bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local Infrasound Monitoring of Lava Eruptions at Nyiragongo Volcano (D.R. Congo) Using Urban and Near‐Source Stations
Authors: Barrière Julien , Oth Adrien , d’Oreye Nicolas , Subira Josué , Smittarello Delphine , Brenot Hugues , Theys Nicolas , Smets Benoît 
Published: September 2023

AbstractDuring eruptions, volcanoes produce air‐pressure waves inaudible for the human ear called infrasound, which are very helpful for detecting early signs of magma at the surface. Compared to violent ash‐rich explosions, recording more discrete atmospheric disturbances from effusive eruptions remains a practical challenge depending on the distance to the source. At Nyiragongo volcano (D.R. Congo), towering above a 1‐million urban area, we analyzed local infrasonic records between January 2018 and April 2022. An acoustic signature from this open‐vent volcano is detected up to the volcano observatory facilities in Goma city center about 17 km from its crater. We compared infrasound signals with space‐based observations of the intra‐crater activity (SO2 emissions, thermal anomalies, crater depth/radius). We thus obtain a comprehensive picture of Nyiragongo's eruptive activity during this period, encompassing the drainage of its lava lake during its third known flank eruption on 22 May 2021.
Electron Heating and Associated Electrostatic Waves in Magnetic Flux Rope Embedded Within Super‐Alfvén Plasma Flow
Authors: Chen Z. Z. , Wang J. , Liu C. M. , Yu J. , He Z. G. , Liu N. G. , Cui J. , Cao J. B. 
Published: September 2023

AbstractMagnetic flux ropes (MFRs) are significant regions for the production of energetic electrons in space and astrophysical plasmas. However, the research on electron heating and acceleration driven by turbulence in MFRs is still quite rare. Utilizing in‐situ measurements from MMS satellite, we study electron heating and associated electrostatic waves in an ion‐scale MFR within terrestrial super‐Alfvén plasma flow. Lower‐hybrid drift waves, generated locally in this MFR, can contribute to the perpendicular heating through their electrostatic potential accelerating electrons. The parallel heating is attributed to antiparallel propagating electron beams. These beams excite the broadband electrostatic waves that can interact with electrons and thermalize electrons. Our study promotes understanding of electron energization driven by plasma waves and wave‐particle interaction in MFRs.
P and S Wave Anisotropic Tomography of the Banda Subduction Zone
Authors: Hua Yuanyuan , Zhao Dapeng , Xu Yi‐Gang 
Published: September 2023

AbstractIn subduction zones with slab‐slab interactions, the pattern of mantle convection is very complex and still unclear. In this study, we jointly invert a large number of P and S wave arrival time data of local earthquakes for 3‐D isotropic and anisotropic velocity structures of the Banda subduction zone. Along the curved Banda arc, the subducting Indo‐Australian slab is detected clearly as a high‐velocity zone, and its azimuthal anisotropy changes along the arc strike, representing fossil anisotropy within the slab and modified anisotropy by the subduction processes. Around the northern edge of the Banda slab, a semi‐toroidal pattern of anisotropy appears in low‐velocity anomalies, representing mantle flow extruded from the Banda arc and escaped from a gap of the Banda‐Molucca slab toward the northeast. Our 3‐D anisotropic tomography uncovers the mantle convection pattern induced by the slab‐slab interactions, shedding new light on the complex dynamical processes in this curved subduction zone.
Properties of Whistler Waves’ Ducting in Plasmas With Systems of Small‐Scale Density Depletions
Authors: Zudin I. Yu. , Zaboronkova T. M. , Gushchin M. E. , Korobkov S. V. , Krafft C. 
Published: September 2023

