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Single-cell sequencing is frequently affected by "omission" due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly "omitted" cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of "omitted" cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
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Algoritmos , Análise de Sequência de RNA , Análise de Célula Única , Análise de Célula Única/métodos , Humanos , Análise de Sequência de RNA/métodos , Biologia Computacional/métodos , RNA-Seq/métodos , Redes Neurais de Computação , Software , Sequenciamento de Nucleotídeos em Larga Escala/métodosRESUMO
[This corrects the article DOI: 10.1371/journal.pone.0266608.].
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[This corrects the article DOI: 10.1039/D4SC02491E.].
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Two-dimensional conductive metal-organic frameworks (2D cMOFs) are an emerging class of crystalline van der Waals layered materials with tunable porosity and high electrical conductivity. They have been used in a variety of applications, such as energy storage and conversion, chemiresistive sensing, and quantum information. Although designing new conductive 2D cMOFs and studying their composition/structure-property relationships have attracted significant attention, there are still very few examples of 2D cMOFs that exhibit room-temperature electrical conductivity above 1 S cm-1, the value exhibited by activated carbon, a well-known porous and conductive material that serves in myriad applications. When such high conductivities are achieved, Ni-diamine linkages are often involved, yet Ni-diamine MOFs remain difficult to access. Here, we report two new 2D cMOFs made through ortho-diamine connections: M3(HITT)2 (M = Ni, Cu; HITT = 2,3,7,8,12,13-hexaiminotetraazanaphthotetraphene). The electrical conductivity of Ni3(HITT)2 reaches 4.5 S cm-1 at 298 K, whereas the conductivity of Cu3(HITT)2 spans from 0.05 (2Cu+Cu2+) to 10-6 (3Cu2+) upon air oxidation, much lower than that of Ni3(HITT)2. Spectroscopic analysis reveals that Ni3(HITT)2 exhibits significantly stronger in-plane π-d conjugation and higher density of charge carriers compared to Cu3(HITT)2, accounting for the higher electrical conductivity of Ni3(HITT)2. Cu2+/Cu+ mixed valency modulates the energy level and carrier density of Cu3(HITT)2, allowing for a variation of electrical conductivity over 4 orders of magnitude. This work provides a deeper understanding of the influence of metal nodes on electrical conductivity and confirms ortho-diamine linkers as privileged among ligands for 2D cMOFs.
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Rare-earth metal complexes of the parent benzene tetraanion and neutral inverse-sandwich rare-earth metal arene complexes have remained elusive. Here, we report the first neutral inverse-sandwich rare-earth metal complexes of the parent benzene tetraanion supported by a monoanionic ß-diketiminate (BDI) ligand. Reduction of the trivalent rare-earth metal diiodide precursors (BDI)MI2(THF) (BDI = HC(C(Me)N[C6H3-(3-pentyl)2-2,6])2; M = Y, 1-Y; M = Sm, 1-Sm) in benzene or para-xylene by potassium graphite yielded the neutral inverse-sandwich rare-earth metal arene complexes [(BDI)M(THF) n ]2(µ-η6,η6-arene) (M = Y, Sm; arene = benzene, 2-M; arene = para-xylene, 3-M). Single crystal X-ray diffraction, spectroscopic and magnetic characterization studies, together with density functional theory (DFT) calculations confirm that these neutral rare-earth metal arene complexes possess an [M3+-(arene)4--M3+] electronic structure with strong metal-arene δ interactions. The arene exchange reactivity shows that 2-Sm has higher stability than 3-Sm. Furthermore, 2-Sm can behave as a four-electron reductant to reduce unsaturated organic substrates. Particularly, while the reaction of 2-Sm with 1,3,5,7-cyclooctatetraene (COT) yielded (BDI)Sm(η8-COT) (4-Sm), 2-Sm reacted with 1,4-diphenylbutadiyne to afford (BDI)Sm(η4-C4Ph2) (5-Sm), the first rare-earth metallacyclopentatriene complex.
