bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulated cell death and inflammasome activation in gut injury following traumatic surgery in vitro and in vivo: implication for postoperative death due to multiorgan dysfunction
Authors: Wu Lingzhi , Zhao Hailin , Zhang Mengxu , Sun Qizhe , Chang Enqiang , Li Xinyi , Ouyang Wen , Le Yuan , Ma Daqing 
Published: November 2023

AbstractPostoperative multi-organ dysfunction (MOD) is associated with significant mortality and morbidity. Necroptosis has been implicated in different types of solid organ injury; however, the mechanisms linking necroptosis to inflammation require further elucidation. The present study examines the involvement of necroptosis and NLR family pyrin domain containing 3 (NLRP3) inflammasome in small intestine injury following traumatic surgery. Kidney transplantation in rats and renal ischaemia-reperfusion (I/R) in mice were used as traumatic and laparotomic surgery models to study necroptosis and inflammasome activation in the small intestinal post-surgery; additional groups also received receptor-interacting protein kinase 1 (RIPK1) inhibitor necrostatin-1s (Nec-1s). To investigate whether necroptosis regulates inflammasome activity in vitro, necroptosis was induced in human colonic epithelial cancer cells (Caco-2) by a combination of tumour necrosis factor-alpha (TNFα), SMAC mimetic LCL-161 and pan-caspase inhibitor Q-VD-Oph (together, TLQ), and necroptosis was blocked by Nec-1s or mixed lineage kinase-domain like (MLKL) inhibitor necrosulfonamide (NSA). Renal transplantation and renal ischaemia-reperfusion (I/R) upregulated the expression of necroptosis mediators (RIPK1; RIPK3; phosphorylated-MLKL) and inflammasome components (P2X purinoceptor subfamily 7, P2X7R; NLRP3; caspase-1) in the small intestines at 24 h, and Nec-1s suppressed the expression of inflammasome components. TLQ treatment induced NLRP3 inflammasome, promoted cleavage of caspase-1 and interleukin-1 beta (IL-1β), and stimulated extracellular ATP release from Caco-2 cells, and MLKL inhibitor NSA prevented TLQ-induced inflammasome activity and ATP release from Caco-2 cells. Our work suggested that necroptosis and inflammasome interactively promote remote postoperative small intestinal injury, at least in part, through ATP purinergic signalling. Necroptosis-inflammasome axis may be considered as novel therapeutic target for tackling postoperative MOD in the critical care settings.
Ecophysiological adaptations shape distributions of closely related trees along a climatic moisture gradient
Authors: Smith Duncan D. , Adams Mark A. , Salvi Amanda M. , Krieg Christopher P. , Ané Cécile , McCulloh Katherine A. , Givnish Thomas J. 
Published: November 2023

AbstractTradeoffs between the energetic benefits and costs of traits can shape species and trait distributions along environmental gradients. Here we test predictions based on such tradeoffs using survival, growth, and 50 photosynthetic, hydraulic, and allocational traits of tenEucalyptusspecies grown in four common gardens along an 8-fold gradient in precipitation/pan evaporation (P/Ep) in Victoria, Australia. Phylogenetically structured tests show that most trait-environment relationships accord qualitatively with theory. Most traits appear adaptive across species within gardens (indicating fixed genetic differences) and within species across gardens (indicating plasticity). However, species from moister climates have lower stomatal conductance than others grown under the same conditions. Responses in stomatal conductance and five related traits appear to reflect greater mesophyll photosynthetic sensitivity of mesic species to lower leaf water potential. Our data support adaptive cross-over, with realized height growth of most species exceeding that of others in climates they dominate. Our findings show that pervasive physiological, hydraulic, and allocational adaptations shape the distributions of dominantEucalyptusspecies along a subcontinental climatic moisture gradient, driven by rapid divergence in speciesP/Epand associated adaptations.
Near-surface magma flow instability drives cyclic lava fountaining at Fagradalsfjall, Iceland
Authors: Scott Samuel , Pfeffer Melissa , Oppenheimer Clive , Bali Enikö , Lamb Oliver D. , Barnie Talfan , Woods Andrew W. , Kjartansdóttir Rikey , Stefánsson Andri 
Published: November 2023

AbstractLava fountains are a common manifestation of basaltic volcanism. While magma degassing plays a clear key role in their generation, the controls on their duration and intermittency are only partially understood, not least due to the challenges of measuring the most abundant gases, H2O and CO2. The 2021 Fagradalsfjall eruption in Iceland included a six-week episode of uncommonly periodic lava fountaining, featuring ~ 100–400 m high fountains lasting a few minutes followed by repose intervals of comparable duration. Exceptional conditions on 5 May 2021 permitted close-range (~300 m), highly time-resolved (every ~ 2 s) spectroscopic measurement of emitted gases during 16 fountain-repose cycles. The observed proportions of major and minor gas molecular species (including H2O, CO2, SO2, HCl, HF and CO) reveal a stage of CO2 degassing in the upper crust during magma ascent, followed by further gas-liquid separation at very shallow depths (~100 m). We explain the pulsatory lava fountaining as the result of pressure cycles within a shallow magma-filled cavity. The degassing at Fagradalsfjall and our explanatory model throw light on the wide spectrum of terrestrial lava fountaining and the subsurface cavities associated with basaltic vents.
Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization
Authors: Dai Dadong , Xie Chuanshuai , Zhou Yayi , Bo Dexin , Zhang Shurong , Mao Shengqiang , Liao Yucheng , Cui Simeng , Zhu Zhaolu , Wang Xueyu , Li Fanling , Peng Donghai , Zheng Jinshui , Sun Ming 
Published: November 2023

AbstractThe formation and consequences of polyploidization in animals with clonal reproduction remain largely unknown. Clade I root-knot nematodes (RKNs), characterized by parthenogenesis and allopolyploidy, show a widespread geographical distribution and extensive agricultural destruction. Here, we generated 4 unzipped polyploid RKN genomes and identified a putative novel alternative telomeric element. Then we reconstructed 4 chromosome-level assemblies and resolved their genome structures as AAB for triploid and AABB for tetraploid. The phylogeny of subgenomes revealed polyploid RKN origin patterns as hybridization between haploid and unreduced gametes. We also observed extensive chromosomal fusions and homologous gene expression decrease after polyploidization, which might offset the disadvantages of clonal reproduction and increase fitness in polyploid RKNs. Our results reveal a rare pathway of polyploidization in parthenogenic polyploid animals and provide a large number of high-precision genetic resources that could be used for RKN prevention and control.
HOP1 and HAP2 are conserved components of the meiosis-related machinery required for successful mating in Leishmania
Authors: Catta-Preta Carolina Moura Costa , Ferreira Tiago Rodrigues , Ghosh Kashinath , Paun Andrea , Sacks David 
Published: November 2023

AbstractWhole genome analysis of Leishmania hybrids generated experimentally in sand flies supports a meiotic mechanism of genetic exchange, with Mendelian segregation of the nuclear genome. Here, we perform functional analyses through the generation of double drug-resistant hybrids in vitro and in vivo (during sand fly infections) to assess the importance of conserved meiosis-related genes in recombination and plasmogamy. We report that HOP1 and a HAP2-paralog (HAP2-2) are essential components of the Leishmania meiosis machinery and cell-to-cell fusion mechanism, respectively, since deletion of either gene in one or both parents significantly reduces or completely abrogates mating competence. These findings significantly advance our understanding of sexual reproduction in Leishmania, with likely relevance to other trypanosomatids, by formally demonstrating the involvement of a meiotic protein homolog and a distinct fusogen that mediates non-canonical, bilateral fusion in the hybridizing cells.
MePMe-seq: antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing
Authors: Hartstock Katja , Kueck Nadine A. , Spacek Petr , Ovcharenko Anna , Hüwel Sabine , Cornelissen Nicolas V. , Bollu Amarnath , Dieterich Christoph , Rentmeister Andrea 
Published: November 2023

AbstractInternal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2′-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans
Authors: Chmielewski David , Wilson Eric A. , Pintilie Grigore , Zhao Peng , Chen Muyuan , Schmid Michael F. , Simmons Graham , Wells Lance , Jin Jing , Singharoy Abhishek , Chiu Wah 
Published: November 2023

AbstractCoronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectrometry. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a role of hinge glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays implicated involvement of N1242-glyan in virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.
NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology
Authors: El Marrahi Anissa , Lipreri Fabio , Kang Ziqi , Gsell Louise , Eroglu Alper , Alber David , Hausser Jean 
Published: November 2023

AbstractAdvances in multiplex histology allow surveying millions of cells, dozens of cell types, and up to thousands of phenotypes within the spatial context of tissue sections. This leads to a combinatorial challenge in (a) summarizing the cellular and phenotypic architecture of tissues and (b) identifying phenotypes with interesting spatial architecture. To address this, we combine ideas from community ecology and machine learning into niche-phenotype mapping (NIPMAP). NIPMAP takes advantage of geometric constraints on local cellular composition imposed by the niche structure of tissues in order to automatically segment tissue sections into niches and their interfaces. Projecting phenotypes on niches and their interfaces identifies previously-reported and previously-unreported spatially-driven phenotypes, concisely summarizes the phenotypic architecture of tissues, and reveals fundamental properties of tissue architecture. NIPMAP is applicable to both protein and RNA multiplex histology of healthy and diseased tissue. An open-source R/Python package implements NIPMAP.
Single-cell analysis identifies genes facilitating rhizobium infection in Lotus japonicus
Authors: Frank Manuel , Fechete Lavinia Ioana , Tedeschi Francesca , Nadzieja Marcin , Nørgaard Malita Malou Malekzadeh , Montiel Jesus , Andersen Kasper Røjkjær , Schierup Mikkel H. , Reid Dugald , Andersen Stig Uggerhøj 
Published: November 2023

AbstractLegume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.
The asymmetric effects of climate risk on higher-moment connectedness among carbon, energy and metals markets
Authors: Zhou Yuqin , Wu Shan , Liu Zhenhua , Rognone Lavinia 
Published: November 2023

AbstractClimate change affects price fluctuations in the carbon, energy and metals markets through physical and transition risks. Climate physical risk is mainly caused by extreme weather, natural disasters and other events caused by climate change, whereas climate transition risk mainly results from the gradual switchover to a low-carbon economy. Given that the connectedness between financial markets may be affected by various factors such as extreme events and economic transformation, understanding the different roles of climate physical risk and transition risk on the higher-moment connectedness across markets has important implications for investors to construct portfolios and regulators to establish regulation system. Here, using the GJRSK model, time-frequency connectedness framework and quantile-on-quantile method, we show asymmetric effects of climate risk on connectedness among carbon, energy and metals markets, with higher impacts of climate physical risk on upward risk spillovers, and greater effects of climate transition risk on the downside risk of kurtosis connectedness.
Domain-dependent strain and stacking in two-dimensional van der Waals ferroelectrics
Authors: Shi Chuqiao , Mao Nannan , Zhang Kena , Zhang Tianyi , Chiu Ming-Hui , Ashen Kenna , Wang Bo , Tang Xiuyu , Guo Galio , Lei Shiming , Chen Longqing , Cao Ye , Qian Xiaofeng , Kong Jing , Han Yimo 
Published: November 2023

AbstractVan der Waals (vdW) ferroelectrics have attracted significant attention for their potential in next-generation nano-electronics. Two-dimensional (2D) group-IV monochalcogenides have emerged as a promising candidate due to their strong room temperature in-plane polarization down to a monolayer limit. However, their polarization is strongly coupled with the lattice strain and stacking orders, which impact their electronic properties. Here, we utilize four-dimensional scanning transmission electron microscopy (4D-STEM) to simultaneously probe the in-plane strain and out-of-plane stacking in vdW SnSe. Specifically, we observe large lattice strain up to 4% with a gradient across ~50 nm to compensate lattice mismatch at domain walls, mitigating defects initiation. Additionally, we discover the unusual ferroelectric-to-antiferroelectric domain walls stabilized by vdW force and may lead to anisotropic nonlinear optical responses. Our findings provide a comprehensive understanding of in-plane and out-of-plane structures affecting domain properties in vdW SnSe, laying the foundation for domain wall engineering in vdW ferroelectrics.
Selective plasticity of fast and slow excitatory synapses on somatostatin interneurons in adult visual cortex
Authors: Grier Bryce D. , Parkins Samuel , Omar Jarra , Lee Hey-Kyoung 
Published: November 2023

AbstractSomatostatin-positive (SOM) interneurons are integral for shaping cortical processing and their dynamic recruitment is likely necessary for adaptation to sensory experience and contextual information. We found that excitatory synapses on SOMs in layer 2/3 (L2/3) of primary visual cortex (V1) of mice can be categorized into fast (F)- and slow (S)-Types based on the kinetics of the AMPA receptor-mediated current. Each SOM contains both types of synapses in varying proportions. The majority of local pyramidal neurons (PCs) make unitary connections with SOMs using both types, followed by those utilizing only S-Type, and a minority with only F-Type. Sensory experience differentially regulates synapses on SOMs, such that local F-Type synapses change with visual deprivation and S-Type synapses undergo plasticity with crossmodal auditory deprivation. Our results demonstrate that the two types of excitatory synapses add richness to the SOM circuit recruitment and undergo selective plasticity enabling dynamic adaptation of the adult V1.
Rotational symmetry breaking in superconducting nickelate Nd0.8Sr0.2NiO2 films
Authors: Ji Haoran , Liu Yi , Li Yanan , Ding Xiang , Xie Zheyuan , Ji Chengcheng , Qi Shichao , Gao Xiaoyue , Xu Minghui , Gao Peng , Qiao Liang , Yang Yi-feng , Zhang Guang-Ming , Wang Jian 
Published: November 2023

AbstractThe infinite-layer nickelates, isostructural to the high-Tc cuprate superconductors, have emerged as a promising platform to host unconventional superconductivity and stimulated growing interest in the condensed matter community. Despite considerable attention, the superconducting pairing symmetry of the nickelate superconductors, the fundamental characteristic of a superconducting state, is still under debate. Moreover, the strong electronic correlation in the nickelates may give rise to a rich phase diagram, where the underlying interplay between the superconductivity and other emerging quantum states with broken symmetry is awaiting exploration. Here, we study the angular dependence of the transport properties of the infinite-layer nickelate Nd0.8Sr0.2NiO2 superconducting films with Corbino-disk configuration. The azimuthal angular dependence of the magnetoresistance (R(φ)) manifests the rotational symmetry breaking from isotropy to four-fold (C4) anisotropy with increasing magnetic field, revealing a symmetry-breaking phase transition. Approaching the low-temperature and large-magnetic-field regime, an additional two-fold (C2) symmetric component in the R(φ) curves and an anomalous upturn of the temperature-dependent critical field are observed simultaneously, suggesting the emergence of an exotic electronic phase. Our work uncovers the evolution of the quantum states with different rotational symmetries in nickelate superconductors and provides deep insight into their global phase diagram.
Spontaneous p53 activation in middle-aged C57BL/6 mice mitigates the lifespan-extending adaptive response induced by low-dose ionizing radiation
Authors: Kohzaki Masaoki , Suzuki Keiji , Ootsuyama Akira , Okazaki Ryuji 
Published: November 2023

AbstractUnderstanding the biological effects of low-dose (<100 mGy) ionizing radiation (LDR) is technically challenging. We investigated age-dependent LDR effects using adaptive response experiments in young (7-to 12-week-old) and middle-aged (40-to 62-week-old) C57BL/6 mice. Compared with 3 Gy irradiation, 0.02 Gy preirradiation followed by 3 Gy irradiation prolonged life in young mice but not middle-aged mice. Preirradiation also suppressed irradiation-induced 53BP1 repair foci in the small intestines, splenic apoptosis, and p53 activity in young mice but not middle-aged mice. Young p53+/− C57BL/6 mice did not show these adaptive responses, indicating that insufficient p53 function in young mice mitigated the adaptive responses. Interestingly, p53 activation in middle-aged mice spontaneously became approximately 4.5-fold greater than that in young mice, possibly masking LDR stresses. Furthermore, adaptive responses in young mice, but not in middle-aged mice, suppressed some senescence-associated secretory phenotype (SASP) factors (IL-6, CCL2, CCL5, CXCL1). Thus, LDR-induced adaptive responses associated with specific SASP factors may be attenuated by a combination of reduced DNA damage sensor/transducer function and chronic p53 activation in middle-aged mice.
Influence of psychopathology and metabolic parameters on quality of life in patients with first-episode psychosis before and after initial antipsychotic treatment
Authors: Dahl Anne Sofie A. , Sørensen Victor , Ambrosen Karen S. , Sørensen Mikkel E. , Mohr Grímur H. , Nielsen Mette Ø. , Bojesen Kirsten B. , Glenthøj Birte Y. , Hahn Margaret , Midtgaard Julie , Ebdrup Bjørn H. 
Published: November 2023

AbstractThe impact of psychological and physical health on quality of life (QoL) in patients with early psychosis remain relatively unexplored. We evaluated the predictive value of psychopathological and metabolic parameters on QoL in antipsychotic-naïve patients with first-episode psychosis before and after initial antipsychotic treatment. At baseline, 125 patients underwent assessments of psychopathology, prevalence of metabolic syndrome (MetS), and QoL. After 6 weeks of antipsychotic monotherapy, 89 patients were re-investigated. At baseline, the prevalence of MetS was 19.3% (n = 22). After 6 weeks, body weight (1.3 kg, p < 0.001) and body mass index (0.4 kg/m2, p < 0.001) increased, and four additional patients developed MetS. Multivariate linear regression revealed that positive and negative symptoms, and to some degree waist circumference, were predictors of QoL at both time points. Our findings suggest that in the earliest stages of antipsychotic treatment, metabolic side-effects may be less influential on QoL than psychopathological severity.
A uniform human multimodal dataset for emotion perception and judgment
Authors: Sun Sai , Cao Runnan , Rutishauser Ueli , Yu Rongjun , Wang Shuo 
Published: November 2023

AbstractFace perception is a fundamental aspect of human social interaction, yet most research on this topic has focused on single modalities and specific aspects of face perception. Here, we present a comprehensive multimodal dataset for examining facial emotion perception and judgment. This dataset includes EEG data from 97 unique neurotypical participants across 8 experiments, fMRI data from 19 neurotypical participants, single-neuron data from 16 neurosurgical patients (22 sessions), eye tracking data from 24 neurotypical participants, behavioral and eye tracking data from 18 participants with ASD and 15 matched controls, and behavioral data from 3 rare patients with focal bilateral amygdala lesions. Notably, participants from all modalities performed the same task. Overall, this multimodal dataset provides a comprehensive exploration of facial emotion perception, emphasizing the importance of integrating multiple modalities to gain a holistic understanding of this complex cognitive process. This dataset serves as a key missing link between human neuroimaging and neurophysiology literature, and facilitates the study of neuropsychiatric populations.