Site-specific protein labeling plays important roles in drug discovery and illuminating biological processes at the molecular level.However,it is challenging to label proteins with high specificity while not affecting...Site-specific protein labeling plays important roles in drug discovery and illuminating biological processes at the molecular level.However,it is challenging to label proteins with high specificity while not affecting their structures and biochemical activities.Over the last few years,a variety of promising strategies have been devised that address these challenges including those that involve introduction of small-size peptide tags or unnatural amino acids(UAAs),chemical labeling of specific protein residues,and affinity-driven labeling.This review summarizes recent developments made in the area of site-specific protein labeling utilizing genetically encoding-and chemical-based methods,and discusses future issues that need to be addressed by researchers in this field.展开更多
Semantic segmentation is a core task in computer vision that allows AI models to interact and understand their surrounding environment. Similarly to how humans subconsciously segment scenes, this ability is crucial fo...Semantic segmentation is a core task in computer vision that allows AI models to interact and understand their surrounding environment. Similarly to how humans subconsciously segment scenes, this ability is crucial for scene understanding. However, a challenge many semantic learning models face is the lack of data. Existing video datasets are limited to short, low-resolution videos that are not representative of real-world examples. Thus, one of our key contributions is a customized semantic segmentation version of the Walking Tours Dataset that features hour-long, high-resolution, real-world data from tours of different cities. Additionally, we evaluate the performance of open-vocabulary, semantic model OpenSeeD on our own custom dataset and discuss future implications.展开更多
In 2012, Ponraj et al. defined a concept of k-product cordial labeling as follows: Let f be a map from V(G)to { 0,1,⋯,k−1 }where k is an integer, 1≤k≤| V(G) |. For each edge uvassign the label f(u)f(v)(modk). f is c...In 2012, Ponraj et al. defined a concept of k-product cordial labeling as follows: Let f be a map from V(G)to { 0,1,⋯,k−1 }where k is an integer, 1≤k≤| V(G) |. For each edge uvassign the label f(u)f(v)(modk). f is called a k-product cordial labeling if | vf(i)−vf(j) |≤1, and | ef(i)−ef(j) |≤1, i,j∈{ 0,1,⋯,k−1 }, where vf(x)and ef(x)denote the number of vertices and edges respectively labeled with x (x=0,1,⋯,k−1). Motivated by this concept, we further studied and established that several families of graphs admit k-product cordial labeling. In this paper, we show that the path graphs Pnadmit k-product cordial labeling.展开更多
Urochordate Ciona spp.are ideal marine model organisms for studying embryogenesis and developmental and evolution-ary biology.However,the effective implementation of genetic labeling and CRISPR/Cas9-based editing tool...Urochordate Ciona spp.are ideal marine model organisms for studying embryogenesis and developmental and evolution-ary biology.However,the effective implementation of genetic labeling and CRISPR/Cas9-based editing tools at cellular resolution remains challenging.This study successfully developed and validated a collection of Gateway-based vectors for cell labeling in Ciona spp.The destination vector sets contained two Gateway cassettes flanked by Minos sites,allowing the N-or C-terminal tagging of a protein of interest with various fluorescent markers.In addition,we optimized the CRISPR/Cas9 and CRISPR/dCas9 systems by incorporating P2A-mCherry,a fluorescent indicator for Cas9 expression at cellular resolution.We demonstrated the effective destruction or inhibition of target genes when CRISPR constructs were introduced into fertilized eggs.Furthermore,we engineered a dual fluorescence sensor system that helps visualize successful gene knockouts at the cellular level in specific tissues.The genetic tools developed in this study offer a robust method for gene expression,cell tracking,and subcellular protein localization while also facilitating tissue-specific functional analysis in Ciona embryos and other model systems.展开更多
Cilia are indispensable for organ development and function,and their dysfunction causes a range of syndromic diseases known as ciliopathies,including obesity,cystic kidney disease,situs inversus,and male infertility(R...Cilia are indispensable for organ development and function,and their dysfunction causes a range of syndromic diseases known as ciliopathies,including obesity,cystic kidney disease,situs inversus,and male infertility(Reiter and Leroux,2017;Wallmeier et al.,2020).To date,over 180 ciliopathy-associated genes have been identified(Reiter and Leroux,2017),yet the underlying mechanisms remain poorly understood.展开更多
Nanoclays have large specific surface area,good adsorption properties,and biocompatibility that have great potential for drug delivery applications[1].Evaluating the in vivo metabolic pathways of nanoclays can help to...Nanoclays have large specific surface area,good adsorption properties,and biocompatibility that have great potential for drug delivery applications[1].Evaluating the in vivo metabolic pathways of nanoclays can help to understand their pharmacodynamic sites and the toxicological effects caused by their in vivo retention time[2].展开更多
Acute lung injury(ALI)is a serious clinical condition with a high mortality rate.Oxidative stress and inflammatory responses play pivotal roles in the pathogenesis of ALI.ONOO^(−)is a key mediator that exacerbates oxi...Acute lung injury(ALI)is a serious clinical condition with a high mortality rate.Oxidative stress and inflammatory responses play pivotal roles in the pathogenesis of ALI.ONOO^(−)is a key mediator that exacerbates oxidative damage and microvascular permeability in ALI.Accurate detection of ONOO^(−)would facilitate early diagnosis and intervention in ALI.Near-infrared fluorescence(NIRF)probes offer new solutions due to their sensitivity,depth of tissue penetration,and imaging capabilities.However,the developed ONOO^(−)fluorescent probes face problems such as interference from other reactive oxygen species and easy intracellular diffusion.To address these issues,we introduced an innovative self-immobilizing NIRF probe,DCI2F-OTf,which was capable of monitoring ONOO^(−)in vitro and in vivo.Importantly,leveraging the high reactivity of the methylene quinone(QM)intermediate,DCI2F-OTf was able to covalently label proteins in the presence of ONOO^(−),enabling in situ imaging.In mice models of ALI,DCI2F-OTf enabled real-time imaging of ONOO^(−)levels and found that ONOO^(−)was tightly correlated with the progression of ALI.Our findings demonstrated that DCI2F-OTf was a promising chemical tool for the detection of ONOO^(−),which could help to gain insight into the pathogenesis of ALI and monitor treatment efficacy.展开更多
