bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86
Authors: Zhou Daming , Supasa Piyada , Liu Chang , Dijokaite-Guraliuc Aiste , Duyvesteyn Helen M. E. , Selvaraj Muneeswaran , Mentzer Alexander J. , Das Raksha , Dejnirattisai Wanwisa , Temperton Nigel , Klenerman Paul , Dunachie Susanna J. , Fry Elizabeth E. , Mongkolsapaya Juthathip , Ren Jingshan , Stuart David I. , Screaton Gavin R. 
Published: March 2024

AbstractUnder pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice
Authors: Luu Laurence D. W. , Pandey Abhimanu , Paramsothy Sudarshan , Ngo Chinh , Castaño-Rodríguez Natalia , Liu Cheng , Kamm Michael A. , Borody Thomas J. , Man Si Ming , Kaakoush Nadeem O. 
Published: March 2024

AbstractHost molecular responses to fecal microbiota transplantation (FMT) in ulcerative colitis are not well understood. Here, we profile the human colonic mucosal transcriptome prior to and following FMT or placebo to identify molecules regulated during disease remission. FMT alters the transcriptome above the effect of placebo (n = 75 vs 3 genes, q < 0.05), including modulation of structural, metabolic and inflammatory pathways. This response is attributed to responders with no consistency observed in non-responders. Regulated pathways in responders include tight junctions, calcium signalling and xenobiotic metabolism. Genes significantly regulated longitudinally in responders post-FMT could discriminate them from responders and non-responders at baseline and non-responders post-FMT, with GBP5 and IRF4 downregulation being associated with remission. Female mice with a deletion of GBP5 are more resistant to developing colitis than their wild-type littermates, showing higher colonic IRF4 phosphorylation. The colonic mucosal response discriminates UC remission following FMT, with GBP5 playing a detrimental role in colitis.
Meta-analysis shows the impacts of ecological restoration on greenhouse gas emissions
Authors: He Tiehu , Ding Weixin , Cheng Xiaoli , Cai Yanjiang , Zhang Yulong , Xia Huijuan , Wang Xia , Zhang Jiehao , Zhang Kerong , Zhang Quanfa 
Published: March 2024

AbstractInternational initiatives set ambitious targets for ecological restoration, which is considered a promising greenhouse gas mitigation strategy. Here, we conduct a meta-analysis to quantify the impacts of ecological restoration on greenhouse gas emissions using a dataset compiled from 253 articles. Our findings reveal that forest and grassland restoration increase CH4 uptake by 90.0% and 30.8%, respectively, mainly due to changes in soil properties. Conversely, wetland restoration increases CH4 emissions by 544.4%, primarily attributable to elevated water table depth. Forest and grassland restoration have no significant effect on N2O emissions, while wetland restoration reduces N2O emissions by 68.6%. Wetland restoration enhances net CO2 uptake, and the transition from net CO2 sources to net sinks takes approximately 4 years following restoration. The net ecosystem CO2 exchange of the restored forests decreases with restoration age, and the transition from net CO2 sources to net sinks takes about 3-5 years for afforestation and reforestation sites, and 6-13 years for clear-cutting and post-fire sites. Overall, forest, grassland and wetland restoration decrease the global warming potentials by 327.7%, 157.7% and 62.0% compared with their paired control ecosystems, respectively. Our findings suggest that afforestation, reforestation, rewetting drained wetlands, and restoring degraded grasslands through grazing exclusion, reducing grazing intensity, or converting croplands to grasslands can effectively mitigate greenhouse gas emissions.
Structure of the intact tail machine of Anabaena myophage A-1(L)
Authors: Yu Rong-Cheng , Yang Feng , Zhang Hong-Yan , Hou Pu , Du Kang , Zhu Jie , Cui Ning , Xu Xudong , Chen Yuxing , Li Qiong , Zhou Cong-Zhao 
Published: March 2024

AbstractThe Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology.
Keto-anthraquinone covalent organic framework for H2O2 photosynthesis with oxygen and alkaline water
Authors: Zhang Xiangcheng , Cheng Silian , Chen Chao , Wen Xue , Miao Jie , Zhou Baoxue , Long Mingce , Zhang Lizhi 
Published: March 2024