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As global climate change continues, drought episodes have become increasingly frequent. Studying plant stress tolerance is urgently needed to ensure food security. The common ice plant is one of the model halophyte plants for plant stress biology research. This study aimed to investigate the functions of a newly discovered transcription factor, Homeobox 7 (HB7), from the ice plant in response to drought stress. An efficient Agrobacterium-mediated transformation method was established in the ice plant, where ectopic McHB7 expression may be sustained for four weeks. The McHB7 overexpression (OE) plants displayed drought tolerance, and the activities of redox enzymes and chlorophyll content in the OE plants were higher than the wild type. Quantitative proteomics revealed 1910 and 495 proteins significantly changed in the OE leaves compared to the wild type under the control and drought conditions, respectively. Most increased proteins were involved in the tricarboxylic acid cycle, photosynthesis, glycolysis, pyruvate metabolism, and oxidative phosphorylation pathways. Some were found to participate in abscisic acid signaling or response. Furthermore, the abscisic acid levels increased in the OE compared with the wild type. McHB7 was revealed to bind to the promoter motifs of Early Responsive to Dehydration genes and abscisic acid-responsive genes, and protein-protein interaction analysis revealed candidate proteins responsive to stresses and hormones (e.g., abscisic acid). To conclude, McHB7 may contribute to enhance plant drought tolerance through abscisic acid signaling.
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Ácido Abscísico , Resistência à Seca , Transdução de Sinais , Estresse Fisiológico , Fatores de Transcrição , Ácido Abscísico/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Homeodomínio/metabolismo , Proteínas de Homeodomínio/genética , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas , Proteômica/métodos , Fatores de Transcrição/metabolismo , Fatores de Transcrição/genéticaRESUMO
Drugs of abuse are thought to promote addiction in part by "hijacking" brain reward systems, but the underlying mechanisms remain undefined. Using whole-brain FOS mapping and in vivo single-neuron calcium imaging, we found that drugs of abuse augment dopaminoceptive ensemble activity in the nucleus accumbens (NAc) and disorganize overlapping ensemble responses to natural rewards in a cell type-specific manner. Combining FOS-Seq, CRISPR-perturbation, and single-nucleus RNA sequencing, we identified Rheb as a molecular substrate that regulates cell type-specific signal transduction in NAc while enabling drugs to suppress natural reward consumption. Mapping NAc-projecting regions activated by drugs of abuse revealed input-specific effects on natural reward consumption. These findings characterize the dynamic, molecular and circuit basis of a common reward pathway, wherein drugs of abuse interfere with the fulfillment of innate needs.
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Homeostase , Núcleo Accumbens , Recompensa , Núcleo Accumbens/metabolismo , Núcleo Accumbens/efeitos dos fármacos , Animais , Camundongos , Neurônios/metabolismo , Drogas Ilícitas/efeitos adversos , Proteína Enriquecida em Homólogo de Ras do Encéfalo/metabolismo , Proteína Enriquecida em Homólogo de Ras do Encéfalo/genética , Masculino , Camundongos Endogâmicos C57BL , Proteínas Proto-Oncogênicas c-fos/metabolismo , Proteínas Proto-Oncogênicas c-fos/genética , Transdução de Sinais , Transtornos Relacionados ao Uso de Substâncias , Análise de Célula Única , Cocaína/farmacologia , Cálcio/metabolismoRESUMO
Muscles featuring high frequency and high stroke linear actuation are essential for animals to achieve superior maneuverability, agility, and environmental adaptability. Artificial muscles are yet to match their biological counterparts, due to inferior actuation speed, magnitude, mode, or adaptability. Inspired by the hierarchical structure of natural muscles, artificial muscles are created that are powerful, responsive, robust, and adaptable. The artificial muscles consist of knots braided from 3D printed liquid crystal elastomer fibers and thin heating threads. The unique hierarchical, braided knot structure offers amplified linear stroke, force rate, and damage-tolerance, as verified by both numerical simulations and experiments. In particular, the square knotted artificial muscle shows reliable cycles of actuation at 1Hz in 3000m depth underwater. Potential application is demonstrated by propelling a model boat. Looking ahead, the knotted artificial muscles can empower novel biomedical devices and soft robots to explore various environments, from inside human body to the mysterious deep sea.