This paper is concerned with design-ing symbol labeling for a low-density parity-check(LDPC)-coded delayed bit-interleaved coded modu-lation(DBICM)scheme in a two-way relay channel(TWRC).We first present some properti...This paper is concerned with design-ing symbol labeling for a low-density parity-check(LDPC)-coded delayed bit-interleaved coded modu-lation(DBICM)scheme in a two-way relay channel(TWRC).We first present some properties of symbol labeling within a phase shift keying(PSK)modula-tion.These properties reduce the candidate labeling search space.Based on this search space,we take DBICM capacity as the cost function and propose a general method for optimizing symbol labeling by em-ploying the differential evolution algorithm.Numeri-cal results show that our labeling obtains a signal-to-noise ratio(SNR)gain up to 0.45 dB with respect to Gray labeling.展开更多
Background:Rabies virus(RABV)-derived neuronal tracing tools are extensively applied in retrograde tracing due to their strict retrograde transsynaptic transfer property and low neurotoxicity.However,the RABV infectio...Background:Rabies virus(RABV)-derived neuronal tracing tools are extensively applied in retrograde tracing due to their strict retrograde transsynaptic transfer property and low neurotoxicity.However,the RABV infection and expression of fluorescence products would be gradually cleared while the infected neurons still survive,a phenomenon known as non-cytolytic immune clearance(NCLIC).This phenomenon introduced the risk of fluorescence loss and led to the omission of a subset of neurons that should be labeled,thereby interfering in the analysis of tracing results.Methods:To compensate for the fluorescence loss problem,in this study,we developed a novel marker footprints(MF)mouse,involving a Cre recombinase-dependent red fluorescent reporter system and systemic expression of glycoprotein(G)and ASLV-A receptor(TVA).Using this mouse model combined with the well-developed RABV-EnvA-ΔG-GFP-Cre viral tool,we developed a novel green-to-red spectral labeling strategy.Results:Neurons in the MF mouse could be co-labeled with green fluorescence from the very quick expression of the viral tool and with red fluorescence from the relatively slow expression of the neuron itself,so neurons undergoing NCLIC with green fluorescence loss could be relabeled red.Furthermore,newly infected neurons could be labeled green and other neurons could be labeled yellow due to the temporal expression difference between the two fluorescent proteins.Conclusions:This is the first polysynaptic retrograde tracing labeling strategy that could label neurons using spectral fluorescence colors with only one injection of the viral tool,enabling its application in recognizing the labeling sequence of neurons in brain regions and enhancing the spatiotemporal resolution of neuronal tracing.展开更多
Liquid-liquid phase separation(LLPS)of proteins and nucleic acids is a common phenomenon in cells that underlies the formation of membraneless organelles.Although the macroscopic behavior of biomolecular coacervates h...Liquid-liquid phase separation(LLPS)of proteins and nucleic acids is a common phenomenon in cells that underlies the formation of membraneless organelles.Although the macroscopic behavior of biomolecular coacervates has been elucidated by microscopy,the detailed dynamic properties of proteins/peptides during the LLPS process remain poorly characterized.Here,site-directed spin labeling-electron paramagnetic resonance(SDSL-EPR)spectroscopy was employed to characterize the dynamic properties of a minimal model LLPS system consisting of positively charged peptides and RNA.The degree of phase separation,indicated by broadening of the EPR spectrum of the spin-labeled peptide due to slow molecular tumbling,was monitored by EPR.In addition,three distinct populations with varying molecular motion during LLPS,featuring different spectral lineshapes,were identified.These populations included a fast motion component(Ⅰ),a slower motion component(Ⅱ)associated with peptides in the dispersed phase and an immobile component(Ⅲ)observed in the dense phase.With gradual titration of the peptides to RNA,the EPR spectrum gradually shifted,refiecting changes in the populations of the components.Together,SDSL-EPR method not only provides new insights into the dynamic behavior of biomolecules during LLPS,but also offers a sensitive method for biomolecular phase separation processes at the molecular level.展开更多
Digital twin technology is revolutionizing personalized healthcare by creating dynamic virtual replicas of individual patients.This paper presents a novel multi-modal architecture leveraging digital twins to enhance p...Digital twin technology is revolutionizing personalized healthcare by creating dynamic virtual replicas of individual patients.This paper presents a novel multi-modal architecture leveraging digital twins to enhance precision in predictive diagnostics and treatment planning of phoneme labeling.By integrating real-time images,electronic health records,and genomic information,the system enables personalized simulations for disease progression modeling,treatment response prediction,and preventive care strategies.In dysarthric speech,which is characterized by articulation imprecision,temporal misalignments,and phoneme distortions,existing models struggle to capture these irregularities.Traditional approaches,often relying solely on audio features,fail to address the full complexity of phoneme variations,leading to increased phoneme error rates(PER)and word error rates(WER).To overcome these challenges,we propose a novel multi-modal architecture that integrates both audio and articulatory data through a combination of Temporal Convolutional Networks(TCNs),Graph Convolutional Networks(GCNs),Transformer Encoders,and a cross-modal attention mechanism.The audio branch of the model utilizes TCNs and Transformer Encoders to capture both short-and long-term dependencies in the audio signal,while the articulatory branch leverages GCNs to model spatial relationships between articulators,such as the lips,jaw,and tongue,allowing the model to detect subtle articulatory imprecisions.A cross-modal attention mechanism fuses the encoded audio and articulatory features,enabling dynamic adjustment of the model’s focus depending on input quality,which significantly improves phoneme labeling accuracy.The proposed model consistently outperforms existing methods,achieving lower Phoneme Error Rates(PER),Word Error Rates(WER),and Articulatory Feature Misclassification Rates(AFMR).Specifically,across all datasets,the model achieves an average PER of 13.43%,an average WER of 21.67%,and an average AFMR of 12.73%.By capturing both the acoustic and articulatory intricacies of speech,this comprehensive approach not only improves phoneme labeling precision but also marks substantial progress in speech recognition technology for individuals with dysarthria.展开更多
