The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

Long-term monitoring of stride length and walking velocity is considered to provide useful information for making decisions on treatment of patients with gait disabilities. The purpose of this study was to develop a device with the following design criteria: lightweight, easy attachment, little hindrance to the natural gait pattern, sufficient memory to record for one day, and practicality in clinical use. The prototype consists of a piezoelectric gyroscope, which detects angular velocity of the thigh of one leg in the sagittal plane, and a microprocessor-based maximum/minimum detector/data logger of a cyclic analog signal associated with the gait cycle. The accuracy of the device was evaluated in 20 normal subjects, seven above-the-knee (A/K) amputees, and ten hemiplegic patients, and relative accuracy within +/-15% was obtained, except for two special cases.

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Since 1986, the centre solenoid (CS)-less formations of ultra-high-beta CT/ST plasmas have been developed in the TS-3 merging experiment using high power heating of magnetic reconnection. In the cohelicity (Type-A) merging, two STs were merged together to build up the plasma beta to βT≈0.5. In the counterhelicity (Type-B) merging, an oblate FRC formed by two merging spheromaks with opposing toroidal field Bt, was transformed into an ultra-high-beta (βT≈0.8) ST by applying external toroidal field Bt. We made the BALLOO code stability analyses of the produced STs and concluded that formations of the first-stable/marginally second-stable STs were obtained by Type-A merging and the second-stable STs by Type-B merging and also unstable STs by both mergings. The ballooning-stable regime calculated from the experimental data was almost consistent with the measured high-n instabilities. The stable regime became larger significantly by increasing the hollowness of current profile and broadness of pressure profile. This paper also addresses normalized betas βN of thus produced STs as large as 6–17 for comparison with the Troyon scaling and a promising B2 scaling of the reconnection heating. These facts indicate that the axial merging is one of the most efficient startup method for high-beta ST without powerful CS.

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases. The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale. In addition, we have developed the Genome Information Broker (GIB, http://gib.genes.nig.ac.jp) that now includes more than 50 complete microbial genome and Arabidopsis genome data. We have also developed a database of the human genome, the Human Genomics Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools.

DKT improved bowel movements, stool properties, and bowel gas. These results suggested that DKT promoted early postoperative bowel functions after total gastrectomy.

BackgroundIn genome-wide studies, over-representation analysis (ORA) against a set of genes is an essential step for biological interpretation. Many gene annotation resources and software platforms for ORA have been proposed. Recently, Medical Subject Headings (MeSH) terms, which are annotations of PubMed documents, have been used for ORA. MeSH enables the extraction of broader meaning from the gene lists and is expected to become an exhaustive annotation resource for ORA. However, the existing MeSH ORA software platforms are still not sufficient for several reasons.ResultsIn this work, we developed an original MeSH ORA framework composed of six types of R packages, including MeSH.db, MeSH.AOR.db, MeSH.PCR.db, the org.MeSH.XXX.db-type packages, MeSHDbi, and meshr.ConclusionsUsing our framework, users can easily conduct MeSH ORA. By utilizing the enriched MeSH terms, related PubMed documents can be retrieved and saved on local machines within this framework.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0453-z) contains supplementary material, which is available to authorized users.