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1.
BMC Syst Biol ; 8 Suppl 4: S9, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25521604

RESUMO

BACKGROUND: Eukaryotic transcriptional regulation is known to be highly connected through the networks of cooperative transcription factors (TFs). Measuring the cooperativity of TFs is helpful for understanding the biological relevance of these TFs in regulating genes. The recent advances in computational techniques led to various predictions of cooperative TF pairs in yeast. As each algorithm integrated different data resources and was developed based on different rationales, it possessed its own merit and claimed outperforming others. However, the claim was prone to subjectivity because each algorithm compared with only a few other algorithms and only used a small set of performance indices for comparison. This motivated us to propose a series of indices to objectively evaluate the prediction performance of existing algorithms. And based on the proposed performance indices, we conducted a comprehensive performance evaluation. RESULTS: We collected 14 sets of predicted cooperative TF pairs (PCTFPs) in yeast from 14 existing algorithms in the literature. Using the eight performance indices we adopted/proposed, the cooperativity of each PCTFP was measured and a ranking score according to the mean cooperativity of the set was given to each set of PCTFPs under evaluation for each performance index. It was seen that the ranking scores of a set of PCTFPs vary with different performance indices, implying that an algorithm used in predicting cooperative TF pairs is of strength somewhere but may be of weakness elsewhere. We finally made a comprehensive ranking for these 14 sets. The results showed that Wang J's study obtained the best performance evaluation on the prediction of cooperative TF pairs in yeast. CONCLUSIONS: In this study, we adopted/proposed eight performance indices to make a comprehensive performance evaluation on the prediction results of 14 existing cooperative TFs identification algorithms. Most importantly, these proposed indices can be easily applied to measure the performance of new algorithms developed in the future, thus expedite progress in this research field.


Assuntos
Algoritmos , Biologia Computacional/métodos , Fatores de Transcrição/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo
2.
Sensors (Basel) ; 14(11): 21858-71, 2014 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-25412220

RESUMO

Wireless sensor networks (WSNs) have emerged as a promising solution for various applications due to their low cost and easy deployment. Typically, their limited power capability, i.e., battery powered, make WSNs encounter the challenge of extension of network lifetime. Many hierarchical protocols show better ability of energy efficiency in the literature. Besides, data reduction based on the correlation of sensed readings can efficiently reduce the amount of required transmissions. Therefore, we use a sub-clustering procedure based on spatial data correlation to further separate the hierarchical (clustered) architecture of a WSN. The proposed algorithm (2TC-cor) is composed of two procedures: the prediction model construction procedure and the sub-clustering procedure. The energy conservation benefits by the reduced transmissions, which are dependent on the prediction model. Also, the energy can be further conserved because of the representative mechanism of sub-clustering. As presented by simulation results, it shows that 2TC-cor can effectively conserve energy and monitor accurately the environment within an acceptable level.

3.
Stud Health Technol Inform ; 201: 63-70, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24943526

RESUMO

The objective of this study is to propose a Cloud Computing based platform for sleep behavior and chronic disease collaborative research. The platform consists of two main components: (1) a sensing bed sheet with textile sensors to automatically record patient's sleep behaviors and vital signs, and (2) a service-oriented cloud computing architecture (SOCCA) that provides a data repository and allows for sharing and analysis of collected data. Also, we describe our systematic approach to implementing the SOCCA. We believe that the new cloud-based platform can provide nurse and other health professional researchers located in differing geographic locations with a cost effective, flexible, secure and privacy-preserved research environment.


Assuntos
Pesquisa Biomédica/organização & administração , Doença Crônica/classificação , Registros Eletrônicos de Saúde/organização & administração , Internet/organização & administração , Polissonografia/métodos , Fases do Sono , Transtornos do Sono-Vigília/fisiopatologia , Comportamento Cooperativo , Humanos , Armazenamento e Recuperação da Informação/métodos , Transtornos do Sono-Vigília/diagnóstico , Telemedicina/organização & administração
4.
BMC Syst Biol ; 8 Suppl 5: S2, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25559499