Self-labeling protein (SLP) tags, such as HaloTag, have gained considerable interest as advanced tools for live cell labeling. However, the chloroalkane-based substrates that can be directly used for protein labeling ...Self-labeling protein (SLP) tags, such as HaloTag, have gained considerable interest as advanced tools for live cell labeling. However, the chloroalkane-based substrates that can be directly used for protein labeling are limited. Here, we report two bioorthogonal small molecule linkers, chloroalkane-tetrazine (CA-Tz) and chloroalkane-azide (CA-N3), which can penetrate cell membranes and facilitate click chemistry-based labeling in live cells. We compare their labeling capability using two clickable silicon rhodamine dyes (SiR-PEG_(3)-TCO and SiR-PEG_(4)-DBCO). Confocal imaging results demonstrate that using CA-Tz and SiR-PEG_(3)-TCO dye exhibits superior intracellular labeling with low nonspecific signals. We subsequently compared the photostability of SiR dyes with that of green fluorescent proteins (mEmerald). Total internal reflection fluorescence (TIRF) imaging indicates that SiR dyes exhibit superior photostability under identical excitation conditions, making them suitable for long-term cell imaging. Furthermore, SiR dyes labeling also shows high structure retention for the fourth-order super-resolution optical fluctuation imaging (SOFI) compared to fluorescent proteins. This study presents clickable HaloTag linkers as effective tools for live cell labeling and imaging, highlighting the high-quality labeling of chloroalkane linkers and clickable dyes for live cell imaging.展开更多
Intelligent fault diagnosis technology plays an indispensable role in ensuring the safety,stability,and efficiency of railway operations.However,existing studies have the following limitations.1)They are typical black-...Intelligent fault diagnosis technology plays an indispensable role in ensuring the safety,stability,and efficiency of railway operations.However,existing studies have the following limitations.1)They are typical black-box models that lacks interpretability as well as they fuse features by simply stacking them,overlooking the discrepancies in the importance of different features,which reduces the credibility and diagnosis accuracy of the models.2)They ignore the effects of potentially mistaken labels in the training datasets disrupting the ability of the models to learn the true data distribution,which degrades the generalization performance of intelligent diagnosis models,especially when the training samples are limited.To address the above items,an interpretable few-shot framework for fault diagnosis with noisy labels is proposed for train transmission systems.In the proposed framework,a feature extractor is constructed by stacked frequency band focus modules,which can capture signal features in different frequency bands and further adaptively concentrate on the features corresponding to the potential fault characteristic frequency.Then,according to prototypical network,a novel metric-based classifier is developed that is tolerant to mislabeled support samples in the case of limited samples.Besides,a new loss function is designed to decrease the impact of label mistakes in query datasets.Finally,fault simulation experiments of subway train transmission systems are designed and conducted,and the effectiveness as well as superiority of the proposed method are proved by ablation experiments and comparison with the existing methods.展开更多
This paper addresses the verification of strong currentstate opacity with respect to real-time observations generated from a discrete-event system that is modeled with time labeled Petri nets. The standard current-sta...This paper addresses the verification of strong currentstate opacity with respect to real-time observations generated from a discrete-event system that is modeled with time labeled Petri nets. The standard current-state opacity cannot completely characterize higher-level security. To ensure the higher-level security requirements of a time-dependent system, we propose a strong version of opacity known as strong current-state opacity. For any path(state-event sequence with time information)π derived from a real-time observation that ends at a secret state, the strong current-state opacity of the real-time observation signifies that there is a non-secret path with the same real-time observation as π. We propose general and non-secret state class graphs, which characterize the general and non-secret states of time-dependent systems, respectively. To capture the observable behavior of non-secret states, a non-secret observer is proposed.Finally, we develop a structure called a real-time concurrent verifier to verify the strong current-state opacity of time labeled Petri nets. This approach is efficient since the real-time concurrent verifier can be constructed by solving a certain number of linear programming problems.展开更多
Straw return has demonstrated significant potential for enhancing carbon(C)sequestration and nitrogen(N)uptake while concurrently promoting plant productivity.However,the specific transport and distribution of C produ...Straw return has demonstrated significant potential for enhancing carbon(C)sequestration and nitrogen(N)uptake while concurrently promoting plant productivity.However,the specific transport and distribution of C produced by photosynthesis and exogenous N within the rice plant-soil system under straw return remains unclear.A long-term straw return pot trial experiment was conducted in a double cropping rice system,incorporating treatments of inorganic fertilizer application with straw removal(F),straw burning and ash return with reducing inorganic fertilizers(SBR),and straw return with reducing inorganic fertilizers(SR)to investigate C sequestration and exogenous N uptake using ^(13)C pulse and ^(15)N isotope tracer techniques.The SR treatment had significantly higher soil ^(13)C abundance,by 24.4 and 25.4%,respectively,^(13)C concentrations in aboveground plant parts,by 18.4 and 35.8%respectively,and ^(15)N concentrations in rice panicles,by 12.8 and 34.3%than the SBR and F treatments.This enhancement contributed to a higher total organic C concentration and increased rice grain yield in the SR treatment.Furthermore,the SR treatment had significantly higher photosynthetic C,by 9.8%,which was directly transferred to soil C.The SR treatment had a higher distribution of photosynthetic C in the leaves and stems,but a lower distribution in the panicle compared to the SBR treatment.This finding is advantageous for sequestering photosynthetic C into the soil through straw return;conversely,opposite trends were observed in ^(15)N distribution.In addition,rice plants in the SR treatment had increased N uptake from urea and soil N sources,enhancing N recovery by 9.2 and 12.5%,respectively,and reducing soil N residues.Correlation analysis showed that the SR treatment increased the concentrations of ^(13)C in leaves and roots while decreasing the ^(15)N abundance in all rice organs,thereby contributing to an increase in rice yield.The partial least square path model suggested that the increase in rice yield under the SR treatment was primarily linked to ^(13)C accumulation within the rice plant-soil system.The results suggest that straw return increases the sequestration of photosynthetic C and exogenous N in the rice plant-soil system and increases N utilization efficiency,which subsequently improves both rice and soil productivity.展开更多
