bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connective tissue inspired elastomer-based hydrogel for artificial skin via radiation-indued penetrating polymerization
Authors: Tian Yuan , Wang Zhihao , Cao Shuiyan , Liu Dong , Zhang Yukun , Chen Chong , Jiang Zhiwen , Ma Jun , Wang Yunlong 
Published: January 2024

AbstractRobust hydrogels offer a candidate for artificial skin of bionic robots, yet few hydrogels have a comprehensive performance comparable to real human skin. Here, we present a general method to convert traditional elastomers into tough hydrogels via a unique radiation-induced penetrating polymerization method. The hydrogel is composed of the original hydrophobic crosslinking network from elastomers and grafted hydrophilic chains, which act as elastic collagen fibers and water-rich substances. Therefore, it successfully combines the advantages of both elastomers and hydrogels and provides similar Young’s modulus and friction coefficients to human skin, as well as better compression and puncture load capacities than double network and polyampholyte hydrogels. Additionally, responsive abilities can be introduced during the preparation process, granting the hybrid hydrogels shape adaptability. With these unique properties, the hybrid hydrogel can be a candidate for artificial skin, fluid flow controller, wound dressing layer and many other bionic application scenarios.
Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly
Authors: Murigneux Emilie , Softic Laurent , Aubé Corentin , Grandi Carmen , Judith Delphine , Bruce Johanna , Le Gall Morgane , Guillonneau François , Schmitt Alain , Parissi Vincent , Berlioz-Torrent Clarisse , Meertens Laurent , Hansen Maike M. K. , Gallois-Montbrun Sarah 
Published: January 2024

AbstractConsiderable progress has been made in understanding the molecular host-virus battlefield during SARS-CoV-2 infection. Nevertheless, the assembly and egress of newly formed virions are less understood. To identify host proteins involved in viral morphogenesis, we characterize the proteome of SARS-CoV-2 virions produced from A549-ACE2 and Calu-3 cells, isolated via ultracentrifugation on sucrose cushion or by ACE-2 affinity capture. Bioinformatic analysis unveils 92 SARS-CoV-2 virion-associated host factors, providing a valuable resource to better understand the molecular environment of virion production. We reveal that G3BP1 and G3BP2 (G3BP1/2), two major stress granule nucleators, are embedded within virions and unexpectedly favor virion production. Furthermore, we show that G3BP1/2 participate in the formation of cytoplasmic membrane vesicles, that are likely virion assembly sites, consistent with a proviral role of G3BP1/2 in SARS-CoV-2 dissemination. Altogether, these findings provide new insights into host factors required for SARS-CoV-2 assembly with potential implications for future therapeutic targeting.
i-shaped antibody engineering enables conformational tuning of biotherapeutic receptor agonists
Authors: Romei Matthew G. , Leonard Brandon , Katz Zachary B. , Le Daniel , Yang Yanli , Day Eric S. , Koo Christopher W. , Sharma Preeti , Bevers III Jack , Kim Ingrid , Dai Huiguang , Farahi Farzam , Lin May , Shaw Andrey S. , Nakamura Gerald , Sockolosky Jonathan T. , Lazar Greg A. 
Published: January 2024

AbstractThe ability to leverage antibodies to agonize disease relevant biological pathways has tremendous potential for clinical investigation. Yet while antibodies have been successful as antagonists, immune mediators, and targeting agents, they are not readily effective at recapitulating the biology of natural ligands. Among the important determinants of antibody agonist activity is the geometry of target receptor engagement. Here, we describe an engineering approach inspired by a naturally occurring Fab-Fab homotypic interaction that constrains IgG in a unique i-shaped conformation. i-shaped antibody (iAb) engineering enables potent intrinsic agonism of five tumor necrosis factor receptor superfamily (TNFRSF) targets. When applied to bispecific antibodies against the heterodimeric IL-2 receptor pair, constrained bispecific IgG formats recapitulate IL-2 agonist activity. iAb engineering provides a tool to tune agonist antibody function and this work provides a framework for the development of intrinsic antibody agonists with the potential for generalization across broad receptor classes.
Scattered tree death contributes to substantial forest loss in California
Authors: Cheng Yan , Oehmcke Stefan , Brandt Martin , Rosenthal Lisa , Das Adrian , Vrieling Anton , Saatchi Sassan , Wagner Fabien , Mugabowindekwe Maurice , Verbruggen Wim , Beier Claus , Horion Stéphanie 
Published: January 2024

