Remote sensing data plays an important role in natural disaster management.However,with the increase of the variety and quantity of remote sensors,the problem of“knowledge barriers”arises when data users in disaster...Remote sensing data plays an important role in natural disaster management.However,with the increase of the variety and quantity of remote sensors,the problem of“knowledge barriers”arises when data users in disaster field retrieve remote sensing data.To improve this problem,this paper proposes an ontology and rule based retrieval(ORR)method to retrieve disaster remote sensing data,and this method introduces ontology technology to express earthquake disaster and remote sensing knowledge,on this basis,and realizes the task suitability reasoning of earthquake disaster remote sensing data,mining the semantic relationship between remote sensing metadata and disasters.The prototype system is built according to the ORR method,which is compared with the traditional method,using the ORR method to retrieve disaster remote sensing data can reduce the knowledge requirements of data users in the retrieval process and improve data retrieval efficiency.展开更多
To resolve the ontology understanding problem, the structural features and the potential important terms of a large-scale ontology are investigated from the perspective of complex networks analysis. Through the empiri...To resolve the ontology understanding problem, the structural features and the potential important terms of a large-scale ontology are investigated from the perspective of complex networks analysis. Through the empirical studies of the gene ontology with various perspectives, this paper shows that the whole gene ontology displays the same topological features as complex networks including ＂small world＂ and ＂scale-free＂,while some sub-ontologies have the ＂scale-free＂ property but no ＂small world＂ effect.The potential important terms in an ontology are discovered by some famous complex network centralization methods.An evaluation method based on information retrieval in MEDLINE is designed to measure the effectiveness of the discovered important terms.According to the relevant literature of the gene ontology terms,the suitability of these centralization methods for ontology important concepts discovering is quantitatively evaluated.The experimental results indicate that the betweenness centrality is the most appropriate method among all the evaluated centralization measures.展开更多
In order to reduce the costs of the ontology construction, a general ontology learning framework （GOLF） is developed. The key technologies of the GOLF including domain concepts extraction and semantic relationships ...In order to reduce the costs of the ontology construction, a general ontology learning framework （GOLF） is developed. The key technologies of the GOLF including domain concepts extraction and semantic relationships between concepts and taxonomy automatic construction are proposed. At the same time ontology evaluation methods are also discussed. The experimental results show that this method produces better performance and it is applicable across different domains. By integrating several machine learning algorithms, this method suffers less ambiguity and can identify domain concepts and relations more accurately. By using generalized corpus WordNet and HowNet, this method is applicable across different domains. In addition, by obtaining source documents from the web on demand, the GOLF can produce up-to-date ontologies.展开更多
To improve the performance of the ontology matching process, a more efficient ontology matching algorithm, which can effectively eliminate unnecessary operations of matching entities, is proposed. By the theoretical a...To improve the performance of the ontology matching process, a more efficient ontology matching algorithm, which can effectively eliminate unnecessary operations of matching entities, is proposed. By the theoretical analysis and proof, a set of matching rules are summarized for depicting inherent relations among matching results of entities. Based on these rules, the proposed algorithm can reuse the matching results of two entities to directly determine the matching results of their adjacent entities. Thereby, redundant operations of matching adjacent entities can be avoided, which can improve the performance of the whole matching process. The experimental results show that, compared with related algorithms, the proposed algorithm has high matching accuracy and can remarkably reduce the consuming time of the whole matching process. So, the proposed algorithm is more competent for the large-scale ontology matching which often occurs in the practical heterogeneous web resources integration project.展开更多
Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported t...Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system.展开更多
To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This g...To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.展开更多