AbstractHydrogen peroxide photosynthesis suffers from insufficient catalytic activity due to the high energy barrier of hydrogen extraction from H2O. Herein, we report that mechanochemically synthesized keto-form anthraquinone covalent organic framework which is able to directly synthesize H2O2 (4784 μmol h−1 g−1 at λ > 400 nm) from oxygen and alkaline water (pH = 13) in the absence of any sacrificial reagents. The strong alkalinity resulted in the formation of OH-(H2O)n clusters in water, which were adsorbed on keto moieties within the framework and then dissociated into O2 and active hydrogen, because the energy barrier of hydrogen extraction was largely lowered. The produced hydrogen reacted with anthraquinone to generate anthrahydroquinone, which was subsequently oxidized by O2 to produce H2O2. This study ultimately sheds light on the importance of hydrogen extraction from H2O for H2O2 photosynthesis and demonstrates that H2O2 synthesis is achievable under alkaline conditions.
Grave-to-cradle photothermal upcycling of waste polyesters over spent LiCoO2
Authors: Lou Xiangxi , Yan Penglei , Jiao Binglei , Li Qingye , Xu Panpan , Wang Lei , Zhang Liang , Cao Muhan , Wang Guiling , Chen Zheng , Zhang Qiao , Chen Jinxing 
Published: March 2024

AbstractLithium-ion batteries (LIBs) and plastics are pivotal components of modern society; nevertheless, their escalating production poses formidable challenges to resource sustainability and ecosystem integrity. Here, we showcase the transformation of spent lithium cobalt oxide (LCO) cathodes into photothermal catalysts capable of catalyzing the upcycling of diverse waste polyesters into high-value monomers. The distinctive Li deficiency in spent LCO induces a contraction in the Co−O6 unit cell, boosting the monomer yield exceeding that of pristine LCO by a factor of 10.24. A comprehensive life-cycle assessment underscores the economic viability of utilizing spent LCO as a photothermal catalyst, yielding returns of 129.6 $·kgLCO−1, surpassing traditional battery recycling returns (13–17 $·kgLCO−1). Solar-driven recycling 100,000 tons of PET can reduce 3.459 × 1011 kJ of electric energy and decrease 38,716 tons of greenhouse gas emissions. This work unveils a sustainable solution for the management of spent LIBs and plastics.
Synergistically optimized electron and phonon transport in high-performance copper sulfides thermoelectric materials via one-pot modulation
Authors: Zhang Yi-Xin , Huang Qin-Yuan , Yan Xi , Wang Chong-Yu , Yang Tian-Yu , Wang Zi-Yuan , Shi Yong-Cai , Shan Quan , Feng Jing , Ge Zhen-Hua 
Published: March 2024

AbstractOptimizing thermoelectric conversion efficiency requires the compromise of electrical and thermal properties of materials, which are hard to simultaneously improve due to the strong coupling of carrier and phonon transport. Herein, a one-pot approach realizing simultaneous second phase and Cu vacancies modulation is proposed, which is effective in synergistically optimizing thermoelectric performance in copper sulfides. Multiple lattice defects, including nanoprecipitates, dislocations, and nanopores are produced by adding a refined ratio of Sn and Se. Phonon transport is significantly suppressed by multiple mechanisms. An ultralow lattice thermal conductivity is therefore obtained. Furthermore, extra Se is added in the copper sulfide for optimizing electrical transport properties by inducing generating Cu vacancies. Ultimately, an excellent figure of merit of ~1.6 at 873 K is realized in the Cu1.992SSe0.016(Cu2SnSe4)0.004 bulk sample. The simple strategy of inducing compositional and structural modulation for improving thermoelectric parameters promotes low-cost high-performance copper sulfides as alternatives in thermoelectric applications.
Spaceflight effects on human vascular smooth muscle cell phenotype and function
Authors: Scotti Marina M. , Wilson Brandon K. , Bubenik Jodi L. , Yu Fahong , Swanson Maurice S. , Allen Josephine B. 
Published: March 2024

AbstractThe cardiovascular system is strongly impacted by the hazards of spaceflight. Astronauts spending steadily increasing lengths of time in microgravity are subject to cardiovascular deconditioning resulting in loss of vascular tone, reduced total blood volume, and diminished cardiac output. Appreciating the mechanisms by which the cells of the vasculature are altered during spaceflight will be integral to understanding and combating these deleterious effects as the human presence in space advances. In this study, we performed RNA-Seq analysis coupled with review by QIAGEN Ingenuity Pathway Analysis software on human aortic smooth muscle cells (HASMCs) cultured for 3 days in microgravity and aboard the International Space Station to assess the transcriptomic changes that occur during spaceflight. The results of our RNA-Seq analysis show that SMCs undergo a wide range of transcriptional alteration while in space, significantly affecting 4422 genes. SMCs largely down-regulate markers of the contractile, synthetic, and osteogenic phenotypes including smooth muscle alpha actin (αSMA), matrix metalloproteinases (MMPs), and bone morphogenic proteins (BMPs). Additionally, components of several cellular signaling pathways were strongly impacted including the STAT3, NFκB, PI3K/AKT, HIF1α, and Endothelin pathways. This study highlights the significant changes in transcriptional behavior SMCs exhibit during spaceflight and puts these changes in context to better understand vascular function in space.
Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion
Authors: Weyh Maria , Jokisch Marie-Lena , Nguyen Tuan-Anh , Fottner Maximilian , Lang Kathrin 
Published: March 2024