Objective: Xueteng-related herbs include Spatholobi Caulis(Jixueteng in Chinese), Sargentodoxae Caulis(Daxueteng in Chinese), Kadsurae Caulis(Dianjixueteng in Chinese), and other medicinal plant stems that release red...Objective: Xueteng-related herbs include Spatholobi Caulis(Jixueteng in Chinese), Sargentodoxae Caulis(Daxueteng in Chinese), Kadsurae Caulis(Dianjixueteng in Chinese), and other medicinal plant stems that release reddish-brown juices after being cut. However, similarity in phonetic spelling and sound leads to their misuse in clinic or commercial circulation. Accurate labeling is imperative as well as effective for species identification.Methods: In this study, the ITS2 sequences of 76 samples of Xueteng-related herbs were obtained and analyzed to identify them. And then they were converted into QR codes using the open source PHP QR code. Also, a DNA barcode reference library was established according to these sequences and was used to authenticate the 25 samples of Xueteng-related herbs collected from the market.Results: The lengths of the ITS2 sequences of different Xueteng-related herbs ranged from 207 to 235 bp and the GC contents were 57.5%-71.0%. Jixueteng, Daxueteng, and Dianjixueteng were clustered into three clades respectively in the neighbor-joining(NJ) phylogenetic tree, and the efficiency of the BLAST method was 100%. The ITS2 sequences of different Xueteng-related herbs were presented vividly and specifically in QR code. Twenty-two of all 25 commercial samples were consistent with the original labels, whereas three samples marked "Dianjixueteng" were authenticated as "Jixueteng".Conclusion: QR code labeling system based on DNA barcode is an effective labeling system of Xuetengrelated herbs for their circulation regulation.展开更多
As one important type of post-translational modifications(PTMs),protein lysine succinylation regulates many important biological processes.It is also closely involved with some major diseases in the aspects of Cardiom...As one important type of post-translational modifications(PTMs),protein lysine succinylation regulates many important biological processes.It is also closely involved with some major diseases in the aspects of Cardiometabolic,liver metabolic,nervous system and so on.Therefore,it is imperative to predict the succinylation sites in proteins for both basic research and drug development.In this paper,a novel predictor called i Succ Lys-BLS was proposed by not only introducing a new machine learning algorithm—Broad Learning System,but also optimizing the imbalanced data by randomly labeling samples.Rigorous cross-validation and independent test indicate that the success rate of i Succ Lys-BLS for positive samples is overwhelmingly higher than its counterparts.展开更多
Bioorthogonal cleavage and ligation reactions together form one more integrated system about the repertoire of bioorthogonal chemistry,capacitating an array of thrilling new biological applications.The bond-cleavage t...Bioorthogonal cleavage and ligation reactions together form one more integrated system about the repertoire of bioorthogonal chemistry,capacitating an array of thrilling new biological applications.The bond-cleavage type and position of biomolecular remain a great challenge,which determines the metabolic pathway of the targets in living systems.Herein we designed two linkages of methylene and carbonyl group attached the N-3 position of the 5-ethynyl-2’-deoxyuridine(EdU)base or the oxygen atom at deoxyribose 3’position to a photocaging group,which would be cleaved by irradiation with 365 nm ultraviolet light.EdU derivatives linked by methylene at the N-3 position had better photodecage efficiency and stability in the absence of light.This paper provides a strategy for studying the nucleoside metabolic pathways in cells,which can easily and conveniently evaluate the effect of the position and type of the linkages.The developed strategy affords a reference for controlling spatial and temporal metabolism of small-molecule drugs,allowing direct manipulation of intact cells under physiological conditions.展开更多
A kind of packet labeling algorithm for autonomous system is introduced. The fairness of the algorithm for each traffic stream in the integrated-services is analyzed. It is shown that the rate of each stream in the in...A kind of packet labeling algorithm for autonomous system is introduced. The fairness of the algorithm for each traffic stream in the integrated-services is analyzed. It is shown that the rate of each stream in the integrated-services would converge to a stable value if the transmittfing or forwarding rates converge to that of the receiving exponentially.展开更多
On the basis of inner-system labeling signaling used in the integrated access system,a kind of inner-system labeling algorithm is introduced in this paper, and the fairness of the algorithm for each traffic stream in ...On the basis of inner-system labeling signaling used in the integrated access system,a kind of inner-system labeling algorithm is introduced in this paper, and the fairness of the algorithm for each traffic stream in the integrated-services is analyzed. The base of this algorithm is Class of Services (CoS), and each packet entering the relative independent area (an autonomous system) would be labeled according to the service type or Quality of Service (QoS) in demand,and be scheduled and managed within the system (the system can be enlarged if conforming to the same protocol). The experimental results show that each of the stream rate in the integratedservices would converge to a stable value if the rates of transmitting converge to that of the receiving exponentially, that is, the effective traffic of each stream would be fair.展开更多
基金supported by the National Key R&D Program of China(No.2021YFC2103600)the National Natural Science Foundation of China(Nos.22278224,22478191)+1 种基金the Project of Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)the State Key Laboratory of Materials Oriented Chemical Engineering(No.KL21-08)。
文摘Site-specific protein labeling plays important roles in drug discovery and illuminating biological processes at the molecular level.However,it is challenging to label proteins with high specificity while not affecting their structures and biochemical activities.Over the last few years,a variety of promising strategies have been devised that address these challenges including those that involve introduction of small-size peptide tags or unnatural amino acids(UAAs),chemical labeling of specific protein residues,and affinity-driven labeling.This review summarizes recent developments made in the area of site-specific protein labeling utilizing genetically encoding-and chemical-based methods,and discusses future issues that need to be addressed by researchers in this field.
