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  • BioMed Central  (121)
  • American Association for the Advancement of Science (AAAS)  (117)
  • 2015-2019  (168)
  • 2000-2004  (67)
  • 1970-1974  (3)
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  • 1
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    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
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    Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-08
    Description: Background: Recently, the Bayesian method becomes more popular for analyzing high dimensional gene expression data as it allows us to borrow information across different genes and provides powerful estimators for evaluating gene expression levels. It is crucial to develop a simple but efficient gene selection algorithm for detecting differentially expressed (DE) genes based on the Bayesian estimators. Results: In this paper, by extending the two-criterion idea of Chen et al. (Chen M-H, Ibrahim JG, Chi Y-Y. A new class of mixture models for differential gene expression in DNA microarray data. J Stat Plan Inference. 2008;138:387–404), we propose two new gene selection algorithms for general Bayesian models and name these new methods as the confident difference criterion methods. One is based on the standardized differences between two mean expression values among genes; the other adds the differences between two variances to it. The proposed confident difference criterion methods first evaluate the posterior probability of a gene having different gene expressions between competitive samples and then declare a gene to be DE if the posterior probability is large. The theoretical connection between the proposed first method based on the means and the Bayes factor approach proposed by Yu et al. (Yu F, Chen M-H, Kuo L. Detecting differentially expressed genes using alibrated Bayes factors. Statistica Sinica. 2008;18:783–802) is established under the normal-normal-model with equal variances between two samples. The empirical performance of the proposed methods is examined and compared to those of several existing methods via several simulations. The results from these simulation studies show that the proposed confident difference criterion methods outperform the existing methods when comparing gene expressions across different conditions for both microarray studies and sequence-based high-throughput studies. A real dataset is used to further demonstrate the proposed methodology. In the real data application, the confident difference criterion methods successfully identified more clinically important DE genes than the other methods. Conclusion: The confident difference criterion method proposed in this paper provides a new efficient approach for both microarray studies and sequence-based high-throughput studies to identify differentially expressed genes.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 3
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    Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4 -dependent auxin response genes (2015)
    BioMed Central
    Details
    Publication Date: 2015-08-15
    Description: Background: Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis. Results: We identified GIRAFFE2.1, a major QTL explaining ~18 % of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth. Conclusions: In combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod information to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 4
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    Patient-reported outcomes in a large community-based pain medicine practice: evaluation for use in phenotype modeling (2015)
    BioMed Central
    Details
    Publication Date: 2015-05-29
    Description: Background: An academic, community medicine partnership was established to build a phenotype-to-outcome model targeting chronic pain. This model will be used to drive clinical decision support for pain medicine in the community setting. The first step in this effort is an examination of the electronic health records (EHR) from clinics that treat chronic pain. The biopsychosocial components provided by both patients and care providers must be of sufficient scope to populate the spectrum of patient types, treatment modalities, and possible outcomes. Methods: The patient health records from a large Midwest pain medicine practice (Michigan Pain Consultants, PC) contains physician notes, administrative codes, and patient-reported outcomes (PRO) on over 30,000 patients during the study period spanning 2010 to mid-2014. The PRO consists of a regularly administered Pain Health Assessment (PHA), a biopsychosocial, demographic, and symptomology questionnaire containing 163 items, which is completed approximately every six months with a compliance rate of over 95 %. The biopsychosocial items (74 items with Likert scales of 0–10) were examined by exploratory factor analysis and descriptive statistics to determine the number of independent constructs available for phenotypes and outcomes. Pain outcomes were examined both in the aggregate and the mean of longitudinal changes in each patient. Results: Exploratory factor analysis of the intake PHA revealed 15 orthogonal factors representing pain levels; physical, social, and emotional functions; the effects of pain on these functions; vitality and health; and measures of outcomes and satisfaction. Seven items were independent of the factors, offering unique information. As an exemplar of outcomes from the follow-up PHAs, patients reported approximately 60 % relief in their pain. When examined in the aggregate, patients showed both a decrease in pain levels and an increase in coping skills with an increased number of visits. When examined individually, 80-85 % of patients presenting with the highest pain levels reported improvement by approximately two points on an 11-point pain scale. Conclusions: We conclude that the data available in a community practice can be a rich source of biopsychosocial information relevant to the phenotypes of chronic pain. It is anticipated that phenotype linkages to best treatments and outcomes can be constructed from this set of records.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
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  • 5
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    Microalbuminuria and left ventricular hypertrophy among newly diagnosed black African hypertensive patients: a cross sectional study from a tertiary hospital in Uganda (2015)
    BioMed Central
    Details
    Publication Date: 2015-05-16