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Materiais Biomiméticos , Água , Materiais Biomiméticos/química , Água/química , Músculos , Impressão Tridimensional , Robótica , Órgãos Artificiais , Animais , Elastômeros/química , Biomimética/métodos , Cristais Líquidos/química , HumanosRESUMO
Mesembryanthemum crystallinum (common ice plant), a facultative CAM plant, shifts from C3 to CAM photosynthesis under salt stress, enhancing water use efficiency. Here we used transcriptomics, proteomics, and targeted metabolomics to profile molecular changes during the diel cycle of C3 to CAM transition. The results confirmed expected changes associated with CAM photosynthesis, starch biosynthesis and degradation, and glycolysis/gluconeogenesis. Importantly, they yielded new discoveries: 1) Transcripts displayed greater circadian regulation than proteins. 2) Oxidative phosphorylation and inositol methylation may play important roles in initiating the transition. 3) V-type H+-ATPases showed consistent transcriptional regulation, aiding in vacuolar malate uptake. 4) A protein phosphatase 2C, a major component in the ABA signaling pathway, may trigger the C3 to CAM transition. Our work highlights the potential molecular switches in the C3 to CAM transition, including the potential role of ABA signaling. SIGNIFICANCE: The common ice plant is a model facultative CAM plant, and under stress conditions it can shift from C3 to CAM photosynthesis within a three-day period. However, knowledge about the molecular changes during the transition and the molecular switches enabling the transition is lacking. Multi-omic analyses not only revealed the molecular changes during the transition, but also highlighted the importance of ABA signaling, inositol methylation, V-type H+-ATPase in initiating the shift. The findings may explain physiological changes and nocturnal stomatal opening, and inform future synthetic biology effort in improving crop water use efficiency and stress resilience.
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Mesembryanthemum , Fotossíntese , Fotossíntese/fisiologia , Mesembryanthemum/metabolismo , Multiômica , Plantas , Inositol/metabolismo , Água/metabolismoRESUMO
Recent studies have examined whether the internal selection mechanism functions similarly for perception and visual working memory (VWM). However, the process of how we access and manipulate object representations distributed in a 3D space remains unclear. In this study, we utilized a memory search task to investigate the effect of depth on object selection and manipulation within VWM. The memory display consisted of colored items half positioned at the near depth plane and the other half at the far plane. During memory maintenance, the participants were instructed to search for a target representation and update its color. The results showed that under object-based attention (Experiments 1, 3, and 5), the update time was faster for targets at the near plane than for those at the far plane. This effect was absent in VWM when deploying spatial attention (Experiment 2) and in visual search regardless of the type of attention deployed (Experiment 4). The differential effects of depth on spatial and object-based attention in VWM suggest that spatial attention primarily relied on 2D location information irrespective of depth, whereas object-based attention seemed to prioritize memory representations at the front plane before shifting to the back. Our findings shed light on the interaction between depth perception and the selection mechanisms within VWM in a 3D context, emphasizing the importance of ordinal, rather than metric, spatial information in guiding object-based attention in VWM.
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Post-extraction alveolar bone atrophy greatly hinders the subsequent orthodontic tooth movement (OTM) or implant placement. In this study, we synthesized biodegradable bifunctional bioactive calcium phosphorus nanoflowers (NFs) loaded with abaloparatide (ABL), namely ABL@NFs, to achieve spatiotemporal management for alveolar bone regeneration. The NFs exhibited a porous hierarchical structure, high drug encapsulation efficacy, and desirable biocompatibility. ABL was initially released to recruit stem cells, followed by sustained release of Ca2+ and PO43- for in situ interface mineralization, establishing an osteogenic "biomineralized environment". ABL@NFs successfully restored morphologically and functionally active alveolar bone without affecting OTM. In conclusion, the ABL@NFs demonstrated promising outcomes for bone regeneration under orthodontic condition, which might provide a desirable reference of man-made "bone powder" in the hard tissue regeneration field.
