bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergent disorder and mechanical memory in periodic metamaterials
Authors: Sirote-Katz Chaviva , Shohat Dor , Merrigan Carl , Lahini Yoav , Nisoli Cristiano , Shokef Yair 
Published: May 2024

AbstractOrdered mechanical systems typically have one or only a few stable rest configurations, and hence are not considered useful for encoding memory. Multistable and history-dependent responses usually emerge from quenched disorder, for example in amorphous solids or crumpled sheets. In contrast, due to geometric frustration, periodic magnetic systems can create their own disorder and espouse an extensive manifold of quasi-degenerate configurations. Inspired by the topological structure of frustrated artificial spin ices, we introduce an approach to design ordered, periodic mechanical metamaterials that exhibit an extensive set of spatially disordered states. While our design exploits the correspondence between frustration in magnetism and incompatibility in meta-mechanics, our mechanical systems encompass continuous degrees of freedom, and thus generalize their magnetic counterparts. We show how such systems exhibit non-Abelian and history-dependent responses, as their state can depend on the order in which external manipulations were applied. We demonstrate how this richness of the dynamics enables to recognize, from a static measurement of the final state, the sequence of operations that an extended system underwent. Thus, multistability and potential to perform computation emerge from geometric frustration in ordered mechanical lattices that create their own disorder.
3D ocean assessments reveal that fisheries reach deep but marine protection remains shallow
Authors: Jacquemont Juliette , Loiseau Charles , Tornabene Luke , Claudet Joachim 
Published: May 2024

AbstractThe wave of new global conservation targets, the conclusion of the High Seas Treaty negotiations, and the expansion of extractive use into the deep sea call for a paradigm shift in ocean conservation. The current reductionist 2D representation of the ocean to set targets and measure impacts will fail at achieving effective biodiversity conservation. Here, we develop a framework that overlays depth realms onto marine ecoregions to conduct the first three-dimensional spatial analysis of global marine conservation achievements and fisheries footprint. Our novel approach reveals conservation gaps of mesophotic, rariphotic, and abyssal depths and an underrepresentation of high protection levels across all depths. In contrast, the 3D footprint of fisheries covers all depths, with benthic fishing occurring down to the lower bathyal and mesopelagic fishing peaking in areas overlying abyssal depths. Additionally, conservation efforts are biased towards areas where the lowest fishing pressures occur, compromising the effectiveness of the marine conservation network. These spatial mismatches emphasize the need to shift towards 3D thinking to achieve ocean sustainability.
Post-resolution macrophages shape long-term tissue immunity and integrity in a mouse model of pneumococcal pneumonia
Authors: Feehan Karen T. , Bridgewater Hannah E. , Stenkiewicz-Witeska Jan , De Maeyer Roel P. H. , Ferguson John , Mack Matthias , Brown Jeremy , Ercoli Giuseppe , Mawer Connar M. , Akbar Arne N. , Glanville James R. W. , Jalali Parinaaz , Bracken Olivia V. , Nicolaou Anna , Kendall Alexandra C. , Sugimoto Michelle A. , Gilroy Derek W. 
Published: May 2024

AbstractResolving inflammation is thought to return the affected tissue back to homoeostasis but recent evidence supports a non-linear model of resolution involving a phase of prolonged immune activity. Here we show that within days following resolution of Streptococcus pneumoniae-triggered lung inflammation, there is an influx of antigen specific lymphocytes with a memory and tissue-resident phenotype as well as macrophages bearing alveolar or interstitial phenotype. The transcriptome of these macrophages shows enrichment of genes associated with prostaglandin biosynthesis and genes that drive T cell chemotaxis and differentiation. Therapeutic depletion of post-resolution macrophages, inhibition of prostaglandin E2 (PGE2) synthesis or treatment with an EP4 antagonist, MF498, reduce numbers of lung CD4+/CD44+/CD62L+ and CD4+/CD44+/CD62L-/CD27+ T cells as well as their expression of the α-integrin, CD103. The T cells fail to reappear and reactivate upon secondary challenge for up to six weeks following primary infection. Concomitantly, EP4 antagonism through MF498 causes accumulation of lung macrophages and marked tissue fibrosis. Our study thus shows that PGE2 signalling, predominantly via EP4, plays an important role during the second wave of immune activity following resolution of inflammation. This secondary immune activation drives local tissue-resident T cell development while limiting tissue injury
Spatiotemporal brain hierarchies of auditory memory recognition and predictive coding
Authors: Bonetti L. , Fernández-Rubio G. , Carlomagno F. , Dietz M. , Pantazis D. , Vuust P. , Kringelbach M. L. 
Published: May 2024