    Description: Background: Microalbuminuria is an early manifestation of kidney damage and independently predicts cardiovascular disease (CVD). Left ventricular hypertrophy (LVH) is also an early marker of cardiac manifestation of target organ damage among hypertensive patients. The prognostic significance of microalbuminuria and its correlation with left ventricular hypertrophy has not been extensively studied in African adult hypertensive populations. This study aimed at determining the prevalence of microalbuminuria, LVH in patients with microalbuminuria and the correlation between microalbuminuria and LVH among newly diagnosed black adult hypertensive patients attending a large outpatient hypertension clinic or admitted on the cardiology ward at Mulago national referral and teaching hospital and Uganda Heart Institute in Kampala, Uganda. Methods: In this cross-sectional study, 256 newly diagnosed eligible black adult hypertensive patients attending the outpatient hypertension clinic or admitted on the cardiology ward at Mulago national referral and teaching hospital and the Uganda Heart Institute, Kampala Uganda were consecutively recruited over a period of 5 months. Data on socio-demographics, clinical and laboratory findings of the study participants was collected using a pre tested questionnaire. Two spot urine samples were collected to assess for microalbuminuria. Echocardiography (ECHO) was done to assess for the left ventricular mass index using the formula of Teicholz as evidence for early hypertensive heart disease. Results: The mean age/standard deviation of the study participants was 54.3 ± 6.2 years with a female predominance (162, 63.3 %). The prevalence of microalbuminuria among newly diagnosed hypertensive patients was 39.5 %. The prevalence of LVH among patients with microalbuminuria was found to be 17 %. There was a positive correlation between microalbuminuria and left ventricular hypertrophy among the newly diagnosed adult hypertensive patients at Mulago Hospital (r = 0.185, p = 0.003). Conclusions: This study demonstrates that microalbuminuria is highly prevalent among newly diagnosed black hypertensive patients and in the presence of LVH. There is also a positive correlation between microalbuminuria and LVH among newly diagnosed hypertensive patients. Since it is a less costly and readily available test, it can be used to predict presence of LVH especially in resource limited settings where ECHO services are not readily available.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 6
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    Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines (2015)
    BioMed Central
    Details
    Publication Date: 2015-05-16
    Description: IntroductionThe normal process of epithelial mesenchymal transition (EMT) is subverted by carcinoma cells to facilitate metastatic spread. Cancer cells rarely undergo a full conversion to the mesenchymal phenotype, and instead adopt positions along the epithelial-mesenchymal axis, a propensity we refer to as epithelial mesenchymal plasticity (EMP). EMP is associated with increased risk of metastasis in breast cancer and consequent poor prognosis. Drivers towards the mesenchymal state in malignant cells include growth factor stimulation or exposure to hypoxic conditions. Methods: We have examined EMP in two cell line models of breast cancer: the PMC42 system (PMC42-ET and PMC42-LA sublines) and MDA-MB-468 cells. Transition to a mesenchymal phenotype was induced across all three cell lines using epidermal growth factor (EGF) stimulation, and in MDA-MB-468 cells by hypoxia. We used RNA sequencing to identify gene expression changes that occur as cells transition to a more-mesenchymal phenotype, and identified the cell signalling pathways regulated across these experimental systems. We then used inhibitors to modulate signalling through these pathways, verifying the conclusions of our transcriptomic analysis. Results: We found that EGF and hypoxia both drive MDA-MB-468 cells to phenotypically similar mesenchymal states. Comparing the transcriptional response to EGF and hypoxia, we have identified differences in the cellular signalling pathways that mediate, and are influenced by, EMT. Significant differences were observed for a number of important cellular signalling components previously implicated in EMT, such as HBEGF and VEGFA.We have shown that EGF- and hypoxia-induced transitions respond differently to treatment with chemical inhibitors (presented individually and in combinations) in these breast cancer cells. Unexpectedly, MDA-MB-468 cells grown under hypoxic growth conditions became even more mesenchymal following exposure to certain kinase inhibitors that prevent growth-factor induced EMT, including the mTOR inhibitor everolimus and the AKT1/2/3 inhibitor AZD5363. Conclusions: While resulting in a common phenotype, EGF and hypoxia induced subtly different signalling systems in breast cancer cells. Our findings have important implications for the use of kinase inhibitor-based therapeutic interventions in breast cancers, where these heterogeneous signalling landscapes will influence the therapeutic response.
    Electronic ISSN: 1478-811X
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 7
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    Association of ADIPOQ gene with type 2 diabetes and related phenotypes in African American men and women: the Jackson Heart Study (2015)
    BioMed Central
    Details
    Publication Date: 2015-12-25
    Description: African Americans experience disproportionately higher prevalence of type 2 diabetes and related risk factors. Little research has been done on the association of ADIPOQ gene on type 2 diabetes, plasma adiponecti...
    Electronic ISSN: 1471-2156
    Topics: Biology
    Published by BioMed Central
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  • 8
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    Certification for gene-edited forests (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Somatic evolution and global expansion of an ancient transmissible cancer lineage (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉The canine transmissible venereal tumor (CTVT) is a cancer lineage that arose several millennia ago and survives by "metastasizing" between hosts through cell transfer. The somatic mutations in this cancer record its phylogeography and evolutionary history. We constructed a time-resolved phylogeny from 546 CTVT exomes and describe the lineage’s worldwide expansion. Examining variation in mutational exposure, we identify a highly context-specific mutational process that operated early in the cancer’s evolution but subsequently vanished, correlate ultraviolet-light mutagenesis with tumor latitude, and describe tumors with heritable hyperactivity of an endogenous mutational process. CTVT displays little evidence of ongoing positive selection, and negative selection is detectable only in essential genes. We illustrate how long-lived clonal organisms capture changing mutagenic environments, and reveal that neutral genetic drift is the dominant feature of long-term cancer evolution.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Black carbon lofts wildfire smoke high into the stratosphere to form a persistent plume (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉In 2017, western Canadian wildfires injected smoke into the stratosphere that was detectable by satellites for more than 8 months. The smoke plume rose from 12 to 23 kilometers within 2 months owing to solar heating of black carbon, extending the lifetime and latitudinal spread. Comparisons of model simulations to the rate of observed lofting indicate that 2% of the smoke mass was black carbon. The observed smoke lifetime in the stratosphere was 40% shorter than calculated with a standard model that does not consider photochemical loss of organic carbon. Photochemistry is represented by using an empirical ozone-organics reaction probability that matches the observed smoke decay. The observed rapid plume rise, latitudinal spread, and photochemical reactions provide new insights into potential global climate impacts from nuclear war.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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