文摘Semantic segmentation is a core task in computer vision that allows AI models to interact and understand their surrounding environment. Similarly to how humans subconsciously segment scenes, this ability is crucial for scene understanding. However, a challenge many semantic learning models face is the lack of data. Existing video datasets are limited to short, low-resolution videos that are not representative of real-world examples. Thus, one of our key contributions is a customized semantic segmentation version of the Walking Tours Dataset that features hour-long, high-resolution, real-world data from tours of different cities. Additionally, we evaluate the performance of open-vocabulary, semantic model OpenSeeD on our own custom dataset and discuss future implications.
文摘In 2012, Ponraj et al. defined a concept of k-product cordial labeling as follows: Let f be a map from V(G)to { 0,1,⋯,k−1 }where k is an integer, 1≤k≤| V(G) |. For each edge uvassign the label f(u)f(v)(modk). f is called a k-product cordial labeling if | vf(i)−vf(j) |≤1, and | ef(i)−ef(j) |≤1, i,j∈{ 0,1,⋯,k−1 }, where vf(x)and ef(x)denote the number of vertices and edges respectively labeled with x (x=0,1,⋯,k−1). Motivated by this concept, we further studied and established that several families of graphs admit k-product cordial labeling. In this paper, we show that the path graphs Pnadmit k-product cordial labeling.
基金supported by the National Key Research and Development Program of China(2022YFC2601302)the Taishan Scholar Program of Shan-dong Province,China(B.D.).
文摘Urochordate Ciona spp.are ideal marine model organisms for studying embryogenesis and developmental and evolution-ary biology.However,the effective implementation of genetic labeling and CRISPR/Cas9-based editing tools at cellular resolution remains challenging.This study successfully developed and validated a collection of Gateway-based vectors for cell labeling in Ciona spp.The destination vector sets contained two Gateway cassettes flanked by Minos sites,allowing the N-or C-terminal tagging of a protein of interest with various fluorescent markers.In addition,we optimized the CRISPR/Cas9 and CRISPR/dCas9 systems by incorporating P2A-mCherry,a fluorescent indicator for Cas9 expression at cellular resolution.We demonstrated the effective destruction or inhibition of target genes when CRISPR constructs were introduced into fertilized eggs.Furthermore,we engineered a dual fluorescence sensor system that helps visualize successful gene knockouts at the cellular level in specific tissues.The genetic tools developed in this study offer a robust method for gene expression,cell tracking,and subcellular protein localization while also facilitating tissue-specific functional analysis in Ciona embryos and other model systems.
基金supported by grants from the National Key Research and Development Program of China(2019YFA0802704)the National Natural Science Foundation of China(31771620)+2 种基金the Natural Science Foundation of Chongqing,China(CSTB2022NSCQMSX1424)Research Startup Fund of Southwest University(SWU117064)Open Research Fund of National Health Commission Key Laboratory of Birth Defects Prevention&Henan Key Laboratory of Population Defects Prevention(ZD202302)。
文摘Cilia are indispensable for organ development and function,and their dysfunction causes a range of syndromic diseases known as ciliopathies,including obesity,cystic kidney disease,situs inversus,and male infertility(Reiter and Leroux,2017;Wallmeier et al.,2020).To date,over 180 ciliopathy-associated genes have been identified(Reiter and Leroux,2017),yet the underlying mechanisms remain poorly understood.
基金supported by National Key Research and Development Program of China(Grant No.:2023YFF0716000)National Natural Science Foundation of China(Grant No.:82071965)+1 种基金Major plan of Jointly Constructed Project by the Science and Technology Department of the State Administration of Traditional Chinese Medicine and the Zhejiang Provincial Administration of Traditional Chinese Medicine,China(Grant No.:GZY-ZJ-KJ-24025)Zhejiang Provincial Natural Science Foundation of China(Grant No.:LQ23H180005).
文摘Nanoclays have large specific surface area,good adsorption properties,and biocompatibility that have great potential for drug delivery applications[1].Evaluating the in vivo metabolic pathways of nanoclays can help to understand their pharmacodynamic sites and the toxicological effects caused by their in vivo retention time[2].
基金supported by the National Natural Science Foundation of China(Nos.22264013,21961010)Hainan Province Science and Technology Special Fund(Nos.ZDYF2021SHFZ219,ZDYF2022SHFZ037)+4 种基金Special Funds of S&T Cooperation and Exchange Projects of Shanxi Province(No.202204041101040)Natural Science Research Talent Project of Hainan Medical University(No.JBGS202101)Postgraduate Innovative Research Project of Hainan(No.Qhys2021-384)Hainan Province Clinical Medical Center(2021)Project for Functional Materials and Molecular Imaging Science Innovation Group of Hainan Medical University.