AbstractOur brain is constantly extracting, predicting, and recognising key spatiotemporal features of the physical world in order to survive. While neural processing of visuospatial patterns has been extensively studied, the hierarchical brain mechanisms underlying conscious recognition of auditory sequences and the associated prediction errors remain elusive. Using magnetoencephalography (MEG), we describe the brain functioning of 83 participants during recognition of previously memorised musical sequences and systematic variations. The results show feedforward connections originating from auditory cortices, and extending to the hippocampus, anterior cingulate gyrus, and medial cingulate gyrus. Simultaneously, we observe backward connections operating in the opposite direction. Throughout the sequences, the hippocampus and cingulate gyrus maintain the same hierarchical level, except for the final tone, where the cingulate gyrus assumes the top position within the hierarchy. The evoked responses of memorised sequences and variations engage the same hierarchical brain network but systematically differ in terms of temporal dynamics, strength, and polarity. Furthermore, induced-response analysis shows that alpha and beta power is stronger for the variations, while gamma power is enhanced for the memorised sequences. This study expands on the predictive coding theory by providing quantitative evidence of hierarchical brain mechanisms during conscious memory and predictive processing of auditory sequences.
Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana
Authors: Huang Wen R. H. , Braam Ciska , Kretschmer Carola , Villanueva Sergio Landeo , Liu Huan , Ferik Filiz , van der Burgh Aranka M. , Boeren Sjef , Wu Jinbin , Zhang Lisha , Nürnberger Thorsten , Wang Yulu , Seidl Michael F. , Evangelisti Edouard , Stuttmann Johannes , Joosten Matthieu H. A. J. 
Published: May 2024

AbstractCell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, −7, and −8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.
Uncovering the spin ordering in magic-angle graphene via edge state equilibration
Authors: Hoke Jesse C. , Li Yifan , May-Mann Julian , Watanabe Kenji , Taniguchi Takashi , Bradlyn Barry , Hughes Taylor L. , Feldman Benjamin E. 
Published: May 2024

AbstractThe flat bands in magic-angle twisted bilayer graphene (MATBG) provide an especially rich arena to investigate interaction-driven ground states. While progress has been made in identifying the correlated insulators and their excitations at commensurate moiré filling factors, the spin-valley polarizations of the topological states that emerge at high magnetic field remain unknown. Here we introduce a technique based on twist-decoupled van der Waals layers that enables measurement of their electronic band structure and–by studying the backscattering between counter-propagating edge states–the determination of the relative spin polarization of their edge modes. We find that the symmetry-broken quantum Hall states that extend from the charge neutrality point in MATBG are spin unpolarized at even integer filling factors. The measurements also indicate that the correlated Chern insulator emerging from half filling of the flat valence band is spin unpolarized and suggest that its conduction band counterpart may be spin polarized.
Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci
Authors: Miliotis Christos , Ma Yuling , Katopodi Xanthi-Lida , Karagkouni Dimitra , Kanata Eleni , Mattioli Kaia , Kalavros Nikolas , Pita-Juárez Yered H. , Batalini Felipe , Ramnarine Varune R. , Nanda Shivani , Slack Frank J. , Vlachos Ioannis S. 
Published: May 2024

AbstractThe landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3′ untranslated region (3′-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3′-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3′-UTR eQTLs in immune-related genes. Our approach identifies numerous 3′-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.
Towards silent and efficient flight by combining bioinspired owl feather serrations with cicada wing geometry
Authors: Wei Zixiao , Wang Stanley , Farris Sean , Chennuri Naga , Wang Ningping , Shinsato Stara , Demir Kahraman , Horii Maya , Gu Grace X. 
Published: May 2024

AbstractAs natural predators, owls fly with astonishing stealth due to the serrated feather morphology that produces advantageous flow characteristics. Traditionally, these serrations are tailored for airfoil edges with simple two-dimensional patterns, limiting their effect on noise reduction while negotiating tradeoffs in aerodynamic performance. Conversely, the intricately structured wings of cicadas have evolved for effective flapping, presenting a potential blueprint for alleviating these aerodynamic limitations. In this study, we formulate a synergistic design strategy that harmonizes noise suppression with aerodynamic efficiency by integrating the geometrical attributes of owl feathers and cicada forewings, culminating in a three-dimensional sinusoidal serration propeller topology that facilitates both silent and efficient flight. Experimental results show that our design yields a reduction in overall sound pressure levels by up to 5.5 dB and an increase in propulsive efficiency by over 20% compared to the current industry benchmark. Computational fluid dynamics simulations validate the efficacy of the bioinspired design in augmenting surface vorticity and suppressing noise generation across various flow regimes. This topology can advance the multifunctionality of aerodynamic surfaces for the development of quieter and more energy-saving aerial vehicles.
Heavy-atom tunnelling in singlet oxygen deactivation predicted by instanton theory with branch-point singularities
Authors: Ansari Imaad M. , Heller Eric R. , Trenins George , Richardson Jeremy O. 
Published: May 2024

