Interaction between Northern Coal Sack in the Cyg OB 7 cloud complex and the multiple super nova remnants including HB 21

We report possible interaction between multiple super nova remnants (SNRs) and Northern Coal Sack (NCS) which is a massive clump (~1000 Mo) in the Cyg OB 7 cloud complex and is forming a massive Class 0 object. We performed molecular observations of the 12CO(J=1-0), 13CO(J=1-0), and C18O(J=1-0) emission lines using the 45m telescope at the Nobeyama Radio Observatory, and we found that there are mainly four velocity components at Vlsr=-20, -6, -4, and 10 km/s. The -6 and -4 km/s components correspond to the systemic velocities of NCS and the Cygnus OB 7 complex, respectively, and the other velocity components originate from distinct smaller clouds. Interestingly, there are apparent correlations and anti-correlations among the spatial distributions of the four components, suggesting that they are physically interacting with one another. On a larger scale, we find that a group of small clouds belonging to the -20 and 10 km/s components are located along two different arcs around some SNRs including HB 21 which has been suggested to be interacting with the Cyg OB 7 cloud complex, and we also find that NCS is located right at the interface of the arcs. The small clouds are likely to be the gas swept up by the stellar wind of the massive stars which created the SNRs. We suggest that the small clouds alined along the two arcs recently encountered NCS and the massive star formation in NCS was triggered by the strong interaction with the small clouds.Comment: To appear in the Publications of the Astronomical Society of Japan (PASJ

Infrared luminosity functions of AKARI Sloan Digital Sky Survey galaxies

By cross-correlating the AKARI all-sky survey in six infrared (IR) bands (9, 18, 65, 90, 140 and 160 μm) with the Sloan Digital Sky Survey (SDSS) galaxies, we identified 2357 IR galaxies with a spectroscopic redshift. This is not just one of the largest samples of local IR galaxies, but AKARI provides crucial far-IR (FIR) bands for accurately measuring the galaxy spectral energy distribution (SED) across the peak of the dust emission at > 100 μ m. By fitting modern IR SED models to the AKARI photometry, we measured the total infrared luminosity (L_(IR)) of individual galaxies. Using this L_(IR), we constructed the luminosity functions (LF) of IR galaxies at a median redshift of z= 0.031. The LF agrees well with that at z= 0.0082 (the Revised Bright Galaxy Sample), showing smooth and continuous evolution towards higher redshift LFs measured in the AKARI North Ecliptic Pole (NEP) deep field. By integrating the IR LF weighted by L_(IR), we measured the local cosmic IR luminosity density of Ω_(IR_= (3.8^(+5.8)_(−1.2)) × 10^8 L_⊙ Mpc^(−3). We separate galaxies into active galactic nuclei (AGN), star-forming galaxies (SFG) and composite by using the [N ii]/Hα versus [O iii]/Hβ line ratios. The fraction of AGN shows a continuous increase with increasing L_(IR) from 25 to 90 per cent at 9 10^(11) L_⊙, coinciding with the break of both the SFG and AGN IR LFs. At L_(IR)≤ 10^(11) L_⊙, SFG dominates IR LFs. Only 1.1 ± 0.1 per cent of Ω_(IR) is produced by luminous infrared galaxies (L_(IR) > 10^(11) L_⊙), and only 0.03 ± 0.01 per cent by ultraluminous infrared galaxies (L_(IR) > 10^(12) L_⊙) in the local Universe. Compared with high-redshift results from the AKARI NEP deep survey, we observed a strong evolution of Ω^(SFG)IR^∝ (1 +z)^(4.1±0.4) and Ω^(AGN)IR^∝ (1+z)^(4.1±0.5). Our results show that all of our measured quantities (IR LFs, L^*, Ω^(AGN)IR, Ω^(SFG)IR) show smooth and steady increase from lower redshift (the Revised Bright Galaxy Sample) to higher redshift (the AKARI NEP deep survey)

