bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalytic carbon–carbon bond cleavage in lignin via manganese–zirconium-mediated autoxidation
Authors: Palumbo Chad T. , Gu Nina X. , Bleem Alissa C. , Sullivan Kevin P. , Katahira Rui , Stanley Lisa M. , Kenny Jacob K. , Ingraham Morgan A. , Ramirez Kelsey J. , Haugen Stefan J. , Amendola Caroline R. , Stahl Shannon S. , Beckham Gregg T. 
Published: January 2024

AbstractEfforts to produce aromatic monomers through catalytic lignin depolymerization have historically focused on aryl–ether bond cleavage. A large fraction of aromatic monomers in lignin, however, are linked by various carbon–carbon (C–C) bonds that are more challenging to cleave and limit the yields of aromatic monomers from lignin depolymerization. Here, we report a catalytic autoxidation method to cleave C–C bonds in lignin-derived dimers and oligomers from pine and poplar. The method uses manganese and zirconium salts as catalysts in acetic acid and produces aromatic carboxylic acids as primary products. The mixtures of the oxygenated monomers are efficiently converted to cis,cis-muconic acid in an engineered strain of Pseudomonas putida KT2440 that conducts aromatic O-demethylation reactions at the 4-position. This work demonstrates that autoxidation of lignin with Mn and Zr offers a catalytic strategy to increase the yield of valuable aromatic monomers from lignin.
Identification of a highly conserved neutralizing epitope within the RBD region of diverse SARS-CoV-2 variants
Authors: Wang Yanqun , Yan An , Song Deyong , Duan Maoqin , Dong Chuangchuang , Chen Jiantao , Jiang Zihe , Gao Yuanzhu , Rao Muding , Feng Jianxia , Zhang Zhaoyong , Qi Ruxi , Ma Xiaomin , Liu Hong , Yu Beibei , Wang Qiaoping , Zong Mengqi , Jiao Jie , Xing Pingping , Pan Rongrong , Li Dan , Xiao Juxue , Sun Junbo , Li Ying , Zhang Linfeng , Shen Zhenduo , Sun Baiping , Zhao Yanyan , Zhang Lu , Dai Jun , Zhao Jingxian , Wang Lan , Dou Changlin , Liu Zheng , Zhao Jincun 
Published: January 2024

AbstractThe constant emergence of SARS-CoV-2 variants continues to impair the efficacy of existing neutralizing antibodies, especially XBB.1.5 and EG.5, which showed exceptional immune evasion properties. Here, we identify a highly conserved neutralizing epitope targeted by a broad-spectrum neutralizing antibody BA7535, which demonstrates high neutralization potency against not only previous variants, such as Alpha, Beta, Gamma, Delta and Omicron BA.1-BA.5, but also more recently emerged Omicron subvariants, including BF.7, CH.1.1, XBB.1, XBB.1.5, XBB.1.9.1, EG.5. Structural analysis of the Omicron Spike trimer with BA7535-Fab using cryo-EM indicates that BA7535 recognizes a highly conserved cryptic receptor-binding domain (RBD) epitope, avoiding most of the mutational hot spots in RBD. Furthermore, structural simulation based on the interaction of BA7535-Fab/RBD complexes dissects the broadly neutralizing effect of BA7535 against latest variants. Therapeutic and prophylactic treatment with BA7535 alone or in combination with BA7208 protected female mice from the circulating Omicron BA.5 and XBB.1 variant infection, suggesting the highly conserved neutralizing epitope serves as a potential target for developing highly potent therapeutic antibodies and vaccines.
The nature of carotenoid S* state and its role in the nonphotochemical quenching of plants
Authors: Accomasso Davide , Londi Giacomo , Cupellini Lorenzo , Mennucci Benedetta 
Published: January 2024

