DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes

BACKGROUND: In systems biology it is common to obtain for the same set of biological entities information from multiple sources. Examples include expression data for the same set of orthologous genes screened in different organisms and data on the same set of culture samples obtained with different high-throughput techniques. A major challenge is to find the important biological processes underlying the data and to disentangle therein processes common to all data sources and processes distinctive for a specific source. Recently, two promising simultaneous data integration methods have been proposed to attain this goal, namely generalized singular value decomposition (GSVD) and simultaneous component analysis with rotation to common and distinctive components (DISCO-SCA). RESULTS: Both theoretical analyses and applications to biologically relevant data show that: (1) straightforward applications of GSVD yield unsatisfactory results, (2) DISCO-SCA performs well, (3) provided proper pre-processing and algorithmic adaptations, GSVD reaches a performance level similar to that of DISCO-SCA, and (4) DISCO-SCA is directly generalizable to more than two data sources. The biological relevance of DISCO-SCA is illustrated with two applications. First, in a setting of comparative genomics, it is shown that DISCO-SCA recovers a common theme of cell cycle progression and a yeast-specific response to pheromones. The biological annotation was obtained by applying Gene Set Enrichment Analysis in an appropriate way. Second, in an application of DISCO-SCA to metabolomics data for Escherichia coli obtained with two different chemical analysis platforms, it is illustrated that the metabolites involved in some of the biological processes underlying the data are detected by one of the two platforms only; therefore, platforms for microbial metabolomics should be tailored to the biological question. CONCLUSIONS: Both DISCO-SCA and properly applied GSVD are promising integrative methods for finding common and distinctive processes in multisource data. Open source code for both methods is provided

Prebiotic effect of inulin-type fructans on faecal microbiota and short-chain fatty acids in type 2 diabetes: a randomised controlled trial

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Prebiotic effect of inulin-type fructans on faecal microbiota and short-chain fatty acids in type 2 diabetes: a randomised controlled trial

publishedVersio

Tilførselsprogrammet 2009. Overvåking av tilførsler og miljøtilstand i Barentshavet og Lofotenområdet

Det er utført nye beregninger av tilførsel av olje, kjemikalier og radioaktive stoffer til Barentshavet. Hovedinntrykket er relativt liten tilførsel av miljøfarlige stoffer til Barentshavet – Lofotenområdet. Nå er imidlertid tørravsetning inkludert i atmosfærisk nedfall og gir vesentlig høyere tilførsel av PAH og PCB enn tidligere kjent. Tilførsel fra luft gir største bidrag til Barentshavet av PCB, PAH, kvikksølv, krom, bly og kadmium. Skipstrafikk dominerer mht. tilførsel av olje og tributyltinn. En ny modell er tatt i bruk for å bedømme transport av miljøfarlige stoffer til Barentshavet og fordelingen innad i havområdet. Overvåking av kjemikalier i sediment og torsk viste i hovedsak lave til moderate konsentrasjoner. Konsentrasjonen av radioaktive stoffer i vann, sediment og torsk var på samme nivåer som registrert på de øvrige overvåkingsstasjonene i Barentshavet. Det er fortsatt store kunnskapsmangler og usikkerheter både i datagrunnlag og i estimatene av tilførsler. Spesielt viktig for den neste rulleringen av programmet er forbedrede tall for tilførsler via luft og forbedring av de marine transport- og spredningsmodellen

Identifying common and distinctive processes underlying multiset data

<p>In many research domains it has become a common practice to rely on multiple sources of data to study the same object of interest. Examples include a systems biology approach to immunology with collection of both gene expression data and immunological readouts for the same set of subjects, and the use of several high-throughput techniques for the same set of fermentation batches. A major challenge is to find the processes underlying such multiset data and to disentangle therein the common processes from those that are distinctive for a specific source. Several integrative methods have been proposed to address this challenge including canonical correlation analysis, simultaneous component analysis, OnPLS, generalized singular value decomposition, DISCO-SCA, and ECU-POWER. To get a better understanding 1) of the methods with respect to finding common and distinctive components and 2) of the relations between these methods, this paper brings the methods together and compares them both on a theoretical level and in terms of analyses of high-dimensional micro-array gene expression data obtained from subjects vaccinated against influenza. (C) 2013 Elsevier B.V. All rights reserved.</p>

The relationship between fatty acid profiles in milk identified by Fourier transform infrared spectroscopy and onset of luteal activity in Norwegian dairy cattle

To investigate the feasibility of milk fatty acids as predictors of onset of luteal activity (OLA), 87 lactations taken from 73 healthy Norwegian Red cattle were surveyed over 2 winter housing seasons. The feasibility of using frozen milk samples for dry-film Fourier transform infrared (FTIR) determination of milk samples was also tested. Morning milk samples were collected thrice weekly (Monday, Wednesday, Friday) for the first 10 wk in milk (WIM). These samples had bronopol (2-bromo-2-nitropropane-1,3-diol) added to them before being frozen at −20°C, thawed, and analyzed by ELISA to determine progesterone concentration and the concentrations of the milk fatty acids C4:0, C14:0, C16:0, C18:0, and cis-9 C18:1 as a proportion of total milk fatty acid content using dry-film FTIR, and averaged by WIM. Onset of luteal activity was defined as the first day that milk progesterone concentrations were >3 ng/mL for 2 successive measurements; the study population was categorized as early (n = 47) or late (n = 40) OLA, using the median value of 21 DIM as the cutoff. Further milk samples were collected 6 times weekly, from morning and afternoon milkings, these were pooled by WIM, and one proportional sample was analyzed fresh for fat, protein, and lactose content by the dairy company Tine SA, using traditional FTIR spectrography in the wet phase of milk. Daily energy-balance calculations were performed in 42 lactations and averaged by WIM. Animals experiencing late OLA had a more negative energy balance in WIM 1, 3, 4, and 5, with the greatest differences been seen in WIM 3 and 4. A higher proportion of the fatty acids were medium chained, C14:0 and C16:0, in the early than in the late OLA group from WIM 1. In WIM 4, the proportion of total fatty acid content that was C16:0 predicted late OLA, with 74% sensitivity and 80% specificity. The long-chain proportion of the fatty acids C18:0 and cis-9 C18:1 were lower in the early than in the late OLA group. Differences were greatest in WIM 4 and 5. Differences in concentrations of cis-9 C18:1 were seen between the groups from WIM 1. No relationship was seen between OLA and milk concentrations of either protein or fat, or between OLA and the milk fat:protein ratio. The differences in milk fatty acid proportions between the 2 groups are most likely related to differences in energy balance. The study shows that frozen milk samples can be tested for fatty acids by FTIR spectroscopy and that FTIR spectroscopy of milk can be used to provide real-time information about cow reproductive function.The relationship between fatty acid profiles in milk identified by Fourier transform infrared spectroscopy and onset of luteal activity in Norwegian dairy cattleacceptedVersio