Abstract
The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of ...actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.
Transcription starts at genomic positions called transcription start sites (TSSs), producing RNAs, and is mainly regulated by genomic elements and transcription factors binding around these TSSs. ...This indicates that TSSs may be a better unit to integrate various data sources related to transcriptional events, including regulation and production of RNAs. However, although several TSS datasets and promoter atlases are available, a comprehensive reference set that integrates all known TSSs is lacking. Thus, we constructed a reference dataset of TSSs (refTSS) for the human and mouse genomes by collecting publicly available TSS annotations and promoter resources, such as FANTOM5, DBTSS, EPDnew, and ENCODE. The data set consists of genomic coordinates of TSS peaks, their gene annotations, quality check results, and conservation between human and mouse. We also developed a web interface to browse the refTSS (http://reftss.clst.riken.jp/). Users can access the resource for collecting and integrating data and information about transcriptional regulation and transcription products.
Display omitted
•We construct a reference data set of transcription start sites (refTSS) by consolidating publicly available transcriptional start site (TSS) information for human and mouse genomes.•The data set provides the genomic coordinates and the associated annotations of TSSs.•Users can use the data set for integrating information about transcriptional regulation and transcribed RNAs.•The refTSS is publicly available via a web interface (http://reftss.clst.riken.jp/) that allows for search and download of the data.
Migration and law in Japan Kondo, Atsushi
Asia & the Pacific policy studies,
01/2015, Letnik:
2, Številka:
1
Journal Article
Recenzirano
Odprti dostop
It has been claimed that Japan is not a country of immigration. Where is Japan's distinctiveness evident, and what features does it share with other countries? This article examines the unique points ...of Japan and investigates problems of residence and citizenship. This article argues that Japan's historical legacy and international human rights have had an impact on Japan's migration and law, takes into consideration the need for new policies and examines some thorny issues. Globalisation and an ageing population are generating a debate on implementing a more liberal admission policy for highly skilled workers, students and nurses/care workers. Thorny issues comprise ethnic discrimination underscored by a colonial legacy and the still existing cold war in East Asia. Drawing a comparison with selected developed countries, this article indicates several challenges for Japan's migration and law. Markedly, Japan is the only developed industrialised democracy that does not have an anti-discrimination law.
Metal–organic frameworks (MOFs) provide access to structures with nanoscale pores, the size and connectivity of which can be controlled by combining the appropriate metals and linkers. To date, there ...have been no reports of using MOFs as templates to make porous, crystalline metal oxides. Microporous titania replicas were made from the MOF template HKUST-1 by dehydration, infiltration with titanium isopropoxide, and subsequent hydrothermal treatment at 200 °C. Etching of the MOF with 1 M aqueous HCl followed by 5% H2O2 yielded a titania replica that retained the morphology of the parent HKUST-1 crystals and contained partially ordered micropores as well as disordered mesopores. Interestingly, the synthesis of porous titania from the HKUST-1 template stabilized the formation of brookite, a rare titania polymorph.
A series of finite element analyses were conducted to clarify the effect of contact and interfacial resistance between constituents on effective thermal conductivities of dispersed composites. ...Equally dispersed fillers in FCC (face-centered cubic) and BCC (body-centered cubic) material systems were extracted from cyclic microstructures as unit cell models. In addition to spherical fillers, a polyhedron called the Wigner-Seitz cell that can realize a fully packed microstructure was chosen as the shape of the filler to investigate the effect of contact between the high volumetric fraction of fillers. The effective thermal conductivities of the resulting composites were calculated based on the FEA results and compared to the theoretical results for various volume fractions of the fillers including the maximum packing fraction. The following conclusions were obtained from the present study: 1. The effect of the contact depending on the shape and configuration of the fillers has more of a significant influence on the effective thermal conductivity than the influence of the increase in the volume fraction of the fillers. 2. When the contact occurred, the effective thermal conductivity became more than double that without contact. 3. Interfacial thermal resistance must be less than the order of 10
m
K/W to obtain improvement in the effective thermal conductivity by compounding the fillers.