AbstractIn plants, light-harvesting complexes serve as antennas to collect and transfer the absorbed energy to reaction centers, but also regulate energy transport by dissipating the excitation energy of chlorophylls. This process, known as nonphotochemical quenching, seems to be activated by conformational changes within the light-harvesting complex, but the quenching mechanisms remain elusive. Recent spectroscopic measurements suggest the carotenoid S* dark state as the quencher of chlorophylls’ excitation. By investigating lutein embedded in different conformations of CP29 (a minor antenna in plants) via nonadiabatic excited state dynamics simulations, we reveal that different conformations of the complex differently stabilize the lutein s-trans conformer with respect to the dominant s-cis one. We show that the s-trans conformer presents the spectroscopic signatures of the S* state and rationalize its ability to accept energy from the closest excited chlorophylls, providing thus a relationship between the complex’s conformation and the nonphotochemical quenching.
Sustainable biomimetic solar distillation with edge crystallization for passive salt collection and zero brine discharge
Authors: Abdelsalam Mohamed A. , Sajjad Muhammad , Raza Aikifa , AlMarzooqi Faisal , Zhang TieJun 
Published: January 2024

AbstractThe urgency of addressing water scarcity and exponential population rise has necessitated the use of sustainable desalination for clean water production, while conventional thermal desalination processes consume fossil fuel with brine rejection. As a promising solution to sustainable solar thermal distillation, we report a scalable mangrove-mimicked device for direct solar vapor generation and passive salt collection without brine discharge. Capillarity-driven salty water supply and continuous vapor generation are ensured by anti-corrosion porous wicking stem and multi-layer leaves, which are made of low-cost superhydrophilic nanostructured titanium meshes. Precipitated salt at the leaf edge forms porous patch during daytime evaporation and get peeled by gravity during night when saline water rewets the leaves, and these salt patches can enhance vaporization by 1.6 times as indicated by our findings. The proposed solar vapor generator achieves a stable photothermal efficiency around 94% under one sun when treating synthetic seawater with a salinity of 3.5 wt.%. Under outdoor conditions, it can produce 2.2 L m−2of freshwater per day from real seawater, which is sufficient for individual drinking needs. This kind of biomimetic solar distillation devices have demonstrated great capability in clean water production and passive salt collection to tackle global water and environmental challenges.
A universal metabolite repair enzyme removes a strong inhibitor of the TCA cycle
Authors: Zmuda Anthony J. , Kang Xiaojun , Wissbroecker Katie B. , Freund Saxhaug Katrina , Costa Kyle C. , Hegeman Adrian D. , Niehaus Thomas D. 
Published: January 2024

AbstractA prevalent side-reaction of succinate dehydrogenase oxidizes malate to enol-oxaloacetate (OAA), a metabolically inactive form of OAA that is a strong inhibitor of succinate dehydrogenase. We purified from cow heart mitochondria an enzyme (OAT1) with OAA tautomerase (OAT) activity that converts enol-OAA to the physiological keto-OAA form, and determined that it belongs to the highly conserved and previously uncharacterized Fumarylacetoacetate_hydrolase_domain-containing protein family. From all three domains of life, heterologously expressed proteins were shown to have strong OAT activity, and ablating the OAT1 homolog caused significant growth defects. In Escherichia coli, expression of succinate dehydrogenase was necessary for OAT1-associated growth defects to occur, and ablating OAT1 caused a significant increase in acetate and other metabolites associated with anaerobic respiration. OAT1 increased the succinate dehydrogenase reaction rate by 35% in in vitro assays with physiological concentrations of both succinate and malate. Our results suggest that OAT1 is a universal metabolite repair enzyme that is required to maximize aerobic respiration efficiency by preventing succinate dehydrogenase inhibition.
FLIP(C1orf112)-FIGNL1 complex regulates RAD51 chromatin association to promote viability after replication stress
Authors: Tischler Jessica D. , Tsuchida Hiroshi , Bosire Rosevalentine , Oda Tommy T. , Park Ana , Adeyemi Richard O. 
Published: January 2024

