SLS-PLAN-IT: A knowledge-based blackboard scheduling system for Spacelab life sciences missions

The primary scheduling tool in use during the Spacelab Life Science (SLS-1) planning phase was the operations research (OR) based, tabular form Experiment Scheduling System (ESS) developed by NASA Marshall. PLAN-IT is an artificial intelligence based interactive graphic timeline editor for ESS developed by JPL. The PLAN-IT software was enhanced for use in the scheduling of Spacelab experiments to support the SLS missions. The enhanced software SLS-PLAN-IT System was used to support the real-time reactive scheduling task during the SLS-1 mission. SLS-PLAN-IT is a frame-based blackboard scheduling shell which, from scheduling input, creates resource-requiring event duration objects and resource-usage duration objects. The blackboard structure is to keep track of the effects of event duration objects on the resource usage objects. Various scheduling heuristics are coded in procedural form and can be invoked any time at the user's request. The system architecture is described along with what has been learned with the SLS-PLAN-IT project

Reconstruction of human protein interolog network using evolutionary conserved network

<p>Abstract</p> <p>Background</p> <p>The recent increase in the use of high-throughput two-hybrid analysis has generated large quantities of data on protein interactions. Specifically, the availability of information about experimental protein-protein interactions and other protein features on the Internet enables human protein-protein interactions to be computationally predicted from co-evolution events (interolog). This study also considers other protein interaction features, including sub-cellular localization, tissue-specificity, the cell-cycle stage and domain-domain combination. Computational methods need to be developed to integrate these heterogeneous biological data to facilitate the maximum accuracy of the human protein interaction prediction.</p> <p>Results</p> <p>This study proposes a relative conservation score by finding maximal quasi-cliques in protein interaction networks, and considering other interaction features to formulate a scoring method. The scoring method can be adopted to discover which protein pairs are the most likely to interact among multiple protein pairs. The predicted human protein-protein interactions associated with confidence scores are derived from six eukaryotic organisms – rat, mouse, fly, worm, thale cress and baker's yeast.</p> <p>Conclusion</p> <p>Evaluation results of the proposed method using functional keyword and Gene Ontology (GO) annotations indicate that some confidence is justified in the accuracy of the predicted interactions. Comparisons among existing methods also reveal that the proposed method predicts human protein-protein interactions more accurately than other interolog-based methods.</p

A Study on Implementation of Southern-Min Taiwanese Tone Sandhi System

PACLIC 19 / Taipei, taiwan / December 1-3, 200

VNTRDB: a bacterial variable number tandem repeat locus database

Variable number tandem repeat-PCR (VNTR-PCR) is a novel method developed for molecular typing of microorganisms. This method has proven useful in epidemiological studies in medical microbiology. Although hundreds of bacterial genomes have been sequenced, variable number tandem repeats (TRs) derived from comparative genome analyses are scarce. This may hamper their application to the surveillance of bacteria in molecular epidemiology. Here, we present a freely accessible variable number tandem repeat database (VNTRDB) that is intended to be a resource for helping in the discovery of putatively polymorphic tandem repeat loci and to aid with assay design by providing the flanking sequences that can be used in subsequent PCR primer design. In order to reveal possible polymorphism, each TR locus was obtained by comparing the sequences between different sets of bacterial genera, species or strains. Through this comparison, TRs which are unique to a genus can also be identified. Moreover, a visualization tool is provided to ensure that the copy number and locus length of repeats are correct. The VNTRDB is available at

A quantitative analysis of monochromaticity in genetic interaction networks

<p>Abstract</p> <p>Background</p> <p>A genetic interaction refers to the deviation of phenotypes from the expected when perturbing two genes simultaneously. Studying genetic interactions help clarify relationships between genes, such as compensation and masking, and identify gene groups of functional modules. Recently, several genome-scale experiments for measuring quantitative (positive and negative) genetic interactions have been conducted. The results revealed that genes in the same module usually interact with each other in a consistent way (pure positive or negative); this phenomenon was designated as monochromaticity. Monochromaticity might be the underlying principle that can be utilized to unveil the modularity of cellular networks. However, no appropriate quantitative measurement for this phenomenon has been proposed.</p> <p>Results</p> <p>In this study, we propose the monochromatic index (MCI), which is able to quantitatively evaluate the monochromaticity of potential functional modules of genes, and the MCI was used to study genetic landscapes in different cellular subsystems. We demonstrated that MCI not only amend the deficiencies of MP-score but also properly incorporate the background effect. The results showed that not only within-complex but also between-complex connections present significant monochromatic tendency. Furthermore, we also found that significantly higher proportion of protein complexes are connected by negative genetic interactions in metabolic network, while transcription and translation system adopts relatively even number of positive and negative genetic interactions to link protein complexes.</p> <p>Conclusion</p> <p>In summary, we demonstrate that MCI improves deficiencies suffered by MP-score, and can be used to evaluate monochromaticity in a quantitative manner. In addition, it also helps to unveil features of genetic landscapes in different cellular subsystems. Moreover, MCI can be easily applied to data produced by different types of genetic interaction methodologies such as Synthetic Genetic Array (SGA), and epistatic miniarray profile (E-MAP).</p