AbstractIn recent years, large-scale tree mortality events linked to global change have occurred around the world. Current forest monitoring methods are crucial for identifying mortality hotspots, but systematic assessments of isolated or scattered dead trees over large areas are needed to reduce uncertainty on the actual extent of tree mortality. Here, we mapped individual dead trees in California using sub-meter resolution aerial photographs from 2020 and deep learning-based dead tree detection. We identified 91.4 million dead trees over 27.8 million hectares of vegetated areas (16.7-24.7% underestimation bias when compared to field data). Among these, a total of 19.5 million dead trees appeared isolated, and 60% of all dead trees occurred in small groups ( ≤ 3 dead trees within a 30 × 30 m grid), which is largely undetected by other state-level monitoring methods. The widespread mortality of individual trees impacts the carbon budget and sequestration capacity of California forests and can be considered a threat to forest health and a fuel source for future wildfires.
Global-scale magnetosphere convection driven by dayside magnetic reconnection
Authors: Dai Lei , Zhu Minghui , Ren Yong , Gonzalez Walter , Wang Chi , Sibeck David , Samsonov Andrey , Escoubet Philippe , Tang Binbin , Zhang Jiaojiao , Branduardi-Raymont Graziella 
Published: January 2024

AbstractPlasma convection on a global scale is a fundamental feature of planetary magnetosphere. The Dungey cycle explains that steady-state convection within the closed part of the magnetosphere relies on magnetic reconnection in the nightside magnetospheric tail. Nevertheless, time-dependent models of the Dungey cycle suggest an alternative scenario where magnetospheric convection can be solely driven by dayside magnetic reconnection. In this study, we provide direct evidence supporting the scenario of dayside-driven magnetosphere convection. The driving process is closely connected to the evolution of Region 1 and Region 2 field-aligned currents. Our global simulations demonstrate that intensified magnetospheric convection and field-aligned currents progress from the dayside to the nightside within 10–20 minutes, following a southward turning of the interplanetary magnetic field. Observational data within this short timescale also reveal enhancements in both magnetosphere convection and the ionosphere’s two-cell convection. These findings provide insights into the mechanisms driving planetary magnetosphere convection, with implications for the upcoming Solar-Wind-Magnetosphere-Ionosphere Link Explorer (SMILE) mission.
A magnetic multi-layer soft robot for on-demand targeted adhesion
Authors: Chen Ziheng , Wang Yibin , Chen Hui , Law Junhui , Pu Huayan , Xie Shaorong , Duan Feng , Sun Yu , Liu Na , Yu Jiangfan 
Published: January 2024

AbstractMagnetic soft robots have shown great potential for biomedical applications due to their high shape reconfigurability, motion agility, and multi-functionality in physiological environments. Magnetic soft robots with multi-layer structures can enhance the loading capacity and function complexity for targeted delivery. However, the interactions between soft entities have yet to be fully investigated, and thus the assembly of magnetic soft robots with on-demand motion modes from multiple film-like layers is still challenging. Herein, we model and tailor the magnetic interaction between soft film-like layers with distinct in-plane structures, and then realize multi-layer soft robots that are capable of performing agile motions and targeted adhesion. Each layer of the robot consists of a soft magnetic substrate and an adhesive film. The mechanical properties and adhesion performance of the adhesive films are systematically characterized. The robot is capable of performing two locomotion modes, i.e., translational motion and tumbling motion, and also the on-demand separation with one side layer adhered to tissues. Simulation results are presented, which have a good qualitative agreement with the experimental results. The feasibility of using the robot to perform multi-target adhesion in a stomach is validated in both ex-vivo and in-vivo experiments.
Sub-micro porous thin polymer membranes for discriminating H2 and CO2
Authors: Yan Xueru , Song Tianqi , Li Min , Wang Zhi , Liu Xinlei 
Published: January 2024

