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Social signal processing
\"Social Signal Processing is the first book to cover all aspects of the modeling, automated detection, analysis, and synthesis of nonverbal behavior in human-human and human-machine interactions. Authoritative surveys address conceptual foundations, machine analysis and synthesis of social signal processing, and applications. Foundational topics include affect perception and interpersonal coordination in communication; later chapters cover technologies for automatic detection and understanding such as computational paralinguistics and facial expression analysis and for the generation of artificial social signals such as social robots and artificial agents. The final section covers a broad spectrum of applications based on social signal processing in healthcare, deception detection, and digital cities, including detection of developmental diseases and analysis of small groups. Each chapter offers a basic introduction to its topic, accessible to students and other newcomers, and then outlines challenges and future perspectives for the benefit of experienced researchers and practitioners in the field\"-- Provided by publisher.
Book
Subcellular Expression Patterns of FKBP Prolyl Isomerase 10 (FKBP10) in Colorectal Cancer and Its Clinical Significance
FKBP10, a member of the FK506-binding protein (FKBP) family, has been implicated in cancer development, although its prognostic function remains controversial. In this study, we analyzed the expression of FKBP10 in tumor tissues using online databases (TCGA) as well as our CRC cohort, and investigated the relationship between its subcellular expression pattern and patient outcomes. Cox regression analysis was used to determine the associations between different subcellular expression patterns of FKBP10 and clinical features of patients. We also discussed the expression level of FKBP10 based on different subcellular expression patterns. Our results showed that FKBP10 was significantly elevated in CRC tissues and exhibited three different subcellular expression patterns which were defined as ‘FKBP10-C’ (concentrated), ‘FKBP10-T’ (transitional) and ‘FKBP10-D’ (dispersive). The FKBP10-D expression pattern was only found in tumor tissues and was associated with unfavorable disease-free survival in CRC patients. High expression levels of FKBP10-C predicted an unfavorable prognosis of recurrence of CRC, while FKBP10-D did not. Our findings suggest that the subcellular expression patterns and expression level of FKBP10 play crucial prognostic roles in CRC, which revealed that FKBP10 may be a viable prognostic and therapeutic target for the diagnosis and treatment of CRC.
Journal Article
Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides
Alternanthera philoxeroides is a notorious invasive weed worldwide, but it still lacks a genome information currently. In this study, we collected 4 groups of A. philoxeroides Illumina RNA-seq data (62.5 Gb) and performed a comprehensive de novo assembling. Totally, 421,372 unigenes were obtained with a total length of 230,842,460 bp, with 43,430 (10.31%) unigenes longer than 1000 bp. Then 119,222 (28.3%) unigenes were functional annotated and 235,885 (56.0%) were grouped into reliable lncRNAs reservoir. Besides, 534 tRNA and 234 rRNAs were identified in assembly sequences. Additionally, 131,624 microsatellites were characterized in 106,761 sequences. Then SSR primers were developed for the amplification of 40,752 microsatellites in 36,329 sequences. The miRNAs are key post-transcriptional regulators, about 86 candidate miRNA sequences were detected from A. philoxeroides assembly, and miRNA target genes prediction revealed possible functions of them in growth and development as well as stress responding processes. These results provide a vital basis for sequence-based studies of A. philoxeroides in the future, especially gene function analysis.
Journal Article
Gene Identification of Pheromone Gland Genes Involved in Type II Sex Pheromone Biosynthesis and Transportation in Female Tea Pest Ectropis grisescens
Moths can biosynthesize sex pheromones in the female sex pheromone glands (PGs) and can distinguish species-specific sex pheromones using their antennae. However, the biosynthesis and transportation mechanism for Type II sex pheromone components has rarely been documented in moths. In this study, we constructed a massive PG transcriptome database (14.72 Gb) from a moth species, Ectropis grisescens, which uses type II sex pheromones and is a major tea pest in China. We further identified putative sex pheromone biosynthesis and transportation-related unigenes: 111 cytochrome P450 monooxygenases (CYPs), 25 odorant-binding proteins (OBPs), and 20 chemosensory proteins (CSPs). Tissue expression and phylogenetic tree analyses showed that one CYP (EgriCYP341-fragment3), one OBP (EgriOBP4), and one CSP (EgriCSP10) gene displayed an enriched expression in the PGs, and that EgriOBP2, 3, and 25 are clustered in the moth pheromone-binding protein clade. We considered these our candidate genes. Our results yielded large-scale PG sequence information for further functional studies.
Journal Article
Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis
Ethylene plays a pivotal role in plant stress resistance and 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is the rate-limiting enzyme in ethylene biosynthesis. Upland cotton (Gossypium hirsutum L.) is the most important natural fiber crop, but the function of ACS in response to abiotic stress has rarely been reported in this plant. We identified 18 GaACS, 18 GrACS, and 35 GhACS genes in Gossypiumarboreum, Gossypium raimondii and Gossypiumhirsutum, respectively, that were classified as types I, II, III, or IV. Collinearity analysis showed that the GhACS genes were expanded from diploid cotton by the whole-genome-duplication. Multiple alignments showed that the C-terminals of the GhACS proteins were conserved, whereas the N-terminals of GhACS10 and GhACS12 were different from the N-terminals of AtACS10 and AtACS12, probably diverging during evolution. Most type II ACS genes were hardly expressed, whereas GhACS10/GhACS12 were expressed in many tissues and in response to abiotic stress; for example, they were highly and hardly expressed at the early stages of cold and heat exposure, respectively. The GhACS genes showed different expression profiles in response to cold, heat, drought, and salt stress by quantitative PCR analysis, which indicate the potential roles of them when encountering the various adverse conditions, and provide insights into GhACS functions in cotton’s adaptation to abiotic stress.