The mechanism for the dehydration of Mg(OH)2 and hydration of MgO was investigated by near-infrared (NIR) spectroscopy. Mg(OH)2 showed three absorption bands in the NIR region at 7339, 7306, and ...7157 cm–1, due to the different hydroxyl groups (7339 cm–1: OH(e) and OH(c) located on the edge and corner of the Mg(OH)2 sheet, 7306 cm–1: OH(t) located on the terrace of Mg(OH)2 sheet, 7157 cm–1: OH(i) located on the interlayer of Mg(OH)2 sheets). During the phase transition from Mg(OH)2 to MgO at approximately 400 °C, the interlayer OH(i) of Mg(OH)2 disappeared by a dehydration reaction and the OH(t) on the (001) plane of Mg(OH)2 was converted to the hydrogen-bonded hydroxyl groups on the (111) plane of MgO (7309 cm–1). Furthermore, when MgO was in contact with water vapor at 85 and 50 °C (RH 85%), the isolated hydroxyl groups of the MgO surface (7360 cm–1) were easily hydrated to form hydrogen-bonded ones (7309 cm–1). When a monolayer Mg(OH)2 sheet was formed on the MgO surface, OH(e), OH(c), and OH(t) were observed at 7345 and 7309 cm–1. As the hydration reaction proceeded, the intermediate state like stacking of several Mg(OH)2 sheets, which are related to the decrease in the OH(t) and the spontaneous increase in the interlayer OH(i), was experimentally confirmed.
Coordination polymers (CPs) or metal-organic frameworks (MOFs) have attracted considerable attention because of the tunable diversity of structures and functions. A 4,4'-bipyridine molecule, which is ...a simple, linear, exobidentate, and rigid ligand molecule, can construct two-dimensional (2D) square grid type CPs. Only the 2D-CPs with appropriate metal cations and counter anions exhibit flexibility and adsorb gas with a gate mechanism and these 2D-CPs are called elastic layer-structured metal-organic frameworks (ELMs). Such a unique property can make it possible to overcome the dilemma of strong adsorption and easy desorption, which is one of the ideal properties for practical adsorbents.
Abstract
Gitelman syndrome is an autosomal recessive inherited salt-losing tubulopathy. It has a prevalence of around 1 in 40,000 people, and heterozygous carriers are estimated at approximately 1%, ...although the exact prevalence is unknown. We estimated the predicted prevalence of Gitelman syndrome based on multiple genome databases, HGVD and jMorp for the Japanese population and gnomAD for other ethnicities, and included all 274 pathogenic missense or nonsense variants registered in HGMD Professional. The frequencies of all these alleles were summed to calculate the total variant allele frequency in
SLC12A3
. The carrier frequency and the disease prevalence were assumed to be twice and the square of the total allele frequency, respectively, according to the Hardy–Weinberg principle. In the Japanese population, the total carrier frequencies were 0.0948 (9.5%) and 0.0868 (8.7%) and the calculated prevalence was 0.00225 (2.3 in 1000 people) and 0.00188 (1.9 in 1000 people) in HGVD and jMorp, respectively. Other ethnicities showed a prevalence varying from 0.000012 to 0.00083. These findings indicate that the prevalence of Gitelman syndrome in the Japanese population is higher than expected and that some other ethnicities also have a higher prevalence than has previously been considered.
Endometriosis-related cervical neoplasms are rare, and their clinicopathological features and association with human papilloma virus infection are unclear. A postmenopausal woman with recently ...diagnosed cervical adenocarcinoma was referred to our hospital. After further investigation, we suspected a stage IIB neoplasm that originated from endometriosis of the cervix or left parametrium. A radical hysterectomy was performed, and pathological examination confirmed a stage IIB cervical endometrioid carcinoma arising from the endometriosis in the cervix to the left parametrium that invaded the cervix; human papilloma virus infection of tumor cells was not detected. Endometriosis-related neoplasms can occur in the cervix or parametrium and present as cervical cancer. The neoplasm described here was not associated with human papilloma virus infection.
The mutant allele frequency of the Pyruvate kinase (PK) gene has been investigated mostly in pure breed cats. We investigated the PK mutant gene in stray and animal hoarding mongrel cats in Hokkaido, ...Japan. We also investigated the kinship of individuals carrying the mutant gene. Genotyping was conducted using the previously reported real-time PCR method. Fourteen microsatellite markers were used to identify the parents and offspring of cats carrying the PK mutant gene, and some kinship such as parent-offspring and siblings was observed. Some stray and animal hoarding cats carried the PK mutation gene and that consanguinity was confirmed among these cats indicated that the PK mutation gene was spread by unregulated interbreeding.
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