bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single cell transcriptome analysis of the THY-Tau22 mouse model of Alzheimer’s disease reveals sex-dependent dysregulations
Authors: Ali Muhammad , Garcia Pierre , Lunkes Laetitia P. , Sciortino Alessia , Thomas Melanie , Heurtaux Tony , Grzyb Kamil , Halder Rashi , Coowar Djalil , Skupin Alex , Buée Luc , Blum David , Buttini Manuel , Glaab Enrico 
Published: March 2024

AbstractAlzheimer’s disease (AD) progression and pathology show pronounced sex differences, but the factors driving these remain poorly understood. To gain insights into early AD-associated molecular changes and their sex dependency for tau pathology in the cortex, we performed single-cell RNA-seq in the THY-Tau22 AD mouse model. By examining cell type-specific and cell type-agnostic AD-related gene activity changes and their sex-dimorphism for individual genes, pathways and cellular sub-networks, we identified both statistically significant alterations and interpreted the upstream mechanisms controlling them. Our results confirm several significant sex-dependent alterations in gene activity in the THY-Tau22 model mice compared to controls, with more pronounced alterations in females. Both changes shared across multiple cell types and cell type-specific changes were observed. The differential genes showed significant over-representation of known AD-relevant processes, such as pathways associated with neuronal differentiation, programmed cell death and inflammatory responses. Regulatory network analysis of these genes revealed upstream regulators that modulate many of the downstream targets with sex-dependent changes. Most key regulators have been previously implicated in AD, such asEgr1,Klf4,Chchd2, complement system genes, and myelin-associated glycoproteins. Comparing with similar data from the Tg2576 AD mouse model and human AD patients, we identified multiple genes with consistent, cell type-specific and sex-dependent alterations across all three datasets. These shared changes were particularly evident in the expression of myelin-associated genes such asMbpandPlp1in oligodendrocytes. In summary, we observed significant cell type-specific transcriptomic changes in the THY-Tau22 mouse model, with a strong over-representation of known AD-associated genes and processes. These include both sex-neutral and sex-specific patterns, characterized by consistent shifts in upstream master regulators and downstream target genes. Collectively, these findings provide insights into mechanisms influencing sex-specific susceptibility to AD and reveal key regulatory proteins that could be targeted for developing treatments addressing sex-dependent AD pathology.
Social buffering in rats reduces fear by oxytocin triggering sustained changes in central amygdala neuronal activity
Authors: Hegoburu Chloe , Tang Yan , Niu Ruifang , Ghosh Supriya , Triana Del Rio Rodrigo , de Araujo Salgado Isabel , Abatis Marios , Alexandre Mota Caseiro David , van den Burg Erwin H. , Grundschober Christophe , Stoop Ron 
Published: March 2024

AbstractThe presence of a companion can reduce fear, but the neural mechanisms underlying this social buffering of fear are incompletely known. We studied social buffering of fear in male and female, and its encoding in the amygdala of male, auditory fear-conditioned rats. Pharmacological, opto,- and/or chemogenetic interventions showed that oxytocin signaling from hypothalamus-to-central amygdala projections underlied fear reduction acutely with a companion and social buffering retention 24 h later without a companion. Single-unit recordings with optetrodes in the central amygdala revealed fear-encoding neurons (showing increased conditioned stimulus-responses after fear conditioning) inhibited by social buffering and blue light-stimulated oxytocinergic hypothalamic projections. Other central amygdala neurons showed baseline activity enhanced by blue light and companion exposure, with increased conditioned stimulus responses that persisted without the companion. Social buffering of fear thus switches the conditioned stimulus from encoding “fear” to “safety” by oxytocin-mediated recruitment of a distinct group of central amygdala “buffer neurons”.
The North Equatorial Current and rapid intensification of super typhoons
Authors: Kang Sok Kuh , Kim Sung-Hun , Lin I.-I. , Park Young-Hyang , Choi Yumi , Ginis Isaac , Cione Joseph , Shin Ji Yun , Kim Eun Jin , Kim Kyeong Ok , Kang Hyoun Woo , Park Jae-Hyoung , Bidlot Jean-Raymond , Ward Brian 
Published: March 2024