文摘Acute lung injury(ALI)is a serious clinical condition with a high mortality rate.Oxidative stress and inflammatory responses play pivotal roles in the pathogenesis of ALI.ONOO^(−)is a key mediator that exacerbates oxidative damage and microvascular permeability in ALI.Accurate detection of ONOO^(−)would facilitate early diagnosis and intervention in ALI.Near-infrared fluorescence(NIRF)probes offer new solutions due to their sensitivity,depth of tissue penetration,and imaging capabilities.However,the developed ONOO^(−)fluorescent probes face problems such as interference from other reactive oxygen species and easy intracellular diffusion.To address these issues,we introduced an innovative self-immobilizing NIRF probe,DCI2F-OTf,which was capable of monitoring ONOO^(−)in vitro and in vivo.Importantly,leveraging the high reactivity of the methylene quinone(QM)intermediate,DCI2F-OTf was able to covalently label proteins in the presence of ONOO^(−),enabling in situ imaging.In mice models of ALI,DCI2F-OTf enabled real-time imaging of ONOO^(−)levels and found that ONOO^(−)was tightly correlated with the progression of ALI.Our findings demonstrated that DCI2F-OTf was a promising chemical tool for the detection of ONOO^(−),which could help to gain insight into the pathogenesis of ALI and monitor treatment efficacy.
文摘This paper is concerned with design-ing symbol labeling for a low-density parity-check(LDPC)-coded delayed bit-interleaved coded modu-lation(DBICM)scheme in a two-way relay channel(TWRC).We first present some properties of symbol labeling within a phase shift keying(PSK)modula-tion.These properties reduce the candidate labeling search space.Based on this search space,we take DBICM capacity as the cost function and propose a general method for optimizing symbol labeling by em-ploying the differential evolution algorithm.Numeri-cal results show that our labeling obtains a signal-to-noise ratio(SNR)gain up to 0.45 dB with respect to Gray labeling.
基金Hubei Natural Science Foundation of China,Grant/Award Number:2024AFB593。
文摘Background:Rabies virus(RABV)-derived neuronal tracing tools are extensively applied in retrograde tracing due to their strict retrograde transsynaptic transfer property and low neurotoxicity.However,the RABV infection and expression of fluorescence products would be gradually cleared while the infected neurons still survive,a phenomenon known as non-cytolytic immune clearance(NCLIC).This phenomenon introduced the risk of fluorescence loss and led to the omission of a subset of neurons that should be labeled,thereby interfering in the analysis of tracing results.Methods:To compensate for the fluorescence loss problem,in this study,we developed a novel marker footprints(MF)mouse,involving a Cre recombinase-dependent red fluorescent reporter system and systemic expression of glycoprotein(G)and ASLV-A receptor(TVA).Using this mouse model combined with the well-developed RABV-EnvA-ΔG-GFP-Cre viral tool,we developed a novel green-to-red spectral labeling strategy.Results:Neurons in the MF mouse could be co-labeled with green fluorescence from the very quick expression of the viral tool and with red fluorescence from the relatively slow expression of the neuron itself,so neurons undergoing NCLIC with green fluorescence loss could be relabeled red.Furthermore,newly infected neurons could be labeled green and other neurons could be labeled yellow due to the temporal expression difference between the two fluorescent proteins.Conclusions:This is the first polysynaptic retrograde tracing labeling strategy that could label neurons using spectral fluorescence colors with only one injection of the viral tool,enabling its application in recognizing the labeling sequence of neurons in brain regions and enhancing the spatiotemporal resolution of neuronal tracing.
基金supported by the National Natural Science Foundation of China(No.21927814)the National Key Research and Development Program of China(Nos.2019YFA0405600,2019YFA0706900,2021YFA1200104,2022YFC3400500)+2 种基金the Strategic Priority Research Program of Chinese Academy of Sciences(Nos.XDB0540200,XDB37040201)Plans for Major Provincial Science&Technology Projects(No.202303a07020004)the Youth Innovation Promotion Association,CAS(No.2022455)。
文摘Liquid-liquid phase separation(LLPS)of proteins and nucleic acids is a common phenomenon in cells that underlies the formation of membraneless organelles.Although the macroscopic behavior of biomolecular coacervates has been elucidated by microscopy,the detailed dynamic properties of proteins/peptides during the LLPS process remain poorly characterized.Here,site-directed spin labeling-electron paramagnetic resonance(SDSL-EPR)spectroscopy was employed to characterize the dynamic properties of a minimal model LLPS system consisting of positively charged peptides and RNA.The degree of phase separation,indicated by broadening of the EPR spectrum of the spin-labeled peptide due to slow molecular tumbling,was monitored by EPR.In addition,three distinct populations with varying molecular motion during LLPS,featuring different spectral lineshapes,were identified.These populations included a fast motion component(Ⅰ),a slower motion component(Ⅱ)associated with peptides in the dispersed phase and an immobile component(Ⅲ)observed in the dense phase.With gradual titration of the peptides to RNA,the EPR spectrum gradually shifted,refiecting changes in the populations of the components.Together,SDSL-EPR method not only provides new insights into the dynamic behavior of biomolecules during LLPS,but also offers a sensitive method for biomolecular phase separation processes at the molecular level.
基金funded by the Ongoing Research Funding program(ORF-2025-867),King Saud University,Riyadh,Saudi Arabia.
文摘Digital twin technology is revolutionizing personalized healthcare by creating dynamic virtual replicas of individual patients.This paper presents a novel multi-modal architecture leveraging digital twins to enhance precision in predictive diagnostics and treatment planning of phoneme labeling.By integrating real-time images,electronic health records,and genomic information,the system enables personalized simulations for disease progression modeling,treatment response prediction,and preventive care strategies.In dysarthric speech,which is characterized by articulation imprecision,temporal misalignments,and phoneme distortions,existing models struggle to capture these irregularities.Traditional approaches,often relying solely on audio features,fail to address the full complexity of phoneme variations,leading to increased phoneme error rates(PER)and word error rates(WER).To overcome these challenges,we propose a novel multi-modal architecture that integrates both audio and articulatory data through a combination of Temporal Convolutional Networks(TCNs),Graph Convolutional Networks(GCNs),Transformer Encoders,and a cross-modal attention mechanism.The audio branch of the model utilizes TCNs and Transformer Encoders to capture both short-and long-term dependencies in the audio signal,while the articulatory branch leverages GCNs to model spatial relationships between articulators,such as the lips,jaw,and tongue,allowing the model to detect subtle articulatory imprecisions.A cross-modal attention mechanism fuses the encoded audio and articulatory features,enabling dynamic adjustment of the model’s focus depending on input quality,which significantly improves phoneme labeling accuracy.The proposed model consistently outperforms existing methods,achieving lower Phoneme Error Rates(PER),Word Error Rates(WER),and Articulatory Feature Misclassification Rates(AFMR).Specifically,across all datasets,the model achieves an average PER of 13.43%,an average WER of 21.67%,and an average AFMR of 12.73%.By capturing both the acoustic and articulatory intricacies of speech,this comprehensive approach not only improves phoneme labeling precision but also marks substantial progress in speech recognition technology for individuals with dysarthria.
