bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lense–Thirring precession after a supermassive black hole disrupts a star
Authors: Pasham Dheeraj R. , Zajaček Michal , Nixon C. J. , Coughlin Eric R. , Śniegowska Marzena , Janiuk Agnieszka , Czerny Bożena , Wevers Thomas , Guolo Muryel , Ajay Yukta , Loewenstein Michael 
Published: May 2024

AbstractAn accretion disk formed around a supermassive black hole after it disrupts a star is expected to be initially misaligned with respect to the equatorial plane of the black hole. This misalignment induces relativistic torques (the Lense–Thirring effect) on the disk, causing the disk to precess at early times, whereas at late times the disk aligns with the black hole and precession terminates1,2. Here we report, using high-cadence X-ray monitoring observations of a tidal disruption event (TDE), the discovery of strong, quasi-periodic X-ray flux and temperature modulations. These X-ray modulations are separated by roughly 15 days and persist for about 130 days during the early phase of the TDE. Lense–Thirring precession of the accretion flow can produce this X-ray variability, but other physical mechanisms, such as the radiation-pressure instability3,4, cannot be ruled out. Assuming typical TDE parameters, that is, a solar-like star with the resulting disk extending at most to the so-called circularization radius, and that the disk precesses as a rigid body, we constrain the disrupting dimensionless spin parameter of the black hole to be 0.05 ≲ ∣a∣ ≲ 0.5.
Osmosensor-mediated control of Ca2+ spiking in pollen germination
Authors: Pei Songyu , Tao Qi , Li Wenke , Qi Guoning , Wang Borong , Wang Yan , Dai Shiwen , Shen Qiujing , Wang Xi , Wu Xiaomei , Xu Shijian , Theprungsirikul Lynn , Zhang Jingyuan , Liang Liang , Liu Yuantao , Chen Kena , Shen Yang , Crawford Bridget M. , Cheng Mengjia , Zhang Qi , Wang Yiqi , Liu Hongli , Yang Benguang , Krichilsky Bryan , Pei Jessica , Song Karen , Johnson Douglas M. , Jiang Zhonghao , Wu Feihua , Swift Gary B. , Yang Huanghe , Liu Zhonghua , Zou Xuexiao , Vo-Dinh Tuan , Liu Feng , Pei Zhen-Ming , Yuan Fang 
Published: May 2024

AbstractHigher plants survive terrestrial water deficiency and fluctuation by arresting cellular activities (dehydration) and resuscitating processes (rehydration). However, how plants monitor water availability during rehydration is unknown. Although increases in hypo-osmolarity-induced cytosolic Ca2+ concentration (HOSCA) have long been postulated to be the mechanism for sensing hypo-osmolarity in rehydration1,2, the molecular basis remains unknown. Because osmolarity triggers membrane tension and the osmosensing specificity of osmosensing channels can only be determined in vivo3–5, these channels have been classified as a subtype of mechanosensors. Here we identify bona fide cell surface hypo-osmosensors in Arabidopsis and find that pollen Ca2+ spiking is controlled directly by water through these hypo-osmosensors—that is, Ca2+ spiking is the second messenger for water status. We developed a functional expression screen in Escherichia coli for hypo-osmosensitive channels and identified OSCA2.1, a member of the hyperosmolarity-gated calcium-permeable channel (OSCA) family of proteins6. We screened single and high-order OSCA mutants, and observed that the osca2.1/osca2.2 double-knockout mutant was impaired in pollen germination and HOSCA. OSCA2.1 and OSCA2.2 function as hypo-osmosensitive Ca2+-permeable channels in planta and in HEK293 cells. Decreasing osmolarity of the medium enhanced pollen Ca2+ oscillations, which were mediated by OSCA2.1 and OSCA2.2 and required for germination. OSCA2.1 and OSCA2.2 convert extracellular water status into Ca2+ spiking in pollen and may serve as essential hypo-osmosensors for tracking rehydration in plants.
Mapping model units to visual neurons reveals population code for social behaviour
Authors: Cowley Benjamin R. , Calhoun Adam J. , Rangarajan Nivedita , Ireland Elise , Turner Maxwell H. , Pillow Jonathan W. , Murthy Mala 
Published: May 2024

