ALBERT

Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.

Description: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.

Description: The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001].

Description: Background: Several epidemiologic studies indicate that maternal gestational weight gain (GWG) influences health outcomes in offspring. Any underlying mechanisms have, however, not been established. A recent study of 88 children based on the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort examined the methylation levels at 1,505 Cytosine-Guanine methylation (CpG) loci and found several to be significantly associated with maternal weight gain between weeks 0 and 18 of gestation. Since these results could not be replicated we wanted to examine associations between 0 and 18 week GWG and genome-wide methylation levels using the Infinium HumanMethylation450 BeadChip (450K) platform on a larger sample size, i.e. 729 newborns sampled from the Norwegian Mother and Child Cohort Study (MoBa). Results: We found no CpG loci associated with 0–18 week GWG after adjusting for the set of covariates used in the ALSPAC study (i.e. child’s sex and maternal age) and for multiple testing (q 〉 0.9, both 1,505 and 473,731 tests). Hence, none of the CpG loci linked with the genes found significantly associated with 0–18 week GWG in the ALSPAC study were significant in our study. Conclusions: The inconsistency in the results with the ALSPAC study with regards to the 0–18 week GWG model may arise for several reasons: sampling from different populations, dissimilar methylome coverage, sample size and/or false positive findings.

Description: Many species use facial features to identify conspecifics, which is necessary to navigate a complex social environment. The fundamental mechanisms underlying face processing are starting to be well understood in a variety of primate species. However, most studies focus on a limited subset of species tested with unfamiliar faces. As well as limiting our understanding of how widely distributed across species these skills are, this also limits our understanding of how primates process faces of individuals they know, and whether social factors (e.g. dominance and social bonds) influence how readily they recognize others. In this study, socially housed crested macaques voluntarily participated in a series of computerized matching-to-sample tasks investigating their ability to discriminate (i) unfamiliar individuals and (ii) members of their own social group. The macaques performed above chance on all tasks. Familiar faces were not easier to discriminate than unfamiliar faces. However, the subjects were better at discriminating higher ranking familiar individuals, but not unfamiliar ones. This suggests that our subjects applied their knowledge of their dominance hierarchies to the pictorial representation of their group mates. Faces of high-ranking individuals garner more social attention, and therefore might be more deeply encoded than other individuals. Our results extend the study of face recognition to a novel species, and consequently provide valuable data for future comparative studies.

Description: Although lasting only a fraction of the year, large storms may represent a significant, but highly variable, control on watershed nitrogen (N) fluxes. We determined the exports of particulate N (PN) and total dissolved N (TDN) including nitrate-N (NO 3 -N) and dissolved organic N (DON) in streamflow from a 12 ha temperate forested watershed. Sampling was performed for 15 storms over September 2010 to December 2012 and included four large tropical storms – Nicole (2010), Irene and Lee (2011) and Sandy (2012). PN composed a substantial portion (39-87%) of the storm event N export with storms constituting 65% of the 2011 PN export. Tropical storm Irene alone generated 1.76 kg N ha −1 of PN which was 27% of the annual watershed N (6.43 kg N ha −1 ) export for 2011. In contrast, tropical storm Sandy (October 2012), yielded low sediment and PN exports, likely due to low precipitation intensity and a freshly-fallen leaf cover that may have reduced soil erosion. Streamwater concentrations of PN, NO 3 -N, and DON ranged from 0–17.5, 0–2.02, and 0.01–0.54 mg N L −1 , respectively. Nitrate-N concentrations displayed a dilution trajectory for peak stormflows suggesting supply limitation, a response that was not as strong for PN. These results underscore the importance of large storms for PN export which is significant given that climate-change predictions indicate an increasing intensity of large tropical storms for the northeast USA. Elevated PN exports could further exacerbate water quality and eutrophication problems in sensitive aquatic ecosystems already subjected to excess dissolved nitrogen loads.