AbstractPolymeric membranes with high permeance and remarkable selectivity for simultaneous H2 purification and CO2 capture under industry-relevant conditions are absent. Herein, sub-micro pores with precise molecular sieving capability are created in ultra-thin (13–30 nm) polymer membranes via controllable transformation of amine-linked polymer (ALP) films into benzimidazole-and-amine-linked polymer (BIALP) layers. The BIALP membranes exhibit stable unprecedented H2/CO2 selectivity of 120 with a H2 permeance of 315 GPU. Furthermore, high pressure (up to 11 bar) and thermal (up to 300 °C) resistance is delivered. This work provides a concept on designing porous polymeric membranes for precise molecular discrimination.
A mesocortical glutamatergic pathway modulates neuropathic pain independent of dopamine co-release
Authors: Li Miao , Yang Guang 
Published: January 2024

AbstractDysfunction in the mesocortical pathway, connecting the ventral tegmental area (VTA) to the prefrontal cortex, has been implicated in chronic pain. While extensive research has focused on the role of dopamine, the contribution of glutamatergic signaling in pain modulation remains unknown. Using in vivo calcium imaging, we observe diminished VTA glutamatergic activity targeting the prelimbic cortex (PL) in a mouse model of neuropathic pain. Optogenetic activation of VTA glutamatergic terminals in the PL alleviates neuropathic pain, whereas inhibiting these terminals in naïve mice induces pain-like responses. Importantly, this pain-modulating effect is independent of dopamine co-release, as demonstrated by CRISPR/Cas9-mediated gene deletion. Furthermore, we show that VTA neurons primarily project to excitatory neurons in the PL, and their activation restores PL outputs to the anterior cingulate cortex, a key region involved in pain processing. These findings reveal a distinct mesocortical glutamatergic pathway that critically modulates neuropathic pain independent of dopamine signaling.
Structure-guided discovery of anti-CRISPR and anti-phage defense proteins
Authors: Duan Ning , Hand Emily , Pheko Mannuku , Sharma Shikha , Emiola Akintunde 
Published: January 2024

AbstractBacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host defenses. Here, we use protein structural similarity and gene co-occurrence analyses to screen >66 million viral protein sequences and >330,000 metagenome-assembled genomes for the identification of anti-phage and counter-defense systems. We predict structures for ~300,000 proteins and perform large-scale, pairwise comparison to known anti-CRISPR (Acr) and anti-phage proteins to identify structural homologs that otherwise may not be uncovered using primary sequence search. This way, we identify a Bacteroidota phage Acr protein that inhibits Cas12a, and an Akkermansia muciniphila anti-phage defense protein, termed BxaP. Gene bxaP is found in loci encoding Bacteriophage Exclusion (BREX) and restriction-modification defense systems, but confers immunity independently. Our work highlights the advantage of combining protein structural features and gene co-localization information in studying host-phage interactions.
Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer
Authors: Zhou Tuoyu , Wu Jingyuan , Tang Haibo , Liu Dali , Jeon Byong-Hun , Jin Weilin , Wang Yiqing , Zheng Yuanzhang , Khan Aman , Han Huawen , Li Xiangkai 
Published: January 2024

AbstractProbiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.
Molecular identification with atomic force microscopy and conditional generative adversarial networks
Authors: Carracedo-Cosme Jaime , Pérez Rubén 
Published: January 2024