AbstractThe rich variety of behaviours observed in animals arises through the interplay between sensory processing and motor control. To understand these sensorimotor transformations, it is useful to build models that predict not only neural responses to sensory input1–5 but also how each neuron causally contributes to behaviour6,7. Here we demonstrate a novel modelling approach to identify a one-to-one mapping between internal units in a deep neural network and real neurons by predicting the behavioural changes that arise from systematic perturbations of more than a dozen neuronal cell types. A key ingredient that we introduce is ‘knockout training’, which involves perturbing the network during training to match the perturbations of the real neurons during behavioural experiments. We apply this approach to model the sensorimotor transformations of Drosophila melanogaster males during a complex, visually guided social behaviour8–11. The visual projection neurons at the interface between the optic lobe and central brain form a set of discrete channels12, and prior work indicates that each channel encodes a specific visual feature to drive a particular behaviour13,14. Our model reaches a different conclusion: combinations of visual projection neurons, including those involved in non-social behaviours, drive male interactions with the female, forming a rich population code for behaviour. Overall, our framework consolidates behavioural effects elicited from various neural perturbations into a single, unified model, providing a map from stimulus to neuronal cell type to behaviour, and enabling future incorporation of wiring diagrams of the brain15 into the model.
Structural insights into the cross-exon to cross-intron spliceosome switch
Authors: Zhang Zhenwei , Kumar Vinay , Dybkov Olexandr , Will Cindy L. , Zhong Jiayun , Ludwig Sebastian E. J. , Urlaub Henning , Kastner Berthold , Stark Holger , Lührmann Reinhard 
Published: May 2024

AbstractEarly spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron1. Alternatively, it can occur through an exon-defined pathway2–5, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5′ splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex6,7. Exon definition promotes the splicing of upstream introns2,8,9 and plays a key part in alternative splicing regulation10–16. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5′ splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.
Acquisition of epithelial plasticity in human chronic liver disease
Authors: Gribben Christopher , Galanakis Vasileios , Calderwood Alexander , Williams Eleanor C. , Chazarra-Gil Ruben , Larraz Miguel , Frau Carla , Puengel Tobias , Guillot Adrien , Rouhani Foad J. , Mahbubani Krishnaa , Godfrey Edmund , Davies Susan E. , Athanasiadis Emmanouil , Saeb-Parsy Kourosh , Tacke Frank , Allison Michael , Mohorianu Irina , Vallier Ludovic 
Published: May 2024

AbstractFor many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1–4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K–AKT–mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.
Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq
Authors: Aguzzoli Heberle Bernardo , Brandon J. Anthony , Page Madeline L. , Nations Kayla A. , Dikobe Ketsile I. , White Brendan J. , Gordon Lacey A. , Fox Grant A. , Wadsworth Mark E. , Doyle Patricia H. , Williams Brittney A. , Fox Edward J. , Shantaraman Anantharaman , Ryten Mina , Goodwin Sara , Ghiban Elena , Wappel Robert , Mavruk-Eskipehlivan Senem , Miller Justin B. , Seyfried Nicholas T. , Nelson Peter T. , Fryer John D. , Ebbert Mark T. W. 
Published: May 2024

AbstractDetermining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson’s disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.
Endosymbionts of citrus leafminer Phyllocnistis citrella Stainton among different citrus orchards in China
Authors: Liu Hao-Qiang , Li Hong-Jun , Pan Qi , Xiang Yao-Zong 
Published: May 2024

AbstractEndosymbionts regulate the behavior of pest species, which could provide insights into their control. The citrus leafminer (Phyllocnistis citrella Stainton) is a widely distributed pest associated with diseases of citrus, especially of young trees. Here, we determined the endosymbiont composition of P. citrella in citrus orchards across China. The resulting dataset comprised average 50,430 high-quality reads for bacterial 16S rRNA V3-V4 regions of endosymbionts from 36 P. citrella larvae sampled from 12 citrus orchards across China. The sequencing depth and sampling size of this dataset were sufficient to reveal most of the endosymbionts of P. citrella. In total, 2,875 bacterial amplicon sequence variants were obtained; taxonomic analysis revealed a total of 372 bacterial genera, most of which were Proteobacteria phylum with Undibacterium being the most abundant genus. This dataset provides the first evidence of P. citrella endosymbionts that could support the development of pest management approaches in citrus orchards.
RUNX1-induced upregulation of PTGS2 enhances cell growth, migration and invasion in colorectal cancer cells
Authors: Zheng Weiwei , Guo Yingchang , Kahar Aihemaiti , Bai Junwei , Zhu Qinhui , Huang Xinli , Li Yuan , Xu Bingyi , Jia Xueshan , Wu Gang , Zhang Chao , Zhu Yuanzeng 
Published: May 2024