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Regeneração Óssea , Osteogênese , Proteína Relacionada ao Hormônio Paratireóideo , Humanos , Osso e Ossos , PorosidadeRESUMO
BACKGROUND: Liver aging, marked by cellular senescence and low-grade inflammation, heightens susceptibility to chronic liver disease and worsens its prognosis. Insulin-like growth factor 2 (IGF2) has been implicated in numerous aging-related diseases. Nevertheless, its role and underlying molecular mechanisms in liver aging remain largely unexplored. METHODS: The expression of IGF2 was examined in the liver of young (2-4 months), middle-aged (9-12 months), and old (24-26 months) C57BL/6 mice. In vivo, we used transgenic IGF2f/f; Alb-Cre mice and D-galactose-induced aging model to explore the role of IGF2 in liver aging. In vitro, we used specific short hairpin RNA against IGF2 to knock down IGF2 in AML12 cells. D-galactose and hydrogen peroxide treatment were used to induce AML12 cell senescence. RESULTS: We observed a significant reduction of IGF2 levels in the livers of aged mice. Subsequently, we demonstrated that IGF2 deficiency promoted senescence phenotypes and senescence-associated secretory phenotypes (SASPs), both in vitro and in vivo aging models. Moreover, IGF2 deficiency impaired mitochondrial function, reducing mitochondrial respiratory capacity, mitochondrial membrane potential, and nicotinamide adenine dinucleotide (NAD)+/NADH ratio, increasing intracellular and mitochondrial reactive oxygen species levels, and disrupting mitochondrial membrane structure. Additionally, IGF2 deficiency markedly upregulated CCAAT/enhancer-binding protein beta (CEBPB). Notably, inhibiting CEBPB reversed the senescence phenotypes and reduced SASPs induced by IGF2 deficiency. CONCLUSIONS: In summary, our findings strongly suggest that IGF2 deficiency promotes liver aging through mitochondrial dysfunction and upregulated CEBPB signaling. These results provide compelling evidence for considering IGF2 as a potential target for interventions aimed at slowing down the process of liver aging.
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Envelhecimento , Galactose , Animais , Camundongos , Envelhecimento/metabolismo , Galactose/metabolismo , Galactose/farmacologia , Fígado/metabolismo , Camundongos Endogâmicos C57BL , Mitocôndrias/metabolismoRESUMO
Poly(glycolic acid) (PGA) is a biodegradable polymer with high gas barrier properties, mechanical strength, and heat deflection temperature. However, PGA's brittleness severely limits its application in packaging, creating a need to develop PGA-based copolymers with improved elasticity that maintain its barrier properties and hydrolytic degradability. In this work, a series of PGBAT (poly(glycolic acid-co-butylene) adipate-co-butylene terephthalate) copolymers containing 21-92% glycolic acid (nGA) with Mw values of 46,700-50,600 g mol-1 were synthesized via melt polycondensation, and the effects of altering the nGA on PGBAT's thermomechanical properties and hydrolysis rate were investigated. Poly(glycolic acid-co-butylene succinate) (PGBS) and poly(glycolic acid-co-butylene terephthalate) (PGBT) copolymers with high nGA were synthesized for comparison. DSC analysis revealed that PGBAT21 (nGA = 21%) and PGBAT92 were semicrystalline, melting between 102.8 and 163.3 °C, while PGBAT44, PGBAT86-89, PGBT80, and PGBS90 were amorphous, with Tg values from -19.0 to 23.7 °C. These high nGA copolymers showed similar rates of hydrolysis to PGA, whereas those containing <50% GA showed almost no mass loss over the testing period. Their mechanical properties were highly dependent upon their crystallinity and improved significantly after annealing. Of the high nGA copolymers, annealed PGBS90 (Mw 97,000 g mol-1) possessed excellent mechanical properties with a modulus of 588 MPa, tensile strength of 30.0 MPa, and elongation at break of 171%, a significant improvement on PGA's elongation at break of 3%. This work demonstrates the potential of enhancing PGA's flexibility by introducing minor amounts of low-cost diols and diacids into its synthesis.
