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  • 1
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    Is atmospheric phosphorus pollution altering global alpine lake stoichiometry? (2015)
    Wiley
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    Publication Date: 2015-08-11
    Description: Anthropogenic activities have significantly altered atmospheric chemistry and changed the global mobility of key macronutrients. Here, we show that contemporary global patterns in nitrogen (N) and phosphorus (P) emissions drive large hemispheric variation in precipitation chemistry. These global patterns of nutrient emission and deposition (N:P) are in turn closely reflected in the water chemistry of naturally oligotrophic lakes ( r 2 =0.81, p 〈0.0001). Observed increases in anthropogenic N deposition play a role in nutrient concentrations ( r 2 =0.20, p 〈0.05); however, atmospheric deposition of P appears to be major contributor to this pattern ( r 2 =0.65, p 〈0.0001). Atmospheric simulations indicate a global increase in P deposition by 1.4 times the preindustrial rate largely due to increased dust and biomass burning emissions. Although changes in the mass flux of global P deposition are smaller than for N, the impacts on primary productivity may be greater because, on average, one unit of increased P deposition has 16X the influence of one unit of N deposition. These stoichiometric considerations, combined with the evidence presented here, suggest that increases in P deposition may be a major driver of alpine lake trophic status, particularly in the Southern Hemisphere. These results underscore the need for the broader scientific community to consider the impact of atmospheric phosphorus deposition on the water quality of naturally oligotrophic lakes.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    The imbalance of new and export production in the Western Antarctic Peninsula, a potentially “leaky” ecosystem (2015)
    Wiley
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    Publication Date: 2015-08-13
    Description: To quantify the balance between new production and vertical nitrogen export of sinking particles, we measured nitrate uptake, net nitrate drawdown, ΔO 2 /Ar-based net community production, sediment trap flux, and 234 Th export at a coastal site near Palmer Station, Antarctica during the phytoplankton growing season from October 2012 to March 2013. We also measured nitrate uptake and 234 Th export throughout the northern western Antarctic Peninsula (WAP) region on a cruise in January 2013. We used a non-steady state 234 Th equation with temporally-varying upwelling rates and an irradiance-based phytoplankton production model to correct our export and new production estimates in the complex coastal site near Palmer Station. Results unequivocally showed that nitrate uptake and net community production were significantly greater than the sinking particle export on region-wide spatial scales and season-long temporal scales. At our coastal site, new production (105±17.4 mg N m −2 d −1 , mean±st.err.) was 5.3 times greater than vertical nitrogen export (20.4±2.4 mg N m −2 d -1 ). On the January cruise in the northern WAP, new production (47.9±14.4 mg N m −2 d -1 ) was 2.4 times greater than export (19.9±1.4 mg N m −2 d −1 ). Much of this imbalance can be attributed to diffusive losses of particulate nitrogen from the surface ocean due to diapycnal mixing, indicative of a “leaky” WAP ecosystem. If these diffusive losses are common in other systems where new production exceeds export, it may be necessary to revise current estimates of the ocean's biological pump.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Issue Information (2015)
    Wiley
    Details
    Publication Date: 2015-08-16
    Description: Cover: In Somes and Oschlies [doi 10.1002/2014GB005050 ], comparison of surface (0–50m) (a) map and (b) zonally averaged DON observations [Letscher et al., 2013] with annual semirecalcitrant DON from the model experiments (c) Redfield DOM (RedDOM), (d) preferential DOP remineralization (pref_DOP_remin), (e) preferential DOP recycling and phytoplankton DOP uptake (nonRedDOP), (f ) non-Redfield DOP with low DOM production (low_nonRedDOP), (g) non-Redfield DOP with high DOM production (high_nonRedDOP), and (h) fast recycling non-Redfield DOP (fast_nonRedDOP). Note that the zonally averaged model results in (b) are taken only from locations where observations exist. See pp. 973–993.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
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  • 6
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    The multiple fates of sinking particles in the North Atlantic Ocean (2015)
    Wiley
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    Publication Date: 2015-08-05
    Description: The direct respiration of sinking organic matter by attached bacteria is often invoked as the dominant sink for settling particles in the mesopelagic ocean. However, other processes, such as enzymatic solubilization and mechanical disaggregation, also contribute to particle flux attenuation by transferring organic matter to the water column. Here, we use observations from the North Atlantic Ocean, coupled to sensitivity analyses of a simple model, to assess the relative importance of particle-attached microbial respiration compared to the other processes that can degrade sinking particles. The observed carbon fluxes, bacterial production rates, and respiration by water column and particle-attached microbial communities each spanned more than an order of magnitude. Rates of substrate-specific respiration on sinking particle material ranged from 0.007 ± 0.003 to 0.173 ± 0.105 d -1 . A comparison of these substrate-specific respiration rates with model results suggested sinking particle material was transferred to the water column by various biological and mechanical processes nearly 3.5 times as fast as it was directly respired. This finding, coupled with strong metabolic demand imposed by measurements of water column respiration (729.3 ± 266.0 mg C m -2 d -1 , on average, over the 50 to 150 m depth interval), suggested a large fraction of the organic matter evolved from sinking particles ultimately met its fate through subsequent remineralization in the water column. At three sites, we also measured very low bacterial growth efficiencies and large discrepancies between depth-integrated mesopelagic respiration and carbon inputs.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    Climate extremes dominate seasonal and interannual variations in carbon export from the Mississippi River Basin (2015)
    Wiley
    Details
    Publication Date: 2015-08-07
    Description: Knowledge about the annual and seasonal patterns of organic and inorganic carbon (C) exports from the major rivers of the world to the coastal ocean are essential for our understanding and potential management of the global C budget so as to limit anthropogenic modification of global climate. Unfortunately our predictive understanding of what controls the timing, magnitude and quality of carbon export is still rudimentary. Here we use a process-based coupled hydrologic/ecosystem biogeochemistry model (the Dynamic Land Ecosystem Model, DLEM) to examine how climate variability and extreme events, changing land use, and atmospheric chemistry have affected the annual and seasonal patterns of C exports from the Mississippi River basin to the Gulf of Mexico. Our process-based simulations estimate that the average annual exports of dissolved organic C (DOC), particulate organic C (POC), and dissolved inorganic C (DIC) in the 2000s was 2.6 ± 0.4 Tg C yr −1 , 3.4 ± 0.3 Tg C yr −1 and 18.8 ± 3.4 Tg C yr −1 , respectively. Although land-use change was the most important agent of change in C export over the past century, climate variability and extreme events (such as flooding and drought) were primarily responsible for seasonal and interannual variations in C export from the basin. The maximum seasonal export of DIC occurred in summer while for maximum DOC and POC occurred in winter. Relative to the 10-year average (2001–2010), our modeling analysis indicates that the years of maximal and minimal C export co-occurred with wet and dry years (2008: 32% above average and 2006: 32% below average). Given IPCC-predicted changes in climate variability and the severity of rain events and droughts of wet and dry years for the remainder of the 21 st Century, our modeling results suggest major changes in the riverine link between the terrestrial and oceanic realms, which are likely to have a major impact on carbon delivery to the coastal ocean.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
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  • 8
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    Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-08
    Description: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 9
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    Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data (2015)
    Oxford University Press
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    Publication Date: 2015-08-08
    Description: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    GS-align for glycan structure alignment and similarity measurement (2015)
    Oxford University Press
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    Publication Date: 2015-08-08
    Description: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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