The basic unit in life is cell.?It contains many protein molecules located at its different organelles. The growth and reproduction of a cell as well as most of its other biological functions are performed via these p...The basic unit in life is cell.?It contains many protein molecules located at its different organelles. The growth and reproduction of a cell as well as most of its other biological functions are performed via these proteins. But proteins in different organelles or subcellular locations have different functions. Facing?the avalanche of protein sequences generated in the postgenomic age, we are challenged to develop high throughput tools for identifying the subcellular localization of proteins based on their sequence information alone. Although considerable efforts have been made in this regard, the problem is far apart from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for drug targets. Using the ML-GKR (Multi-Label Gaussian Kernel Regression) method,?we developed a new predictor called “pLoc-mGpos” by in-depth extracting the key information from GO (Gene Ontology) into the Chou’s general PseAAC (Pseudo Amino Acid Composition)?for predicting the subcellular localization of Gram-positive bacterial proteins with both single and multiple location sites. Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mGpos predictor is remarkably superior to “iLoc-Gpos”, the state-of-the-art predictor for the same purpose.?To maximize the convenience of most experimental scientists, a user-friendly web-server for the new powerful predictor has been established at http://www.jci-bioinfo.cn/pLoc-mGpos/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.展开更多
BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,...BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,several studies use genes involved in essential cellular functions[glyceraldehyde-3-phosphate dehydro-genase(GAPDH),18S rRNA,andβ-actin]without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes.Furthermore,such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recom-mend two or more genes.It impacts the credibility of these studies and causes dis-tortions in the gene expression findings.For tissue engineering,the accuracy of gene expression drives the best experimental or therapeutical approaches.We cultivated DPSCs under two conditions:Undifferentiated and osteogenic dif-ferentiation,both for 35 d.We evaluated the gene expression of 10 candidates for RGs[ribosomal protein,large,P0(RPLP0),TATA-binding protein(TBP),GAPDH,actin beta(ACTB),tubulin(TUB),aminolevulinic acid synthase 1(ALAS1),tyro-sine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,zeta(YWHAZ),eukaryotic translational elongation factor 1 alpha(EF1a),succinate dehydrogenase complex,subunit A,flavoprotein(SDHA),and beta-2-micro-globulin(B2M)]every 7 d(1,7,14,21,28,and 35 d)by RT-qPCR.The data were analysed by the four main algorithms,ΔCt method,geNorm,NormFinder,and BestKeeper and ranked by the RefFinder method.We subdivided the samples into eight subgroups.RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm.The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs.Either theΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes.However,geNorm analysis showed RPLP0/EF1αin the first place.These algorithms’two least stable RGs were B2M/GAPDH.For BestKeeper,ALAS1 was ranked as the most stable RG,and SDHA as the least stable RG.The pair RPLP0/TBP was detected in most subgroups as the most stable RGs,following the RefFinfer ranking.CONCLUSION For the first time,we show that RPLP0/TBP are the most stable RGs,whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.展开更多
Context and Objective: Over the past few decades, terminologies developed for clinical descriptions have been increasingly used as key resources for knowledge management, data integration, and decision support to the ...Context and Objective: Over the past few decades, terminologies developed for clinical descriptions have been increasingly used as key resources for knowledge management, data integration, and decision support to the extent that today they have become essential in the biomedical and health field. Among these clinical terminologies, some may possess the characteristics of one or several types of representation. This is the case for the Systematized Nomenclature of Human and Veterinary Medicine—Clinical Terms (SNOMED CT), which is both a clinical medical terminology and a formal ontology based on the principles of semantic web. Methods: We present and discuss, on one hand, the compliance of SNOMED CT with the requirements of a reference clinical terminology and, on the other hand, the specifications of the features and constructions of descriptive of SNOMED CT. Results: We demonstrate the consistency of the reference clinical terminology SNOMED CT with the principles stated in James J. Cimino’s desiderata and we also show that SNOMED CT contains an ontology based on the EL profile of OWL2 with some simplifications. Conclusions: The duality of SNOMED CT shown is crucial for understanding the versatility, depth, and scope in the health field.展开更多
With a few exceptions, physics theories are based in a conception of time and space;our two major theories, general relativity, and quantum field theory, differ in their conceptions. Key issues herein include mathemat...With a few exceptions, physics theories are based in a conception of time and space;our two major theories, general relativity, and quantum field theory, differ in their conceptions. Key issues herein include mathematics, logic, intuition, experiment, and ontology, with emphasis on simultaneity and dimensionality of the world. The treatment is through ontological comparison of two theories, space-time theory (special relativity) and energy-time theory (local absolute space and universal time). These two theories share many of the same equations but have different ontology.展开更多
Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(...Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.展开更多