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Addiction prioritizes drug use over innate needs by "hijacking" brain circuits that direct motivation, but how this develops remains unclear. Using whole-brain FOS mapping and in vivo single-neuron calcium imaging, we find that drugs of abuse augment ensemble activity in the nucleus accumbens (NAc) and disorganize overlapping ensemble responses to natural rewards in a cell-type-specific manner. Combining "FOS-Seq", CRISPR-perturbations, and snRNA-seq, we identify Rheb as a shared molecular substrate that regulates cell-type-specific signal transductions in NAc while enabling drugs to suppress natural reward responses. Retrograde circuit mapping pinpoints orbitofrontal cortex which, upon activation, mirrors drug effects on innate needs. These findings deconstruct the dynamic, molecular, and circuit basis of a common reward circuit, wherein drug value is scaled to promote drug-seeking over other, normative goals.
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Global climate change and population growth are persistently posing threats to natural resources (e.g., freshwater) and agricultural production. Crassulacean acid metabolism (CAM) evolved from C3 photosynthesis as an adaptive form of photosynthesis in hot and arid regions. It features the nocturnal opening of stomata for CO2 assimilation, diurnal closure of stomata for water conservation, and high water-use efficiency. To cope with global climate challenges, the CAM mechanism has attracted renewed attention. Facultative CAM is a specialized form of CAM that normally employs C3 or C4 photosynthesis but can shift to CAM under stress conditions. It not only serves as a model for studying the molecular mechanisms underlying the CAM evolution, but also provides a plausible solution for creating stress-resilient crops with facultative CAM traits. This review mainly discusses the recent research effort in defining the C3 to CAM transition of facultative CAM plants, and highlights challenges and future directions in this important research area with great application potential.
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Metabolismo Ácido das Crassuláceas , Fotossíntese , Agricultura , Mudança Climática , Produtos AgrícolasRESUMO
With the birth of next-generation sequencing (NGS) technology, genomic data in public databases have increased exponentially. Unfortunately, exogenous contamination or intracellular parasite sequences in assemblies could confuse genomic analysis. Meanwhile, they can provide a valuable resource for studies of host-microbe interactions. Here, we used a strategy based on DNA barcodes to scan protistan contamination in the GenBank WGS/TSA database. The results showed a total of 13,952 metazoan/animal assemblies in GenBank, where 17,036 contigs were found to be protistan contaminants in 1507 assemblies (10.8%), with even higher contamination rates in taxa of Cnidaria (150/281), Crustacea (237/480), and Mollusca (107/410). Taxonomic analysis of the protists derived from these contigs showed variations in abundance and evenness of protistan contamination across different metazoan taxa, reflecting host preferences of Apicomplexa, Ciliophora, Oomycota and Symbiodiniaceae for mammals and birds, Crustacea, insects, and Cnidaria, respectively. Finally, mitochondrial proteins COX1 and CYTB were predicted from these contigs, and the phylogenetic analysis corroborated the protistan origination and heterogeneous distribution of the contaminated contigs. Overall, in this study, we conducted a large-scale scan of protistan contaminant in genomic resources, and the protistan sequences detected will help uncover the protist diversity and relationships of these picoeukaryotes with Metazoa.
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Platelet-rich fibrin (PRF) is an autologous growth factor carrier that promotes bone tissue regeneration, but its effectiveness is restrained by poor storage capabilities, uncontrollable concentration of growth factors, unstable shape, etc. Herein, we developed a photocrosslinkable composite hydrogel by incorporating lyophilized PRF exudate (LPRFe) into the carboxymethyl chitosan methacryloyl (CMCSMA)/gelatin methacryloyl (GelMA) hydrogel to effectively solve the dilemma of PRF. The hydrogel possessed suitable physical properties and sustainable release ability of growth factors in LPRFe. The LPRFe-loaded hydrogel could improve the adhesion, proliferation, migration, and osteogenic differentiation of rat bone mesenchymal stem cells (BMSCs). Furthermore, the animal experiments demonstrated that the hydrogel possessed excellent biocompatibility and biodegradability, and the introduction of LPRFe in the hydrogel can effectively accelerate the bone healing process. Conclusively, the combination of LPRFe with CMCSMA/GelMA hydrogel may be a promising therapeutic approach for bone defects.