AbstractThe reactive singlet state of oxygen (O2) can decay to the triplet ground state nonradiatively in the presence of a solvent. There is a controversy about whether tunnelling is involved in this nonadiabatic spin-crossover process. Semiclassical instanton theory provides a reliable and practical computational method for elucidating the reaction mechanism and can account for nuclear quantum effects such as zero-point energy and multidimensional tunnelling. However, the previously developed instanton theory is not directly applicable to this system because of a branch-point singularity which appears in the flux correlation function. Here we derive a new instanton theory for cases dominated by the singularity, leading to a new picture of tunnelling in nonadiabatic processes. Together with multireference electronic-structure theory, this provides a rigorous framework based on first principles that we apply to calculate the decay rate of singlet oxygen in water. The results indicate a new reaction mechanism that is 27 orders of magnitude faster at room temperature than the classical process through the minimum-energy crossing point. We find significant heavy-atom tunnelling contributions as well as a large temperature-dependent H2O/D2O kinetic isotope effect of approximately 20, in excellent agreement with experiment.
Cell of origin epigenetic priming determines susceptibility to Tet2 mutation
Authors: Schiroli Giulia , Kartha Vinay , Duarte Fabiana M. , Kristiansen Trine A. , Mayerhofer Christina , Shrestha Rojesh , Earl Andrew , Hu Yan , Tay Tristan , Rhee Catherine , Buenrostro Jason D. , Scadden David T. 
Published: May 2024

AbstractHematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin’s epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
Human CD4-binding site antibody elicited by polyvalent DNA prime-protein boost vaccine neutralizes cross-clade tier-2-HIV strains
Authors: Wang Shixia , Chan Kun-Wei , Wei Danlan , Ma Xiuwen , Liu Shuying , Hu Guangnan , Park Saeyoung , Pan Ruimin , Gu Ying , Nazzari Alexandra F. , Olia Adam S. , Xu Kai , Lin Bob C. , Louder Mark K. , McKee Krisha , Doria-Rose Nicole A. , Montefiori David , Seaman Michael S. , Zhou Tongqing , Kwong Peter D. , Arthos James , Kong Xiang-Peng , Lu Shan 
Published: May 2024

AbstractThe vaccine elicitation of HIV tier-2-neutralization antibodies has been a challenge. Here, we report the isolation and characterization of a CD4-binding site (CD4bs) specific monoclonal antibody, HmAb64, from a human volunteer immunized with a polyvalent DNA prime-protein boost HIV vaccine. HmAb64 is derived from heavy chain variable germline gene IGHV1-18 and light chain germline gene IGKV1-39. It has a third heavy chain complementarity-determining region (CDR H3) of 15 amino acids. On a cross-clade panel of 208 HIV-1 pseudo-virus strains, HmAb64 neutralized 20 (10%), including tier-2 strains from clades B, BC, C, and G. The cryo-EM structure of the antigen-binding fragment of HmAb64 in complex with a CNE40 SOSIP trimer revealed details of its recognition; HmAb64 uses both heavy and light CDR3s to recognize the CD4-binding loop, a critical component of the CD4bs. This study demonstrates that a gp120-based vaccine can elicit antibodies capable of tier 2-HIV neutralization.
Superlative mechanical energy absorbing efficiency discovered through self-driving lab-human partnership
Authors: Snapp Kelsey L. , Verdier Benjamin , Gongora Aldair E. , Silverman Samuel , Adesiji Adedire D. , Morgan Elise F. , Lawton Timothy J. , Whiting Emily , Brown Keith A. 
Published: May 2024

AbstractEnergy absorbing efficiency is a key determinant of a structure’s ability to provide mechanical protection and is defined by the amount of energy that can be absorbed prior to stresses increasing to a level that damages the system to be protected. Here, we explore the energy absorbing efficiency of additively manufactured polymer structures by using a self-driving lab (SDL) to perform >25,000 physical experiments on generalized cylindrical shells. We use a human-SDL collaborative approach where experiments are selected from over trillions of candidates in an 11-dimensional parameter space using Bayesian optimization and then automatically performed while the human team monitors progress to periodically modify aspects of the system. The result of this human-SDL campaign is the discovery of a structure with a 75.2% energy absorbing efficiency and a library of experimental data that reveals transferable principles for designing tough structures.
Explainable chemical artificial intelligence from accurate machine learning of real-space chemical descriptors
Authors: Gallegos Miguel , Vassilev-Galindo Valentin , Poltavsky Igor , Martín Pendás Ángel , Tkatchenko Alexandre 
Published: May 2024

