bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ketamine evoked disruption of entorhinal and hippocampal spatial maps
Authors: Masuda Francis Kei , Aery Jones Emily A. , Sun Yanjun , Giocomo Lisa M. 
Published: October 2023

AbstractKetamine, a rapid-acting anesthetic and acute antidepressant, carries undesirable spatial cognition side effects including out-of-body experiences and spatial memory impairments. The neural substrates that underlie these alterations in spatial cognition however, remain incompletely understood. Here, we used electrophysiology and calcium imaging to examine ketamine’s impacts on the medial entorhinal cortex and hippocampus, which contain neurons that encode an animal’s spatial position, as mice navigated virtual reality and real world environments. Ketamine acutely increased firing rates, degraded cell-pair temporal firing-rate relationships, and altered oscillations, leading to longer-term remapping of spatial representations. In the reciprocally connected hippocampus, the activity of neurons that encode the position of the animal was suppressed after ketamine administration. Together, these findings demonstrate ketamine-induced dysfunction of the MEC-hippocampal circuit at the single cell, local-circuit population, and network levels, connecting previously demonstrated physiological effects of ketamine on spatial cognition to alterations in the spatial navigation circuit.
UV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean
Authors: Sun Jiaqi , Huang Shiyu , Lu Qing , Li Shuo , Zhao Shizhen , Zheng Xiaojian , Zhou Qian , Zhang Wenxiao , Li Jie , Wang Lili , Zhang Ke , Zheng Wenyu , Feng Xianzhong , Liu Baohui , Kong Fanjiang , Xiang Fengning 
Published: October 2023

AbstractPlant height is a key agronomic trait that affects yield and is controlled by both phytohormone gibberellin (GA) and ultraviolet-B (UV-B) irradiation. However, whether and how plant height is modulated by UV-B-mediated changes in GA metabolism are not well understood. It has not been reported that the E3 ubiquitin ligase Anaphase Promoting Complex/Cyclosome (APC/C) is involved in the regulation of plant growth in response to environmental factors. We perform a forward genetic screen in soybean and find that a mutation in Glycine max Increased Leaf Petiole Angle1 (GmILPA1), encoding a subunit of the APC/C, lead to dwarfism under UV-B irradiation. UV-B promotes the accumulation of GmILPA1, which ubiquitinate the GA catabolic enzyme GA2 OXIDASE-like (GmGA2ox-like), resulting in its degradation in a UV-B-dependent manner. Another E3 ligase, GmUBL1, also ubiquitinate GmGA2ox-like and enhance the GmILPA1-mediated degradation of GmGA2ox-like, which suggest that GmILPA1-GmGA2ox-like module counteract the UV-B-mediated reduction of bioactive GAs. We also determine that GmILPA1 is a target of selection during soybean domestication and breeding. The deletion (Indel-665) in the promoter might facilitate the adaptation of soybean to high UV-B irradiation. This study indicates that an evolutionary GmILPA1 variant has the capability to develop ideal plant architecture with soybean cultivars.
Chemoproteomic capture of RNA binding activity in living cells
Authors: Heindel Andrew J. , Brulet Jeffrey W. , Wang Xiantao , Founds Michael W. , Libby Adam H. , Bai Dina L. , Lemke Michael C. , Leace David M. , Harris Thurl E. , Hafner Markus , Hsu Ku-Lung 
Published: October 2023

AbstractProteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
Structural conservation of insulin/IGF signalling axis at the insulin receptors level in Drosophila and humans
Authors: Viola Cristina M. , Frittmann Orsolya , Jenkins Huw T. , Shafi Talha , De Meyts Pierre , Brzozowski Andrzej M. 
Published: October 2023