Daily newspapers publish a tremendous amount of information disseminated through the Internet.Freely available and easily accessible large online repositories are not indexed and are in an un-processable format.The ma...Daily newspapers publish a tremendous amount of information disseminated through the Internet.Freely available and easily accessible large online repositories are not indexed and are in an un-processable format.The major hindrance in developing and evaluating existing/new monolingual text in an image is that it is not linked and indexed.There is no method to reuse the online news images because of the unavailability of standardized benchmark corpora,especially for South Asian languages.The corpus is a vital resource for developing and evaluating text in an image to reuse local news systems in general and specifically for the Urdu language.Lack of indexing,primarily semantic indexing of the daily news items,makes news items impracticable for any querying.Moreover,the most straightforward search facility does not support these unindexed news resources.Our study addresses this gap by associating and marking the newspaper images with one of the widely spoken but under-resourced languages,i.e.,Urdu.The present work proposed a method to build a benchmark corpus of news in image form by introducing a web crawler.The corpus is then semantically linked and annotated with daily news items.Two techniques are proposed for image annotation,free annotation and fixed cross examination annotation.The second technique got higher accuracy.Build news ontology in protégéusing OntologyWeb Language(OWL)language and indexed the annotations under it.The application is also built and linked with protégéso that the readers and journalists have an interface to query the news items directly.Similarly,news items linked together will provide complete coverage and bring together different opinions at a single location for readers to do the analysis themselves.展开更多
Alzheimer’s disease is a progressive neurodegenerative disorder and the most common cause of dementia that principally affects older adults.Pathogenic factors,such as oxidative stress,an increase in acetylcholinester...Alzheimer’s disease is a progressive neurodegenerative disorder and the most common cause of dementia that principally affects older adults.Pathogenic factors,such as oxidative stress,an increase in acetylcholinesterase activity,mitochondrial dysfunction,genotoxicity,and neuroinflammation are present in this syndrome,which leads to neurodegeneration.Neurodegenerative pathologies such as Alzheimer’s disease are considered late-onset diseases caused by the complex combination of genetic,epigenetic,and environmental factors.There are two main types of Alzheimer’s disease,known as familial Alzheimer’s disease(onset<65 years)and late-onset or sporadic Alzheimer’s disease(onset≥65 years).Patients with familial Alzheimer’s disease inherit the disease due to rare mutations on the amyloid precursor protein(APP),presenilin 1 and 2(PSEN1 and PSEN2)genes in an autosomaldominantly fashion with closely 100%penetrance.In contrast,a different picture seems to emerge for sporadic Alzheimer’s disease,which exhibits numerous non-Mendelian anomalies suggesting an epigenetic component in its etiology.Importantly,the fundamental pathophysiological mechanisms driving Alzheimer’s disease are interfaced with epigenetic dysregulation.However,the dynamic nature of epigenetics seems to open up new avenues and hope in regenerative neurogenesis to improve brain repair in Alzheimer’s disease or following injury or stroke in humans.In recent years,there has been an increase in interest in using natural products for the treatment of neurodegenerative illnesses such as Alzheimer’s disease.Through epigenetic mechanisms,such as DNA methylation,non-coding RNAs,histone modification,and chromatin conformation regulation,natural compounds appear to exert neuroprotective effects.While we do not purport to cover every in this work,we do attempt to illustrate how various phytochemical compounds regulate the epigenetic effects of a few Alzheimer’s disease-related genes.展开更多
Noncoding RNAs instruct the Cas9 nuclease to site speifillyl cleave DNA in the CRISPR/Cas9 system.Despite the high incidence of hepatocellular carcinoma(HCC),the patient's outcome is poor.As a result of the emerge...Noncoding RNAs instruct the Cas9 nuclease to site speifillyl cleave DNA in the CRISPR/Cas9 system.Despite the high incidence of hepatocellular carcinoma(HCC),the patient's outcome is poor.As a result of the emergence of therapeutic resistance in HCC patients,dlinicians have faced difficulties in treating such tumor.In addition,CRISPR/Cas9 screens were used to identify genes that improve the dlinical response of HCC patients.It is the objective of this article to summarize the current understanding of the use of the CRISPR/Cas9 system for the treatment of cancer,with a particular emphasis on HCC as part of the current state of knowledge.Thus,in order to locate recent developments in oncology research,we examined both the Scopus database and the PubMed database.The ability to selectively interfere with gene expression in combinatorial CRISPR/Cas9 screening can lead to the discovery of new effective HCC treatment regimens by combining clinically approved drugs.Drug resistance can be overcome with the help of the CRISPR/Cas9 system.HCC signature genes and resistance to treatment have been uncovered by genome-scale CRISPR activation screening although this method is not without limitations.It has been extensively examined whether CRISPR can be used as a tool for disease research and gene therapy.CRISPR and its applications to tumor research,particularly in HCC,are examined in this study through a review of the literature.展开更多
基金supported by the National Key Research and Development Program of China(2020YFC1512304).
