RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here

A flexible representation of omic knowledge for thorough analysis of microarray data

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site

Fabrication and characterization of field-effect transistor device with C_2v isomer of Pr@C₈₂

A field-effect transistor (FET) device was fabricated with thin films of C2v isomer of Pr@C82. This device apparently showed n-channel normally-on type FET properties, where non-zero current was observed at gate-source voltage of 0 VGS, of 0V. Normally off FET properties were observed by subtraction of the non-zero current from the drain current.Thus the normally on properties are ascribed to the high bulk current caused by the small energy gap ≈0.3 eV. The field-effect mobility for this FET was 1.5 x 10-4 cm2 V-1 s-1 at 320 K, being comparable to those of other endohedral metallofullerene FET devices.</p

Lubiprostone Decreases the Small Bowel Transit Time by Capsule Endoscopy: An Exploratory, Randomised, Double-Blind, Placebo-Controlled 3-Way Crossover Study

The aim of this study was to investigate the usefulness of lubiprostone for bowel preparation and as a propulsive agent in small bowel endoscopy. Six healthy male volunteers participated in this randomized, 3-way crossover study. The subjects received a 24 μg tablet of lubiprostone 60 minutes prior to the capsule ingestion for capsule endoscopy (CE) and a placebo tablet 30 minutes before the capsule ingestion (L-P regimen), a placebo tablet 60 minutes prior to CE and a 24 μg tablet of lubiprostone 30 minutes prior to CE (P-L regimen), or a placebo tablet 60 minutes prior to r CE and a placebo tablet again 30 minutes prior to CE (P-P regimen). The quality of the capsule endoscopic images and the amount of water in the small bowel were assessed on 5-point scale. The median SBTT was 178.5 (117–407) minutes in the P-P regimen, 122.5 (27–282) minutes in the L-P regimen, and 110.5 (11–331) minutes in the P-L regimen (P=0.042). This study showed that the use of lubiprostone significantly decreased the SBTT. We also confirmed that lubiprostone was effective for inducing water secretion into the small bowel during CE

Accuracy of Non-invasive Arterial Input Functions and Error in Quantitative Images in the Cerebellar Reference Method

PURPOSE: We developed and validated the accuracy of a method to calculate the arterial input function (AIF) from PET images only, without the need for the arterial blood sampling, in the absolute quantitation of functional parametric values in 15O- gas PET examinations.METHODS: We extended the method reported by Iguchi et al. (2013) to derive the arterial input function, thus absolute quantitative functional parametric images of cerebral perfusion and oxygen metabolism by a reference tissue approach. We compared shapes of the AIF and reproducibility of the absolute functional values. Existing test data that were carried out with the continuous arterial blood sampling were used for this study.RESULTS: The estimated AIF shapes agreed well with those estimated from the continuous arterial blood sampling. The error range of the absolute quantitative values was approximately ±20%, with a fairly well reproducibility in the relative values being less than 3%.CONCLUSION: The AIFs by this method were reproducible. Although the absolute quantitative values varied depending on the assumed functional values in the reference region in individual cases, the relative images showed fairly good agreement with the results from the standard technique that employed the arterial blood sampling. The present technique may provide significant contribution to clinical examination.</p

maxillofacial features of Apert syndrome

Apert syndrome is a rare craniosynostosis syndrome characterized by irregular craniosynostosis, midface hypoplasia, and syndactyly of the hands and feet. Previous studies analyzed individuals with Apert syndrome and reported some facial and intraoral features caused by severe maxillary hypoplasia. However, these studies were performed by analyzing both individuals who had and those had not received a palate repair surgery, which had a high impact on the maxillary growth and occlusion. To highlight the intrinsic facial and intraoral features of Apert syndrome, five Japanese individuals with Apert syndrome from 5 years and 2 months to 9 years and 10 months without cleft palate were analyzed in this study. A concave profile and a skeletal Class III jaw-base relationship caused by severe maxillary hypoplasia were seen in all patients. The patients exhibited anterior and posterior crossbites possibly due to a small dental arch of Maxilla

The medaka fish Tol2 transposable element is in an early stage of decay: identification of a nonautonomous copy

The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The Tol2 element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Here we report the presence of a nonautonomous Tol2 copy that was identified by surveying the medaka genome sequence database. This copy contained 3 local sequence alterations that affected the deduced amino acid sequence of the transposase: a deletion of 15 nucleotides resulting in a deletion of 5 amino acids, a base substitution causing a single amino acid change, and another base substitution giving rise to a stop codon. Transposition assays using cultured human cells revealed that the transposase activity was reduced by the 15-nucleotide deletion and abolished by the nonsense mutation. This is the first example of a nonautonomous Tol2 copy. Thus, Tol2 is in an early stage of decay in the medaka genome, and is therefore a unique element to observe an almost whole decay process that progresses in natural populations.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Effects of Perioperative Oral Management in Patients with Cancer

Perioperative oral management (POM) is used to prevent pneumonia in patients with cancer. However, the factors that expose hospitalized patients to increased risk of developing pneumonia remain unclear. For example, no study to date has compared the incidence of pneumonia in hospitalized patients by cancer primary lesion, or POM implementation, or not. We determined which patients were most likely to benefit from POM and examined the effects of POM on pneumonia prevention and mortality. In a total of 9441 patients with cancer who underwent surgery during hospitalization, there were 8208 patients in the No POM group, and 1233 in the POM group. We examined between-group differences in the incidence of pneumonia and associated outcomes during hospitalization. There was no significant between-group difference in the incidence of pneumonitis, however, patients with lung, or head and neck cancers, demonstrated a lower incidence of postoperative pneumonia. Among patients with lung and pancreatic cancers, mortality was significantly lower in the POM group. POM appears effective at reducing the risk of postoperative pneumonia in patients with certain cancers. Further, mortality was significantly lower in patients with lung and pancreatic cancers who received POM; hence, POM may be an effective adjuvant therapy for patients with cancer