477 research outputs found
FOAM (functional ontology assignments for metagenomes):a hidden markov model (HMM) database with environmental focus
A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/
The California Planet Survey. I. Four New Giant Exoplanets
We present precise Doppler measurements of four stars obtained during the past decade at Keck Observatory by the California Planet Survey (CPS). These stars, namely, HD 34445, HD 126614, HD 13931, and Gl 179, all show evidence for a single planet in Keplerian motion. We also present Doppler measurements from the Hobby-Eberly Telescope (HET) for two of the stars, HD 34445 and Gl 179, that confirm the Keck detections and significantly refine the orbital parameters. These planets add to the statistical properties of giant planets orbiting near or beyond the ice line, and merit follow-up by astrometry, imaging, and space-borne spectroscopy. Their orbital parameters span wide ranges of planetary minimum mass (M sin i = 0.38-1.9 M(Jup)), orbital period (P = 2.87-11.5 yr), semimajor axis (a = 2.1-5.2 AU), and eccentricity (e = 0.02-0.41). HD 34445 b (P = 2.87 yr, M sin i = 0.79 MJup, e = 0.27) is a massive planet orbiting an old, G-type star. We announce a planet, HD 126614 Ab, and an M dwarf, HD 126614 B, orbiting the metal-rich star HD 126614 (which we now refer to as HD 126614 A). The planet, HD 126614 Ab, has minimum mass M sin i = 0.38 MJup and orbits the stellar primary with period P = 3.41 yr and orbital separation a = 2.3 AU. The faint M dwarf companion, HD 126614 B, is separated from the stellar primary by 489 mas (33 AU) and was discovered with direct observations using adaptive optics and the PHARO camera at Palomar Observatory. The stellar primary in this new system, HD 126614 A, has the highest measured metallicity ([ Fe/ H] = + 0.56) of any known planet-bearing star. HD 13931 b (P = 11.5 yr, M sin i = 1.88 MJup, e = 0.02) is a Jupiter analog orbiting a near solar twin. Gl 179 b (P = 6.3 yr, M sin i = 0.82 M(Jup), e = 0.21) is a massive planet orbiting a faint M dwarf. The high metallicity of Gl 179 is consistent with the planet-metallicity correlation among M dwarfs, as documented recently by Johnson & Apps.NSF AST-0702821NASA NNX06AH52GMcDonald Observator
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases
Spinneret: Aiding Creative Ideation through Non-Obvious Concept Associations
Mind mapping is a popular way to explore a design space in creative thinking
exercises, allowing users to form associations between concepts. Yet, most
existing digital tools for mind mapping focus on authoring and organization,
with little support for addressing the challenges of mind mapping such as
stagnation and design fixation. We present Spinneret, a functional approach to
aid mind mapping by providing suggestions based on a knowledge graph. Spinneret
uses biased random walks to explore the knowledge graph in the neighborhood of
an existing concept node in the mind map, and provides "suggestions" for the
user to add to the mind map. A comparative study with a baseline mind-mapping
tool reveals that participants created more diverse and distinct concepts with
Spinneret, and reported that the suggestions inspired them to think of ideas
they would otherwise not have explored.Comment: ACM CHI 202
Light-ion production in the interaction of 175 MeV quasi-mono-energetic neutrons with iron and with bismuth
Nuclear data for neutron-induced reactions in the intermediate energy range
of 20 to 200 MeV are of great importance for the development of nuclear
reaction codes since little data exist in that range. Also several different
applications benefit from such data, notably accelerator-driven incineration of
nuclear waste. The Medley setup was used for a series of measurements of p, d,
t, He and -particle production by 175 MeV quasi-mono-energetic
neutrons on various target nuclei. The measurements were performed at the The
Svedberg Laboratory in Uppsala, Sweden. Eight detector telescopes placed at
angles between 20 and 160 were used. Medley uses the -- technique to discriminate among the particle types and is
able to measure double-differential cross sections over a wide range of
particle energies. This paper briefly describes the experimental setup,
summarizes the data analysis and reports on recent changes in the previously
reported preliminary data set on bismuth. Experimental data are compared with
INCL4.5-Abla07, MCNP6 using CEM03.03, TALYS and PHITS model calculations as
well as with nuclear data evaluations. The models agree fairly well overall but
in some cases systematic differences are found.Comment: 16 pages, 19 figures; submitted to Phys. Rev.