AbstractThe insulin-related hormones regulate key life processes in Metazoa, from metabolism to growth, lifespan and aging, through an evolutionarily conserved insulin signalling axis (IIS). In humans the IIS axis is controlled by insulin, two insulin-like growth factors, two isoforms of the insulin receptor (hIR-A and -B), and its homologous IGF-1R. In Drosophila, this signalling engages seven insulin-like hormones (DILP1-7) and a single receptor (dmIR). This report describes the cryoEM structure of the dmIR ectodomain:DILP5 complex, revealing high structural homology between dmIR and hIR. The excess of DILP5 yields dmIR complex in an asymmetric ‘T’ conformation, similar to that observed in some complexes of human IRs. However, dmIR binds three DILP5 molecules in a distinct arrangement, showing also dmIR-specific features. This work adds structural support to evolutionary conservation of the IIS axis at the IR level, and also underpins a better understanding of an important model organism.
Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis
Authors: Wang Qian , Liu Ning , Deng Yaming , Guan Yuze , Xiao Hongli , Nitka Tara A. , Yang Hui , Yadav Anju , Vukovic Lela , Mathews Irimpan I. , Chen Xi , Kim Chu-Young 
Published: October 2023

AbstractMonensin A is a prototypical natural polyether polyketide antibiotic. It acts by binding a metal cation and facilitating its transport across the cell membrane. Biosynthesis of monensin A involves construction of a polyene polyketide backbone, subsequent epoxidation of the alkenes, and, lastly, formation of cyclic ethers via epoxide-opening cyclization. MonCI, a flavin-dependent monooxygenase, is thought to transform all three alkenes in the intermediate polyketide premonensin A into epoxides. Our crystallographic study has revealed that MonCI’s exquisite stereocontrol is due to the preorganization of the active site residues which allows only one specific face of the alkene to approach the reactive C(4a)-hydroperoxyflavin moiety. Furthermore, MonCI has an unusually large substrate-binding cavity that can accommodate premonensin A in an extended or folded conformation which allows any of the three alkenes to be placed next to C(4a)-hydroperoxyflavin. MonCI, with its ability to perform multiple epoxidations on the same substrate in a stereospecific manner, demonstrates the extraordinary versatility of the flavin-dependent monooxygenase family of enzymes.
Polarized microtubule remodeling transforms the morphology of reactive microglia and drives cytokine release
Authors: Adrian Max , Weber Martin , Tsai Ming-Chi , Glock Caspar , Kahn Olga I. , Phu Lilian , Cheung Tommy K. , Meilandt William J. , Rose Christopher M. , Hoogenraad Casper C. 
Published: October 2023

AbstractMicroglial reactivity is a pathological hallmark in many neurodegenerative diseases. During stimulation, microglia undergo complex morphological changes, including loss of their characteristic ramified morphology, which is routinely used to detect and quantify inflammation in the brain. However, the underlying molecular mechanisms and the relation between microglial morphology and their pathophysiological function are unknown. Here, proteomic profiling of lipopolysaccharide (LPS)-reactive microglia identifies microtubule remodeling pathways as an early factor that drives the morphological change and subsequently controls cytokine responses. We find that LPS-reactive microglia reorganize their microtubules to form a stable and centrosomally-anchored array to facilitate efficient cytokine trafficking and release. We identify cyclin-dependent kinase 1 (Cdk-1) as a critical upstream regulator of microtubule remodeling and morphological change in-vitro and in-situ. Cdk-1 inhibition also rescues tau and amyloid fibril-induced morphology changes. These results demonstrate a critical role for microtubule dynamics and reorganization in microglial reactivity and modulating cytokine-mediated inflammatory responses.
In situ electron paramagnetic resonance spectroscopy using single nanodiamond sensors
Authors: Qin Zhuoyang , Wang Zhecheng , Kong Fei , Su Jia , Huang Zhehua , Zhao Pengju , Chen Sanyou , Zhang Qi , Shi Fazhan , Du Jiangfeng 
Published: October 2023

