基于组件技术的简标制作管理系统的设计和实现

本文提出了“简标”的概念 ,并在组件化的思想指导下 ,探讨了简标标绘及管理软件的系统结构及实现流程 ,实现了图元 。

Simplified criteria for diagnosing superficial esophageal squamous neoplasms using Narrow Band Imaging magnifying endoscopy

AIM To simplify the diagnostic criteria for superficial esophageal squamous cell carcinoma(SESCC) on Narrow Band Imaging combined with magnifying endoscopy(NBI-ME).METHODS This study was based on the post-hoc analysis of a randomized controlled trial. We performed NBI-ME for 147 patients with present or a history of squamous cell carcinoma in the head and neck, or esophagus between January 2009 and June 2011. Two expert endoscopistsdetected 89 lesions that were suspicious for SESCC lesions, which had been prospectively evaluated for the following 6 NBI-ME findings in real time: "intervascular background coloration"; "proliferation of intrapapillary capillary loops(IPCL)"; and "dilation", "tortuosity", "change in caliber", and "various shapes(VS)" of IPCLs(i.e., Inoue's tetrad criteria). The histologic examination of specimens was defined as the gold standard for diagnosis. A stepwise logistic regression analysis was used to identify candidates for the simplified criteria from among the 6 NBI-ME findings for diagnosing SESCCs. We evaluated diagnostic performance of the simplified criteria compared with that of Inoue's criteria.RESULTS Fifty-four lesions(65%) were histologically diagnosed as SESCCs and the others as low-grade intraepithelial neoplasia or inflammation. In the univariate analysis, proliferation, tortuosity, change in caliber, and VS were significantly associated with SESCC(P < 0.01). The combination of VS and proliferation was statistically extracted from the 6 NBI-ME findings by using the stepwise logistic regression model. We defined the combination of VS and proliferation as simplified dyad criteria for SESCC. The areas under the curve of the simplified dyad criteria and Inoue's tetrad criteria were 0.70 and 0.73, respectively. No significant difference was shown between them. The sensitivity, specificity, and accuracy of diagnosis for SESCC were 77.8%, 57.1%, 69.7% and 51.9%, 80.0%, 62.9% for the simplified dyad criteria and Inoue's tetrad criteria, respectively.CONCLUSION The combination of proliferation and VS may serve as simplified criteria for the diagnosis of SESCC using NBIME.

Taxonomic Status of Daduhe Loquat （Eriobotrya prinoides var. dadunensis）

The taxonomic status of Daduhe loquat （E. prinoides var. dadunensis） was studied through analyzing genetic relationships among Oakleaf loquat （E. prinoides）, Daduhe loquat and Common loquat （E. japonica） using inter simple sequence repeats （ISSR） molecular marker and morphologic marker in this paper. Based on ISSR marker research, the similarity coefficient between Oakleaf loquat and Common loquat was lower than the similarity coefficient between Oakleaf loquat and Daduhe loquat while the similarity coefficient between Daduhe loquat and Common loquat was intermediate. The highest additivity was obtained when Daduhe loquat was regarded as the undetermined hybrid （45.8%）. The specific bands of Oakleaf loquat and Common loquat were present in Daduhe loquat. Based on morphologic traits research, Daduhe loquat was also between Oakleaf loquat and Common loquat but a little leaning to Oakleaf loquat. All the results support that Daduhe loquat was hybrid of Oakleaf loquat and Common loquat.

De novo Assembly of Pen Shell(Atrina pectinata) Transcriptome and Screening of Its Genic Microsatellites

The pen shell(Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes(18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats(SSRs) were identified, of them the most abundant type was mono-nucleotide repeats(12902, 55.01%), which was followed by di-nucleotide(8132, 34.68%), tri-nucleotide(2010, 8.57%), tetra-nucleotide(401, 1.71%), and penta-nucleotide(7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.

Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats(SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class(44.08%), followed by mononucleotides(29.67%), trinucleotides(18.96%), tetranucleotides(5.66%), hexanucleotides(1.07%), and pentanucleotides(0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci(90.0%) were successfully amplified with specific products and 24(80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17(with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

The Minimum Fill-in for the Corona of Two Graphs

In this paper, we determine the minimum fill-ins of the corona G. H of two graphs G and H when the minimum fill-in of G,H were known as F(G),F(H). Our result is that

Identification and Characterization of 43 Microsatellite Markers Derived from Expressed Sequence Tags of the Sea Cucumber (Apostichopus japonicus)

The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from Gen-Bank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles, and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

Molecular Identification and Cultivar Fingerprints of Prunus persica (L.) Batsch Germplasms