文摘Remote sensing data plays an important role in natural disaster management.However,with the increase of the variety and quantity of remote sensors,the problem of“knowledge barriers”arises when data users in disaster field retrieve remote sensing data.To improve this problem,this paper proposes an ontology and rule based retrieval(ORR)method to retrieve disaster remote sensing data,and this method introduces ontology technology to express earthquake disaster and remote sensing knowledge,on this basis,and realizes the task suitability reasoning of earthquake disaster remote sensing data,mining the semantic relationship between remote sensing metadata and disasters.The prototype system is built according to the ORR method,which is compared with the traditional method,using the ORR method to retrieve disaster remote sensing data can reduce the knowledge requirements of data users in the retrieval process and improve data retrieval efficiency.
基金The National Basic Research Program of China (973Program) (No.2005CB321802)Program for New Century Excellent Talents in University (No.NCET-06-0926)the National Natural Science Foundation of China (No.60873097,90612009)
文摘To resolve the ontology understanding problem, the structural features and the potential important terms of a large-scale ontology are investigated from the perspective of complex networks analysis. Through the empirical studies of the gene ontology with various perspectives, this paper shows that the whole gene ontology displays the same topological features as complex networks including ＂small world＂ and ＂scale-free＂,while some sub-ontologies have the ＂scale-free＂ property but no ＂small world＂ effect.The potential important terms in an ontology are discovered by some famous complex network centralization methods.An evaluation method based on information retrieval in MEDLINE is designed to measure the effectiveness of the discovered important terms.According to the relevant literature of the gene ontology terms,the suitability of these centralization methods for ontology important concepts discovering is quantitatively evaluated.The experimental results indicate that the betweenness centrality is the most appropriate method among all the evaluated centralization measures.
基金The National Basic Research Program of China(973Program)(No.2003CB317000),the Natural Science Foundation of Zhejiang Province (No.Y105625).
文摘In order to reduce the costs of the ontology construction, a general ontology learning framework （GOLF） is developed. The key technologies of the GOLF including domain concepts extraction and semantic relationships between concepts and taxonomy automatic construction are proposed. At the same time ontology evaluation methods are also discussed. The experimental results show that this method produces better performance and it is applicable across different domains. By integrating several machine learning algorithms, this method suffers less ambiguity and can identify domain concepts and relations more accurately. By using generalized corpus WordNet and HowNet, this method is applicable across different domains. In addition, by obtaining source documents from the web on demand, the GOLF can produce up-to-date ontologies.
基金R & D Infrastructure and Facility Development(No2005DKA64201)the National High Technology Research and De-velopment Program of China (863Program) (No2006AA12Z202)
文摘To improve the performance of the ontology matching process, a more efficient ontology matching algorithm, which can effectively eliminate unnecessary operations of matching entities, is proposed. By the theoretical analysis and proof, a set of matching rules are summarized for depicting inherent relations among matching results of entities. Based on these rules, the proposed algorithm can reuse the matching results of two entities to directly determine the matching results of their adjacent entities. Thereby, redundant operations of matching adjacent entities can be avoided, which can improve the performance of the whole matching process. The experimental results show that, compared with related algorithms, the proposed algorithm has high matching accuracy and can remarkably reduce the consuming time of the whole matching process. So, the proposed algorithm is more competent for the large-scale ontology matching which often occurs in the practical heterogeneous web resources integration project.