AbstractAn ultimate goal of electron paramagnetic resonance (EPR) spectroscopy is to analyze molecular dynamics in place where it occurs, such as in a living cell. The nanodiamond (ND) hosting nitrogen-vacancy (NV) centers will be a promising EPR sensor to achieve this goal. However, ND-based EPR spectroscopy remains elusive, due to the challenge of controlling NV centers without well-defined orientations inside a flexible ND. Here, we show a generalized zero-field EPR technique with spectra robust to the sensor’s orientation. The key is applying an amplitude modulation on the control field, which generates a series of equidistant Floquet states with energy splitting being the orientation-independent modulation frequency. We acquire the zero-field EPR spectrum of vanadyl ions in aqueous glycerol solution with embedded single NDs, paving the way towards in vivo EPR.
Record ages of non-Markovian scale-invariant random walks
Authors: Régnier Léo , Dolgushev Maxim , Bénichou Olivier 
Published: October 2023

AbstractHow long is needed for an observable to exceed its previous highest value and establish a new record? This time, known as the age of a record plays a crucial role in quantifying record statistics. Until now, general methods for determining record age statistics have been limited to observations of either independent random variables or successive positions of a Markovian (memoryless) random walk. Here we develop a theoretical framework to determine record age statistics in the presence of memory effects for continuous non-smooth processes that are asymptotically scale-invariant. Our theoretical predictions are confirmed by numerical simulations and experimental realisations of diverse representative non-Markovian random walk models and real time series with memory effects, in fields as diverse as genomics, climatology, hydrology, geology and computer science. Our results reveal the crucial role of the number of records already achieved in time series and change our view on analysing record statistics.
Electronic Janus lattice and kagome-like bands in coloring-triangular MoTe2 monolayers
Authors: Lei Le , Dai Jiaqi , Dong Haoyu , Geng Yanyan , Cao Feiyue , Wang Cong , Xu Rui , Pang Fei , Liu Zheng-Xin , Li Fangsen , Cheng Zhihai , Wang Guang , Ji Wei 
Published: October 2023

AbstractPolymorphic structures of transition metal dichalcogenides (TMDs) host exotic electronic states, like charge density wave and superconductivity. However, the number of these structures is limited by crystal symmetries, which poses a challenge to achieving tailored lattices and properties both theoretically and experimentally. Here, we report a coloring-triangle (CT) latticed MoTe2 monolayer, termed CT-MoTe2, constructed by controllably introducing uniform and ordered mirror-twin-boundaries into a pristine monolayer via molecular beam epitaxy. Low-temperature scanning tunneling microscopy and spectroscopy (STM/STS) together with theoretical calculations reveal that the monolayer has an electronic Janus lattice, i.e., an energy-dependent atomic-lattice and a Te pseudo-sublattice, and shares the identical geometry with the Mo5Te8 layer. Dirac-like and flat electronic bands inherently existing in the CT lattice are identified by two broad and two prominent peaks in STS spectra, respectively, and verified with density-functional-theory calculations. Two types of intrinsic domain boundaries were observed, one of which maintains the electronic-Janus-lattice feature, implying potential applications as an energy-tunable electron-tunneling barrier in future functional devices.
Fibroblast growth factor 18 stimulates the proliferation of hepatic stellate cells, thereby inducing liver fibrosis
Authors: Tsuchiya Yuichi , Seki Takao , Kobayashi Kenta , Komazawa-Sakon Sachiko , Shichino Shigeyuki , Nishina Takashi , Fukuhara Kyoko , Ikejima Kenichi , Nagai Hidenari , Igarashi Yoshinori , Ueha Satoshi , Oikawa Akira , Tsurusaki Shinya , Yamazaki Soh , Nishiyama Chiharu , Mikami Tetuo , Yagita Hideo , Okumura Ko , Kido Taketomo , Miyajima Atsushi , Matsushima Kouji , Imasaka Mai , Araki Kimi , Imamura Toru , Ohmuraya Masaki , Tanaka Minoru , Nakano Hiroyasu 
Published: October 2023