AbstractSuper Typhoon Mangkhut, which traversed the North Equatorial Current (NEC; 8–17 °N) in the western North Pacific in 2018, was the most intense Category-5 tropical cyclone (TC) with the longest duration in history—3.5 days. Here we show that the combination of two factors—high ocean heat content (OHC) and increased stratification — makes the NEC region the most favored area for a rapid intensification (RI) of super typhoons, instead of the Eddy Rich Zone (17–25 °N), which was considered the most relevant for RI occurrence. The high OHC results from a northward deepening thermocline in geostrophic balance with the westward-flowing NEC. The stratification is derived from precipitation associated with the Inter-Tropical Convergence Zone in the summer peak typhoon season. These factors, which are increasingly significant over the past four decades, impede the TC-induced sea surface cooling, thus enhancing RI of TCs and simultaneously maintaining super typhoons over the NEC region.
Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons
Authors: del Blanco Beatriz , Niñerola Sergio , Martín-González Ana M. , Paraíso-Luna Juan , Kim Minji , Muñoz-Viana Rafael , Racovac Carina , Sanchez-Mut Jose V. , Ruan Yijun , Barco Ángel 
Published: March 2024

AbstractKdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a’s function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements
Authors: Hayashi Naoki , Lai Yong , Fuerte-Stone Jay , Mimee Mark , Lu Timothy K. 
Published: March 2024

AbstractSophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.
Circulation of hydraulically ponded turbidity currents and the filling of continental slope minibasins
Authors: Reece J. Kevin , Dorrell Robert M. , Straub Kyle M. 
Published: March 2024

AbstractNatural depressions on continental margins termed minibasins trap turbidity currents, a class of sediment-laden seafloor density driven flow. These currents are the primary downslope vectors for clastic sediment, particulate organic carbon, and microplastics. Here, we establish a method that facilitates long-distance self-suspension of dilute sediment-laden flows, enabling study of turbidity currents with appropriately scaled natural topography. We show that flow dynamics in three-dimensional minibasins are dominated by circulation cell structures. While fluid rotation is mainly along a horizontal plane, inwards spiraling flow results in strong upwelling jets that reduce the ability of minibasins to trap particulate organic carbon, microplastics, and fine-grained clastic sediment. Circulation cells are the prime mechanism for distributing particulates in minibasins and set the geometry of deposits, which are often intricate and below the resolution of geophysical surveys. Fluid and sediment are delivered to circulation cells by turbidity currents that runup the distal wall of minibasins. The magnitude of runup increases with the discharge rate of currents entering minibasins, which influences the amount of sediment that is either trapped in minibasins or spills to downslope environs and determines the height that deposits onlap against minibasin walls.
Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes
Authors: Palani Sowmiya , Machida Yuka , Alvey Julia R. , Mishra Vandana , Welter Allison L. , Cui Gaofeng , Bragantini Benoît , Botuyan Maria Victoria , Cong Anh T. Q. , Mer Georges , Schellenberg Matthew J. , Machida Yuichi J. 
Published: March 2024

Abstract
FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme’s biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A’s function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
Tri-system integration in metal-oxide nanocomposites via in-situ solution-processed method for ultrathin flexible transparent electrodes
Authors: Kim John Jinwook , Shuji Kojima , Zheng Jiawei , He Xinjun , Sajjad Ahmad , Zhang Hong , Su Haibin , Choy Wallace C. H. 
Published: March 2024

AbstractFor stable operation of ultrathin flexible transparent electrodes (uFTEs), it is critical to implement effective risk management during concurrent multi-loading operation of electrical bias and mechanical folding cycles in high-humidity environments. Despite extensive efforts in preparing solution-processed uFTEs with cost-effective and high-throughput means, achieving in-situ nano-adhesion in heterogeneous metal-oxide nanocomposites remains challenging. In this work, we observed by serendipity liquid-like behaviour of transparent metal-oxide-semiconductor zinc oxide nanoparticles (ZnONPs) onto silver nanowires (AgNWs) developed by in-situ solution processed method (iSPM). This enabled us to address the long-standing issue of vulnerability in the nanocomposite caused by the interface of dissimilar materials between AgNWs and ZnONPs, resulting in a remarkably improved multi-loading operation. Importantly, substrate-integrated uFTEs constituted of the metal-oxide nanocomposite electrode semi-embedded in the polymer matrix of greatly thin <0.5 μm thickness is successfully demonstrated with the smooth surface topography, promoted by the tri-system integration including (i) AgNW-AgNW, (ii) ZnONP-ZnONP, and (iii) AgNW-ZnONP systems. Our finding unveils the complex interfacial dynamics associated with the heterogeneous interface system between AgNWs and ZnONPs and holds great promise in understanding the in-situ nano-adhesion process and increasing the design flexibility of next generation solution-processed uFTEs.
Room temperature chirality switching and detection in a helimagnetic MnAu2 thin film
Authors: Masuda Hidetoshi , Seki Takeshi , Ohe Jun-ichiro , Nii Yoichi , Masuda Hiroto , Takanashi Koki , Onose Yoshinori 
Published: March 2024