AbstractPost-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to −1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein–DNA and protein–protein interactions in biological processes from replication to ubiquitin signalling.
A high-quality chromosome-level genome assembly of the Chinese medaka Oryzias sinensis
Authors: Dong Zhongdian , Wang Jiangman , Chen Guozhu , Guo Yusong , Zhao Na , Wang Zhongduo , Zhang Bo 
Published: March 2024

AbstractOryzias sinensis, also known as Chinese medaka or Chinese ricefish, is a commonly used animal model for aquatic environmental assessment in the wild as well as gene function validation or toxicology research in the lab. Here, a high-quality chromosome-level genome assembly of O. sinensis was generated using single-tube long fragment read (stLFR) reads, Nanopore long-reads, and Hi-C sequencing data. The genome is 796.58 Mb, and a total of 712.17 Mb of the assembled sequences were anchored to 23 pseudo-chromosomes. A final set of 22,461 genes were annotated, with 98.67% being functionally annotated. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of genome assembly and gene annotation reached 95.1% (93.3% single-copy) and 94.6% (91.7% single-copy), respectively. Furthermore, we also use ATAC-seq to uncover chromosome transposase-accessibility as well as related genome area function enrichment for Oryzias sinensis. This study offers a new improved foundation for future genomics research in Chinese medaka.
High-capacity data hiding for medical images based on the mask-RCNN model
Authors: Saidi Hadjer , Tibermacine Okba , Elhadad Ahmed 
Published: March 2024

AbstractThis study introduces a novel approach for integrating sensitive patient information within medical images with minimal impact on their diagnostic quality. Utilizing the mask region-based convolutional neural network for identifying regions of minimal medical significance, the method embeds information using discrete cosine transform-based steganography. The focus is on embedding within “insignificant areas”, determined by deep learning models, to ensure image quality and confidentiality are maintained. The methodology comprises three main steps: neural network training for area identification, an embedding process for data concealment, and an extraction process for retrieving embedded information. Experimental evaluations on the CHAOS dataset demonstrate the method’s effectiveness, with the model achieving an average intersection over union score of 0.9146, indicating accurate segmentation. Imperceptibility metrics, including peak signal-to-noise ratio, were employed to assess the quality of stego images, with results showing high capacity embedding with minimal distortion. Furthermore, the embedding capacity and payload analysis reveal the method’s high capacity for data concealment. The proposed method outperforms existing techniques by offering superior image quality, as evidenced by higher peak signal-to-noise ratio values, and efficient concealment capacity, making it a promising solution for secure medical image handling.
Analyzing fine scaling quantum effects on the buckling of axially-loaded carbon nanotubes based on the density functional theory and molecular mechanics method
Authors: Mirnezhad M. , Ansari R. , Falahatgar S. R. , Aghdasi P. 
Published: March 2024

AbstractIn this paper, the quantum effects of fine scaling on the buckling behavior of carbon nanotubes (CNTs) under axial loading are investigated. Molecular mechanics and quantum mechanics are respectively utilized to study the buckling behavior and to obtain the molecular mechanics coefficients of fine-scale nanotubes. The results of buckling behavior of CNTs with different chiralities with finite and infinite dimensions are given, and a comparison study is presented on them. The differences between finite and infinite nanotubes reflect the quantum effects of fine scaling on the buckling behavior. In addition, the results show that the dimensional changes highly affect the mechanical properties and the buckling behavior of CNTs to certain dimensions. Moreover, dimensional changes have a significant effect on the critical buckling strain. Beside, in addition to the structure dimensions, the arrangement of structural and boundary atoms have a major influence on the buckling behavior.
Quantum scissor from exact generalized photon number statistics
Authors: Batin Abdul Q , Ghosh Suranjana , Panigrahi Prasanta K. , Roy Utpal 
Published: March 2024

AbstractWe report the close form expressions of the photon number statistics for a generalized coherent state and a generalized photon-added coherent state, which are shown to be crucial for proposing a variety of quantum scissor operations. The analytically obtained distributions are also capable of predicting the precise laser intensity windows for realizing a variety of quantum scissors. Truncating a photon added state overcomes the selection rule of obtaining the lower order Fock states. Photon addition also enables us to obtain a higher order Fock state in a lower order superposition. The importance of circular geometry is also demonstrated for engineering such quantum scissors.
Biodegradable poly(ethylene glycol-glycerol-itaconate-sebacate) copolyester elastomer with significantly reinforced mechanical properties by in-situ construction of bacterial cellulose interpenetrating network
Authors: Tang Lisheng , Jin Yuanyuan , He Xiaoyan , Huang Ran 
Published: March 2024