AbstractLiver fibrosis results from chronic liver injury triggered by factors such as viral infection, excess alcohol intake, and lipid accumulation. However, the mechanisms underlying liver fibrosis are not fully understood. Here, we demonstrate that the expression of fibroblast growth factor 18 (Fgf18) is elevated in mouse livers following the induction of chronic liver fibrosis models. Deletion of Fgf18 in hepatocytes attenuates liver fibrosis; conversely, overexpression of Fgf18 promotes liver fibrosis. Single-cell RNA sequencing reveals that overexpression of Fgf18 in hepatocytes results in an increase in the number of Lrat+ hepatic stellate cells (HSCs), thereby inducing fibrosis. Mechanistically, FGF18 stimulates the proliferation of HSCs by inducing the expression of Ccnd1. Moreover, the expression of FGF18 is correlated with the expression of profibrotic genes, such as COL1A1 and ACTA2, in human liver biopsy samples. Thus, FGF18 promotes liver fibrosis and could serve as a therapeutic target to treat liver fibrosis.
Cloaking a qubit in a cavity
Authors: Lledó Cristóbal , Dassonneville Rémy , Moulinas Adrien , Cohen Joachim , Shillito Ross , Bienfait Audrey , Huard Benjamin , Blais Alexandre 
Published: October 2023

AbstractCavity quantum electrodynamics (QED) uses a cavity to engineer the mode structure of the vacuum electromagnetic field such as to enhance the interaction between light and matter. Exploiting these ideas in solid-state systems has lead to circuit QED which has emerged as a valuable tool to explore the rich physics of quantum optics and as a platform for quantum computation. Here we introduce a simple approach to further engineer the light-matter interaction in a driven cavity by controllably decoupling a qubit from the cavity’s photon population, effectively cloaking the qubit from the cavity. This is realized by driving the qubit with an external tone tailored to destructively interfere with the cavity field, leaving the qubit to interact with a cavity which appears to be in the vacuum state. Our experiment demonstrates how qubit cloaking can be exploited to cancel the ac-Stark shift and measurement-induced dephasing, and to accelerate qubit readout. In addition to qubit readout, applications of this method include qubit logical operations and the preparation of non-classical cavity states in circuit QED and other cavity-based setups.
ELMAS: a one-year dataset of hourly electrical load profiles from 424 French industrial and tertiary sectors
Authors: Bellinguer Kevin , Girard Robin , Bocquet Alexis , Chevalier Antoine 
Published: October 2023

AbstractThe combination of ongoing urban expansion and electrification of uses challenges the power grid. In such a context, information regarding customers’ consumption is vital to assess the expected load at strategic nodes over time, and to guide power system planning strategies. Comprehensive household consumption databases are widely available today thanks to the roll-out of smart meters, while the consumption of tertiary premises is seldom shared mainly due to privacy concerns. To fill this gap, the French main distribution system operator, Enedis, commissioned Mines Paris to derive load profiles of industrial and tertiary sectors for its prospective tools. The ELMAS dataset is an open dataset of 18 electricity load profiles derived from hourly consumption time series collected continuously over one year from a total of 55,730 customers. These customers are divided into 424 fields of activity, and three levels of capacity subscription. A clustering approach is employed to gather activities sharing similar temporal patterns, before averaging the associated time series to ensure anonymity.
Variable cardiac responses in rhesus macaque monkeys after discrete mediodorsal thalamus manipulations
Authors: Méndez Juan Carlos , Perry Brook A. L. , Premereur Elsie , Pelekanos Vassilis , Ramadan Tamara , Mitchell Anna S. 
Published: October 2023

AbstractThe control of some physiological parameters, such as the heart rate, is known to have a role in cognitive and emotional processes. Cardiac changes are also linked to mental health issues and neurodegeneration. Thus, it is not surprising that many of the brain structures typically associated with cognition and emotion also comprise a circuit—the central automatic network—responsible for the modulation of cardiovascular output. The mediodorsal thalamus (MD) is involved in higher cognitive processes and is also known to be connected to some of the key neural structures that regulate cardiovascular function. However, it is unclear whether the MD has any role in this circuitry. Here, we show that discrete manipulations (microstimulation during anaesthetized functional neuroimaging or localized cytotoxin infusions) to either the magnocellular or the parvocellular MD subdivisions led to observable and variable changes in the heart rate of female and male rhesus macaque monkeys. Considering the central positions that these two MD subdivisions have in frontal cortico-thalamocortical circuits, our findings suggest that MD contributions to autonomic regulation may interact with its identified role in higher cognitive processes, representing an important physiological link between cognition and emotion.
Spatial differences influence nitrogen uptake, grain yield, and land-use advantage of wheat/soybean relay intercropping systems
Authors: Raza Muhammad Ali , Din Atta Mohi Ud , Zhiqi Wang , Gul Hina , Ur Rehman Sana , Bukhari Birra , Haider Imran , Rahman Muhammad Habib Ur , Liang Xue , Luo Shuanglong , El Sabagh Ayman , Qin Ruijun , Zhongming Ma 
Published: October 2023