Eight common genetic variants associated with serum dheas levels suggest a key role in ageing mechanisms
Dehydroepiandrosterone sulphate (DHEAS) is the most abundant circulating steroid secreted by adrenal glands-yet its function is unknown. Its serum concentration declines significantly with increasing age, which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-related diseases or diminished longevity. We conducted a meta-analysis of genome-wide association data with 14,846 individuals and identified eight independent common SNPs associated with serum DHEAS concentrations. Genes at or near the identified loci include ZKSCAN5 (rs11761528; p = 3.15×10-36), SULT2A1 (rs2637125; p = 2.61×10-19), ARPC1A (rs740160; p = 1.56×10-16), TRIM4 (rs17277546; p = 4.50×10-11), BMF (rs7181230; p = 5.44×10-11), HHEX (rs2497306; p = 4.64×10-9), BCL2L11 (rs6738028; p = 1.72×10-8), and CYP2C9 (rs2185570; p = 2.29×10-8). These genes are associated with type 2 diabetes, lymphoma, actin filament assembly, drug and xenobiotic metabolism, and zinc finger proteins. Several SNPs were associated with changes in gene expression levels, and the related genes are connected to biological pathways linking DHEAS with ageing. This study provides much needed insight into the function of DHEAS
A second horizon scan of biogeography:golden ages, Midas touches, and the Red Queen
Are we entering a new ‘Golden Age’ of biogeography, with continued development of infrastructure
and ideas? We highlight recent developments, and the challenges and opportunities they bring, in
light of the snapshot provided by the 7th biennial meeting of the International Biogeography Society
(IBS 2015). We summarize themes in and across 15 symposia using narrative analysis and word
clouds, which we complement with recent publication trends and ‘research fronts’. We find that
biogeography is still strongly defined by core sub-disciplines that reflect its origins in botanical,
zoological (particularly bird and mammal), and geographic (e.g., island, montane) studies of the
1800s. That core is being enriched by large datasets (e.g. of environmental variables, ‘omics’,
species’ occurrences, traits) and new techniques (e.g., advances in genetics, remote sensing,
modeling) that promote studies with increasing detail and at increasing scales; disciplinary
breadth is being diversified (e.g., by developments in paleobiogeography and microbiology) and
integrated through the transfer of approaches and sharing of theory (e.g., spatial modeling and
phylogenetics in evolutionary–ecological contexts). Yet some subdisciplines remain on the fringe
(e.g., marine biogeography, deep-time paleobiogeography), new horizons and new theory may be
overshadowed by popular techniques (e.g., species distribution modelling), and hypotheses, data,
and analyses may each be wanting. Trends in publication suggest a shift away from traditional
biogeography journals to multidisciplinary or open access journals. Thus, there are currently many stewardship of, the planet (e.g., Intergovernmental Science-Policy Platform on Biodiversity and
Ecosystem Services). As in the past, biogeographers doubtless will continue to be engaged by
new data and methods in exploring the nexus between biology and geography for decades into
the future. But golden ages come and go, and they need not touch every domain in a discipline
nor affect subdisciplines at the same time; moreover, what appears to be a Golden Age may
sometimes have an undesirable ‘Midas touch’. Contexts within and outwith biogeography—e.g.,
methods, knowledge, climate, biodiversity, politics—are continually changing, and at times it can
be challenging to establish or maintain relevance. In so many races with the Red Queen, we
suggest that biogeography will enjoy greatest success if we also increasingly engage with the
epistemology of our disciplinePeer reviewe
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FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus
A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/
Epidemiology and Clinical Features of Patients with Visceral Leishmaniasis Treated by an MSF Clinic in Bakool Region, Somalia, 2004–2006
Our paper describes the epidemiological features of visceral leishmaniasis in the Bakool region, South Central Somalia, over the years 2004 to 2006. Since 2000, Médecins Sans Frontières has been providing care for patients suffering from visceral leishmaniasis in Huddur, located in a region endemic for visceral leishmaniasis. By the end of 2005, we witnessed a dramatic increase in the number of patients admitted to the Huddur centre with visceral leishmaniasis. In our paper, we provide a description of the profile of patients admitted, thus giving an insight into the epidemiology of visceral leishmaniasis in a part of the world where relatively little has been documented and where the true magnitude of this neglected disease remains unknown
Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease.
Osteocytes are master regulators of the skeleton. We mapped the transcriptome of osteocytes from different skeletal sites, across age and sexes in mice to reveal genes and molecular programs that control this complex cellular-network. We define an osteocyte transcriptome signature of 1239 genes that distinguishes osteocytes from other cells. 77% have no previously known role in the skeleton and are enriched for genes regulating neuronal network formation, suggesting this programme is important in osteocyte communication. We evaluated 19 skeletal parameters in 733 knockout mouse lines and reveal 26 osteocyte transcriptome signature genes that control bone structure and function. We showed osteocyte transcriptome signature genes are enriched for human orthologs that cause monogenic skeletal disorders (P = 2.4 × 10-22) and are associated with the polygenic diseases osteoporosis (P = 1.8 × 10-13) and osteoarthritis (P = 1.6 × 10-7). Thus, we reveal the molecular landscape that regulates osteocyte network formation and function and establish the importance of osteocytes in human skeletal disease
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