AbstractFrequency modulation (FM) atomic force microscopy (AFM) with metal tips functionalized with a CO molecule at the tip apex (referred as High-Resolution AFM, HR-AFM) has provided access to the internal structure of molecules with totally unprecedented resolution. We propose a model to extract the chemical information from those AFM images in order to achieve a complete identification of the imaged molecule. Our Conditional Generative Adversarial Network (CGAN) converts a stack of constant-height HR-AFM images at various tip-sample distances into a ball-and-stick depiction, where balls of different color and size represent the chemical species and sticks represent the bonds, providing complete information on the structure and chemical composition. The CGAN has been trained and tested with the QUAM-AFM data set, that contains simulated AFM images for a collection of 686000 organic molecules that include all the chemical species relevant in organic chemistry. Tests with a large set of theoretical images and few experimental examples demonstrate the accuracy and potential of our approach for molecular identification.
Candidate ferroelectrics via ab initio high-throughput screening of polar materials
Authors: Ricci Francesco , Reyes-Lillo Sebastian E. , Mack Stephanie A. , Neaton Jeffrey B. 
Published: January 2024

AbstractFerroelectrics are a class of polar and switchable functional materials with diverse applications, from microelectronics to energy conversion. Computational searches for new ferroelectric materials have been constrained by accurate prediction of the polarization and switchability with electric field, properties that, in principle, require a comparison with a nonpolar phase whose atomic-scale unit cell is continuously deformable from the polar ground state. For most polar materials, such a higher-symmetry nonpolar phase does not exist or is unknown. Here, we introduce a general high-throughput workflow that screens polar materials as potential ferroelectrics. We demonstrate our workflow on 1978 polar structures in the Materials Project database, for which we automatically generate a nonpolar reference structure using pseudosymmetries, and then compute the polarization difference and energy barrier between polar and nonpolar phases, comparing the predicted values to known ferroelectrics. Focusing on a subset of 182 potential ferroelectrics, we implement a systematic ranking strategy that prioritizes candidates with large polarization and small polar-nonpolar energy differences. To assess stability and synthesizability, we combine information including the computed formation energy above the convex hull, the Inorganic Crystal Structure Database id number, a previously reported machine learning-based synthesizability score, and ab initio phonon band structures. To distinguish between previously reported ferroelectrics, materials known for alternative applications, and lesser-known materials, we combine this ranking with a survey of the existing literature on these candidates through Google Scholar and Scopus databases, revealing ~130 promising materials uninvestigated as ferroelectric. Our workflow and large-scale high-throughput screening lays the groundwork for the discovery of novel ferroelectrics, revealing numerous candidates materials for future experimental and theoretical endeavors.
Adaptive finite differencing in high accuracy electronic structure calculations
Authors: Briggs E. L. , Lu Wenchang , Bernholc J. 
Published: January 2024

AbstractA multi-order Adaptive Finite Differencing (AFD) method is developed for the kinetic energy operator in real-space, grid-based electronic structure codes. It uses atomic pseudo orbitals produced by the corresponding pseudopotential codes to optimize the standard finite difference (SFD) operators for improved precision. Results are presented for a variety of test systems and Bravais lattice types, including the well-known Δ test for 71 elements in the periodic table, the Mott insulator NiO, and borax decahydrate, which contains covalent, ionic, and hydrogen bonds. The tests show that an 8th-order AFD operator leads to the same average Δ value as that achieved by plane-wave codes and is typically far more accurate and has a much lower computational cost than a 12th-order SFD operator. The scalability of real-space electronic calculations is demonstrated for a 2016-atom NiO cell, for which the computational time decreases nearly linearly when scaled from 18 to 144 CPU-GPU nodes.
On the dynamical stability of copper-doped lead apatite
Authors: Kim Sun-Woo , Wang Kang , Chen Siyu , Conway Lewis J. , Pascut G. Lucian , Errea Ion , Pickard Chris J. , Monserrat Bartomeu 
Published: January 2024