AbstractHomologous recombination (HR) plays critical roles in repairing lesions that arise during DNA replication and is thus essential for viability. RAD51 plays important roles during replication and HR, however, how RAD51 is regulated downstream of nucleofilament formation and how the varied RAD51 functions are regulated is not clear. We have investigated the protein c1orf112/FLIP that previously scored in genome-wide screens for mediators of DNA inter-strand crosslink (ICL) repair. Upon ICL agent exposure, FLIP loss leads to marked cell death, elevated chromosomal instability, increased micronuclei formation, altered cell cycle progression and increased DNA damage signaling. FLIP is recruited to damage foci and forms a complex with FIGNL1. Both proteins have epistatic roles in ICL repair, forming a stable complex. Mechanistically, FLIP loss leads to increased RAD51 amounts and foci on chromatin both with or without exogenous DNA damage, defective replication fork progression and reduced HR competency. We posit that FLIP is essential for limiting RAD51 levels on chromatin in the absence of damage and for RAD51 dissociation from nucleofilaments to properly complete HR. Failure to do so leads to replication slowing and inability to complete repair.
A nanoparticle-based sonodynamic therapy reduces Helicobacter pylori infection in mouse without disrupting gut microbiota
Authors: Liu Tao , Chai Shuang , Li Mingyang , Chen Xu , Xie Yutao , Zhao Zehui , Xie Jingjing , Yu Yunpeng , Gao Feng , Zhu Feng , Yang Lihua 
Published: January 2024

AbstractInfection by Helicobacter pylori, a prevalent global pathogen, currently requires antibiotic-based treatments, which often lead to antimicrobial resistance and gut microbiota dysbiosis. Here, we develop a non-antibiotic approach using sonodynamic therapy mediated by a lecithin bilayer-coated poly(lactic-co-glycolic) nanoparticle preloaded with verteporfin, Ver-PLGA@Lecithin, in conjunction with localized ultrasound exposure of a dosage permissible for ultrasound medical devices. This study reveals dual functionality of Ver-PLGA@Lecithin. It effectively neutralizes vacuolating cytotoxin A, a key virulence factor secreted by H. pylori, even in the absence of ultrasound. When coupled with ultrasound exposure, it inactivates H. pylori by generating reactive oxygen species, offering a potential solution to overcome antimicrobial resistance. In female mouse models bearing H. pylori infection, this sonodynamic therapy performs comparably to the standard triple therapy in reducing gastric infection. Significantly, unlike the antibiotic treatments, the sonodynamic therapy does not negatively disrupt gut microbiota, with the only major impact being upregulation of Lactobacillus, which is a bacterium widely used in yogurt products and probiotics. This study presents a promising alternative to the current antibiotic-based therapies for H. pylori infection, offering a reduced risk of antimicrobial resistance and minimal disturbance to the gut microbiota.
Structural and biochemical insights into the mechanism of the Gabija bacterial immunity system
Authors: Huo Yanwu , Kong Lingfei , Zhang Ye , Xiao Min , Du Kang , Xu Sunyuntao , Yan Xiaoxue , Ma Jun , Wei Taotao 
Published: January 2024

AbstractThe Gabija system is a newly discovered bacterial immune system that consists of GajA and GajB. Here we report the cryo-EM structure of the Gabija complex from Bacillus cereus VD045 at 3.6 Å, which provides the direct evidence of interactions between GajA and GajB. The Gabija complex is an octameric ring structure with four GajA and four GajB. GajA is an OLD nucleases family protein, while GajB belongs to the SF1 helicases. The Gabija complex has sequence-specific DNA nuclease activity and prefers circular rather than linear DNA as substrate, its activity is more sensitive to concentrations change of nucleotides compared to GajA alone. Our data suggest a mechanism of Gabija immunity: the nuclease activity of Gabija complex is inhibited under physiological conditions, while it is activated by depletion of NTP and dNTP upon the replication and transcription of invading phages and cleave the circular DNA to prevent phage DNA replication.
Efficient conversion of propane in a microchannel reactor at ambient conditions
Authors: Li Chunsong , Zhang Haochen , Liu Wenxuan , Sheng Lin , Cheng Mu-Jeng , Xu Bingjun , Luo Guangsheng , Lu Qi 
Published: January 2024