AbstractHelimagnetic structures, in which the magnetic moments are spirally ordered, host an internal degree of freedom called chirality corresponding to the handedness of the helix. The chirality seems quite robust against disturbances and is therefore promising for next-generation magnetic memory. While the chirality control was recently achieved by the magnetic field sweep with the application of an electric current at low temperature in a conducting helimagnet, problems such as low working temperature and cumbersome control and detection methods have to be solved in practical applications. Here we show chirality switching by electric current pulses at room temperature in a thin-film MnAu2 helimagnetic conductor. Moreover, we have succeeded in detecting the chirality at zero magnetic fields by means of simple transverse resistance measurement utilizing the spin Berry phase in a bilayer device composed of MnAu2 and a spin Hall material Pt. These results may pave the way to helimagnet-based spintronics.
Canonical and non-canonical integrin-based adhesions dynamically interconvert
Authors: Lukas Fabian , Matthaeus Claudia , López-Hernández Tania , Lahmann Ines , Schultz Nicole , Lehmann Martin , Puchkov Dmytro , Pielage Jan , Haucke Volker , Maritzen Tanja 
Published: March 2024

AbstractAdhesions are critical for anchoring cells in their environment, as signaling platforms and for cell migration. In line with these diverse functions different types of cell-matrix adhesions have been described. Best-studied are the canonical integrin-based focal adhesions. In addition, non-canonical integrin adhesions lacking focal adhesion proteins have been discovered. These include reticular adhesions also known as clathrin plaques or flat clathrin lattices, that are enriched in clathrin and other endocytic proteins, as well as extensive adhesion networks and retraction fibers. How these different adhesion types that share a common integrin backbone are related and whether they can interconvert is unknown. Here, we identify the protein stonin1 as a marker for non-canonical αVβ5 integrin-based adhesions and demonstrate by live cell imaging that canonical and non-canonical adhesions can reciprocally interconvert by the selective exchange of components on a stable αVβ5 integrin scaffold. Hence, non-canonical adhesions can serve as points of origin for the generation of canonical focal adhesions.
Neuromorphic antennal sensory system
Authors: Jiang Chengpeng , Xu Honghuan , Yang Lu , Liu Jiaqi , Li Yue , Takei Kuniharu , Xu Wentao 
Published: March 2024

AbstractInsect antennae facilitate the nuanced detection of vibrations and deflections, and the non-contact perception of magnetic or chemical stimuli, capabilities not found in mammalian skin. Here, we report a neuromorphic antennal sensory system that emulates the structural, functional, and neuronal characteristics of ant antennae. Our system comprises electronic antennae sensor with three-dimensional flexible structures that detects tactile and magnetic stimuli. The integration of artificial synaptic devices adsorbed with solution-processable MoS2 nanoflakes enables synaptic processing of sensory information. By emulating the architecture of receptor-neuron pathway, our system realizes hardware-level, spatiotemporal perception of tactile contact, surface pattern, and magnetic field (detection limits: 1.3 mN, 50 μm, 9.4 mT). Vibrotactile-perception tasks involving profile and texture classifications were accomplished with high accuracy (> 90%), surpassing human performance in “blind” tactile explorations. Magneto-perception tasks including magnetic navigation and touchless interaction were successfully completed. Our work represents a milestone for neuromorphic sensory systems and biomimetic perceptual intelligence.
A root cap-localized NAC transcription factor controls root halotropic response to salt stress in Arabidopsis
Authors: Zheng Lulu , Hu Yongfeng , Yang Tianzhao , Wang Zhen , Wang Daoyuan , Jia Letian , Xie Yuanming , Luo Long , Qi Weicong , Lv Yuanda , Beeckman Tom , Xuan Wei , Han Yi 
Published: March 2024

AbstractPlants are capable of altering root growth direction to curtail exposure to a saline environment (termed halotropism). The root cap that surrounds root tip meristematic stem cells plays crucial roles in perceiving and responding to environmental stimuli. However, how the root cap mediates root halotropism remains undetermined. Here, we identified a root cap-localized NAC transcription factor, SOMBRERO (SMB), that is required for root halotropism. Its effect on root halotropism is attributable to the establishment of asymmetric auxin distribution in the lateral root cap (LRC) rather than to the alteration of cellular sodium equilibrium or amyloplast statoliths. Furthermore, SMB is essential for basal expression of the auxin influx carrier gene AUX1 in LRC and for auxin redistribution in a spatiotemporally-regulated manner, thereby leading to directional bending of roots away from higher salinity. Our findings uncover an SMB-AUX1-auxin module linking the role of the root cap to the activation of root halotropism.
Interrogating site dependent kinetics over SiO2-supported Pt nanoparticles
Authors: Kim Taek-Seung , O’Connor Christopher R. , Reece Christian 
Published: March 2024