[Objective] The aim was to study the molecular identification and cultivar fingerprints of Prunus persica (L.) Batsch germplasms.[Method] Sixty peach genotypes,representing China common local cultivars and European samples were screened by microsatellites (simple sequence repeats,SSRs) and Inter-Simple Sequence Repeat (ISSR) markers.[Result] 26 reproducible bands were amplified by Nine SSR primers,and 24 of which were polymorphic; 236 bands were amplified by 30 ISSR primers,and 113 of which were polymorphic.31 genotypes were discriminated with 1-3 distinct polymorphic bands generated from the primers ISSR and SSR.Seven cultivar-specific ISSR fragments and two SSR unique alleles obtained from this study were available to be converted into Sequence Characterized Amplified Region (SCAR) markers.The genetic similarity coefficient (GS) estimated from these molecular data averaged were 0.939 (ranged from 0.856 to 0.983) for ISSR and 0.646 (ranged from 0.240 to 1.000) for SSR,respectively.The combined grouping association indicated that most local Chinese peach cultivars and exotic accessions were clustered together.This could be related to the mode of introduction and maintenance of the peach cultivars involving limited foundation germplasm,exchange of cultivars between plantations,and periodic development of new recombinant cultivars following sexual reproduction.[Conclusion] The results obtained in this work would help to improve the conservation,molecular identification and management of peach germplasm in breeding.

Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone (Haliotis discus hannai)

Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone (Haliotis discus hannai).Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences,after redundancy elimination.Seventeen polymorphic EST-SSRs were developed.The number of alleles per locus varied from 2-17,with an average of 6.8 alleles per locus.The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922,respectively.Twelve of the 17 loci (70.6%) were successfully amplified in H.diversicolor.Seventeen loci segregated in three families,with three showing the presence of null alleles (17.6%).The adequate level of variability and low frequency of null alleles observed in H.discus hannai,together with the high rate of transportability across Haliotis species,make this set of EST-SSR markers an important tool for comparative mapping,marker-assisted selection,and evolutionary studies,not only in the Pacific abalone,but also in related species.

Identification and Analysis of SSRs Derived from Protein-coding Genes in Grape

SSR(Simple Sequence Repeats), also known as microsatellites or STRs(short tandem repeats), are a type of PCRbased markers. So far, the version of grape genome has been updated constantly, but SSRs derived from protein-coding genes in grape have not yet been identified. In this study, 4 337 SSR-containing genes were found among 29 971 protein-coding genes in grape(Vitis vinifera L.), and 5 384 SSRs were found. There were 96 types of repeat motifs in SSRs derived from protein-coding genes in grape, and the most frequently occurring repeat motif was A/T. Among various repeat motifs in dinucleotide SSRs, the most frequently occurring repeat motif was AG/CT. Moreover, many genes exhibited codon usage bias, which was affected by the mutation pressure. GO annotation, KEGG annotation and domain analysis of these genes were performed.Several genes were found to be closely related to the synthesis and metabolism of secondary metabolites, synthesis of flavones or anthocyanins, development and morphology of plant organs, and tolerance to biotic or abiotic stresses, including transcription factors in MYB, Hsf, NBS and TPC families. This study laid a solid foundation for the development of SSR markers and research of QTLs controlling complex agronomic traits in grape.

Advance of Study on SSR Molecular Marker in Citrus and Its Close Relatives

Simple sequences repeat （SSR） molecular maker, as a new type of DNA molecular marker, the second generation based on the polymerase chain reaction （PCR）, is valuable and of great potential as genetic markers for its characteristics of abundant quantity, high polymorphic, reproducibility, specific site amplification, high occurring frequency, and co-dominant inheritance etc. This paper outlined its principles and characteristics, and introduced its application to variety identification, phylogenetic relationship analysis, genetic diversity analysis, DNA fingerprinting and linkage map constructing etc. in recent years in Citrus and its close relatives.

睡虎地秦简日书“四法日”小考

睡虎地秦简日书甲种825—830简标题为"啻",其内容是: 春三月:啻(帝)为室申,剽卯,殺辰,四法庚辛。夏三月:啻(帝)为室寅剽午,殺未,四法壬癸。秋三月:啻(帝)为室巳,剽酉,殺成

Screening for simple sequence repeat markers in Puccinia striiformis tritici based on genomic sequence

Puccinia striiformis f. sp. tritici （Pst） is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatelUte markers from the genomic sequence of an isolate of Chinese Pst race C^32. Polymorphism at each simple sequence repeat （SSR） locus was determined using 32 Pst isolates from 7 countries. The number of alleles varied from 2 to 7 across isolates, and the observed and expected heterozygosities ranged from 0.33 to 0.97 （mean 0.62） and 0.23 to 0.73 （mean 0.51 ）, respectively. As expected the genomic SSR markers were more polymorphic than the expressed sequence tag （EST）-SSR markers developed previously. These markers will be more useful for population genetics and molecular genetics studies in Pst.

Developing new SSR markers from ESTs of pea(Pisum sativum L.)

