HEAT: a New Tool for Gene Set Enrichment Analysis Using Comprehensive Annotation of Human Genes in H-InvDB

H-InvDB Enrichment Analysis Tool (HEAT) is a new data-mining tool for gene set enrichment analysis based on comprehensive annotations of human genes in H-InvDB. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. The advantage of HEAT is the wide variety of annotation items used for its analysis: chromosomal bands, InterPro functional domains, Gene Ontology terms, KEGG pathways, H-InvDB gene families/groups, SCOP structural domains, subcellular localization predicted by using the Wolf-PSORT program, tissue-specific gene expression as defined in the H-ANGEL database, and transcription factor binding sites in promoter regions based on JASPAR. HEAT accepts lists of human gene identifiers (IDs) including HUGO gene symbols, accession numbers of INSD (DDBJ/EMBL/GenBank), UniProt accession numbers, Gene IDs, Ensembl Gene IDs, H-InvDB Transcript IDs (HIT) and Locus IDs (HIX), etc. Then, HEAT converts the accepted IDs into HIX using the ID Converter System ("http://biodb.jp/":http://biodb.jp/), collects various annotations of H-InvDB representative transcripts, and conducts statistical tests by using Fisher's exact probability. The output of HEAT is a simple report of annotations commonly found among the query genes, which is very useful to grasp the property of a particular gene set. HEAT is freely available at "http://hinv.jp/HEAT/":http://hinv.jp/HEAT/

The frog skin-derived antimicrobial peptide esculentin-1a(1-21)nh2 promotes the migration of human hacat keratinocytes in an egf receptor-dependent manner: a novel promoter of human skin wound healing?

One of the many functions of skin is to protect the organism against a wide range of pathogens. Antimicrobial peptides (AMPs) produced by the skin epithelium provide an effective chemical shield against microbial pathogens. However, whereas antibacterial/antifungal activities of AMPs have been extensively characterized, much less is known regarding their wound healing-modulatory properties. By using an in vitro re-epithelialisation assay employing special cell-culture inserts, we detected that a derivative of the frog-skin AMP esculentin-1a, named esculentin-1a(1-21)NH2, significantly stimulates migration of immortalized human keratinocytes (HaCaT cells) over a wide range of peptide concentrations (0.025-4 μM), and this notably more efficiently than human cathelicidin (LL-37). This activity is preserved in primary human epidermal keratinocytes. By using appropriate inhibitors and an enzyme-linked immunosorbent assay we found that the peptide-induced cell migration involves activation of the epidermal growth factor receptor and STAT3 protein. These results suggest that esculentin-1a(1-21)NH2 now deserves to be tested in standard wound healing assays as a novel candidate promoter of skin re-epithelialisation. The established ability of esculentin-1a(1-21)NH2 to kill microbes without harming mammalian cells, namely its high anti-Pseudomonal activity, makes this AMP a particularly attractive candidate wound healing promoter, especially in the management of chronic, often Pseudomonas-infected, skin ulcers

Relationships between the Use and Environment of an Unagi-nonedoko-like Green Space in Downtown Kyoto City

It is becoming necessary to consider the effective use of vacant lots that have developed due to the demolition of Kyo-machiya (traditional houses) in Kyoto. These long, narrow lots are called Unagi-no-nedoko (“beds of eel”). Their spatial characteristics might make them unsuitable as green spaces because there is the possibility of creating a dark, small, exclusive, and dangerous atmosphere. Thus, we investigated the influence of the environment of an Unagi–no-nedoko-like green space on user awareness and behavior. The results found that the inner area of the green space was as quiet as an indoor room and was recognized as a “relaxing” environment, which caused users to stay longer. Moreover, users found the whole area “large” and “open.” These findings demonstrate that the spatial characteristics of Unagi-no-nedoko do not necessarily make them uncomfortable as green spaces, and it is possible to use such lots as green spaces in downtown Kyoto