RESUMO

BACKGROUND: Transcriptional regulation of gene expression is usually accomplished by multiple interactive transcription factors (TFs). Therefore, it is crucial to understand the precise cooperative interactions among TFs. Various kinds of experimental data including ChIP-chip, TF binding site (TFBS), gene expression, TF knockout and protein-protein interaction data have been used to identify cooperative TF pairs in existing methods. The nucleosome occupancy data is not yet used for this research topic despite that several researches have revealed the association between nucleosomes and TFBSs. RESULTS: In this study, we developed a novel method to infer the cooperativity between two TFs by integrating the TF-gene documented regulation, TFBS and nucleosome occupancy data. TF-gene documented regulation and TFBS data were used to determine the target genes of a TF, and the genome-wide nucleosome occupancy data was used to assess the nucleosome occupancy on TFBSs. Our method identifies cooperative TF pairs based on two biologically plausible assumptions. If two TFs cooperate, then (i) they should have a significantly higher number of common target genes than random expectation and (ii) their binding sites (in the promoters of their common target genes) should tend to be co-depleted of nucleosomes in order to make these binding sites simultaneously accessible to TF binding. Each TF pair is given a cooperativity score by our method. The higher the score is, the more likely a TF pair has cooperativity. Finally, a list of 27 cooperative TF pairs has been predicted by our method. Among these 27 TF pairs, 19 pairs are also predicted by existing methods. The other 8 pairs are novel cooperative TF pairs predicted by our method. The biological relevance of these 8 novel cooperative TF pairs is justified by the existence of protein-protein interactions and co-annotation in the same MIPS functional categories. Moreover, we adopted three performance indices to compare our predictions with 11 existing methods' predictions. We show that our method performs better than these 11 existing methods in identifying cooperative TF pairs in yeast. Finally, the cooperative TF network constructed from the 27 predicted cooperative TF pairs shows that our method has the power to find cooperative TF pairs of different biological processes. CONCLUSION: Our method is effective in identifying cooperative TF pairs in yeast. Many of our predictions are validated by the literature, and our method outperforms 11 existing methods. We believe that our study will help biologists to understand the mechanisms of transcriptional regulation in eukaryotic cells.


Assuntos
Proteínas Fúngicas/metabolismo , Nucleossomos/metabolismo , Mapeamento de Interação de Proteínas/métodos , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo , Algoritmos , Sequência de Aminoácidos , Sítios de Ligação , Bases de Dados de Proteínas , Armazenamento e Recuperação da Informação , Dados de Sequência Molecular , Ligação Proteica , Análise de Sequência de Proteína/métodos , Transcrição Genética/fisiologia
5.
Plant Cell Physiol ; 54(2): e7, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23314755

RESUMO

Both floral development and evolutionary trends of orchid flowers have long attracted the interest of biologists. However, expressed sequences derived from the flowers of other orchid subfamilies are still scarce except for a few species in Epidendroideae. In order to broadly increase our scope of Orchidaceae genetic information, we updated the OrchidBase to version 2.0 which has 1,562,071 newly added floral non-redundant transcribed sequences (unigenes) collected comprehensively from 10 orchid species across five subfamilies of Orchidaceae. A total of 662,671,362 reads were obtained by using next-generation sequencing (NGS) Solexa Illumina sequencers. After assembly, on average 156,207 unigenes were generated for each species. The average length of a unigene is 347 bp. We made a detailed annotation including general information, relative expression level, gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping and gene network prediction. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. We have re-designed the user interface in the new version. Users can enter the Phalaenopsis transcriptome or Orchidaceae floral transcriptome to browse or search the unigenes. OrchidBase 2.0 is freely available at http://orchidbase.itps.ncku.edu.tw/.


Assuntos
Bases de Dados Genéticas , Flores/metabolismo , Genes de Plantas , Orchidaceae/metabolismo , Software , Transcriptoma , Etiquetas de Sequências Expressas , Flores/genética , Biblioteca Gênica , Internet , Anotação de Sequência Molecular , Orchidaceae/classificação , Orchidaceae/genética , Filogenia
6.
Gene ; 518(1): 91-100, 2013 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-23262337

RESUMO

Orchids are one of the most species rich of all angiosperm families. Their extraordinary floral diversity, especially conspicuous labellum morphology, makes them the successful species during evolution process. Because of the fine and delicate development of the perianth, orchid provides a rich subject for studying developmental biology. However, study on molecular mechanism underling orchid floral development is still in its infancy. In this study, we developed an oligomicroarray containing 14,732 unigenes based on the information of expressed sequence tags derived from Phalaenopsis orchids. We applied the oligomicroarray to compare transcriptome among different types of floral organs including sepal, petal and labellum. We discovered that 173, 11, and 285 unigenes were highly differentially expressed in sepal, petal, and labellum, respectively. These unigenes were annotated with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and transcription factor family. Unigenes involved in energy metabolism, lipid metabolism, and terpenoid metabolism are significantly differentially distributed between labellum and two types of tepal (sepal and petal). Labellum-dominant unigenes encoding MADS-box and sepal-dominant unigenes encoding WRKY transcription factors were also identified. Further studies are required but data suggest that it will be possible to identify genes better adapted to sepal, petal and labellum function. The developed functional genomic tool will narrow the gap between approaches based on model organisms with plenty genomic resources and species that are important for developmental and evolutionary studies.