AbstractTo address the concern that biodegradable elastomers are environmental-friendly but usually associated with poor properties for practical utilization, we report a star-crosslinked poly(ethylene glycol-glycerol-itaconate-sebacate) (PEGIS) elastomer synthesized by esterification, polycondensation and UV curing, and reinforced by bacterial cellulose (BC). The interpenetrating network of primary BC backbone and vulcanized elastomer is achieved by the “in-situ secondary network construction” strategy. With the well dispersion of BC without agglomeration, the mechanical properties of PEGIS are significantly enhanced in tensile strength, Young’s modulus and elongation at break. The reinforcement strategy is demonstrated to be efficient and offers a route to the development of biodegradable elastomers for a variety of applications in the future.
Optical coherence tomography and optical coherence tomography angiography findings in optic nerve hypoplasia and their relationships with visual acuity
Authors: Kang Min Chae , Park Kyung-Ah , Oh Sei Yeul 
Published: March 2024

AbstractThis study aimed to quantitatively assess the thickness of the peripapillary retinal nerve fiber layer (pRNFL) thickness, as well as the microvascular alterations in the macula and peripapillary regions, in optic nerve hypoplasia (ONH) patients compared to normal controls. This was achieved through the utilization of spectral-domain optical coherence tomography (SD-OCT) and optical coherence tomography angiography (OCTA), with a specific focus on elucidating the association between these structural alterations and visual acuity. We included a total of 17 eyes of 12 ONH patients, and 34 eyes of age-matched 34 healthy controls. The pRNFL thickness was quantified using SD-OCT, while OCTA facilitated the visualization and measurement of the microvascular structure images of the superficial retinal capillary plexus (SRCP), deep retinal capillary plexus (DRCP), and radial peripapillary capillary (RPC) segment in the macula and peripapillary area. pRNFL thickness was measured for eight sectors (superior, temporal, inferior, nasal, superotemporal, superonasal, inferotemporal, and inferonasal). SRCP, DRCP, and RPC were measured for four sectors (superior, temporal, inferior, and nasal). Age, gender, and spherical equivalent refractive errors were statistically adjusted for the analysis. Associations of structural parameters with visual acuity in ONH patients were analyzed using Spearman correlation analysis. pRNFL thickness was significantly thinner in ONH patients than in controls for all sectors. Vessel densities of temporal and nasal sectors in DRCP were significantly higher in ONH patients, but vessel densities of the inferior sector in RPC were significantly lower than those in controls. For all sectors, pRNFL thickness was strongly associated with visual acuity in ONH patients. ONH patients showed significant pRNFL thinning and microvascular alterations compared to controls, and pRNFL thickness was strongly associated with visual function. OCT and OCTA are useful tools for evaluating optic disc hypoplasia and its functional status.
Transient expression of anti-HrpE scFv antibody reduces the hypersensitive response in non-host plant against bacterial phytopathogen Xanthomonas citri subsp. citri
Authors: Raeisi Hamideh , Safarnejad Mohammad Reza , Alavi Seyed Mehdi , de Oliveira Andrade Maxuel , Farrokhi Naser , Elahinia Seyed Ali 
Published: March 2024

AbstractCitrus canker is a bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that affects the citrus industry worldwide. Hrp pili subunits (HrpE), an essential component of Type III secretion system (T3SS) bacteria, play a crucial role in the pathogenesis of Xcc by transporting effector proteins into the host cell and causing canker symptoms. Therefore, development of antibodies that block HrpE can suppress disease progression. In this study, a specific scFv detecting HrpE was developed using phage display technique and characterized using sequencing, ELISA, Western blotting, and molecular docking. In addition, a plant expression vector of pCAMBIA-scFvH6 was constructed and agroinfiltrated into Nicotiana tabacum cv. Samson leaves. The hypersensitive response (HR) in the leaves of transformed and non-transformed plants was evaluated by inoculating leaves with Xcc. After three rounds of biopanning of the phage library, a specific human scFv antibody, named scFvH6, was identified that showed high binding activity against HrpE in ELISA and Western blotting. Molecular docking results showed that five intermolecular hydrogen bonds are involved in HrpE-scFvH6 interaction, confirming the specificity and high binding activity of scFvH6. Successful transient expression of pCAMBIA-scFvH6 in tobacco leaves was verified using immunoassay tests. The binding activity of plant-produced scFvH6 to detect HrpE in Western blotting and ELISA was similar to that of bacterial-produced scFvH6 antibody. Interestingly, tobacco plants expressing scFvH6 showed a remarkable reduction in HR induced by Xcc compared with control plants, so that incidence of necrotic lesions was significantly higher in non-transformed controls (≥ 1.5 lesions/cm2) than in the plants producing scFvH6 (≤ 0.5 lesions/cm2) after infiltration with Xcc inoculum. Our results revealed that the expression of scFvH6 in tobacco leaves can confer resistance to Xcc, indicating that this approach could be considered to provide resistance to citrus bacterial canker disease.