An Aggressive Signet Ring Cell Carcinoma of the Prostate in a Japanese Man

Signet ring cell carcinoma (SRCC) of the prostate is rare, with approximately 100 case reports to date. Here we report a very aggressive case of SRCC of the prostate in a Japanese man. The patient received estramustine, docetaxel, and carboplatin combination chemotherapy, followed by TS-1 and CPT-11 combination therapy. Unfortunately, the disease progressed, and he died of general metastatic disease treated over 16 month with systemic chemotherapy

X-rays from the Power Sources of the Cepheus A Star-Forming Region

We report an observation of X-ray emission from the exciting region of Cepheus A with the Chandra/ACIS instrument. What had been an unresolved X-ray source comprising the putative power sources is now resolved into at least 3 point-like sources, each with similar X-ray properties and differing radio and submillimeter properties. The sources are HW9, HW3c, and a new source that is undetected at other wavelengths "h10." They each have inferred X-ray luminosities >= 10^31 erg s^-1 with hard spectra, T >= 10^7 K, and high low-energy absorption equivalent to tens to as much as a hundred magnitudes of visual absorption. The star usually assumed to be the most massive and energetic, HW2, is not detected with an upper limit about 7 times lower than the detections. The X-rays may arise via thermal bremsstrahlung in diffuse emission regions associated with a gyrosynchrotron source for the radio emission, or they could arise from powerful stellar winds. We also analyzed the Spitzer/IRAC mid-IR observation from this star-formation region and present the X-ray results and mid-IR classifications of the nearby stars. HH 168 is not as underluminous in X-rays as previously reported.Comment: Accepted in the ApJ, 30 pages, 11 figures, in one .pdf fil

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts

We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219 765 human transcripts in 43 159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources—‘Navigation search’, ‘H-InvDB Enrichment Analysis Tool (HEAT)’ and web service APIs. ‘Navigation search’ is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility

Effect of an Oral Adsorbent, AST-120, on Dialysis Initiation and Survival in Patients with Chronic Kidney Disease

The oral adsorbent AST-120 has the potential to delay dialysis initiation and improve survival of patients on dialysis. We evaluated the effect of AST-120 on dialysis initiation and its potential to improve survival in patients with chronic kidney disease. The present retrospective pair-matched study included 560 patients, grouped according to whether or not they received AST-120 before dialysis (AST-120 and non-AST-120 groups). The cumulative dialysis initiation free rate and survival rate were compared by the Kaplan-Meier method. Multivariate analysis was used to determine the impact of AST-120 on dialysis initiation. Our results showed significant differences in the 12- and 24-month dialysis initiation free rate (P < 0.001), although no significant difference was observed in the survival rate between the two groups. In conclusion, AST-120 delays dialysis initiation in chronic kidney disease (CKD) patients but has no effect on survival. AST-120 is an effective therapy for delaying the progression of CKD

Efficacy of SMART Stent Placement for Salvage Angioplasty in Hemodialysis Patients with Recurrent Vascular Access Stenosis

Vascular access stenosis is a major complication in hemodialysis patients. We prospectively observed 50 patients in whom 50 nitinol shape-memory alloy-recoverable technology (SMART) stents were used as salvage therapy for recurrent peripheral venous stenosis. Twenty-five stents each were deployed in native arteriovenous fistula (AVF) and synthetic arteriovenous polyurethane graft (AVG) cases. Vascular access patency rates were calculated by Kaplan-Meier analysis. The primary patency rates in AVF versus AVG at 3, 6, and 12 months were 80.3% versus 75.6%, 64.9% versus 28.3%, and 32.3% versus 18.9%, respectively. The secondary patency rates in AVF versus AVG at 3, 6, and 12 months were 88.5% versus 75.5%, 82.6% versus 61.8%, and 74.4% versus 61.8%, respectively. Although there were no statistically significant difference in patency between AVF and AVG, AVG showed poor tendency in primary and secondary patency. The usefulness of SMART stents was limited in a short period of time in hemodialysis patients with recurrent vascular access stenosis