基金funded by the National Natural Science Foundation of China (Nos. 62235007 and 22204070)the National Key Research and Development Program (No. 2020YFA0909000)+2 种基金Guangdong Provincial Key Laboratory of Advanced Biomaterials (No. 2022B1212010003)Shenzhen Science and Technology Innovation Project (Nos. KQTD20170810111314625, SGDX20211123114002003 and JCYJ20210324115807021)Shenzhen Bay Laboratory (No. SZBL2021080601002).
文摘Self-labeling protein (SLP) tags, such as HaloTag, have gained considerable interest as advanced tools for live cell labeling. However, the chloroalkane-based substrates that can be directly used for protein labeling are limited. Here, we report two bioorthogonal small molecule linkers, chloroalkane-tetrazine (CA-Tz) and chloroalkane-azide (CA-N3), which can penetrate cell membranes and facilitate click chemistry-based labeling in live cells. We compare their labeling capability using two clickable silicon rhodamine dyes (SiR-PEG_(3)-TCO and SiR-PEG_(4)-DBCO). Confocal imaging results demonstrate that using CA-Tz and SiR-PEG_(3)-TCO dye exhibits superior intracellular labeling with low nonspecific signals. We subsequently compared the photostability of SiR dyes with that of green fluorescent proteins (mEmerald). Total internal reflection fluorescence (TIRF) imaging indicates that SiR dyes exhibit superior photostability under identical excitation conditions, making them suitable for long-term cell imaging. Furthermore, SiR dyes labeling also shows high structure retention for the fourth-order super-resolution optical fluctuation imaging (SOFI) compared to fluorescent proteins. This study presents clickable HaloTag linkers as effective tools for live cell labeling and imaging, highlighting the high-quality labeling of chloroalkane linkers and clickable dyes for live cell imaging.
基金supported in part by the National Key R&D Program of China under Grant 2022YFB4300601in part by the State Key Laboratory of Advanced Rail Autonomous Operation under Grant RAO2023ZZ003.
文摘Intelligent fault diagnosis technology plays an indispensable role in ensuring the safety,stability,and efficiency of railway operations.However,existing studies have the following limitations.1)They are typical black-box models that lacks interpretability as well as they fuse features by simply stacking them,overlooking the discrepancies in the importance of different features,which reduces the credibility and diagnosis accuracy of the models.2)They ignore the effects of potentially mistaken labels in the training datasets disrupting the ability of the models to learn the true data distribution,which degrades the generalization performance of intelligent diagnosis models,especially when the training samples are limited.To address the above items,an interpretable few-shot framework for fault diagnosis with noisy labels is proposed for train transmission systems.In the proposed framework,a feature extractor is constructed by stacked frequency band focus modules,which can capture signal features in different frequency bands and further adaptively concentrate on the features corresponding to the potential fault characteristic frequency.Then,according to prototypical network,a novel metric-based classifier is developed that is tolerant to mislabeled support samples in the case of limited samples.Besides,a new loss function is designed to decrease the impact of label mistakes in query datasets.Finally,fault simulation experiments of subway train transmission systems are designed and conducted,and the effectiveness as well as superiority of the proposed method are proved by ablation experiments and comparison with the existing methods.
基金supported by the Special Fund for Scientific and Technological Innovation Strategy of Guangdong Province(2022A0505030025)the Science and Technology Fund,FDCT,Macao SAR(0064/2021/A2)
文摘This paper addresses the verification of strong currentstate opacity with respect to real-time observations generated from a discrete-event system that is modeled with time labeled Petri nets. The standard current-state opacity cannot completely characterize higher-level security. To ensure the higher-level security requirements of a time-dependent system, we propose a strong version of opacity known as strong current-state opacity. For any path(state-event sequence with time information)π derived from a real-time observation that ends at a secret state, the strong current-state opacity of the real-time observation signifies that there is a non-secret path with the same real-time observation as π. We propose general and non-secret state class graphs, which characterize the general and non-secret states of time-dependent systems, respectively. To capture the observable behavior of non-secret states, a non-secret observer is proposed.Finally, we develop a structure called a real-time concurrent verifier to verify the strong current-state opacity of time labeled Petri nets. This approach is efficient since the real-time concurrent verifier can be constructed by solving a certain number of linear programming problems.
基金supported by the National Natural Science Foundation of China(32160503)the Earmarked Fund for Jiangxi Agriculture Research System,China(JXARS-01)the National Key R&D Program of China(2023YFD2301303).