基金supported by the National Natural Science Foundation of China,No.81870975(to SZ)。
文摘Exosomes exhibit complex biological functions and mediate a variety of biological processes,such as promoting axonal regeneration and functional recove ry after injury.Long non-coding RNAs(IncRNAs)have been reported to play a crucial role in axonal regeneration.Howeve r,the role of the IncRNA-microRNAmessenger RNA(mRNA)-competitive endogenous RNA(ceRNA)network in exosome-mediated axonal regeneration remains unclear.In this study,we performed RNA transcriptome sequencing analysis to assess mRNA expression patterns in exosomes produced by cultured fibroblasts(FC-EXOs)and Schwann cells(SCEXOs).Diffe rential gene expression analysis,Gene Ontology analysis,Kyoto Encyclopedia of Genes and Genomes analysis,and protein-protein intera ction network analysis were used to explo re the functions and related pathways of RNAs isolated from FC-EXOs and SC-EXOs.We found that the ribosome-related central gene Rps5 was enriched in FC-EXOs and SC-EXOs,which suggests that it may promote axonal regeneration.In addition,using the miRWalk and Starbase prediction databases,we constructed a regulatory network of ceRNAs targeting Rps5,including 27 microRNAs and five IncRNAs.The ceRNA regulatory network,which included Ftx and Miat,revealed that exsosome-derived Rps5 inhibits scar formation and promotes axonal regeneration and functional recovery after nerve injury.Our findings suggest that exosomes derived from fibro blast and Schwann cells could be used to treat injuries of peripheral nervous system.
基金Acknowledgments This research was supported by the Natural National Science Foundation of China （No. 30571173, No. 31201274）, National High Technology Research and Development Program of China （863 Program） （No. 2012AA10A307）.
文摘To better know FM （Fusarium moniliforme） induced genes in maize ear rot, GO （gene ontology） method was performed to analyze detail physiological functions in the defensive response after pathogen infection. This gene annotation system was widely used to investigate large numbers of genes involving in real active role or regulator in cell response. First of all, differentially expressed genes were isolated by using genechip platform at 96 h post-inoculation with FM in maize inbred Bt-1. In total, 482 differentially expressed unique genes were screened out in inbred Bt-1 when compared to mock-inoculated bract tissues. Then, each gene was annotated to define functional class by GO method. Finally, these large FM-responsive genes with significant differentially change were sorted into cellular component, molecular function and biological process with complicated network by molecular annotation system. The demonstrated information in the GO analysis could provide another view for understanding the molecular mechanism and indicate a deeply complicated network with gene function underlying disease development in the host tissue. The findings in this study provide important bases to probe the molecular processes, the alteration of metabolism and the immune mechanism upon the FM infection in maize.
文摘The basic unit in life is cell.?It contains many protein molecules located at its different organelles. The growth and reproduction of a cell as well as most of its other biological functions are performed via these proteins. But proteins in different organelles or subcellular locations have different functions. Facing?the avalanche of protein sequences generated in the postgenomic age, we are challenged to develop high throughput tools for identifying the subcellular localization of proteins based on their sequence information alone. Although considerable efforts have been made in this regard, the problem is far apart from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for drug targets. Using the ML-GKR (Multi-Label Gaussian Kernel Regression) method,?we developed a new predictor called “pLoc-mGpos” by in-depth extracting the key information from GO (Gene Ontology) into the Chou’s general PseAAC (Pseudo Amino Acid Composition)?for predicting the subcellular localization of Gram-positive bacterial proteins with both single and multiple location sites. Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mGpos predictor is remarkably superior to “iLoc-Gpos”, the state-of-the-art predictor for the same purpose.?To maximize the convenience of most experimental scientists, a user-friendly web-server for the new powerful predictor has been established at http://www.jci-bioinfo.cn/pLoc-mGpos/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.