AbstractThe ducting of whistler waves by systems of small‐scale field‐aligned plasma density depletions is studied. Similarly to our previous paper (Zudin et al., 2019, https://doi.org/10.1029/2019ja026637), we carry out analytical calculations and numerical simulations for the parameters of an active experiment in which very low frequency whistler waves emitted by a ground‐based transmitter at a frequency of 18 kHz were received onboard the DEMETER satellite at 700 km above the SURA heating facility. Random‐sized density depletions with a level around 10%–20% and perpendicular sizes ranging from 10 m up to about 300 m are considered. The properties of ducted waves are determined by the perpendicular size of individual depletions. Particularly, depletions with a width of more then d0 ∼ 100 m form separate ducting structures, that is, coupled waveguides capable of exchanging energy by means of mode overlap. Depletions with a width of less than d0 ∼ 100 m form a common waveguide structure, whose properties are equivalent to those of a wider irregularity with a smoothed density profile. Two important differences are revealed in ducting properties of density depletions compared to density enhancements considered in Zudin et al. (2019, https://doi.org/10.1029/2019ja026637). First, depletions support highly oblique Gendrin mode waves, rather than quasi‐longitudinal whistlers as in the case of density enhancements. Second, the characteristic perpendicular size d0 ∼ 100 m of density depletions separating the regimes of “coupled waveguides” and of “equivalent ducting structure” with smoothed density profile is by an order of magnitude smaller than for density enhancements of the same 10–20% relative level.
Blocking insulin-like growth factor 1 receptor signaling pathway inhibits neuromuscular junction regeneration after botulinum toxin-A treatment
Authors: Ishihara Hiroki , Otani Yoshinori , Tanaka Kazuki , Miyajima Hisao , Ngo Huy Xuan , Fujitani Masashi 
Published: September 2023

AbstractBotulinum toxin-A (BTX) administration into muscle is an established treatment for conditions with excessive muscle contraction. However, botulinum therapy has short-term effectiveness, and high-dose injection of BTX could induce neutralizing antibodies against BTX. Therefore, prolonging its effects could be beneficial in a clinical situation. Insulin-like growth factor-1 receptor (IGF1R) and its ligands, insulin-like growth factor (IGF) -I and II, regulate the physiological and pathological processes of the nervous system. It has been suggested that IGF1R is involved in the process after BTX administration, but the specific regeneration mechanism remains unclear. Therefore, this study aimed to determine how inhibition of IGF1R signaling pathway affects BTX-induced muscle paralysis. The results showed that anti-IGF1R antibody administration inhibited the recovery from BTX-induced neurogenic paralysis, and the synaptic components at the neuromuscular junction (NMJ), mainly post-synaptic components, were significantly affected by the antibody. In addition, the wet weight or frequency distribution of the cross-sectional area of the muscle fibers was regulated by IGF1R, and sequential antibody administration following BTX treatment increased the number of Pax7+-satellite cells in the gastrocnemius (GC) muscle, independent of NMJ recovery. Moreover, BTX treatment upregulated mammalian target of rapamycin (mTOR)/S6 kinase signaling pathway, HDAC4, Myog, Fbxo32/MAFbx/Atrogin-1 pathway, and transcription of synaptic components, but not autophagy. Finally, IGF1R inhibition affected only mTOR/S6 kinase translational signaling in the GC muscle. In conclusion, the IGF1R signaling pathway is critical for NMJ regeneration via specific translational signals. IGF1R inhibition could be highly beneficial in clinical practice by decreasing the number of injections and total dose of BTX due to the prolonged duration of the effect.
LncRNA Neat1 targets NonO and miR-128-3p to promote antigen-specific Th17 cell responses and autoimmune inflammation
Authors: Chen Sisi , Wang Jiali , Zhang Kailang , Ma Binyun , Li Xiaorong , Wei Ruihua , Nian Hong 
Published: September 2023