AbstractMachine-learned computational chemistry has led to a paradoxical situation in which molecular properties can be accurately predicted, but they are difficult to interpret. Explainable AI (XAI) tools can be used to analyze complex models, but they are highly dependent on the AI technique and the origin of the reference data. Alternatively, interpretable real-space tools can be employed directly, but they are often expensive to compute. To address this dilemma between explainability and accuracy, we developed SchNet4AIM, a SchNet-based architecture capable of dealing with local one-body (atomic) and two-body (interatomic) descriptors. The performance of SchNet4AIM is tested by predicting a wide collection of real-space quantities ranging from atomic charges and delocalization indices to pairwise interaction energies. The accuracy and speed of SchNet4AIM breaks the bottleneck that has prevented the use of real-space chemical descriptors in complex systems. We show that the group delocalization indices, arising from our physically rigorous atomistic predictions, provide reliable indicators of supramolecular binding events, thus contributing to the development of Explainable Chemical Artificial Intelligence (XCAI) models.
Priming with LSD1 inhibitors promotes the persistence and antitumor effect of adoptively transferred T cells
Authors: Qiu Fengqi , Jiang Peishan , Zhang Guiheng , An Jie , Ruan Kexin , Lyu Xiaowen , Zhou Jianya , Sheng Wanqiang 
Published: May 2024

AbstractThe antitumor efficacy of adoptively transferred T cells is limited by their poor persistence, in part due to exhaustion, but the underlying mechanisms and potential interventions remain underexplored. Here, we show that targeting histone demethylase LSD1 by chemical inhibitors reshapes the epigenome of in vitro activated and expanded CD8+ T cells, and potentiates their antitumor efficacy. Upon T cell receptor activation and IL-2 signaling, a timely and transient inhibition of LSD1 suffices to improve the memory phenotype of mouse CD8+ T cells, associated with a better ability to produce multiple cytokines, resist exhaustion, and persist in both antigen-dependent and -independent manners after adoptive transfer. Consequently, OT1 cells primed with LSD1 inhibitors demonstrate an enhanced antitumor effect in OVA-expressing solid tumor models implanted in female mice, both as a standalone treatment and in combination with PD-1 blockade. Moreover, priming with LSD1 inhibitors promotes polyfunctionality of human CD8+ T cells, and increases the persistence and antitumor efficacy of human CD19-CAR T cells in both leukemia and solid tumor models. Thus, pharmacological inhibition of LSD1 could be exploited to improve adoptive T cell therapy.
Parental experiences orchestrate locust egg hatching synchrony by regulating nuclear export of precursor miRNA
Authors: Zhu Ya′nan , He Jing , Wang Jiawen , Guo Wei , Liu Hongran , Song Zhuoran , Kang Le 
Published: May 2024

AbstractParental experiences can affect the phenotypic plasticity of offspring. In locusts, the population density that adults experience regulates the number and hatching synchrony of their eggs, contributing to locust outbreaks. However, the pathway of signal transmission from parents to offspring remains unclear. Here, we find that transcription factor Forkhead box protein N1 (FOXN1) responds to high population density and activates the polypyrimidine tract-binding protein 1 (Ptbp1) in locusts. FOXN1–PTBP1 serves as an upstream regulator of miR-276, a miRNA to control egg-hatching synchrony. PTBP1 boosts the nucleo-cytoplasmic transport of pre-miR-276 in a “CU motif”-dependent manner, by collaborating with the primary exportin protein exportin 5 (XPO5). Enhanced nuclear export of pre-miR-276 elevates miR-276 expression in terminal oocytes, where FOXN1 activates Ptbp1 and leads to egg-hatching synchrony in response to high population density. Additionally, PTBP1-prompted nuclear export of pre-miR-276 is conserved in insects, implying a ubiquitous mechanism to mediate transgenerational effects.
Pressure stabilizes ferrous iron in bridgmanite under hydrous deep lower mantle conditions
Authors: Zhang Li , Chen Yongjin , Yang Ziqiang , Liu Lu , Yang Yanping , Dalladay-Simpson Philip , Wang Junyue , Mao Ho-kwang 
Published: May 2024

AbstractEarth’s lower mantle is a potential water reservoir. The physical and chemical properties of the region are in part controlled by the Fe3+/ΣFe ratio and total iron content in bridgmanite. However, the water effect on the chemistry of bridgmanite remains unclear. We carry out laser-heated diamond anvil cell experiments under hydrous conditions and observe dominant Fe2+ in bridgmanite (Mg, Fe)SiO3 above 105 GPa under the normal geotherm conditions corresponding to depth > 2300 km, whereas Fe3+-rich bridgmanite is obtained at lower pressures. We further observe FeO in coexistence with hydrous NiAs-type SiO2 under similar conditions, indicating that the stability of ferrous iron is a combined result of H2O effect and high pressure. The stability of ferrous iron in bridgmanite under hydrous conditions would provide an explanation for the nature of the low-shear-velocity anomalies in the deep lower mantle. In addition, entrainment from a hydrous dense layer may influence mantle plume dynamics and contribute to variations in the redox conditions of the mantle.