基金Supported by São Paulo Research Foundation(FAPESP),No.2010/08918-9 and 2020/11564-6the KBSP Young Investigator Fellowship,No.2011/00204-0+2 种基金the DBF Fellowship,No.2019/27492-7the LMG Fellowship,No.2014/01395-1the CFB Fellowship,No.2014/14278-3.
文摘BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,several studies use genes involved in essential cellular functions[glyceraldehyde-3-phosphate dehydro-genase(GAPDH),18S rRNA,andβ-actin]without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes.Furthermore,such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recom-mend two or more genes.It impacts the credibility of these studies and causes dis-tortions in the gene expression findings.For tissue engineering,the accuracy of gene expression drives the best experimental or therapeutical approaches.We cultivated DPSCs under two conditions:Undifferentiated and osteogenic dif-ferentiation,both for 35 d.We evaluated the gene expression of 10 candidates for RGs[ribosomal protein,large,P0(RPLP0),TATA-binding protein(TBP),GAPDH,actin beta(ACTB),tubulin(TUB),aminolevulinic acid synthase 1(ALAS1),tyro-sine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,zeta(YWHAZ),eukaryotic translational elongation factor 1 alpha(EF1a),succinate dehydrogenase complex,subunit A,flavoprotein(SDHA),and beta-2-micro-globulin(B2M)]every 7 d(1,7,14,21,28,and 35 d)by RT-qPCR.The data were analysed by the four main algorithms,ΔCt method,geNorm,NormFinder,and BestKeeper and ranked by the RefFinder method.We subdivided the samples into eight subgroups.RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm.The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs.Either theΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes.However,geNorm analysis showed RPLP0/EF1αin the first place.These algorithms’two least stable RGs were B2M/GAPDH.For BestKeeper,ALAS1 was ranked as the most stable RG,and SDHA as the least stable RG.The pair RPLP0/TBP was detected in most subgroups as the most stable RGs,following the RefFinfer ranking.CONCLUSION For the first time,we show that RPLP0/TBP are the most stable RGs,whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.
文摘Context and Objective: Over the past few decades, terminologies developed for clinical descriptions have been increasingly used as key resources for knowledge management, data integration, and decision support to the extent that today they have become essential in the biomedical and health field. Among these clinical terminologies, some may possess the characteristics of one or several types of representation. This is the case for the Systematized Nomenclature of Human and Veterinary Medicine—Clinical Terms (SNOMED CT), which is both a clinical medical terminology and a formal ontology based on the principles of semantic web. Methods: We present and discuss, on one hand, the compliance of SNOMED CT with the requirements of a reference clinical terminology and, on the other hand, the specifications of the features and constructions of descriptive of SNOMED CT. Results: We demonstrate the consistency of the reference clinical terminology SNOMED CT with the principles stated in James J. Cimino’s desiderata and we also show that SNOMED CT contains an ontology based on the EL profile of OWL2 with some simplifications. Conclusions: The duality of SNOMED CT shown is crucial for understanding the versatility, depth, and scope in the health field.
文摘With a few exceptions, physics theories are based in a conception of time and space;our two major theories, general relativity, and quantum field theory, differ in their conceptions. Key issues herein include mathematics, logic, intuition, experiment, and ontology, with emphasis on simultaneity and dimensionality of the world. The treatment is through ontological comparison of two theories, space-time theory (special relativity) and energy-time theory (local absolute space and universal time). These two theories share many of the same equations but have different ontology.
基金supported by the Major Program of National Agricultural Science and Technology of China(NK20220607)the West Light Foundation of the Chinese Academy of Sciences(2022XBZG_XBQNXZ_A_001)the Sichuan Science and Technology Program,China(2022ZDZX0014)。
文摘Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.
基金King Saud University through Researchers Supporting Project number(RSP-2021/387),King Saud University,Riyadh,Saudi Arabia.