Evolutionary conservation of DNA-contact residues in DNA-binding domains

<p>Abstract</p> <p>Background</p> <p>DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues.</p> <p>Results</p> <p>Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues.</p> <p>Conclusion</p> <p>This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.</p

Epidemiology and Clinical Peculiarities of Norovirus and Rotavirus Infection in Hospitalized Young Children with Acute Diarrhea in Taiwan, 2009

Background/PurposeAcute diarrhea is one of the most common morbidities in pediatrics worldwide. We conducted a study to investigate the incidence of norovirus in young children hospitalized with acute diarrhea in Taiwan and its clinical peculiarity compared with rotavirus gastroenteritis.MethodsBetween January and December, 2009, patients younger than 5 years and admitted to hospital with acute diarrhea were randomly selected; and their stool samples were collected and tested for presence of rotavirus and norovirus by enzyme immunoassay and reverse transcription-polymerase chain reaction, respectively. The clinical manifestations and laboratory findings of the enrolled patients were analyzed.ResultsA total of 989 cases were enrolled with a mean age of 21.6 ± 13.7 months and a male proportion of 56.0%. Rotavirus and norovirus was detected in 20.2% and 14.6% of all patients, respectively. Genogroup II was the predominant strain of norovirus (80.6%). Children aged 6-36 months accounted for the majority of patients positive for rotavirus and norovirus (73.0% and 81.3%, respectively). The incidences of norovirus and rotavirus infection were higher during winter and early spring. Most patients with rotavirus and norovirus diarrhea experienced vomiting (74.9% vs. 74.8%, respectively) and fever (94.7% vs. 71.3%, respectively).ConclusionMost young diarrheal patients presenting with vomiting were likely to have norovirus or rotavirus infection. Patients with norovirus diarrhea experienced an absence of, or low-grade fever and longer duration of vomiting compared with those positive for rotavirus infection. A family history of current gastroenteritis may suggest the possibility of norovirus infection

Prevalence of intestinal parasitic infections among school children in capital areas of the Democratic Republic of São Tomé and Príncipe, West Africa

Background: Although the Democratic Republic of Sao Tome and Principe (DRSTP) has undertaken school children-based deworming programs against intestinal parasitic infections (IPIs) using a single dose of mebendazole annually since 2005, it remains unclear as to the outcome to date. The present study intends to  investigate the recent IPIs status among school children living in capital areas of the DRSTP.Methods: A total of 252 school children (121 boys and 131 girls) of grades 4 and 5 from 4 primary schools located in the capital areas participated in the present study and their fresh fecal specimens were examined for the presence of any parasites using the merthiolate- iodine-formaldehyde concentration method as conducted.Results: The overall prevalence of IPIs was 64.7% (163/ 252). No significant gender difference in prevalence between boys (67.8%) and girls (61.8%) was found (p = 0.3). The majority of school children were infected with a single species of parasite (55.8%). Altogether, 12 different intestinal parasite species were identified in DRSTP school children, of which 9 species were pathogenic and the remaining 3 were non-pathogenic.Conclusion: Improving the detection method, sanitation facilities and personal hygiene as well as utilizing combined drugs are all important measures to greatly reduce IPIs in DRSTP school children.Keywords: Democratic Republic of Sao Tome and Principe, school children, intestinal parasitic infection

POINeT: protein interactome with sub-network analysis and hub prioritization

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools.</p> <p>Results</p> <p>We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3) to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles.</p> <p>Conclusion</p> <p>The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to selected tissues can be revealed. The straightforward interface of POINeT makes PPI search and analysis just a few clicks away. The modular design permits further functional enhancement without hampering the simplicity. POINeT is available at <url>http://poinet.bioinformatics.tw/</url>.</p

Thrombomodulin Regulates Keratinocyte Differentiation and Promotes Wound Healing

The membrane glycoprotein thrombomodulin (TM) has been implicated in keratinocyte differentiation and wound healing, but its specific function remains undetermined. The epidermis-specific TM knockout mice were generated to investigate the function of TM in these biological processes. Primary cultured keratinocytes obtained from TMlox/lox; K5-Cre mice, in which TM expression was abrogated, underwent abnormal differentiation in response to calcium induction. Poor epidermal differentiation, as evidenced by downregulation of the terminal differentiation markers loricrin and filaggrin, was observed in TMlox/lox; K5-Cre mice. Silencing TM expression in human epithelial cells impaired calcium-induced extracellular signal–regulated kinase pathway activation and subsequent keratinocyte differentiation. Compared with wild-type mice, the cell spreading area and wound closure rate were lower in keratinocytes from TMlox/lox; K5-Cre mice. In addition, the lower density of neovascularization and smaller area of hyperproliferative epithelium contributed to slower wound healing in TMlox/lox; K5-Cre mice than in wild-type mice. Local administration of recombinant TM (rTM) accelerated healing rates in the TM-null skin. These data suggest that TM has a critical role in skin differentiation and wound healing. Furthermore, rTM may hold therapeutic potential for the treatment of nonhealing chronic wounds