AbstractColorectal cancer (CRC) arises via the progressive accumulation of dysregulation in key genes including oncogenes and tumor-suppressor genes. Prostaglandin-endoperoxide synthase 2 (PTGS2, also called COX2) acts as an oncogenic driver in CRC. Here, we explored the upstream transcription factors (TFs) responsible for elevating PTGS2 expression in CRC cells. The results showed that PTGS2 silencing repressed cell growth, migration and invasion in HCT116 and SW480 CRC cells. The two fragments (499–981 bp) and (1053–1434 bp) were confirmed as the core TF binding profiles of the PTGS2 promoter. PTGS2 expression positively correlated with RUNX1 level in colon adenocarcinoma (COAD) samples using the TCGA-COAD dataset. Furthermore, RUNX1 acted as a positive regulator of PTGS2 expression by promoting transcriptional activation of the PTGS2 promoter via the 1086–1096 bp binding motif. In conclusion, our study demonstrates that PTGS2 upregulation induced by the TF RUNX1 promotes CRC cell growth, migration and invasion, providing an increased rationale for the use of PTGS2 inhibitors in CRC prevention and treatment.
Effect of partner presence on emotion regulation during parent–child interactions
Authors: Enav Yael , Knudtson Marguerite , Goldenberg Amit , Gross James J. 
Published: May 2024

AbstractHaving people around, especially if they provide social support, often leads to positive outcomes both physically and mentally. Mere social presence is especially beneficial when it comes from a loved one or romantic partner. In these studies, we aim to expand the understanding of how the presence of one’s romantic partner affects emotion regulation in parental situations. Specifically, we examined how partner presence influences the parent’s emotional intensity, emotion regulation, and interpretation of their child’s emotion regulation. We examined these questions in parents of both non-autistic children (Study 1) as well as autistic children (Study 2), which we hypothesize leads to more intense emotional interactions. The parents of autistic children were better able to regulate their emotions when their partners were present compared to when they were absent. Furthermore, in both studies, parents’ ratings of their children’s ability to regulate their emotions were higher when their parent’s partner was present compared to when the partner was absent. However, in both studies, we found no significant difference in the parents’ emotional intensity when their partners were present compared to when their partners were absent during the emotionally charged interaction with their child. Our findings help highlight the impact of partner presence on parent and child emotion regulation.
How different text display patterns affect cybersickness in augmented reality
Authors: Zhang Jianing , Che Xiaoping , Chang Enyao , Qu Chenxin , Di Xiaofei , Liu Haiming , Su Jingxin 
Published: May 2024

AbstractCybersickness remains a pivotal factor that impacts user experience in Augmented Reality (AR). Research probing into the relationship between AR reading tasks and cybersickness, particularly focusing on text display patterns and user characteristics, has been scant. Moreover, the influence of cybersickness on searching ability and the broader spectrum of user experience has not been rigorously tested. Recent investigations have aimed to pinpoint the variables that contribute to cybersickness during AR reading sessions. In one such study, 40 participants underwent a series of controlled experiments with randomized text display patterns, including variations in text speed and text movement modes. Post-experiment, participants completed a questionnaire that helped quantify their experiences and the degree of cybersickness encountered. The data highlighted that satiety, text speed, and text movement mode are significant contributors to cybersickness. When participants experienced higher levels of cybersickness, font color stood out as a particularly influential factor, whereas gender differences seemed to affect the onset of cybersickness more noticeably at lower levels. This study also drew attention to the impact of cybersickness on search ability within AR environments. It was noted that as cybersickness intensity increased, search ability was markedly compromised. In sum, the research underscores the importance of text display patterns and user characteristics, such as past AR experience, in understanding cybersickness and its detrimental effects on user experience and search ability, particularly under conditions of intense cybersickness.
Slope stability considering multi-fissure seepage under rainfall conditions
Authors: Jia Jianqing , Mao Chengxin , Tenorio Victor O. 
Published: May 2024

AbstractFissures form the channel for rainwater infiltration, which accelerate the infiltration of rainwater into slope bodies, hence its important impact on the seepage field and stability of the slope. In this paper, taking one landslide of Liang-Wan freeway as the research object, firstly, the equivalent permeability coefficient method is used to homogenize the fissured soil. Then considering the boundary conditions of rainfall infiltration and groundwater level, a fluid–structure coupling model is established based on saturated–unsaturated seepage theory, and evolution characteristics of seepage, displacement and stress of the slope are studied. Based on these, the slope stability coefficient is determined. The results show that the rising rate of pore water pressure and volume water content of topsoil increases when multi-fissure seepage is considered, and the pore water velocity is larger in the local seepage range of fissures. With the increase of buried depth, the closer to groundwater level, the influence of multi-fissure seepage gradually weakens. The theoretical calculation results of slope displacement are more consistent with the field monitoring results. With the increase of rainfall time, the stability coefficient of slope decreases gradually, and the rate and range of decrease are greater.
A new continental hydrogen play in Damara Belt (Namibia)
Authors: Roche V. , Geymond U. , Boka-Mene M. , Delcourt N. , Portier E. , Revillon S. , Moretti I. 
Published: May 2024