文摘Daily newspapers publish a tremendous amount of information disseminated through the Internet.Freely available and easily accessible large online repositories are not indexed and are in an un-processable format.The major hindrance in developing and evaluating existing/new monolingual text in an image is that it is not linked and indexed.There is no method to reuse the online news images because of the unavailability of standardized benchmark corpora,especially for South Asian languages.The corpus is a vital resource for developing and evaluating text in an image to reuse local news systems in general and specifically for the Urdu language.Lack of indexing,primarily semantic indexing of the daily news items,makes news items impracticable for any querying.Moreover,the most straightforward search facility does not support these unindexed news resources.Our study addresses this gap by associating and marking the newspaper images with one of the widely spoken but under-resourced languages,i.e.,Urdu.The present work proposed a method to build a benchmark corpus of news in image form by introducing a web crawler.The corpus is then semantically linked and annotated with daily news items.Two techniques are proposed for image annotation,free annotation and fixed cross examination annotation.The second technique got higher accuracy.Build news ontology in protégéusing OntologyWeb Language(OWL)language and indexed the annotations under it.The application is also built and linked with protégéso that the readers and journalists have an interface to query the news items directly.Similarly,news items linked together will provide complete coverage and bring together different opinions at a single location for readers to do the analysis themselves.
文摘Alzheimer’s disease is a progressive neurodegenerative disorder and the most common cause of dementia that principally affects older adults.Pathogenic factors,such as oxidative stress,an increase in acetylcholinesterase activity,mitochondrial dysfunction,genotoxicity,and neuroinflammation are present in this syndrome,which leads to neurodegeneration.Neurodegenerative pathologies such as Alzheimer’s disease are considered late-onset diseases caused by the complex combination of genetic,epigenetic,and environmental factors.There are two main types of Alzheimer’s disease,known as familial Alzheimer’s disease(onset<65 years)and late-onset or sporadic Alzheimer’s disease(onset≥65 years).Patients with familial Alzheimer’s disease inherit the disease due to rare mutations on the amyloid precursor protein(APP),presenilin 1 and 2(PSEN1 and PSEN2)genes in an autosomaldominantly fashion with closely 100%penetrance.In contrast,a different picture seems to emerge for sporadic Alzheimer’s disease,which exhibits numerous non-Mendelian anomalies suggesting an epigenetic component in its etiology.Importantly,the fundamental pathophysiological mechanisms driving Alzheimer’s disease are interfaced with epigenetic dysregulation.However,the dynamic nature of epigenetics seems to open up new avenues and hope in regenerative neurogenesis to improve brain repair in Alzheimer’s disease or following injury or stroke in humans.In recent years,there has been an increase in interest in using natural products for the treatment of neurodegenerative illnesses such as Alzheimer’s disease.Through epigenetic mechanisms,such as DNA methylation,non-coding RNAs,histone modification,and chromatin conformation regulation,natural compounds appear to exert neuroprotective effects.While we do not purport to cover every in this work,we do attempt to illustrate how various phytochemical compounds regulate the epigenetic effects of a few Alzheimer’s disease-related genes.
文摘Noncoding RNAs instruct the Cas9 nuclease to site speifillyl cleave DNA in the CRISPR/Cas9 system.Despite the high incidence of hepatocellular carcinoma(HCC),the patient's outcome is poor.As a result of the emergence of therapeutic resistance in HCC patients,dlinicians have faced difficulties in treating such tumor.In addition,CRISPR/Cas9 screens were used to identify genes that improve the dlinical response of HCC patients.It is the objective of this article to summarize the current understanding of the use of the CRISPR/Cas9 system for the treatment of cancer,with a particular emphasis on HCC as part of the current state of knowledge.Thus,in order to locate recent developments in oncology research,we examined both the Scopus database and the PubMed database.The ability to selectively interfere with gene expression in combinatorial CRISPR/Cas9 screening can lead to the discovery of new effective HCC treatment regimens by combining clinically approved drugs.Drug resistance can be overcome with the help of the CRISPR/Cas9 system.HCC signature genes and resistance to treatment have been uncovered by genome-scale CRISPR activation screening although this method is not without limitations.It has been extensively examined whether CRISPR can be used as a tool for disease research and gene therapy.CRISPR and its applications to tumor research,particularly in HCC,are examined in this study through a review of the literature.