Description: Consideration of petrographic and U-Pb provenance data and paleocurrent analysis of Kungurian (upper Leonardian) Cutler Group strata in the salt anticline province of the Paradox Basin of Utah demonstrates striking contrasts in composition and inferred sources of stratigraphically adjacent eolian and fluvial facies. Eolian strata, termed here the Castle Valley Sandstone, exposed in the Castle Valley northeast of Moab, Utah, and long correlated with the White Rim Sandstone, were deposited on the southwestern flank of a NW-trending diapiric salt wall. The eolian strata, which overlie red fluvial sandstone and conglomerate of the undifferentiated Cutler Formation, are as much as 183 m thick in outcrop and consist of two eolianite members separated by a thin sheet-flood deposit that contains pebbles derived from the salt wall and upturned conglomeratic strata adjacent to it. Both eolian and underlying fluvial deposits thin and onlap eastward onto the now-collapsed salt wall. Fluvial strata at Castle Valley and in exposures to the northeast were transported northwestward, parallel to the salt wall. Large-scale foresets in the lower eolianite member indicate dominant northeasterly wind directions (present coordinates) and transport directly away from the contemporary Uncompahgre uplift, whereas foresets in the upper member indicate variable northeasterly and northwesterly paleowinds. The eolian strata thus accumulated on the lee side of the salt wall, but sandstone composition and northwesterly wind components indicate net transport from the northwest, comparable with dominant southeastward sand transport, away from the Pangean shoreline, documented for the greater White Rim erg to the west and northwest. The NW and NE winds are both predicted by late Paleozoic atmospheric circulation models for western Pangea. Cutler fluvial sandstones are compositional arkoses (mean Qt 56 F 42 L 2 ) containing basement-derived detrital components that include potassium feldspar, plagioclase, biotite, and zircons with a restricted, bimodal age distribution of ~1790–1689 Ma and ~1466–1406 Ma. These grain ages exactly match known basement ages in the nearby Uncompahgre uplift. In contrast, the Castle Valley Sandstone ranges from quartz-rich arkose to subarkose and exhibits a consistent upsection decrease in feldspar content, from Qt 71 F 27 L 2 in the lower eolianite member to Qt 90 F 10 L 0 in the upper member. Like the underlying fluvial arkose, the lower eolianite member contains potassium feldspar, plagioclase, and mica derived from the Uncompahgre uplift, but the locally derived zircon age groups constitute only 23%–37% and 13% of the zircon grain ages in the lower and upper eolianite members, respectively; whereas older Archean and Paleoproterozoic grains, including ca. 1.5 Ga grains uncommon in the Laurentian detrital-zircon record, and Grenville, Neoproterozoic, and early Paleozoic grains constitute the bulk of the zircons. Quartzarenite of the greater White Rim erg contains detrital-zircon populations similar to those of the upper eolianite member. The Grenville and younger grains are interpreted as having an eastern Laurentian (Appalachian) source, whereas the ca. 1.5 Ga grains probably had an ultimate source in Baltica. Sediment-transport directions indicate that zircon grains not directly attributable to local basement of the Ancestral Rocky Mountains, including grains with a likely Baltica source, were transported to the western shoreline of Laurentia by transcontinental fluvial systems and then southeastward to their depositional site at the erg margin in salt-withdrawal minibasins.

Description: : The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr Contact: pafilis@hcmr.gr or lars.juhl.jensen@cpr.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Organic Letters DOI: 10.1021/ol503508k

Description: Population growth in cities has resulted in the rapid expansion of urbanized land. Most research and management of stream ecosystems affected by urban expansion has focused on the maintenance and restoration of biotic communities rather than their basal resources. We examined the potential for urbanization to induce bottom-up ecosystem effects by looking at its influence on dissolved organic matter (DOM) composition and bioavailability and microbial enzyme activity. We selected 113 headwater streams across a gradient of urbanization in central and southern Maine and used elemental and optical analyses, including parallel factor analysis of excitation-emission matrices, to characterize DOM composition. Results show that fluorescent and stoichiometric DOM composition changed significantly across the rural to urban gradient. Specifically, the proportion of humic-like allochthonous DOM decreased while that of more bioavailable autochthonous DOM increased in the more urbanized streams. In laboratory incubations, increased autochthonous DOM was associated with a doubling in the decay rate of dissolved organic carbon as well as increased activity of C-acquiring enzymes. These results suggest that urbanization replaces upstream humic material with more local sources of DOM that turnover more rapidly and may drive bottom-up changes in microbial communities and affect the quality and quantity of downstream DOM delivery.

Description: The effect of sodium on refractory phase formation in a model Calcium Aluminate Cement–bonded refractory was investigated from 700°C to 1500°C. Sodium reacts with α-alumina to form sodium β-alumina (β-Al 2 O 3 ) via the intermediate NaAlO 2 . Formation of β-Al 2 O 3 disrupts the reaction path of calcia with alumina, delaying crystallization of calcium hexaluminate, CaO·6Al 2 O 3 , from 1350°C to 1500°C. β-Al 2 O 3 is also shown to reduce Young's modulus and delay sintering. The presence of NaAlO 2 and β-Al 2 O 3 result in an increase in internal friction. Increased linear expansion of up to 47% is observed when 1 wt% Na is added. The expansion is shown to scale with the amount of dopant with only 0.3 wt% Na leading to an additional 31% linear expansion. On cooling, the presence of β-Al 2 O 3 can be demonstrated by a peak in internal friction between 1200°C and 1000°C which could be caused by Na + ion hopping along the spinel-like planes.