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/

Vascular Adhesion Protein-1 Blockade Suppresses Ocular Inflammation After Retinal Laser Photocoagulation in Mice

PURPOSE. To investigate the effect of the vascular adhesion protein-1 (VAP-1) inhibitor RTU-1096 on retinal morphologic changes and ocular inflammation after retinal laser photocoagulation in mice. METHODS. C57BL/6JJcl mice were fed a diet containing RTU-1096, a specific inhibitor for VAP-1, or a control diet ad libitum for 7 days. Laser photocoagulation was performed on the peripheral retina of the animals. The semicarbazide sensitive amine oxidase (SSAO) activities in plasma and chorioretinal tissues were measured. Optical coherence tomography (OCT) images were acquired before and at 1, 3, and 7 days after laser photocoagulation, and thickness of the individual retinal layers was measured. Intravitreal leukocyte infiltration was assessed by histologic analysis. The expression level of intercellular adhesion molecule-1 (ICAM-1) in retinal tissues were examined by quantitative real-time PCR. RESULTS. One day after laser photocoagulation, the thickness of the outer nuclear layer (ONL) increased in the laser group compared with in the control group, and RTU-1096 administration abrogated the ONL thickening. Histologic analysis and OCT observation revealed that laser photocoagulation caused infiltration of inflammatory cells and the appearance of hyperreflective foci at the vitreoretinal surface, both of which were suppressed by RTU-1096 administration. In addition, systemic administration of RTU-1096 reduced upregulation of the leukocyte adhesion molecules ICAM-1 in the retina. CONCLUSIONS. The current data indicate that VAP-1/SSAO inhibition may be a potential therapeutic strategy for the prevention of macular edema secondary to scatter laser photocoagulation in patients with ischemic retinal diseases such as diabetic retinopathy

Author Identification : One view on the infrastructure building in Open Access environment

DRF国際会議2009：オープンアクセスリポジトリの現在と未来:世界とアジアへの視点から＝International Conference 2009：Open access repositories now and in the future : from the global and Asia-Pacific points of view(Dec.3-4,2009, Tokyo)のポスターセッション用資

Biorhythm-Based Awakening Timing Modulation

Abstract-The purpose of the present study is to control human biological rhythm and life cycle by optimization of awakening timing. We developed a wearable interface for controlling awakening time named "BRAC (Biological Rhythm based Awakening timing Controller)". BRAC could estimate bio-rhythm by pulse wave from finger tip and send awake signal to user. An ordinary alarm clock operates according to set times that have to be set in advance. However, humans have a rhythm in their sleep, which affects one's sleep depth and wake-up timing. We consider the simplest way to control or reset human's biorhythm or life style is to optimize the awakening timing and the sleeping hours. We examined the relationship between controlling awakening timing based on autonomous nerve rhythm and equilibrium function. Our findings suggest indicate that the prototype "BRAC" could evaluate user's biological rhythm and awakes user at the time optimized for physical function of equilibrium

Myocardial velocity gradient as a noninvasively determined index of left ventricular diastolic dysfunction in patients with hypertrophic cardiomyopathy