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Quitosana , Fibrina Rica em Plaquetas , Ratos , Animais , Hidrogéis/farmacologia , Quitosana/farmacologia , Osteogênese , Gelatina/farmacologiaRESUMO
Bats have received increasing attention because of some unique biological features they possess. TRIM is a large family of proteins that participate in diverse cellular functions, such as antiviral immunity, DNA damage repair, tumor suppression, and aging. These functional areas appear to be highly consistent with the special characteristics of bats, such as tolerance to viruses and DNA damage generated in flight, low cancer incidence, and longevity. However, there is still a lack of systematic study of the TRIM family in bats. Here, we explored the TRIM family of bats using the genomes of 16 representative species. The results showed that the bat TRIM family contains 70 members, with 24 under positive selection and 7 duplicated. Additional transcriptomic analysis revealed the tissue-specific expressions of TRIM9, 46, 54, 55, 63, and 72. Additionally, following interferon or viral stimulation, TRIM orthologs associated with antiviral immunity reported in humans were also upregulated in bat cells. The present study systematically analyzed the composition, evolution, and expression of bat TRIM genes. It may provide a theoretical basis for studies of bat TRIM in the fields of antiviral immunity, longevity, and tolerance to DNA damage.
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Quirópteros , Vírus , Animais , Humanos , Proteínas com Motivo Tripartido/genética , Vírus/genética , Antivirais/metabolismo , Genoma , FilogeniaRESUMO
To elucidate the role of post-translational modifications (PTMs) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein's structure and virulence, we generated a high-resolution map of 87 PTMs using liquid chromatography with tandem mass spectrometry data on the extracted spike protein from SARS-CoV-2 virions and then reconstituted its structure heterogeneity caused by PTMs. Nonetheless, Alphafold2, a high-accuracy artificial intelligence tool to perform protein structure prediction, relies solely on primary amino acid sequence, whereas the impact of PTM, which often modulates critical protein structure and function, is much ignored. To overcome this challenge, we proposed the mutagenesis approach-an in silico, site-directed amino acid substitution to mimic the influence of PTMs on protein structure due to altered physicochemical properties in the post-translationally modified amino acids-and then reconstituted the spike protein's structure from the substituted sequences by Alphafold2. For the first time, the proposed method revealed predicted protein structures resulting from PTMs, a problem that Alphafold2 has yet to address. As an example, we performed computational analyses of the interaction of the post-translationally modified spike protein with its host factors such as angiotensin-converting enzyme 2 to illuminate binding affinity. Mechanistically, this study suggested the structural analysis of post-translationally modified protein via mutagenesis and deep learning. To summarize, the reconstructed spike protein structures showed that specific PTMs can be used to modulate host factor binding, guide antibody design, and pave the way for new therapeutic targets. The code and Supplementary Materials are freely available at https://github.com/LTZHKUSTGZ/SARS-CoV-2-spike-protein-PTM.
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Pancharatnam-Berry (PB) metasurfaces have demonstrated mighty capability to manipulate electromagnetic (EM) waves, and exhibited potential applications for devices with broadband and efficient functionality. However, it remains a challenge to simultaneously achieve broadband and efficient wavefront manipulation for terahertz (THz) components with simple profiles. Herein, we introduce a simple ultra-thin PB metasurface with superior properties in the THz region. The structure is composed of a simple metallic C-Shaped Split Ring Resonator (CSRR) patterned on a flexible polyimide support layer. It is verified that the circular transmission efficiency is close to the theoretical limit of the single-layer metasurface in the range of 0.6 - 1.2 THz. Furthermore, we design metasurfaces based on the PB meta-atoms with spatially rotated orientation to achieve beam steering and superposition of vortex waves. The results are basically in line with expectations, validating the good performances of our proposal. This simple and easily deployable metasurface will give rise to more possibilities for the design of THz functional devices.