Assuntos
Flores/genética , Perfilação da Expressão Gênica/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Orchidaceae/genética , Metabolismo Energético/genética , Etiquetas de Sequências Expressas , Flores/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Metabolismo dos Lipídeos/genética , Proteínas de Domínio MADS/genética , Proteínas de Domínio MADS/metabolismo , Redes e Vias Metabólicas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
7.
PLoS One ; 8(12): e83791, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24386279

RESUMO

Transcription factor binding site (TFBS) identification plays an important role in deciphering gene regulatory codes. With comprehensive knowledge of TFBSs, one can understand molecular mechanisms of gene regulation. In the recent decades, various computational approaches have been proposed to predict TFBSs in the genome. The TFBS dataset of a TF generated by each algorithm is a ranked list of predicted TFBSs of that TF, where top ranked TFBSs are statistically significant ones. However, whether these statistically significant TFBSs are functional (i.e. biologically relevant) is still unknown. Here we develop a post-processor, called the functional propensity calculator (FPC), to assign a functional propensity to each TFBS in the existing computationally predicted TFBS datasets. It is known that functional TFBSs reveal strong positional preference towards the transcriptional start site (TSS). This motivates us to take TFBS position relative to the TSS as the key idea in building our FPC. Based on our calculated functional propensities, the TFBSs of a TF in the original TFBS dataset could be reordered, where top ranked TFBSs are now the ones with high functional propensities. To validate the biological significance of our results, we perform three published statistical tests to assess the enrichment of Gene Ontology (GO) terms, the enrichment of physical protein-protein interactions, and the tendency of being co-expressed. The top ranked TFBSs in our reordered TFBS dataset outperform the top ranked TFBSs in the original TFBS dataset, justifying the effectiveness of our post-processor in extracting functional TFBSs from the original TFBS dataset. More importantly, assigning functional propensities to putative TFBSs enables biologists to easily identify which TFBSs in the promoter of interest are likely to be biologically relevant and are good candidates to do further detailed experimental investigation. The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/.


Assuntos
Biologia Computacional/métodos , Proteínas de Ligação a DNA/metabolismo , Regiões Promotoras Genéticas , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo , Sítios de Ligação , Regulação Fúngica da Expressão Gênica , Especificidade por Substrato
8.
Sensors (Basel) ; 12(10): 14158-78, 2012 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-23202042

RESUMO

A growing number of educational studies apply sensors to improve student learning in real classroom settings. However, how can sensors be integrated into classrooms to help instructors find out students' reading concentration rates and thus better increase learning effectiveness? The aim of the current study was to develop a reading concentration monitoring system for use with e-books in an intelligent classroom and to help instructors find out the students' reading concentration rates. The proposed system uses three types of sensor technologies, namely a webcam, heartbeat sensor, and blood oxygen sensor to detect the learning behaviors of students by capturing various physiological signals. An artificial bee colony (ABC) optimization approach is applied to the data gathered from these sensors to help instructors understand their students' reading concentration rates in a classroom learning environment. The results show that the use of the ABC algorithm in the proposed system can effectively obtain near-optimal solutions. The system has a user-friendly graphical interface, making it easy for instructors to clearly understand the reading status of their students.


Assuntos
Atenção/fisiologia , Monitorização Fisiológica/instrumentação , Leitura , Estudantes/psicologia , Algoritmos , Animais , Inteligência Artificial , Abelhas/fisiologia , Livros , Humanos , Aplicativos Móveis , Monitorização Fisiológica/métodos , Instituições Acadêmicas
9.
J Med Syst ; 35(5): 1299-312, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21424848

RESUMO

When facing damages caused by falls, a well designed smart sensor system to detect falls can be both medically and economically helpful. This research introduces a portable terrain adaptable fall detection system, by placing accelerometers and gyroscopes in parts of the body and transmit data through wireless transmitter modules to mobile devices to get the related information and combining it with the center of gravity clustering algorithm introduced in this research which computes the human body behavior patterns according the relationship between the center of gravity in the body and the feet portion of the body. Compared with the research in the past, this system is not only highly accurate and robust, but also able to adapt to different types of terrains, which solves the problems that other researches have for detection errors when the client is climbing the stairs or walking on a slant.