AbstractLong non-coding RNAs (lncRNAs) interaction with RNA-Binding proteins (RBPs) plays an important role in immunological processes. The generation of antigen-specific Th17 cells is closely associated with autoimmune pathogenesis. However, the function of lncRNA-RBP interactions in the regulation of pathogenic Th17 cell responses during autoimmunity remains poorly understood. Here, we found that lncRNA Neat1, highly expressed in Th17 cells, promoted antigen-specific Th17 cell responses. Both global and CD4+ T cell-specific knockdown of Neat1 protected mice against the development of experimental autoimmune uveitis (EAU). Mechanistically, Neat1 regulated RNA-Binding protein NonO, thus relieving IL-17 and IL-23R from NonO-mediated transcriptional repression and supporting antigen-specific Th17 cell responses. In addition, Neat1 also modulated miR-128-3p/NFAT5 axis to increase the expression of IL-17 and IL-23R, leading to augmented Th17 cell responses. Our findings elucidate a previously unrecognized mechanistic insight into the action of Neat1 in promoting antigen-specific Th17 responses and autoimmunity, and may facilitate the development of therapeutic targets for T cell-mediated autoimmune diseases.
ATP7B R778L mutant hepatocytes resist copper toxicity by activating autophagy and inhibiting necroptosis
Authors: Tang Shan , Liang Chen , Hou Wei , Hu Zhongjie , Chen Xinyue , Zhao Jing , Zhang Wei , Duan Zhongping , Bai Li , Zheng Sujun 
Published: September 2023

AbstractWilson’s disease (WD) is an inherited disease characterized by copper metabolism disorder caused by mutations in the adenosine triphosphatase copper transporting β gene (ATP7B). Currently, WD cell and animal model targeting the most common R778L mutation in Asia is lacking. In addition, the mechanisms by which hepatocytes resist copper toxicity remain to be further elucidated. In this study, we aimed to construct a novel WD cell model with R778L mutation and dissected the molecular basics of copper resistance. A novel HepG2 cell line stably expressing the ATP7B R778L gene (R778L cell) was constructed. The expression of necroptosis- and autophagy-related molecules was detected by PCR and Western blot (WB) in wild-type (WT) HepG2 and R778L cells with or without CuSO4 treatment. In addition, we detected and compared the levels of autophagy and necroptosis in CuSO4-treated R778L cells with the activation and inhibition of autophagy. Moreover, the mRNA and protein levels of autophagy and necroptosis signaling molecules were compared in R778L cells with the overexpression and knockdown of Unc-51 Like Autophagy Activating Kinase 1 (ULK1) and Autophagy Related 16 Like 1 (ATG16L1). We successfully constructed an R778L mutation HepG2 cell line. CuSO4 triggered the enhanced expression of autophagy and necroptosis signaling molecules in WT HepG2 cells and R778L cells. Remarkably, higher levels of autophagy and necroptosis were observed in R778L cells compared with those in WT cells. Autophagy activation led to weakened necroptosis mediated by RIPK3 and MLKL, conversely, autophagy inhibition brought about enhanced necroptosis. At the molecular level, ULK1- and ATG16L1 overexpression resulted in reduced necroptosis levels and vice versa. ULK1- and ATG16L1-mediated autophagy activation protects hepatocytes against RIPK3- and MLKL-mediated necroptosis in our new WD cell model treated with CuSO4. Targeted therapy by autophagy activation or necroptosis inhibition may be a novel and effective strategy to treat WD.
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
Authors: Li Yang , Zhang Chengxin , Feng Chenjie , Pearce Robin , Lydia Freddolino P. , Zhang Yang 
Published: September 2023

AbstractRNAs are fundamental in living cells and perform critical functions determined by their tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem. We present a novel method, DRfold, to predict RNA tertiary structures by simultaneous learning of local frame rotations and geometric restraints from experimentally solved RNA structures, where the learned knowledge is converted into a hybrid energy potential to guide RNA structure assembly. The method significantly outperforms previous approaches by >73.3% in TM-score on a sequence-nonredundant dataset containing recently released structures. Detailed analyses showed that the major contribution to the improvements arise from the deep end-to-end learning supervised with the atom coordinates and the composite energy function integrating complementary information from geometry restraints and end-to-end learning models. The open-source DRfold program with fast training protocol allows large-scale application of high-resolution RNA structure modeling and can be further improved with future expansion of RNA structure databases.
Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Authors: Tran Khoa A. , Addala Venkateswar , Johnston Rebecca L. , Lovell David , Bradley Andrew , Koufariotis Lambros T. , Wood Scott , Wu Sunny Z. , Roden Daniel , Al-Eryani Ghamdan , Swarbrick Alexander , Williams Elizabeth D. , Pearson John V. , Kondrashova Olga , Waddell Nicola 
Published: September 2023