AbstractThe recent claim of room temperature superconductivity in a copper-doped lead apatite compound, called LK-99, has sparked remarkable interest and controversy. Subsequent experiments have largely failed to reproduce the claimed superconductivity, while theoretical works have identified multiple key features including strong electronic correlation, structural instabilities, and dopability constraints. A puzzling claim of several recent theoretical studies is that both parent and copper-doped lead apatite structures are dynamically unstable at the harmonic level, questioning decades of experimental reports of the parent compound structures and the recently proposed copper-doped structures. In this work, we demonstrate that both parent and copper-doped lead apatite structures are dynamically stable at room temperature. Anharmonic phonon–phonon interactions play a key role in stabilizing some copper-doped phases, while most phases are largely stable even at the harmonic level. We also show that dynamical stability depends on both volume and correlation strength, suggesting controllable ways of exploring the copper-doped lead apatite structural phase diagram. Our results fully reconcile the theoretical description of the structures of both parent and copper-doped lead apatite with the experiment.
CSF α-synuclein seed amplification kinetic profiles are associated with cognitive decline in Parkinson’s disease
Authors: Brockmann Kathrin , Lerche Stefanie , Baiardi Simone , Rossi Marcello , Wurster Isabel , Quadalti Corinne , Roeben Benjamin , Mammana Angela , Zimmermann Milan , Hauser Ann‑Kathrin , Deuschle Christian , Schulte Claudia , Liepelt-Scarfone Inga , Gasser Thomas , Parchi Piero 
Published: January 2024

AbstractSeed amplification assays have been implemented in Parkinson’s disease to reveal disease-specific misfolded alpha-synuclein aggregates in biospecimens. While the assays’ qualitative dichotomous seeding response is valuable to stratify and enrich cohorts for alpha-synuclein pathology in general, more quantitative parameters that are associated with clinical dynamics of disease progression and that might potentially serve as exploratory outcome measures in clinical trials targeting alpha-synuclein would add important information. To evaluate whether the seeding kinetic parameters time required to reach the seeding threshold (LAG phase), the peak of fluorescence response (Imax), and the area under the curve (AUC) are associated with clinical trajectories, we analyzed LAG, Imax, and AUC in relation to the development of cognitive decline in a longitudinal cohort of 199 people with Parkinson’s disease with positive CSF alpha-synuclein seeding status. Patients were stratified into tertiles based on their individual CSF alpha-synuclein seeding kinetic properties. The effect of the kinetic parameters on longitudinal development of cognitive impairment defined by MoCA ≤25 was analyzed by Cox-Regression. Patients with a higher number of positive seeding replicates and tertile groups of shorter LAG, higher Imax, and higher AUC showed a higher prevalence of and a shorter duration until cognitive impairment longitudinally (3, 6, and 3 years earlier with p ≤ 0.001, respectively). Results remained similar in separate subgroup analyses of patients with and without GBA mutation. We conclude that a more prominent alpha-synuclein seeding kinetic profile translates into a more rapid development of cognitive decline.
hUC-MSCs-derived MFGE8 ameliorates locomotor dysfunction via inhibition of ITGB3/ NF-κB signaling in an NMO mouse model
Authors: Xu Huiming , Jiang Wei , Li Xuejia , Jiang Jiaohua , Afridi Shabbir Khan , Deng Longhui , Li Rui , Luo Ermei , Zhang Zhaoqing , Huang Yu-Wen Alvin , Cui Yaxiong , So Kwok-Fai , Chen Haijia , Qiu Wei , Tang Changyong 
Published: January 2024

AbstractNeuromyelitis optica (NMO) is a severe autoimmune inflammatory disease of the central nervous system that affects motor function and causes relapsing disability. Human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) have been used extensively in the treatment of various inflammatory diseases, due to their potent regulatory roles that can mitigate inflammation and repair damaged tissues. However, their use in NMO is currently limited, and the mechanism underlying the beneficial effects of hUC-MSCs on motor function in NMO remains unclear. In this study, we investigate the effects of hUC-MSCs on the recovery of motor function in an NMO systemic model. Our findings demonstrate that milk fat globule epidermal growth 8 (MFGE8), a key functional factor secreted by hUC-MSCs, plays a critical role in ameliorating motor impairments. We also elucidate that the MFGE8/Integrin αvβ3/NF-κB signaling pathway is partially responsible for structural and functional recovery, in addition to motor functional enhancements induced by hUC-MSC exposure. Taken together, these findings strongly support the involvement of MFGE8 in mediating hUC-MSCs-induced improvements in motor functional recovery in an NMO mouse model. In addition, this provides new insight on the therapeutic potential of hUC-MSCs and the mechanisms underlying their beneficial effects in NMO.