AbstractObjectivesWe investigated the utility of the peak negative myocardial velocity gradient (MVG) derived from tissue Doppler imaging (TDI) for evaluation of diastolic dysfunction in patients with hypertrophic cardiomyopathy (HCM).BackgroundHypertrophic cardiomyopathy is characterized by impaired diastolic function with abnormal stiffness and prolonged relaxation. However, it remains difficult to evaluate these defects noninvasively.MethodsBoth TDI and conventional echocardiography were performed in 36 patients with HCM and in 47 control subjects. Left ventricular (LV) pressure was measured simultaneously in all HCM patients and in 26 controls.ResultsThe peak negative MVG occurred soon after the isovolumic relaxation period during the initial phase of rapid filling (auxotonic relaxation). It was significantly smaller in HCM patients than in control subjects (2.32 ± 0.52/s vs. 4.82 ± 1.15/s, p < 0.0001); the cutoff value for differentiation between all HCM patients and 47 normal individuals was determined as 3.2/s. Both the left ventricular end-diastolic pressure (LVEDP) (19.6 ± 6.1 mm Hg vs. 6.5 ± 1.7 mm Hg, p < 0.0001) and the time constant of LV pressure decay during isovolumic diastole (tau) (44.0 ± 6.7 ms vs. 32.1 ± 5.5 ms, p < 0.0001) were increased in HCM patients compared with controls. The peak negative MVG was negatively correlated with both LVEDP (r= −0.75, p < 0.0001) and tau (r= −0.58, p < 0.0001).ConclusionsA reduced peak negative MVG reflects both prolonged relaxation and elevated LVEDP. The peak negative MVG might thus provide a noninvasive index of diastolic function, yielding unique information about auxotonic relaxation in patients with HCM

Walking and Sports Participation and Mortality From Coronary Heart Disease and Stroke

ObjectivesWe aimed to examine the impact of exercise on mortality from cardiovascular disease (CVD) in Asian populations.BackgroundFew data have been available in Asian countries, where job-related physical activity is higher than that in Western countries.MethodsBetween 1988 and 1990, 31,023 men and 42,242 women in Japan, ages 40 to 79 years with no history of stroke, coronary heart disease (CHD), or cancer, completed a self-administered questionnaire. Systematic mortality surveillance was performed through 1999, and 1,946 cardiovascular deaths were identified. We chose the second lowest categories of walking and sports participation as the reference to reduce a potential effect of ill health.ResultsMen and women who reported having physical activity in the highest category (i.e., walking ≥1 h/day or doing sports ≥5 h/week) had a 20% to 60% lower age-adjusted risk of mortality from CVD, compared with those in the second lowest physical activity category (i.e., walking 0.5 h/day, or sports participation for 1 to 2 h/week). Adjustment for known risk factors, exclusion of individuals who died within two years of baseline inquiry, or gender-specific analysis did not substantially alter these associations. The multivariate-adjusted hazard ratios (95% confidence interval) for the highest versus the second lowest categories of walking or sports participation were 0.71 (0.54 to 0.94) and 0.80 (0.48 to 1.31), respectively, for ischemic stroke (IS); 0.84 (0.64 to 1.09) and 0.51 (0.32 to 0.82), respectively, for CHD; and 0.84 (0.75 to 0.95) and 0.73 (0.60 to 0.90), respectively, for CVD.ConclusionsPhysical activity through walking and sports participation might reduce the risk of mortality from IS and CHD

Nitrosomonas europaea MazF Specifically Recognises the UGG Motif and Promotes Selective RNA Degradation

Toxin-antitoxin (TA) systems are implicated in prokaryotic stress adaptation. Previously, bioinformatics analysis predicted that such systems are abundant in some slowly growing chemolithotrophs; e.g., Nitrosomonas europaea. Nevertheless, the molecular functions of these stress-response modules remain largely unclear, limiting insight regarding their physiological roles. Herein, we show that one of the putative MazF family members, encoded at the ALW85_RS04820 locus, constitutes a functional toxin that engenders a TA pair with its cognate MazE antitoxin. The coordinate application of a specialised RNA-Seq and a fluorescence quenching technique clarified that a unique triplet, UGG, serves as the determinant for MazF cleavage. Notably, statistical analysis predicted that two transcripts, which are unique in the autotroph, comprise the prime targets of the MazF endoribonuclease: hydroxylamine dehydrogenase (hao), which is essential for ammonia oxidation, and a large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL), which plays an important role in carbon assimilation. Given that N. europaea obtains energy and reductants via ammonia oxidation and the carbon for its growth from carbon dioxide, the chemolithotroph might use the MazF endoribonuclease to modulate its translation profile and subsequent biochemical reactions