AbstractA detailed knowledge of reaction kinetics is key to the development of new more efficient heterogeneous catalytic processes. However, the ability to resolve site dependent kinetics has been largely limited to surface science experiments on model systems. Herein, we can bypass the pressure, materials, and temperature gaps, resolving and quantifying two distinct pathways for CO oxidation over SiO2-supported 2 nm Pt nanoparticles using transient pressure pulse experiments. We find that the pathway distribution directly correlates with the distribution of well-coordinated (e.g., terrace) and under-coordinated (e.g., edge, vertex) CO adsorption sites on the 2 nm Pt nanoparticles as measured by in situ DRIFTS. We conclude that well-coordinated sites follow classic Langmuir-Hinshelwood kinetics, but under-coordinated sites follow non-standard kinetics with CO oxidation being barrierless but conversely also slow. This fundamental method of kinetic site deconvolution is broadly applicable to other catalytic systems, affording bridging of the complexity gap in heterogeneous catalysis.
Surface hydrophobization of zeolite enables mass transfer matching in gas-liquid-solid three-phase hydrogenation under ambient pressure
Authors: Wang Shuai , Hu Riming , Ren Jianyu , Lv Yipin , Song Lianghao , Zhao Huaiqing , Jiang Xuchuan , Gao Daowei , Chen Guozhu 
Published: March 2024

AbstractAttaining high hydrogenation performance under mild conditions, especially at ambient pressure, remains a considerable challenge due to the difficulty in achieving efficient mass transfer at the gas-liquid-solid three-phase interface. Here, we present a zeolite nanoreactor with joint gas-solid-liquid interfaces for boosting H2 gas and substrates to involve reactions. Specifically, the Pt active sites are encapsulated within zeolite crystals, followed by modifying the external zeolite surface with organosilanes. The silane sheath with aerophilic/hydrophobic properties can promote the diffusion of H2 and the mass transfer of reactant/product molecules. In aqueous solutions, the gaseous H2 molecules can rapidly diffuse into the zeolite channels, thereby augmenting H2 concentration surround Pt sites. Simultaneously, the silane sheath with lipophilicity nature promotes the enrichment of the aldehydes/ketones on the catalyst and facilitates the hydrophilia products of alcohol rediffusion back to the aqueous phase. By modifying the wettability of the catalyst, the hydrogenation of aldehydes/ketones can be operated in water at ambient H2 pressure, resulting in a noteworthy turnover frequency up to 92.3 h−1 and a 4.3-fold increase in reaction rate compared to the unmodified catalyst.
A self-regulatory cell-wall-sensing module at cell edges controls plant growth
Authors: Elliott Liam , Kalde Monika , Schürholz Ann-Kathrin , Zhang Xinyu , Wolf Sebastian , Moore Ian , Kirchhelle Charlotte 
Published: March 2024

AbstractMorphogenesis of multicellular organs requires coordination of cellular growth. In plants, cell growth is determined by turgor pressure and the mechanical properties of the cell wall, which also glues cells together. Because plants have to integrate tissue-scale mechanical stresses arising through growth in a fixed tissue topology, they need to monitor cell wall mechanical status and adapt growth accordingly. Molecular factors have been identified, but whether cell geometry contributes to wall sensing is unknown. Here we propose that plant cell edges act as cell-wall-sensing domains during growth. We describe two Receptor-Like Proteins, RLP4 and RLP4-L1, which occupy a unique polarity domain at cell edges established through a targeted secretory transport pathway. We show that RLP4s associate with the cell wall at edges via their extracellular domain, respond to changes in cell wall mechanics and contribute to directional growth control in Arabidopsis.
Ultra-sensitive, highly linear, and hysteresis-free strain sensors enabled by gradient stiffness sliding strategy
Authors: Xue Fuhua , Peng Qingyu , Ding Renjie , Li Pengyang , Zhao Xu , Zheng Haowen , Xu Liangliang , Tang Zhigong , Zhang Xinxing , He Xiaodong 
Published: March 2024

AbstractDeveloping strain sensors with both high sensitivity and high linearity has always been the goal of researchers. Compared to resistive strain sensors, capacitive strain sensors have incomparable linearity advantages, but have always been limited by low sensitivity. Here, we report a gradient stiffness sliding design strategy that addresses this problem, significantly improving sensitivity while maintaining high linearity. By controlling the distribution of the locally enhanced electric field and the heterogeneous deformation of the substrate, a strain sensor with excellent performance is successfully prepared, exhibiting a giant gauge factor (9.1 × 106) and linearity (R2 = 0.9997) over the entire sensing range, together with almost no hysteresis and fast response time (17 ms). The gradient stiffness sliding design is a general strategy expected to be applied to other types of sensors to achieve ultra-high sensitivity and ultra-high linearity at the same time.