Copepod carcasses as microbial hot spots for pelagic denitrification

Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O-2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O-2 level. The extent of anoxia gradually expanded with decreasing ambient O-2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes (nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in (15)NO3-amended seawater demonstrated denitrification, of which on average 34%+/- 17% (n=28) was sustained by nitrification. However, the activity was highly variable and was strongly dependent on the ambient O-2 levels. While denitrification was present even at air-saturation (302 mol L-1), the average carcass specific activity increased several orders of magnitude to approximate to 1 nmol d(-1) at 20% air-saturation (55 mol O-2 L-1) at an ambient temperature of 7 degrees C. Sinking carcasses of C. finmarchicus therefore represent hotspots of pelagic denitrification, but the quantitative importance as a sink for bioavailable nitrogen is strongly dependent on the ambient O-2 level. The importance of carcass associated denitrification could be highly significant in O-2 depleted environments such as Oxygen Minimum Zones (OMZ)

Vacuum stability, neutrinos, and dark matter

Motivated by the discovery hint of the Standard Model (SM) Higgs mass around 125 GeV at the LHC, we study the vacuum stability and perturbativity bounds on Higgs scalar of the SM extensions including neutrinos and dark matter (DM). Guided by the SM gauge symmetry and the minimal changes in the SM Higgs potential we consider two extensions of neutrino sector (Type-I and Type-III seesaw mechanisms) and DM sector (a real scalar singlet (darkon) and minimal dark matter (MDM)) respectively. The darkon contributes positively to the $\beta$ function of the Higgs quartic coupling $\lambda$ and can stabilize the SM vacuum up to high scale. Similar to the top quark in the SM we find the cause of instability is sensitive to the size of new Yukawa couplings between heavy neutrinos and Higgs boson, namely, the scale of seesaw mechanism. MDM and Type-III seesaw fermion triplet, two nontrivial representations of $SU(2)_{L}$ group, will bring the additional positive contributions to the gauge coupling $g_{2}$ renormalization group (RG) evolution and would also help to stabilize the electroweak vacuum up to high scale.Comment: 18 pages, 15 figures; published versio

Non-standard interactions versus non-unitary lepton flavor mixing at a neutrino factory

The impact of heavy mediators on neutrino oscillations is typically described by non-standard four-fermion interactions (NSIs) or non-unitarity (NU). We focus on leptonic dimension-six effective operators which do not produce charged lepton flavor violation. These operators lead to particular correlations among neutrino production, propagation, and detection non-standard effects. We point out that these NSIs and NU phenomenologically lead, in fact, to very similar effects for a neutrino factory, for completely different fundamental reasons. We discuss how the parameters and probabilities are related in this case, and compare the sensitivities. We demonstrate that the NSIs and NU can, in principle, be distinguished for large enough effects at the example of non-standard effects in the $\mu$-$\tau$-sector, which basically corresponds to differentiating between scalars and fermions as heavy mediators as leading order effect. However, we find that a near detector at superbeams could provide very synergistic information, since the correlation between source and matter NSIs is broken for hadronic neutrino production, while NU is a fundamental effect present at any experiment.Comment: 32 pages, 5 figures. Final version published in JHEP. v3: Typo in Eq. (27) correcte

Proposal for a multilevel university cybermetric analysis model

The final publication is available at Springer via http://dx.doi.org/10.1007/s11192-012-0868-5Universities’ online seats have gradually become complex systems of dynamic information where all their institutions and services are linked and potentially accessible. These online seats now constitute a central node around which universities construct and document their main activities and services. This information can be quantitative measured by cybermetric techniques in order to design university web rankings, taking the university as a global reference unit. However, previous research into web subunits shows that it is possible to carry out systemic web analyses, which open up the possibility of carrying out studies which address university diversity, necessary for both describing the university in greater detail and for establishing comparable ranking units. To address this issue, a multilevel university cybermetric analysis model is proposed, based on parts (core and satellite), levels (institutional and external) and sublevels (contour and internal), providing a deeper analysis of institutions. Finally the model is integrated into another which is independent of the technique used, and applied by analysing Harvard University as an example of use.Orduña Malea, E.; Ontalba Ruipérez, JA. (2013). Proposal for a multilevel university cybermetric analysis model. Scientometrics. 95(3):863-884. doi:10.1007/s11192-012-0868-5S863884953Acosta Márquez, T., Igartua Perosanz, J.J. & Gómez Isla, J. (2009). Páginas web de las universidades españolas. Enred: revista digital de la Universidad de Salamanca, 5 [online; discontinued].Aguillo, I. F. (1998). Hacia un concepto documental de sede web. El Profesional de la Información, 7(1–2), 45–46.Aguillo, I. F. (2009). Measuring the institutions’ footprint in the web. 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Journal of the American Society for Information Science and Technology, 55(14), 1216–1227.Buenadicha, M., Chamorro, A., Miranda, F. J., & González, O. R. (2001). A new web assessment index: Spanish Universities Analysis. Internet Research, 11(3), 226–234.Castells, M. (2001). La galaxia Internet. Barcelona: Plaza y Janés.Chu, H., He, S., & Thelwall, M. (2002). Library and Information Science Schools in Canada and USA: a Webometric perspective. Journal of Education for Library and Information Science, 43(2), 110–125.Crowston, K., & Williams, M. (2000). Reproduced and Emergent Genres of Communication on the World Wide Web. The Information Society: an International Journal, 16(3), 201–215.Goldfarb, A. (2006). The (teaching) role of universities in the diffusion of the Internet. International Journal of Industrial Organization, 24(2), 203–225.Ingwersen, P. (1998). The calculation of web impact factors. Journal of Documentation, 54(2), 236–243.Katz, R. N. (2008a). The tower and the cloud: Higher education in the age of cloud computing. USA: Educause.Katz, R. N. (2008b). The gathering cloud: is this the end of the middle. In R. N. Katz (Ed.), The tower and the cloud: Higher education in the age of cloud computing (p. 2008). USA: Educause.Li, X. (2005). National and international university departmental Web site interlinking: a webometric analysis. [Unpublished doctoral dissertation]. Wolverhampton, UK: University of Wolverhampton.Li, X., Thelwall, M., Musgrove, P., & Wilkinson, D. (2003). The relationship between the links/Web Impact Factors of computer science departments in UK and their RAE (Research Assessment Exercise) ranking in 2001. Scientometrics, 57(2), 239–255.Middleton, I., McConnell, M., & Davidson, G. (1999). Presenting a model for the structure and content of a University World Wide Web site. Journal of Information Science, 25(3), 217–219.Orduña-Malea, E. (2012). 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Use of news articles and announcements on official websites of universities. Turkish Online Journal of Educational Technology, 10(2), 287–296