Journal Article
Characterization and expression analysis of four members genes of flavanone 3-hydroxylase families from Chamaemelum nobile
Chamaemelum nobile is a traditional Chinese herbal medicine, whose secondary metabolites used in the pharmacology of Chinese medicine. Among them, the flavonoids have great research value. Flavanone 3-hydroxylase (F3H) is one of the core enzymes in the early steps of flavonoid biosynthesis. This study aimed to elucidate the structures, functions, and expression levels of F3H families from C. nobile. Four members of the F3H family were screened from C. nobile transcriptome data and performed bioinformatics analysis. Results showed that CnF3H1~4 had a high similarity with the other F3H plants, and all genes contained two conserved isopenicillin N synthase-like and oxoglutarate/iron-dependent dioxygenase domains. Further analysis revealed that the four CnF3H proteins contained some differences in binding sites. The results of secondary and 3-D structures displayed that the composition and proportion of the four CnF3H secondary structures were basically the same, and their 3D structures were consistent with the secondary structures. The phylogenetic tree displayed that CnF3H2, CnF3H3, and CnF3H4 were grouped with Asteraceae. The expression patterns of CnF3Hs in the roots, stems, leaves, and flowers of C. nobile were evaluated using the value of RPKM. The results indicated that CnF3Hs had significant difference in the expression of different tissues. Especially, CnF3H1~3 and CnF3H4 had the highest expression levels in the flowers and roots, respectively. Hence, CnF3Hs played a significant role in the flavonoid metabolism.
Journal Article
Molecular Cloning and Expression Analysis of a MADS-Box Gene (GbMADS2) from Ginkgo biloba
As a kind of transcription factors gene family, MADS-box genes play an important role in plant development processes. To find genes involved in the floral transition of Ginkgo biloba, a MADS-box gene, designated as GbMADS2, was cloned from G. biloba based on EST sequences by RT-PCR. Sequence analysis results showed that the cDNA sequence of GbMADS2 contained a 663 bp length ORF encoding 221 amino acids protein, which displayed typical structure of plant MADS-box protein including MADS, I, and K domains and C terminus. The sequence of GbMADS2 protein was highly homologous to those of MADS-box proteins from other plant species with the highest homologous to AGAMOUS (CyAG) from Cycas revoluta. The phylogenetic tree analysis revealed that GbMADS2 belonged to AGAMOUS clade genes. Real-time PCR analysis indicated that expression levels of GbMADS2 gene in female and male flower were significantly higher than those in root, stem, and leaves, and that GbMADS2 expression level increased along with time of flower development. The spatial and time-course expression profile of GbMADS2 implied that GbMADS2 might be involved in development of reproductive organs. The isolation and expression analysis of GbMADS2 provided basis for further studying the molecular mechanism of flower development in G. biloba.
Journal Article
SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies
Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method for rapid and effective detection of spatially expressed genes in large spatial transcriptomic studies. SPARK-X not only produces effective type I error control and high power but also brings orders of magnitude computational savings. We apply SPARK-X to analyze three large datasets, one of which is only analyzable by SPARK-X. In these data, SPARK-X identifies many spatially expressed genes including those that are spatially expressed within the same cell type, revealing new biological insights.
Journal Article
Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis
Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.
Journal Article
Molecular Cloning and Expression Analysis of a MADS-Box Gene (GbMADS2) from Ginkgo biloba
As a kind of transcription factors gene family, MADS-box genes play an important role in plant development processes. To find genes involved in the floral transition of Ginkgo biloba, a MADS-box gene, designated as GbMADS2 , was cloned from G. biloba based on EST sequences by RT-PCR. Sequence analysis results showed that the cDNA sequence of GbMADS2 contained a 663 bp length ORF encoding 221 amino acids protein, which displayed typical structure of plant MADS-box protein including MADS, I, and K domains and C terminus. The sequence of GbMADS2 protein was highly homologous to those of MADS-box proteins from other plant species with the highest homologous to AGAMOUS ( CyAG) from Cycas revoluta . The phylogenetic tree analysis revealed that GbMADS2 belonged to AGAM OUS clade genes. Real-time PCR analysis indicated that expression levels of GbMADS2 gene in female and male flower were significantly higher than those in root, stem, and leaves, and that GbMADS2 expression level increased along with time of flower development. The spatial and time-course expression profile of GbMADS2 implied that GbMADS2 might be involved in development of reproductive organs. The isolation and expression analysis of GbMADS2 provided basis for further studying the molecular mechanism of flower development in G. biloba.
Journal Article