correlated with Pb content in the roots. The potential targets of the 41 phasiRNAs were enriched in ion transport and import. Only the expression of PHAS_1 (ZmTAS3j, Trans-Acting Short Interference RNA3) was regulated by its cis-expression quantitative trait locus and thus affected the Pb content in the roots. Using the Nicotiana benthamiana transient expression system, 5′-rapid amplification of cDNA ends, and Arabidopsis heterologously expressed, we verified that ZmTAS3j was cleaved by zma-miR390 and thus generated tasiRNA targeting ARF genes (tasiARFs), and that the 5′ and 3′ zma-miR390 target sites of ZmTAS3j were both necessary for efficient biosynthesis and functional integrity of tasiARFs. We validated the involvement of the zma-miR390–ZmTAS3j–tasiARF–ZmARF3–ZmHMA3 pathway in Pb accumulation in maize seedlings using genetic, molecular, and cytological methods. Moreover, the increased Pb tolerance in ZmTAS3j-overexpressed lines was likely attributed to the zma-miR390–ZmTAS3j–tasiARF–ZmARF3–SAURs pathway, which elevated indole acetic acid levels and thus reactive oxygen species-scavenging capacity in maize roots. Our study reveals the importance of the TAS3-derived tasiRNA pathway in plant adaptation to Pb stress.
E3 ligase SlCOP1-1 stabilizes transcription factor SlOpaque2 and enhances fruit resistance to Botrytis cinerea in tomato
Authors: Gao Guangtong , Zhou Leilei , Liu Jinying , Wang Peiwen , Gong Pichang , Tian Shiping , Qin Guozheng , Wang Weihao , Wang Yuying 
Published: July 2024

Abstract
CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a pivotal repressor in plant photomorphogenesis, has been extensively studied in various plant processes. However, the specific roles of COP1 in fruit remain poorly understood. Here, we functionally characterized SlCOP1-1 (also known as LeCOP1), an Arabidopsis (Arabidopsis thaliana) COP1 ortholog, in tomato (Solanum lycopersicum) fruit ripening and disease resistance. Despite the clear upregulation of SlCOP1-1 during fruit ripening, knockout or overexpression (OE) of SlCOP1-1 in tomatoes only minimally affected ripening. Intriguingly, these genetic manipulations substantially altered fruit resistance to the fungal pathogen Botrytis cinerea. Proteomic analysis revealed differential accumulation of proteins associated with fruit disease resistance upon SlCOP1-1 knockout or OE. To unravel the mechanism of SlCOP1-1 in disease resistance, we conducted a screen for SlCOP1-1-interacting proteins and identified the stress-related bZIP transcription factor SlOpaque2. We provide evidence that SlOpaque2 functions in tomato resistance to B. cinerea, and SlCOP1-1-mediated mono-ubiquitination and stabilization of SlOpaque2 contributes to fruit resistance against B. cinerea. Our findings uncover a regulatory role of COP1 in controlling fruit disease resistance, enriching our understanding of the regulatory network orchestrating fruit responses to disease.
From global diffusion to local semantics: unpacking the scientization of central banks
Authors: Ibrocevic Edin 
Published: July 2024

Abstract
This article investigates the scientization of central banks and analyzes the evolving knowledge production. Existing literature suggests that scientized knowledge production either becomes globally more similar over time or is driven by local political economy considerations. However, research on the structure of central bank knowledge production is lacking. To address this, I conduct semantic network analysis on 75 000 central bank working papers and articles from top economics journals. Findings show global organizational forms of knowledge production have diffused, but semantics remain localized. The semantic structure becomes increasingly clustered over time, with a notable division between the Federal Reserve System (FED) and non-FED clusters. Only Federal Reserve produces knowledge aligned with top academic journals. Cluster differences are not solely due to mandates or political contexts but depend on specific policy environments. This research illuminates the evolution of knowledge production within central banks and underscores the influence of organizational and policy contexts.