文摘Straw return has demonstrated significant potential for enhancing carbon(C)sequestration and nitrogen(N)uptake while concurrently promoting plant productivity.However,the specific transport and distribution of C produced by photosynthesis and exogenous N within the rice plant-soil system under straw return remains unclear.A long-term straw return pot trial experiment was conducted in a double cropping rice system,incorporating treatments of inorganic fertilizer application with straw removal(F),straw burning and ash return with reducing inorganic fertilizers(SBR),and straw return with reducing inorganic fertilizers(SR)to investigate C sequestration and exogenous N uptake using ^(13)C pulse and ^(15)N isotope tracer techniques.The SR treatment had significantly higher soil ^(13)C abundance,by 24.4 and 25.4%,respectively,^(13)C concentrations in aboveground plant parts,by 18.4 and 35.8%respectively,and ^(15)N concentrations in rice panicles,by 12.8 and 34.3%than the SBR and F treatments.This enhancement contributed to a higher total organic C concentration and increased rice grain yield in the SR treatment.Furthermore,the SR treatment had significantly higher photosynthetic C,by 9.8%,which was directly transferred to soil C.The SR treatment had a higher distribution of photosynthetic C in the leaves and stems,but a lower distribution in the panicle compared to the SBR treatment.This finding is advantageous for sequestering photosynthetic C into the soil through straw return;conversely,opposite trends were observed in ^(15)N distribution.In addition,rice plants in the SR treatment had increased N uptake from urea and soil N sources,enhancing N recovery by 9.2 and 12.5%,respectively,and reducing soil N residues.Correlation analysis showed that the SR treatment increased the concentrations of ^(13)C in leaves and roots while decreasing the ^(15)N abundance in all rice organs,thereby contributing to an increase in rice yield.The partial least square path model suggested that the increase in rice yield under the SR treatment was primarily linked to ^(13)C accumulation within the rice plant-soil system.The results suggest that straw return increases the sequestration of photosynthetic C and exogenous N in the rice plant-soil system and increases N utilization efficiency,which subsequently improves both rice and soil productivity.
基金supported by the CAMS Innovation Fund for Medical Sciences(CIFMS,2016-I2M-3-016)the Key Projects of the National Science and Technology Pillar Program(No.2011BAI07B08)
文摘Objective: Xueteng-related herbs include Spatholobi Caulis(Jixueteng in Chinese), Sargentodoxae Caulis(Daxueteng in Chinese), Kadsurae Caulis(Dianjixueteng in Chinese), and other medicinal plant stems that release reddish-brown juices after being cut. However, similarity in phonetic spelling and sound leads to their misuse in clinic or commercial circulation. Accurate labeling is imperative as well as effective for species identification.Methods: In this study, the ITS2 sequences of 76 samples of Xueteng-related herbs were obtained and analyzed to identify them. And then they were converted into QR codes using the open source PHP QR code. Also, a DNA barcode reference library was established according to these sequences and was used to authenticate the 25 samples of Xueteng-related herbs collected from the market.Results: The lengths of the ITS2 sequences of different Xueteng-related herbs ranged from 207 to 235 bp and the GC contents were 57.5%-71.0%. Jixueteng, Daxueteng, and Dianjixueteng were clustered into three clades respectively in the neighbor-joining(NJ) phylogenetic tree, and the efficiency of the BLAST method was 100%. The ITS2 sequences of different Xueteng-related herbs were presented vividly and specifically in QR code. Twenty-two of all 25 commercial samples were consistent with the original labels, whereas three samples marked "Dianjixueteng" were authenticated as "Jixueteng".Conclusion: QR code labeling system based on DNA barcode is an effective labeling system of Xuetengrelated herbs for their circulation regulation.
基金the National Natural Science Foundation of China(61761023,31760315)the Natural Science Foundation of Jiangxi Province,China(20202BABL202004,20202BAB202007)the Scientific Research Plan of the Department of Education of Jiangxi Province(GJJ190695)。
文摘As one important type of post-translational modifications(PTMs),protein lysine succinylation regulates many important biological processes.It is also closely involved with some major diseases in the aspects of Cardiometabolic,liver metabolic,nervous system and so on.Therefore,it is imperative to predict the succinylation sites in proteins for both basic research and drug development.In this paper,a novel predictor called i Succ Lys-BLS was proposed by not only introducing a new machine learning algorithm—Broad Learning System,but also optimizing the imbalanced data by randomly labeling samples.Rigorous cross-validation and independent test indicate that the success rate of i Succ Lys-BLS for positive samples is overwhelmingly higher than its counterparts.
基金supported by the National Natural Science Foundation of China(Nos.21432008,91753201 and 21721005)the large-scale instrument and equipment sharing foundation of Wuhan University。
文摘Bioorthogonal cleavage and ligation reactions together form one more integrated system about the repertoire of bioorthogonal chemistry,capacitating an array of thrilling new biological applications.The bond-cleavage type and position of biomolecular remain a great challenge,which determines the metabolic pathway of the targets in living systems.Herein we designed two linkages of methylene and carbonyl group attached the N-3 position of the 5-ethynyl-2’-deoxyuridine(EdU)base or the oxygen atom at deoxyribose 3’position to a photocaging group,which would be cleaved by irradiation with 365 nm ultraviolet light.EdU derivatives linked by methylene at the N-3 position had better photodecage efficiency and stability in the absence of light.This paper provides a strategy for studying the nucleoside metabolic pathways in cells,which can easily and conveniently evaluate the effect of the position and type of the linkages.The developed strategy affords a reference for controlling spatial and temporal metabolism of small-molecule drugs,allowing direct manipulation of intact cells under physiological conditions.
文摘A kind of packet labeling algorithm for autonomous system is introduced. The fairness of the algorithm for each traffic stream in the integrated-services is analyzed. It is shown that the rate of each stream in the integrated-services would converge to a stable value if the transmittfing or forwarding rates converge to that of the receiving exponentially.
文摘On the basis of inner-system labeling signaling used in the integrated access system,a kind of inner-system labeling algorithm is introduced in this paper, and the fairness of the algorithm for each traffic stream in the integrated-services is analyzed. The base of this algorithm is Class of Services (CoS), and each packet entering the relative independent area (an autonomous system) would be labeled according to the service type or Quality of Service (QoS) in demand,and be scheduled and managed within the system (the system can be enlarged if conforming to the same protocol). The experimental results show that each of the stream rate in the integratedservices would converge to a stable value if the rates of transmitting converge to that of the receiving exponentially, that is, the effective traffic of each stream would be fair.