Assuntos
Acidentes por Quedas , Monitorização Ambulatorial/instrumentação , Telemetria/instrumentação , Tecnologia sem Fio , Algoritmos , Humanos
10.
Plant Cell Physiol ; 52(2): 238-43, 2011 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21245031

RESUMO

Orchids are one of the most ecological and evolutionarily significant plants, and the Orchidaceae is one of the most abundant families of the angiosperms. Genetic databases will be useful not only for gene discovery but also for future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of the database is an automated system written in Perl and C#, and consists of the following components: automatic pre-processing of EST reads, assembly of raw sequences, annotation of the assembled sequences and storage of the analyzed information in SQL databases. A web application was implemented with HTML and a Microsoft .NET Framework C# program for browsing and querying the database, creating dynamic web pages on the client side, analyzing gene ontology (GO) and mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers with a high-quality genetic resource for data mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.


Assuntos
Bases de Dados Genéticas , Perfilação da Expressão Gênica , Orchidaceae/genética , Mineração de Dados , Etiquetas de Sequências Expressas , Biblioteca Gênica , Internet , Anotação de Sequência Molecular , Análise de Sequência de DNA , Interface Usuário-Computador
11.
Nurse Educ Today ; 31(8): e8-e15, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21196068

RESUMO

In clinical nursing courses, students are trained to identify the status of the target patients. The mastery of such ability and skills is very important since patients frequently need to be cared for immediately. In this pilot study, a repertory grid-oriented clinical mobile learning system is developed for a nursing training program. With the assistance of the mobile learning system, the nursing school students are able to learn in an authentic learning scenario, in which they can physically face the target patients, with the personal guidance and supplementary materials from the learning system to support them. To show the effectiveness of this innovative approach, an experiment has been conducted on the "respiratory system" unit of a nursing course. The experimental results show that the innovative approach is helpful to students in improving their learning achievements. Moreover, from the questionnaire surveys, it was found that most students showed favorable attitudes toward the usage of the mobile learning system and their participation in the training program.


Assuntos
Atitude do Pessoal de Saúde , Computadores de Mão , Sistemas de Apoio a Decisões Clínicas , Educação em Enfermagem/métodos , Estudantes de Enfermagem/psicologia , Competência Clínica , Humanos , Aprendizagem , Avaliação em Enfermagem , Pesquisa em Educação de Enfermagem , Pesquisa em Avaliação de Enfermagem , Projetos Piloto , Doenças Respiratórias/enfermagem , Taiwan
12.
Sensors (Basel) ; 10(12): 11400-13, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-22163534

RESUMO

Wireless sensor networks have garnered considerable attention recently. Networks typically have many sensor nodes, and are used in commercial, medical, scientific, and military applications for sensing and monitoring the physical world. Many researchers have attempted to improve wireless sensor network management efficiency. A Simple Network Management Protocol (SNMP)-based sensor network management system was developed that is a convenient and effective way for managers to monitor and control sensor network operations. This paper proposes a novel WSNManagement system that can show the connections stated of relationships among sensor nodes and can be used for monitoring, collecting, and analyzing information obtained by wireless sensor networks. The proposed network management system uses collected information for system configuration. The function of performance analysis facilitates convenient management of sensors. Experimental results show that the proposed method enhances the alive rate of an overall sensor node system, reduces the packet lost rate by roughly 5%, and reduces delay time by roughly 0.2 seconds. Performance analysis demonstrates that the proposed system is effective for wireless sensor network management.