A population of luminous accreting black holes with hidden mergers

Major galaxy mergers are thought to play an important part in fuelling the growth of supermassive black holes. However, observational support for this hypothesis is mixed, with some studies showing a correlation between merging galaxies and luminous quasars and others showing no such association. Recent observations have shown that a black hole is likely to become heavily obscured behind merger-driven gas and dust, even in the early stages of the merger, when the galaxies are well separated (5 to 40 kiloparsecs). Merger simulations further suggest that such obscuration and black-hole accretion peaks in the final merger stage, when the two galactic nuclei are closely separated (less than 3 kiloparsecs). Resolving this final stage requires a combination of high-spatial-resolution infrared imaging and high-sensitivity hard-X-ray observations to detect highly obscured sources. However, large numbers of obscured luminous accreting supermassive black holes have been recently detected nearby (distances below 250 megaparsecs) in X-ray observations. Here we report high-resolution infrared observations of hard-X-ray-selected black holes and the discovery of obscured nuclear mergers, the parent populations of supermassive-black-hole mergers. We find that obscured luminous black holes (bolometric luminosity higher than 2x10^44 ergs per second) show a significant (P<0.001) excess of late-stage nuclear mergers (17.6 per cent) compared to a sample of inactive galaxies with matching stellar masses and star formation rates (1.1 per cent), in agreement with theoretical predictions. Using hydrodynamic simulations, we confirm that the excess of nuclear mergers is indeed strongest for gas-rich major-merger hosts of obscured luminous black holes in this final stage.Comment: To appear in the 8 November 2018 issue of Nature. This is the authors' version of the wor

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Disparate Associations of HLA Class I Markers with HIV-1 Acquisition and Control of Viremia in an African Population

BACKGROUND:Acquisition of human immunodeficiency virus type 1 (HIV-1) infection is mediated by a combination of characteristics of the infectious and the susceptible member of a transmission pair, including human behavioral and genetic factors, as well as viral fitness and tropism. Here we report on the impact of established and potential new HLA class I determinants of heterosexual HIV-1 acquisition in the HIV-1-exposed seronegative (HESN) partners of serodiscordant Zambian couples. METHODOLOGY/PRINCIPAL FINDINGS:We assessed the relationships of behavioral and clinically documented risk factors, index partner viral load, and host genetic markers to HIV-1 transmission among 568 cohabiting couples followed for at least nine months. We genotyped subjects for three classical HLA class I genes known to influence immune control of HIV-1 infection. From 1995 to December 2006, 240 HESNs seroconverted and 328 remained seronegative. In Cox proportional hazards models, HLA-A*68:02 and the B*42-C*17 haplotype in HESN partners were significantly and independently associated with faster HIV-1 acquisition (relative hazards = 1.57 and 1.55; p = 0.007 and 0.013, respectively) after controlling for other previously established contributing factors in the index partner (viral load and specific class I alleles), in the HESN partner (age, gender), or in the couple (behavioral and clinical risk score). Few if any previously implicated class I markers were associated here with the rate of acquiring infection. CONCLUSIONS/SIGNIFICANCE:A few HLA class I markers showed modest effects on acquisition of HIV-1 subtype C infection in HESN partners of discordant Zambian couples. However, the striking disparity between those few markers and the more numerous, different markers found to determine HIV-1 disease course makes it highly unlikely that, whatever the influence of class I variation on the rate of infection, the mechanism mediating that phenomenon is identical to that involved in disease control

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations

Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens