bluuebunny/crossref_metadata_2025_split huggingface dataset:
RIPK1-dependent necroptosis promotes vasculogenic mimicry formation via eIF4E in triple-negative breast cancer
Authors: Li Fan , Sun Huizhi , Yu Yihui , Che Na , Han Jiyuan , Cheng Runfen , Zhao Nan , Guo Yuhong , Huang Chongbiao , Zhang Danfang 
Published: May 2023

AbstractNecroptosis is a caspase-independent form of programmed cell death. Receptor interacting protein kinase 1 (RIPK1) is a key molecule in the initiation of necroptosis and the formation of the necrotic complex. Vasculogenic mimicry (VM) provides a blood supply to tumor cells that is not dependent on endothelial cells. However, the relationship between necroptosis and VM in triple-negative breast cancer (TNBC) is not fully understood. In this study, we found that RIPK1-dependent necroptosis promoted VM formation in TNBC. Knockdown of RIPK1 significantly suppressed the number of necroptotic cells and VM formation. Moreover, RIPK1 activated the p-AKT/eIF4E signaling pathway during necroptosis in TNBC. eIF4E was blocked by knockdown of RIPK1 or AKT inhibitors. Furthermore, we found that eIF4E promoted VM formation by promoting epithelial-mesenchymal transition (EMT) and the expression and activity of MMP2. In addition to its critical role in necroptosis-mediated VM, eIF4E was essential for VM formation. Knockdown of eIF4E significantly suppressed VM formation during necroptosis. Finally, through clinical significance, the results found that eIF4E expression in TNBC was positively correlated with the mesenchymal marker vimentin, the VM marker MMP2, and the necroptosis markers MLKL and AKT. In conclusion, RIPK1-dependent necroptosis promotes VM formation in TNBC. Necroptosis promotes VM formation by activating RIPK1/p-AKT/eIF4E signaling in TNBC. eIF4E promotes EMT and MMP2 expression and activity, leading to VM formation. Our study provides a rationale for necroptosis-mediated VM and also providing a potential therapeutic target for TNBC.
Development and validation of an online tool to assess perceived portion size norms of discretionary foods
Authors: Liu Qingzhou , Wang Leanne , Guo Siyi , Allman-Farinelli Margaret , Rangan Anna 
Published: May 2023

Abstract
Background
Perceived portion size norms (typical perception of how much of a given food individuals choose to eat at a single occasion) may have shifted towards larger sizes due to the ubiquity of large serving sizes. However, there is a lack of validated tools to assess such norms for energy-dense and nutrient-poor discretionary foods. This study aimed to develop and validate an online tool to examine the perceived portion size norms of discretionary foods.

Methods
An online image-series tool of 15 commonly consumed discretionary foods was developed, with eight successive portion size options included for each food. Using a randomised-crossover design, adult consumers (18–65 years) completed the validation study in a laboratory session (April-May 2022) by reporting their perceived portion size norms for each food twice, once based on food images on a computer and another time based on equivalent real food portion size options at food stations in the laboratory. Agreement between methods for each test food was examined using cross-classification and intra-class correlation (ICC).

Results
A sample of 114 subjects were recruited (mean age 24.8 years). Cross-classification indicated >90% of selections were matched in the same or adjacent portion size option. ICC was 0.85 across all foods, demonstrating a good level of agreement.

Conclusion
This novel online image-series tool developed to examine perceived portion size norms of discretionary foods showed good agreement with equivalent real food portion size options and may be valuable to investigate perceived portion size norms of common discretionary foods in future studies.
Wetting and complex remodeling of membranes by biomolecular condensates
Authors: Mangiarotti Agustín , Chen Nannan , Zhao Ziliang , Lipowsky Reinhard , Dimova Rumiana 
Published: May 2023

AbstractCells compartmentalize parts of their interiors into liquid-like condensates, which can be reconstituted in vitro. Although these condensates interact with membrane-bound organelles, their potential for membrane remodeling and the underlying mechanisms of such interactions are not well-understood. Here, we demonstrate that interactions between protein condensates - including hollow ones, and membranes can lead to remarkable morphological transformations and provide a theoretical framework to describe them. Modulation of solution salinity or membrane composition drives the condensate-membrane system through two wetting transitions, from dewetting, through a broad regime of partial wetting, to complete wetting. When sufficient membrane area is available, fingering or ruffling of the condensate-membrane interface is observed, an intriguing phenomenon producing intricately curved structures. The observed morphologies are governed by the interplay of adhesion, membrane elasticity, and interfacial tension. Our results highlight the relevance of wetting in cell biology, and pave the way for the design of synthetic membrane-droplet based biomaterials and compartments with tunable properties.
AMPK is a mechano-metabolic sensor linking cell adhesion and mitochondrial dynamics to Myosin-dependent cell migration
Authors: Crosas-Molist Eva , Graziani Vittoria , Maiques Oscar , Pandya Pahini , Monger Joanne , Samain Remi , George Samantha L. , Malik Saba , Salise Jerrine , Morales Valle , Le Guennec Adrien , Atkinson R. Andrew , Marti Rosa M. , Matias-Guiu Xavier , Charras Guillaume , Conte Maria R. , Elosegui-Artola Alberto , Holt Mark , Sanz-Moreno Victoria 
Published: May 2023

AbstractCell migration is crucial for cancer dissemination. We find that AMP-activated protein kinase (AMPK) controls cell migration by acting as an adhesion sensing molecular hub. In 3-dimensional matrices, fast-migrating amoeboid cancer cells exert low adhesion/low traction linked to low ATP/AMP, leading to AMPK activation. In turn, AMPK plays a dual role controlling mitochondrial dynamics and cytoskeletal remodelling. High AMPK activity in low adhering migratory cells, induces mitochondrial fission, resulting in lower oxidative phosphorylation and lower mitochondrial ATP. Concurrently, AMPK inactivates Myosin Phosphatase, increasing Myosin II-dependent amoeboid migration. Reducing adhesion or mitochondrial fusion or activating AMPK induces efficient rounded-amoeboid migration. AMPK inhibition suppresses metastatic potential of amoeboid cancer cells in vivo, while a mitochondrial/AMPK-driven switch is observed in regions of human tumours where amoeboid cells are disseminating. We unveil how mitochondrial dynamics control cell migration and suggest that AMPK is a mechano-metabolic sensor linking energetics and the cytoskeleton.
Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries
Authors: Cho Hunyong , Ren Zhi , Divaris Kimon , Roach Jeffrey , Lin Bridget M. , Liu Chuwen , Azcarate-Peril M. Andrea , Simancas-Pallares Miguel A. , Shrestha Poojan , Orlenko Alena , Ginnis Jeannie , North Kari E. , Zandona Andrea G. Ferreira , Ribeiro Apoena Aguiar , Wu Di , Koo Hyun 
Published: May 2023

AbstractStreptococcus mutanshas been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity ofSelenomonas sputigena, Prevotella salivaeandLeptotrichia wadei, either individually or withS. mutans. We show thatS. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulatingS. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability ofS. sputigenato colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected withS. mutans, S. sputigenacauses extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
Nonthermal acceleration of protein hydration by sub-terahertz irradiation
Authors: Sugiyama Jun-ichi , Tokunaga Yuji , Hishida Mafumi , Tanaka Masahito , Takeuchi Koh , Satoh Daisuke , Imashimizu Masahiko 
Published: May 2023

AbstractThe collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxation (DR) measurements to investigate how externally applied sub-THz electromagnetic fields perturb the rapid collective dynamics and influence the considerably slower chemical processes in protein–water systems. We analyzed an aqueous lysozyme solution, whose hydration is not thermally equilibrated. By detecting time-lapse differences in microwave DR, we demonstrated that sub-THz irradiation gradually decreases the dielectric permittivity of the lysozyme solution by reducing the orientational polarization of water molecules. Comprehensive analysis combining THz and nuclear magnetic resonance spectroscopies suggested that the gradual decrease in the dielectric permittivity is not induced by heating but is due to a slow shift toward the hydrophobic hydration structure in lysozyme. Our findings can be used to investigate hydration-mediated protein functions based on sub-THz irradiation.
Anion redox as a means to derive layered manganese oxychalcogenides with exotic intergrowth structures
Authors: Sasaki Shunsuke , Giri Souvik , Cassidy Simon J. , Dey Sunita , Batuk Maria , Vandemeulebroucke Daphne , Cibin Giannantonio , Smith Ronald I. , Holdship Philip , Grey Clare P. , Hadermann Joke , Clarke Simon J. 
Published: May 2023

AbstractTopochemistry enables step-by-step conversions of solid-state materials often leading to metastable structures that retain initial structural motifs. Recent advances in this field revealed many examples where relatively bulky anionic constituents were actively involved in redox reactions during (de)intercalation processes. Such reactions are often accompanied by anion-anion bond formation, which heralds possibilities to design novel structure types disparate from known precursors, in a controlled manner. Here we present the multistep conversion of layered oxychalcogenides Sr2MnO2Cu1.5Ch2 (Ch = S, Se) into Cu-deintercalated phases where antifluorite type [Cu1.5Ch2]2.5- slabs collapsed into two-dimensional arrays of chalcogen dimers. The collapse of the chalcogenide layers on deintercalation led to various stacking types of Sr2MnO2Ch2 slabs, which formed polychalcogenide structures unattainable by conventional high-temperature syntheses. Anion-redox topochemistry is demonstrated to be of interest not only for electrochemical applications but also as a means to design complex layered architectures.
An asymmetric electrolyte to simultaneously meet contradictory requirements of anode and cathode
Authors: Chen Shengmei , Ying Yiran , Ma Longtao , Zhu Daming , Huang Haitao , Song Li , Zhi Chunyi 
Published: May 2023

AbstractOne of the major obstacles hindering the application of zinc metal batteries is the contradictory demands from the Zn metal anode and cathodes. At the anode side, water induces serious corrosion and dendrite growth, remarkably suppressing the reversibility of Zn plating/stripping. At the cathode side, water is essential because many cathode materials require both H+ and Zn2+ insertion/extraction to achieve a high capacity and long lifespan. Herein, an asymmetric design of inorganic solid-state electrolyte combined with hydrogel electrolyte is presented to simultaneously meet the as-mentioned contrary requirements. The inorganic solid-state electrolyte is toward the Zn anode to realize a dendrite-free and corrosion-free highly reversible Zn plating/stripping, and the hydrogel electrolyte enables consequent H+ and Zn2+ insertion/extraction at the cathode side for high performance. Therefore, there is no hydrogen and dendrite growth detected in cells with a super high-areal-capacity up to 10 mAh·cm−2 (Zn//Zn), ~5.5 mAh·cm−2 (Zn//MnO2) and ~7.2 mAh·cm−2 (Zn//V2O5). These Zn//MnO2 and Zn//V2O5 batteries show remarkable cycling stability over 1000 cycles with 92.4% and over 400 cycles with 90.5% initial capacity retained, respectively.
Vaccinia E5 is a major inhibitor of the DNA sensor cGAS
Authors: Yang Ning , Wang Yi , Dai Peihong , Li Tuo , Zierhut Christian , Tan Adrian , Zhang Tuo , Xiang Jenny Zhaoying , Ordureau Alban , Funabiki Hironori , Chen Zhijian , Deng Liang 
Published: May 2023

AbstractThe DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is not well understood. In this study, we screened 80 vaccinia genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS. E5 is responsible for abolishing cGAMP production during vaccinia virus (Western Reserve strain) infection of dendritic cells. E5 localizes to the cytoplasm and nucleus of infected cells. Cytosolic E5 triggers ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, and thereby improves antigen-specific T cell responses.
Base editing-mediated one-step inactivation of the Dnmt gene family reveals critical roles of DNA methylation during mouse gastrulation
Authors: Li Qing , Lu Jiansen , Yin Xidi , Chang Yunjian , Wang Chao , Yan Meng , Feng Li , Cheng Yanbo , Gao Yun , Xu Beiying , Zhang Yao , Wang Yingyi , Cui Guizhong , Xu Luang , Sun Yidi , Zeng Rong , Li Yixue , Jing Naihe , Xu Guo-Liang , Wu Ligang , Tang Fuchou , Li Jinsong 
Published: May 2023

AbstractDuring embryo development, DNA methylation is established by DNMT3A/3B and subsequently maintained by DNMT1. While much research has been done in this field, the functional significance of DNA methylation in embryogenesis remains unknown. Here, we establish a system of simultaneous inactivation of multiple endogenous genes in zygotes through screening for base editors that can efficiently introduce a stop codon. Embryos with mutations in Dnmts and/or Tets can be generated in one step with IMGZ. Dnmt-null embryos display gastrulation failure at E7.5. Interestingly, although DNA methylation is absent, gastrulation-related pathways are down-regulated in Dnmt-null embryos. Moreover, DNMT1, DNMT3A, and DNMT3B are critical for gastrulation, and their functions are independent of TET proteins. Hypermethylation can be sustained by either DNMT1 or DNMT3A/3B at some promoters, which are related to the suppression of miRNAs. The introduction of a single mutant allele of six miRNAs and paternal IG-DMR partially restores primitive streak elongation in Dnmt-null embryos. Thus, our results unveil an epigenetic correlation between promoter methylation and suppression of miRNA expression for gastrulation and demonstrate that IMGZ can accelerate deciphering the functions of multiple genes in vivo.
Probing the atomically diffuse interfaces in Pd@Pt core-shell nanoparticles in three dimensions
Authors: Li Zezhou , Xie Zhiheng , Zhang Yao , Mu Xilong , Xie Jisheng , Yin Hai-Jing , Zhang Ya-Wen , Ophus Colin , Zhou Jihan 
Published: May 2023

AbstractDeciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We quantify the rich structural variety of core-shell nanoparticles with heteroepitaxy in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is found to be atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle’s morphology or crystallographic texture. The high concentration of Pd in the diffusive interface is highly related to the free Pd atoms dissolved from the Pd seeds, which is confirmed by atomic images of Pd and Pt single atoms and sub-nanometer clusters using cryogenic electron microscopy. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into precise nanomaterial manipulation and chemical property regulation.
Intramolecular charge transfer enables highly-efficient X-ray luminescence in cluster scintillators
Authors: Zhang Nan , Qu Lei , Dai Shuheng , Xie Guohua , Han Chunmiao , Zhang Jing , Huo Ran , Hu Huan , Chen Qiushui , Huang Wei , Xu Hui 
Published: May 2023

AbstractLuminescence clusters composed of organic ligands and metals have gained significant interests as scintillators owing to their great potential in high X-ray absorption, customizable radioluminescence, and solution processability at low temperatures. However, X-ray luminescence efficiency in clusters is primarily governed by the competition between radiative states from organic ligands and nonradiative cluster-centered charge transfer. Here we report that a class of Cu4I4 cubes exhibit highly emissive radioluminescence in response to X-ray irradiation through functionalizing biphosphine ligands with acridine. Mechanistic studies show that these clusters can efficiently absorb radiation ionization to generate electron-hole pairs and transfer them to ligands during thermalization for efficient radioluminescence through precise control over intramolecular charge transfer. Our experimental results indicate that copper/iodine-to-ligand and intraligand charge transfer states are predominant in radiative processes. We demonstrate that photoluminescence and electroluminescence quantum efficiencies of the clusters reach 95% and 25.6%, with the assistance of external triplet-to-singlet conversion by a thermally activated delayed fluorescence matrix. We further show the utility of the Cu4I4 scintillators in achieving a lowest X-ray detection limit of 77 nGy s−1 and a high X-ray imaging resolution of 12 line pairs per millimeter. Our study offers insights into universal luminescent mechanism and ligand engineering of cluster scintillators.
Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide
Authors: Li Xiaolong , Singh Nishant Kumar , Collins David R. , Ng Robert , Zhang Angela , Lamothe-Molina Pedro A. , Shahinian Peter , Xu Shutong , Tan Kemin , Piechocka-Trocha Alicja , Urbach Jonathan M. , Weber Jeffrey K. , Gaiha Gaurav D. , Takou Mbah Overbeck Christian , Huynh Tien , Cheever Sophia , Chen James , Birnbaum Michael , Zhou Ruhong , Walker Bruce D. , Wang Jia-huai 
Published: May 2023

AbstractCytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.
Semantic novelty modulates neural responses to visual change across the human brain
Authors: Nentwich Maximilian , Leszczynski Marcin , Russ Brian E. , Hirsch Lukas , Markowitz Noah , Sapru Kaustubh , Schroeder Charles E. , Mehta Ashesh D. , Bickel Stephan , Parra Lucas C. 
Published: May 2023

AbstractOur continuous visual experience in daily life is dominated by change. Previous research has focused on visual change due to stimulus motion, eye movements or unfolding events, but not their combined impact across the brain, or their interactions with semantic novelty. We investigate the neural responses to these sources of novelty during film viewing. We analyzed intracranial recordings in humans across 6328 electrodes from 23 individuals. Responses associated with saccades and film cuts were dominant across the entire brain. Film cuts at semantic event boundaries were particularly effective in the temporal and medial temporal lobe. Saccades to visual targets with high visual novelty were also associated with strong neural responses. Specific locations in higher-order association areas showed selectivity to either high or low-novelty saccades. We conclude that neural activity associated with film cuts and eye movements is widespread across the brain and is modulated by semantic novelty.
Spatially-optimized urban greening for reduction of population exposure to land surface temperature extremes
Authors: Massaro Emanuele , Schifanella Rossano , Piccardo Matteo , Caporaso Luca , Taubenböck Hannes , Cescatti Alessandro , Duveiller Gregory 
Published: May 2023

AbstractThe population experiencing high temperatures in cities is rising due to anthropogenic climate change, settlement expansion, and population growth. Yet, efficient tools to evaluate potential intervention strategies to reduce population exposure to Land Surface Temperature (LST) extremes are still lacking. Here, we implement a spatial regression model based on remote sensing data that is able to assess the population exposure to LST extremes in urban environments across 200 cities based on surface properties like vegetation cover and distance to water bodies. We define exposure as the number of days per year where LST exceeds a given threshold multiplied by the total urban population exposed, in person ⋅ day. Our findings reveal that urban vegetation plays a considerable role in decreasing the exposure of the urban population to LST extremes. We show that targeting high-exposure areas reduces vegetation needed for the same decrease in exposure compared to uniform treatment.