AbstractSerpentinization is commonly presented as the main source of natural hydrogen (H2) in the continental domains. However, recent works in Australia and Brazil showed that Archean–Paleoproterozoic banded iron formations could be another natural source of H2 gas. Although the reaction that produces hydrogen is similar (Fe2+ oxidation—H2O reduction process), the iron content may be higher in banded iron formations than in mafic igneous lithologies, potentially generating H2 more efficiently. Here, we present structural evidence that reported H2 emissions from Waterberg Basin, Namibia are associated with underlying Neoproterozoic banded iron formations—the Chuos Formation. Magnetite, a known H2-generating mineral, is ubiquitous and accompanied by other suspected H2-generating minerals (biotite and siderite) in Chuos Formation. Magnetite occurs either as pervasive cm to dm continuous metamorphic laminations in foliation and fractures planes and/or diffusely disseminated in metachert and metacarbonate levels. From this, we infer that metamorphism does not negatively affect the Fe2+ content that is required to generate hydrogen. H2 seepages in Waterberg Basin suggest that an active H2-generating system may exist at depth and that the presence of potential traps and reservoirs is likely based on field observations.
Wildfire smoke reduces lake ecosystem metabolic rates unequally across a trophic gradient
Authors: Smits Adrianne P. , Scordo Facundo , Tang Minmeng , Cortés Alicia , Farruggia Mary Jade , Culpepper Joshua , Chandra Sudeep , Jin Yufang , Valbuena Sergio A. , Watanabe Shohei , Schladow Geoffrey , Sadro Steven 
Published: May 2024

AbstractWildfire smoke covers entire continents, depositing aerosols and reducing solar radiation fluxes to millions of freshwater ecosystems, yet little is known about impacts on lakes. Here, we quantified trends in the spatial extent of smoke cover in California, USA, and assessed responses of gross primary production and ecosystem respiration to smoke in 10 lakes spanning a gradient in water clarity and nutrient concentrations. From 2006 − 2022, the maximum extent of medium or high-density smoke occurring between June-October increased by 300,000 km2. In the three smokiest years (2018, 2020, 2021), lakes experienced 23 − 45 medium or high-density smoke days, characterized by 20% lower shortwave radiation fluxes and five-fold higher atmospheric fine particulate matter concentrations. Ecosystem respiration generally declined during smoke cover, especially in low-nutrient, cold lakes, whereas responses of primary production were more variable. Lake attributes and seasonal timing of wildfires will mediate the effects of smoke on lakes.
The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate
Authors: Bhattacharjee Pushpak , Wang Die , Anderson Dovile , Buckler Joshua N , de Geus Eveline , Yan Feng , Polekhina Galina , Schittenhelm Ralf , Creek Darren J , Harris Lawrence D , Sadler Anthony J 
Published: May 2024

AbstractDuring infection viruses hijack host cell metabolism to promote their replication. Here, analysis of metabolite alterations in macrophages exposed to poly I:C recognises that the antiviral effector Protein Kinase RNA-activated (PKR) suppresses glucose breakdown within the pentose phosphate pathway (PPP). This pathway runs parallel to central glycolysis and is critical to producing NADPH and pentose precursors for nucleotides. Changes in metabolite levels between wild-type and PKR-ablated macrophages show that PKR controls the generation of ribose 5-phosphate, in a manner distinct from its established function in gene expression but dependent on its kinase activity. PKR phosphorylates and inhibits the Ribose 5-Phosphate Isomerase A (RPIA), thereby preventing interconversion of ribulose- to ribose 5-phosphate. This activity preserves redox control but decreases production of ribose 5-phosphate for nucleotide biosynthesis. Accordingly, the PKR-mediated immune response to RNA suppresses nucleic acid production. In line, pharmacological targeting of the PPP during infection decreases the replication of the Herpes simplex virus. These results identify an immune response-mediated control of host cell metabolism and suggest targeting the RPIA as a potential innovative antiviral treatment.
Yttria-stabilized zirconia (8YSZ) synthesis in a supercritical CO2-assisted process: a parametric study for achieving cubic phase stability
Authors: Avédikian Loan , Vulliet Julien , David Thomas , Hertz Audrey 
Published: May 2024

Supercritical CO2 solvent enables the synthesis of crystallized oxide particles with high specific surfaces. A route was developed to generate nano-structured YSZ powders which may be suitable for porous SOC electrodes or dense electrolytes.