AbstractCereal/legume intercropping is becoming a popular production strategy for higher crop yields and net profits with reduced inputs and environmental impact. However, the effects of different spatial arrangements on the growth, grain yield, nitrogen uptake, and land-use advantage of wheat/soybean relay intercropping are still unclear, particularly under arid irrigated conditions. Therefore, in a three-year field study from 2018 to 2021, soybean was relay intercropped with wheat in different crop configurations (0.9 m, narrow strips; 1.8 m, medium strips; and 2.7 m, wide strips), and the results of intercropping systems were compared with their sole systems. Results revealed that intercrops with wide strips outperformed the narrow and medium strips, when the objective was to obtain higher total leaf area, dry matter, nitrogen uptake, and grain yield on a given land area due to reduced interspecific competition between intercrops. Specifically, at maturity, wide strips increased the dry matter accumulation (37% and 58%) and its distribution in roots (37% and 55%), straw (40% and 61%), and grains (30% and 46%) of wheat and soybean, respectively, compared to narrow strips. This enhanced dry matter in wide strips improved the soybean’s competitive ability (by 17%) but reduced the wheat’s competitive ability (by 12%) compared with narrow strips. Noticeably, all intercropping systems accumulated a significantly higher amount of nitrogen than sole systems, revealing that wheat/soybean relay intercropping requires fewer anthropogenic inputs (nitrogen) and exerts less pressure on the ecosystem than sole systems. Overall, in wide strips, intercropped wheat and soybean achieved 62% and 71% of sole wheat and soybean yield, respectively, which increased the greater total system yield (by 19%), total land equivalent ratio (by 24%), and net profit (by 34%) of wide strips compared to narrow strips. Our study, therefore, implies that the growth parameters, grain yields, nutrient accumulation, and land-use advantage of intercrop species could be improved with the proper spatial arrangement in cereal/legume intercropping systems.
Adaptive structure evolution and biologically plausible synaptic plasticity for recurrent spiking neural networks
Authors: Pan Wenxuan , Zhao Feifei , Zeng Yi , Han Bing 
Published: October 2023

AbstractThe architecture design and multi-scale learning principles of the human brain that evolved over hundreds of millions of years are crucial to realizing human-like intelligence. Spiking neural network based Liquid State Machine (LSM) serves as a suitable architecture to study brain-inspired intelligence because of its brain-inspired structure and the potential for integrating multiple biological principles. Existing researches on LSM focus on different certain perspectives, including high-dimensional encoding or optimization of the liquid layer, network architecture search, and application to hardware devices. There is still a lack of in-depth inspiration from the learning and structural evolution mechanism of the brain. Considering these limitations, this paper presents a novel LSM learning model that integrates adaptive structural evolution and multi-scale biological learning rules. For structural evolution, an adaptive evolvable LSM model is developed to optimize the neural architecture design of liquid layer with separation property. For brain-inspired learning of LSM, we propose a dopamine-modulated Bienenstock-Cooper-Munros (DA-BCM) method that incorporates global long-term dopamine regulation and local trace-based BCM synaptic plasticity. Comparative experimental results on different decision-making tasks show that introducing structural evolution of the liquid layer, and the DA-BCM regulation of the liquid layer and the readout layer could improve the decision-making ability of LSM and flexibly adapt to rule reversal. This work is committed to exploring how evolution can help to design more appropriate network architectures and how multi-scale neuroplasticity principles coordinated to enable the optimization and learning of LSMs for relatively complex decision-making tasks.