AbstractThe oxidative dehydrogenation of propane, primarily sourced from shale gas, holds promise in meeting the surging global demand for propylene. However, this process necessitates high operating temperatures, which amplifies safety concerns in its application due to the use of mixed propane and oxygen. Moreover, these elevated temperatures may heighten the risk of overoxidation, leading to carbon dioxide formation. Here we introduce a microchannel reaction system designed for the oxidative dehydrogenation of propane within an aqueous environment, enabling highly selective and active propylene production at room temperature and ambient pressure with mitigated safety risks. A propylene selectivity of over 92% and production rate of 19.57 mmol mCu−2 h−1 are simultaneously achieved. This exceptional performance stems from the in situ creation of a highly active, oxygen-containing Cu catalytic surface for propane activation, and the enhanced propane transfer via an enlarged gas-liquid interfacial area and a reduced diffusion path by establishing a gas-liquid Taylor flow using a custom-made T-junction microdevice. This microchannel reaction system offers an appealing approach to accelerate gas-liquid-solid reactions limited by the solubility of gaseous reactant.
A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice
Authors: Greiss Ferdinand , Lardon Nicolas , Schütz Leonie , Barak Yoav , Daube Shirley S. , Weinhold Elmar , Noireaux Vincent , Bar-Ziv Roy 
Published: January 2024

AbstractRealizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.
Transgenic expression of cif genes from Wolbachia strain wAlbB recapitulates cytoplasmic incompatibility in Aedes aegypti
Authors: McNamara Cameron J. , Ant Thomas H. , Harvey-Samuel Tim , White-Cooper Helen , Martinez Julien , Alphey Luke , Sinkins Steven P. 
Published: January 2024

AbstractThe endosymbiotic bacteria Wolbachia can invade insect populations by modifying host reproduction through cytoplasmic incompatibility (CI), an effect that results in embryonic lethality when Wolbachia-carrying males mate with Wolbachia-free females. Here we describe a transgenic system for recreating CI in the major arbovirus vector Aedes aegypti using CI factor (cif) genes from wAlbB, a Wolbachia strain currently being deployed to reduce dengue transmission. CI-like sterility is induced when cifA and cifB are co-expressed in testes; this sterility is rescued by maternal cifA expression, thereby reproducing the pattern of Wolbachia-induced CI. Expression of cifB alone is associated with extensive DNA damage and disrupted spermatogenesis. The strength of rescue by maternal cifA expression is dependent on the comparative levels of cifA/cifB expression in males. These findings are consistent with CifB acting as a toxin and CifA as an antitoxin, with CifA attenuating CifB toxicity in both the male germline and in developing embryos. These findings provide important insights into the interactions between cif genes and their mechanism of activity and provide a foundation for the building of a cif gene-based drive system in Ae. aegypti.
Ultrafast Bragg coherent diffraction imaging of epitaxial thin films using deep complex-valued neural networks
Authors: Yu Xi , Wu Longlong , Lin Yuewei , Diao Jiecheng , Liu Jialun , Hallmann Jörg , Boesenberg Ulrike , Lu Wei , Möller Johannes , Scholz Markus , Zozulya Alexey , Madsen Anders , Assefa Tadesse , Bozin Emil S. , Cao Yue , You Hoydoo , Sheyfer Dina , Rosenkranz Stephan , Marks Samuel D. , Evans Paul G. , Keen David A. , He Xi , Božović Ivan , Dean Mark P. M. , Yoo Shinjae , Robinson Ian K. 
Published: January 2024

AbstractDomain wall structures form spontaneously due to epitaxial misfit during thin film growth. Imaging the dynamics of domains and domain walls at ultrafast timescales can provide fundamental clues to features that impact electrical transport in electronic devices. Recently, deep learning based methods showed promising phase retrieval (PR) performance, allowing intensity-only measurements to be transformed into snapshot real space images. While the Fourier imaging model involves complex-valued quantities, most existing deep learning based methods solve the PR problem with real-valued based models, where the connection between amplitude and phase is ignored. To this end, we involve complex numbers operation in the neural network to preserve the amplitude and phase connection. Therefore, we employ the complex-valued neural network for solving the PR problem and evaluate it on Bragg coherent diffraction data streams collected from an epitaxial La2-xSrxCuO4 (LSCO) thin film using an X-ray Free Electron Laser (XFEL). Our proposed complex-valued neural network based approach outperforms the traditional real-valued neural network methods in both supervised and unsupervised learning manner. Phase domains are also observed from the LSCO thin film at an ultrafast timescale using the complex-valued neural network.
Soft, full Wheatstone bridge 3D pressure sensors for cardiovascular monitoring
Authors: Park Yoonseok , Luan Haiwen , Kwon Kyeongha , Chung Ted S. , Oh Seyong , Yoo Jae-Young , Chung Gooyoon , Kim Junha , Kim Suhyeon , Kwak Sung Soo , Choi Junhwan , Phan Hoang-Phuong , Yoo Seonggwang , Jeong Hyoyoung , Shin Jaeho , Won Sang Min , Yoon Hong-Joon , Jung Yei Hwan , Rogers John A. 
Published: January 2024