AbstractCells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumour purities and cell lineages, to compare the performance of nine TME deconvolution methods (BayesPrism, Scaden, CIBERSORTx, MuSiC, DWLS, hspe, CPM, Bisque, and EPIC).Some methods are more robust in deconvolving mixtures with high tumour purity levels. Most methods tend to mis-predict normal epithelial for cancer epithelial as tumour purity increases, a finding that is validated in two independent datasets. The breast cancer molecular subtype influences this mis-prediction. BayesPrism and DWLS have the lowest combined numbers of false positives and false negatives, and have the best performance when deconvolving granular immune lineages. Our findings highlight the need for more single-cell characterisation of rarer cell types, and suggest that tumour cell compositions should be considered when deconvolving the TME.
Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities
Authors: Lin Yu-Han , Xu Meng-Yun , Hsu Chuan-Chih , Damei Florensia Ariani , Lee Hui-Chun , Tsai Wei-Lun , Hoang Cuong V. , Chiang Yin-Ru , Ma Lay-Sun 
Published: September 2023

AbstractThe diversification of effector function, driven by a co-evolutionary arms race, enables pathogens to establish compatible interactions with hosts. Structurally conserved plant pathogenesis-related PR-1 and PR-1-like (PR-1L) proteins are involved in plant defense and fungal virulence, respectively. It is unclear how fungal PR-1L counters plant defense. Here, we show that Ustilago maydis UmPR-1La and yeast ScPRY1, with conserved phenolic resistance functions, are Ser/Thr-rich region mediated cell-surface localization proteins. However, UmPR-1La has gained specialized activity in sensing phenolics and eliciting hyphal-like formation to guide fungal growth in plants. Additionally, U. maydis hijacks maize cathepsin B-like 3 (CatB3) to release functional CAPE-like peptides by cleaving UmPR-1La’s conserved CNYD motif, subverting plant CAPE-primed immunity and promoting fungal virulence. Surprisingly, CatB3 avoids cleavage of plant PR-1s, despite the presence of the same conserved CNYD motif. Our work highlights that UmPR-1La has acquired additional dual roles to suppress plant defense and sustain the infection process of fungal pathogens.
Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice
Authors: Monsorno Katia , Ginggen Kyllian , Ivanov Andranik , Buckinx An , Lalive Arnaud L. , Tchenio Anna , Benson Sam , Vendrell Marc , D’Alessandro Angelo , Beule Dieter , Pellerin Luc , Mameli Manuel , Paolicelli Rosa Chiara 
Published: September 2023

AbstractMicroglia, the innate immune cells of the central nervous system, actively participate in brain development by supporting neuronal maturation and refining synaptic connections. These cells are emerging as highly metabolically flexible, able to oxidize different energetic substrates to meet their energy demand. Lactate is particularly abundant in the brain, but whether microglia use it as a metabolic fuel has been poorly explored. Here we show that microglia can import lactate, and this is coupled with increased lysosomal acidification. In vitro, loss of the monocarboxylate transporter MCT4 in microglia prevents lactate-induced lysosomal modulation and leads to defective cargo degradation. Microglial depletion of MCT4 in vivo leads to impaired synaptic pruning, associated with increased excitation in hippocampal neurons, enhanced AMPA/GABA ratio, vulnerability to seizures and anxiety-like phenotype. Overall, these findings show that selective disruption of the MCT4 transporter in microglia is sufficient to alter synapse refinement and to induce defects in mouse brain development and adult behavior.
A plant cytorhabdovirus modulates locomotor activity of insect vectors to enhance virus transmission
Authors: Gao Dong-Min , Qiao Ji-Hui , Gao Qiang , Zhang Jiawen , Zang Ying , Xie Liang , Zhang Yan , Wang Ying , Fu Jingyan , Zhang Hua , Han Chenggui , Wang Xian-Bing 
Published: September 2023