The Far-Infrared Surveyor (FIS) for AKARI

The Far-Infrared Surveyor (FIS) is one of two focal plane instruments on the AKARI satellite. FIS has four photometric bands at 65, 90, 140, and 160 um, and uses two kinds of array detectors. The FIS arrays and optics are designed to sweep the sky with high spatial resolution and redundancy. The actual scan width is more than eight arcmin, and the pixel pitch is matches the diffraction limit of the telescope. Derived point spread functions (PSFs) from observations of asteroids are similar to the optical model. Significant excesses, however, are clearly seen around tails of the PSFs, whose contributions are about 30% of the total power. All FIS functions are operating well in orbit, and its performance meets the laboratory characterizations, except for the two longer wavelength bands, which are not performing as well as characterized. Furthermore, the FIS has a spectroscopic capability using a Fourier transform spectrometer (FTS). Because the FTS takes advantage of the optics and detectors of the photometer, it can simultaneously make a spectral map. This paper summarizes the in-flight technical and operational performance of the FIS.Comment: 23 pages, 10 figures, and 2 tables. Accepted for publication in the AKARI special issue of the Publications of the Astronomical Society of Japa

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

<p>Abstract</p> <p>Background</p> <p>The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.</p> <p>Results</p> <p>Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs.</p> <p>Conclusions</p> <p>Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.</p

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

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

Effects of Amino Acid, Enzyme Mixture and Phytase Added to Low Protein and Low Phosphorus Diet on Performance and Excretion of Nitrogen and Phosphorus in Broilers.

In the purpose to reducing excretion of nitrogen (N) and phosphorus (P) without the influence of the growth performances and abdominal fat in broilers, a feeding trial and balance test were conducted. Four diets were prepared. The control diets (C) contained 23% crude protein (CP) for 0 to 21 days of age and 19% CP for 22 to 49 days of age, respectively. In the second diets (L), CP were reduced to 19 and 16% for both phases and crystal amino acids were added to be 110% of requirements at both phases. In the third diets (LE), an enzyme mixture (cellulase, xylanase and pectinase) was added to L. In the fourth diets (LEP), non-phytate P were reduced to 0.32% and 0.28% for both phases, and phytase was added. Eight hundred one-day-old broiler chicks, equal number of male and female, were divided into 4 treatments and given free access to one of the diets for 49 days of age, and body weight (BW), feed intake and mortality were recorded. At the end of experiment, 50 chicks per each treatment were slaughtered by bleeding through a jugular vein and eviscerated for the determination of abdominal fat. Using another 10 male broiler chicks per each treatment, excretion of dry matter (DM), N and P were determined by the balance test. There were no significant differences in BW gain, feed intake, feed conversion ratio and mortality among four treatments. Abdominal fat of broilers fed L was significantly heavier than that of other three treatments, and no significant differences were found in abdominal fat among other three treatments. Excretion of DM and N in L, LE and LEP decreased to 91, 84 and 82%, and 73, 70 and 70% of C, respectively. Excretion of P of broilers fed LEP decreased to a half of other three treatments, and there were no differences in P excretion among other three treatments

Effects of Microbial Phytase on Phytate Phosphorus Utilization in Plant Feedstuffs for Broiler Chicks

The reported effects of dietary supplemented microbial phytase on the utilization of phytate phosphorus (pP) differ widely by investigators. In order to clarify the differences, the contents of total phosphorus (P) and pP in commonly used five plant feedstuffs, corn (C), soybean meal (SM), defatted rice bran (RB), wheat bran (WB) and high level flour wheat bran (FWB) were determined, and the effect of microbial phytase on utilization of pP in these feedstuffs was studied using male broiler chicks. The contents of total P in plant feedstuffs were determined to be 0.25, 0.67, 2.81, 1.04 and 0.54%, and those of pP to be 0.15, 0.31, 2.02, 0.71 and 0.32% in C, SM, RB, WB and FWB, respectively. The ratios of pP to total P ranged from 47.2% (for SM) to 71.8% (for RB). The experimental diets were formulated using C, SM, RB, WB or FWB as a sole source of pP. Male broiler chicks were fed the diets supplemented by 0 or 500 phytase units/kg of diet microbial phytase for 10 days from 7 to 17 days of age. There were large differences in pP retention among plant feedstuffs without microbial phytase. Especially the retention was low (5.4%) in the C and high (73.4%) in the WB. The pP retention in SM, RB and FWB were 52.3, 42.5 and 51.1%, respectively. On the other hand, with the addition of microbial phytase, pP retention in C, SM, RB, WB and FWB increased to 69.9, 75.0, 78.6, 86.6 and 84.1%, respectively