AbstractVariations in parameters associated with the ambient environment can introduce noise in soft, body-worn sensors. For example, many piezoresistive pressure sensors exhibit a high degree of sensitivity to fluctuations in temperature, thereby requiring active compensation strategies. The research presented here addresses this challenge with a multilayered 3D microsystem design that integrates four piezoresistive sensors in a full-Wheatstone bridge configuration. An optimized layout of the sensors relative to the neutral mechanical plane leads to both an insensitivity to temperature and an increased sensitivity to pressure, relative to previously reported devices that rely on similar operating principles. Integrating this 3D pressure sensor into a soft, flexible electronics platform yields a system capable of real-time, wireless measurements from the surface of the skin. Placement above the radial and carotid arteries yields high-quality waveforms associated with pulsatile blood flow, with quantitative correlations to blood pressure. The results establish the materials and engineering aspects of a technology with broad potential in remote health monitoring.
Multidimensional well-being of US households at a fine spatial scale using fused household surveys
Authors: Ummel Kevin , Poblete-Cazenave Miguel , Akkiraju Karthik , Graetz Nick , Ashman Hero , Kingdon Cora , Herrera Tenorio Steven , Singhal Aaryaman Sunny , Cohen Daniel Aldana , Rao Narasimha D. 
Published: January 2024

AbstractSocial science often relies on surveys of households and individuals. Dozens of such surveys are regularly administered by the U.S. government. However, they field independent, unconnected samples with specialized questions, limiting research questions to those that can be answered by a single survey. The presented data comprise the fusion onto the American Community Survey (ACS) microdata of select donor variables from the Residential Energy Consumption Survey (RECS) of 2015, the National Household Travel Survey (NHTS) of 2017, the American Housing Survey (AHS) of 2019, and the Consumer Expenditure Survey - Interview (CEI) for the years 2015–2019. This results in an integrated microdataset of household attributes and well-being dimensions that can be analyzed to address research questions in ways that are not currently possible. The underlying statistical techniques, designed under the fusionACS project, are included in an open-sourceRpackage, fusionModel, that provides generic tools for the creation, analysis, and validation of fused microdata.
Clinical and immunological relevance of SLAMF6 expression in the tumor microenvironment of breast cancer and melanoma
Authors: Oba Takaaki , Long Mark D. , Ito Ken-ichi , Ito Fumito 
Published: January 2024

AbstractCompelling evidence shows that the frequency of T cells in the tumor microenvironment correlates with prognosis as well as response to immunotherapy. However, considerable heterogeneity exists within tumor-infiltrating T cells, and significance of their genomic and transcriptomic landscape on clinical outcomes remains to be elucidated. Signaling lymphocyte activation molecule 6 (SLAMF6) is expressed on intra-tumoral progenitor-exhausted T cells, which exhibit the capacity to proliferate, self-renew and produce terminally-exhausted T cells in pre-clinical models and patients. Here, we investigated the impact of SLAMF6 expression on prognosis in two immunologically different tumor types using publicly available databases. Our findings demonstrate that high SLAMF6 expression is associated with better prognosis, expression of TCF7 (encoding T-cell factor 1), and increased gene signatures associated with conventional type 1 dendritic cells and effector function of T cells in melanoma and breast cancer. Single-cell profiling of breast cancer tumor microenvironment reveals SLAMF6 expression overlaps CD8 T cells with a T-effector signature, which includes subsets expressing TCF7, memory and effector-related genes, analogous to progenitor-exhausted T cells. These findings illustrate the significance of SLAMF6 in the tumor as a marker for better effector responses, and provide insights into the predictive and prognostic determinants for cancer patients.