The development of expressed sequence tags(ESTs) from pea has provided a useful source for mining novel simple sequence repeat(SSR) markers.In the present research,in order to find EST-derived SSR markers,18 552 pea ESTs from the National Center for Biotechnology Information(NCBI) database were downloaded and assembled into 10 086 unigenes.A total of 586 microsatellites in 530 unigenes were identified,indicating that merely 5.25% of sequences contained SSRs.The most abundant SSRs within pea were tri-nucleotide repeat motifs,and among all the tri-nucleotide repeats,the motif GAA was the most abundant type.In total,49 SSRs were used for primer design.EST-SSR loci were subsequently screened on 10 widely adapted varieties in China.Of these,nine loci showed polymorphic profiles that revealed two to three alleles per locus.The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41.Furthermore,transferable analysis revealed that some of these loci showed transferability to faba bean.Because of their polymorphism and transferability,these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry(Myrica rubra) and their application in seedling identification

Chinese bayberry （Myrica rubra Sieb. et Zucc.） is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat （SSR） molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content （PIC） varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera （syn. More/la cerifera） and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between ＇Biqi＇ and ＇Dongkui＇. A neighbor-joining （N J） tree was con- structed to assess the genetic relationships among accessions, and the elite accessions ＇Y2010-70＇, ＇Y2012-140＇, and ＇Y2012-145＇, were characterized as potential new genotypes for cultivation.

Development of genic SSR markers from transcriptome sequencing of pear buds

A total of 8375 genic simple sequence repeat（SSR） loci were discovered from a unigene set assembled from 116282 transcriptomic unigenes in this study.Dinucleotide repeat motifs were the most common with a frequency of 65.11%,followed by trinucleotide（32.81%）.A total of 4100 primer pairs were designed from the SSR loci.Of these,343 primer pairs（repeat length≥15 bp） were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions.After the preliminary test,104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11%（101） of these.Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions.These markers displayed a high level of polymorphism.The number of alleles at these SSR loci ranged from 2 to 17,with a mean of 9.43 alleles per locus,and the polymorphism information content（PIC） values ranged from 0.26 to 0.91.The UPGMA（unweighted pair-group method with arithmetic average） cluster analysis grouped the 28 Pyrus accessions into two groups： Oriental pears and Occidental pears,which are congruent to the traditional taxonomy,demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships,enriching rare Pyrus EST-SSR resources,and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding

The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat （SSR） genotyping data. The amplified fragments from SSR primers were highly polymorphic in the badey accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 badey accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China.

Efimov-like states and quantum funneling effects on synthetic hyperbolic surfaces

Engineering lattice models with tailored inter-site tunnelings and onsite energies could synthesize essentially arbitrary Riemannian surfaces with highly tunable local curvatures.Here,we point out that discrete synthetic Poincaréhalf-planes and Poincarédisks,which are created by lattices in flat planes,support infinitely degenerate eigenstates for any nonzero eigenenergies.Such Efimov-like states exhibit a discrete scaling symmetry and imply an unprecedented apparatus for studying quantum anomaly using hyperbolic surfaces.Furthermore,all eigenstates are exponentially localized in the hyperbolic coordinates,signifying the first example of quantum funneling effects in Hermitian systems.As such,any initial wave packet travels towards the edge of the Poincaréhalf-plane or its equivalent on the Poincarédisk,delivering an efficient scheme to harvest light and atoms in two dimensions.Our findings unfold the intriguing properties of hyperbolic spaces and suggest that Efimov states may be regarded as a projection from a curved space with an extra dimension.

EFFICIENT ALGORITHMS FOR IDENTIFYING ORTHOLOGOUS SIMPLE SEQUENCE REPEATS OF DISEASE GENES

Dynamic mutations of simple sequence repeats （SSRs） have been demonstrated to affect normal gene function and cause different genetic disorders. Several conserved and even partial functional SSR patterns are discovered in inherited orthologous disease genes. To explore a wide range of SSRs in genetic diseases, a comprehensive system focusing on identifying orthologous SSRs of disease genes through a comparative genomics mechanism is constructed and accomplished by adopting online Mendelian inheritance in man （OMIM） and NCBI HomoloGene databases as the fundamental resources of human genetic diseases and homologous gene information. In addition, an efficient and effective algorithm for searching SSR patterns is also developed for providing annotated SSR information among various model species. By integrating these data resources and mining technologies, biologists and doctors can systematically retrieve novel and important conserved SSR information among orthologous disease genes. The proposed system, Orthologous SSR for Disease Genes （OSDG）, is the first comprehensive framework for identifying orthologous SSRs as potential causative factors of genetic disorders and is freely available at http：//osdg.cs.ntou.edu.tw/.

Community Detection with the Weighted Parsimony Criterion

Community detection in networks has been studied extensively in the last decade. Many criteria, expressing the quality of the partitions obtained, as well as a few exact algorithms and a large number of heuristics have been proposed. The parsimony criterion consists in minimizing the number of edges added or removed from the given network in order to transform it into a set of disjoint cliques.Recently Zhang, Qiu and Zhang have proposed a weighted parsimony model in which a weight coefficient is introduced to balance the numbers of inserted and deleted edges. These authors propose rules to select a good value of the coefficient, use simulated annealing to find optimal or near-optimal solutions and solve a series of real and artificial instances. In the present paper, an algorithm is proposed for solving exactly the weighted parsimony problem for all values of the parameter. This algorithm is based on iteratively solving the problem for a set of given values of the parameter using a row generation algorithm. This procedure is combined with a search procedure to find all lowest breakpoints of the value curve(i.e., the weighted sum of inserted and deleted edges). Computational results on a series of artificial and real world networks from the literature are reported. It appears that several partitions for the same network may be informative and that the set of solutions usually contains at least one intuitively appealing partition.