AbstractTransmission of many plant viruses relies on phloem-feeding insect vectors. However, how plant viruses directly modulate insect behavior is largely unknown. Barley yellow striate mosaic virus (BYSMV) is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus). Here, we show that BYSMV infects the central nervous system (CNS) of SBPHs, induces insect hyperactivity, and prolongs phloem feeding duration. The BYSMV accessory protein P6 interacts with the COP9 signalosome subunit 5 (LsCSN5) of SBPHs and suppresses LsCSN5-regulated de-neddylation from the Cullin 1 (CUL1), hereby inhibiting CUL1-based E3 ligases-mediated degradation of the circadian clock protein Timeless (TIM). Thus, virus infection or knockdown of LsCSN5 compromises TIM oscillation and induces high insect locomotor activity for transmission. Additionally, expression of BYSMV P6 in the CNS of transgenic Drosophila melanogaster disturbs circadian rhythm and induces high locomotor activity. Together, our results suggest the molecular mechanisms whereby BYSMV modulates locomotor activity of insect vectors for transmission.
Food inflation and child undernutrition in low and middle income countries
Authors: Headey Derek , Ruel Marie 
Published: September 2023

AbstractThe 21st Century has been marked by increased volatility in food prices, with global price spikes in 2007-08, 2010-11, and again in 2021-22. The impact of food inflation on the risk of child undernutrition is not well understood, however. This study explores the potential impacts of food inflation on wasting and stunting among 1.27 million pre-school children from 44 developing countries. On average, a 5 percent increase in the real price of food increases the risk of wasting by 9 percent and severe wasting by 14 percent. These risks apply to young infants, suggesting a prenatal pathway, as well as to older children who typically experience a deterioration in diet quality in the wake of food inflation. Male children and children from poor and rural landless households are more severely impacted. Food inflation during pregnancy and the first year after birth also increases the risk of stunting for children 2-5 years of age. This evidence provides a strong rationale for interventions to prevent food inflation and mitigate its impacts on vulnerable children and their mothers.
Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice
Authors: Deshpande Rajashree A. , Marin-Gonzalez Alberto , Barnes Hannah K. , Woolley Phillip R. , Ha Taekjip , Paull Tanya T. 
Published: September 2023

AbstractThe Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
Theoretical design of a space bioprocessing system to produce recombinant proteins
Authors: Soundararajan Mathangi , Paddock Matthew B. , Dougherty Michael , Jones Harry W. , Hogan John A. , Donovan Frances M. , Galazka Jonathan M. , Settles A. Mark 
Published: September 2023

AbstractSpace-based biomanufacturing has the potential to improve the sustainability of deep space exploration. To advance biomanufacturing, bioprocessing systems need to be developed for space applications. Here, commercial technologies were assessed to design space bioprocessing systems to supply a liquid amine carbon dioxide scrubber with active carbonic anhydrase produced recombinantly. Design workflows encompassed biomass dewatering of 1 L Escherichia coli cultures through to recombinant protein purification. Non-crew time equivalent system mass (ESM) analyses had limited utility for selecting specific technologies. Instead, bioprocessing system designs focused on minimizing complexity and enabling system versatility. Three designs that differed in biomass dewatering and protein purification approaches had nearly equivalent ESM of 357–522 kg eq. Values from the system complexity metric (SCM), technology readiness level (TRL), integration readiness level (IRL), and degree of crew assistance metric identified a simpler, less costly, and easier to operate design for automated biomass dewatering, cell lysis, and protein affinity purification.
Quantum networks with neutral atom processing nodes
Authors: Covey Jacob P. , Weinfurter Harald , Bernien Hannes 
Published: September 2023

AbstractQuantum networks providing shared entanglement over a mesh of quantum nodes will revolutionize the field of quantum information science by offering novel applications in quantum computation, enhanced precision in networks of sensors and clocks, and efficient quantum communication over large distances. Recent experimental progress with individual neutral atoms demonstrates a high potential for implementing the crucial components of such networks. We highlight latest developments and near-term prospects on how arrays of individually controlled neutral atoms are suited for both efficient remote entanglement generation and large-scale quantum information processing, thereby providing the necessary features for sharing high-fidelity and error-corrected multi-qubit entangled states between the nodes. We describe both the functionality requirements and several examples for advanced, large-scale quantum networks composed of neutral atom processing nodes.