Assuntos
Redes de Comunicação de Computadores/instrumentação , Redes de Comunicação de Computadores/organização & administração , Tecnologia de Sensoriamento Remoto/instrumentação , Tecnologia sem Fio/instrumentação , Segurança Computacional/instrumentação , Capacitação de Usuário de Computador , Eficiência Organizacional , Humanos , Sistemas de Informação Administrativa , Modelos Biológicos , Tecnologia de Sensoriamento Remoto/métodos , Processamento de Sinais Assistido por Computador/instrumentação , Interface Usuário-Computador , Tecnologia sem Fio/organização & administração
13.
Sensors (Basel) ; 9(12): 10117-35, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-22303165

RESUMO

Current research on routing in wireless sensor computing concentrates on increasing the service lifetime, enabling scalability for large number of sensors and supporting fault tolerance for battery exhaustion and broken nodes. A sensor node is naturally exposed to various sources of unreliable communication channels and node failures. Sensor nodes have many failure modes, and each failure degrades the network performance. This work develops a novel mechanism, called Reliable Routing Mechanism (RRM), based on a hybrid cluster-based routing protocol to specify the best reliable routing path for sensor computing. Table-driven intra-cluster routing and on-demand inter-cluster routing are combined by changing the relationship between clusters for sensor computing. Applying a reliable routing mechanism in sensor computing can improve routing reliability, maintain low packet loss, minimize management overhead and save energy consumption. Simulation results indicate that the reliability of the proposed RRM mechanism is around 25% higher than that of the Dynamic Source Routing (DSR) and ad hoc On-demand Distance Vector routing (AODV) mechanisms.

14.
J Comput Biol ; 13(10): 1775-89, 2006 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-17238844

RESUMO

The expression of genes in mammalian cells can be constitutive, transient, or inducible. Transcripts of transient and inducible genes are difficult to discover using the EST approach. Transiently expressed genes, however, are crucial to embryo development and the pathogenesis of disease because they determine the outcome of disease. Using our new bioinformatics approach, which we believe will facilitate verification of novel transcripts in developing embryos or pathogen-induced cells; we aimed to identify novel exons in transiently expressed genes. First of all, the proposed method uses a general gene predictor that must be able to produce all possibly optimal or suboptimal candidate exons in human. After applying signal processing, an anchoring procedure in the method transforms and groups the candidate sequences into many numeric hashing-signals clusters rapidly. In the meanwhile, an entropy-based theorem in the method can be used to remove the most error matches, repeat matches. Finally, the method generates the resulting exons identified by alignment with other genomic or EST sequence in cross-species. Our results indicated that 3,223 filtered target exons were potential novel exons. The theoretical threshold determined using the computational method for filtering repeat matches had 95.3% sensitivity and 81.8% specificity. The inferential threshold, however, was close to the experimental threshold, which is a practical expected value for considering both sensitivity and specificity. Therefore, our results proved the feasibility of the method. Combining the anchoring method embedded an entropy-based filter with an inherently unreliable gene predictor can be used to obtain a small scope of exons that may be potentially novel because the combination avoids many drawbacks of some traditional gene predictors.


Assuntos
Genoma Humano , Algoritmos , Análise por Conglomerados , Éxons , Etiquetas de Sequências Expressas , Estudos de Viabilidade , Perfilação da Expressão Gênica , Humanos , Análise de Sequência
15.
IEEE Trans Inf Technol Biomed ; 7(3): 163-70, 2003 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-14518729

RESUMO

A novel diagnostic scheme to develop quantitative indexes of diabetes is introduced in this paper. The fractal dimension of the vascular distribution is estimated because we discovered that the fractal dimension of a severe diabetic patient's retinal vascular distribution appears greater than that of a normal human's. The issue of how to yield an accurate fractal dimension is to use high-quality images. To achieve a better image-processing result, an appropriate image-processing algorithm is adopted in this paper. Another important fractal feature introduced in this paper is the measure of lacunarity, which describes the characteristics of fractals that have the same fractal dimension but different appearances. For those vascular distributions in the same fractal dimension, further classification can be made using the degree of lacunarity. In addition to the image-processing technique, the resolution of original image is also discussed here. In this paper, the influence of the image resolution upon the fractal dimension is explored. We found that a low-resolution image cannot yield an accurate fractal dimension. Therefore, an approach for examining the lower bound of image resolution is also proposed in this paper. As for the classification of diagnosis results, four different approaches are compared to achieve higher accuracy. In this study, the fractal dimension and the measure of lacunarity have shown their significance in the classification of diabetes and are adequate for use as quantitative indexes.


Assuntos
Algoritmos , Diabetes Mellitus/patologia , Retinopatia Diabética/patologia , Fractais , Interpretação de Imagem Assistida por Computador/métodos , Oftalmoscopia/métodos , Complicações do Diabetes , Diabetes Mellitus/diagnóstico , Retinopatia Diabética/diagnóstico , Retinopatia Diabética/etiologia , Humanos , Aumento da Imagem/métodos , Reconhecimento Automatizado de Padrão , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
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