Spatial and temporal trends in Precambrian nitrogen cycling: a Mesoproterozoic offshore nitrate minimum

We thank NSF EAR FESD grant #1338810 (RB), NASA grant NNX16AI37G (RB), the Agouron Institute (RB), the NASA Astrobiology Institute’s Virtual Planetary Laboratory (RB), the NSF Graduate Research Fellowship Program (MAK), and the Department of Earth and Space Sciences, University of Washington Goodspeed Geology Fellowship (MCK), Misch Fellowship (MCK), and the Kenneth C. Robbins Field Study Fellowship (2014, MCK) for funding.Fixed nitrogen is an essential nutrient for eukaryotes. As N2 fixation and assimilation of nitrate are catalyzed by metalloenzymes, it has been hypothesized that in Mesoproterozoic oceans nitrate was limited in offshore environments by low trace metal concentrations and high rates of denitrification in anoxic and episodically euxinic deep water masses, restricting eukaryotes to near-shore environments and limiting their evolutionary innovation. To date this hypothesis has only been tested in the Belt Supergroup (∼1.4 Ga), with results that support an onshore-offshore nitrate gradient as a potential control on eukaryote ecology. Here we present bulk nitrogen and organic carbon isotopic data from non-isochronous cross-basinal facies across the Bangemall (∼1.5 Ga) and the Roper (∼1.4-1.5 Ga) basins to better understand the extent and variability of onshore-offshore nitrogen isotope gradients in the Mesoproterozoic. Both basins show an average ∼1-2‰ enrichment in δ15Nbulk from deep to shallow facies, with a maximum range from -1‰ offshore to +7.5‰ onshore. Unlike the Belt basin, the Bangemall and Roper basins show some offshore δ15Nbulk values that are enriched beyond the isotopic range induced by biological N2 fixation alone. This suggests a mixture of aerobic and anaerobic metabolisms offshore. In shallow waters, where δ15Nbulk enrichment peaks, an aerobic nitrogen cycle was evidently operating vigorously. Even though isotopic signatures of aerobic nitrogen cycling are seen in all parts of the Bangemall and Roper basins, our data are consistent with a lateral gradient in nitrate availability within the photic zone, with higher concentrations in near-shore environments than offshore. The variability in δ15Nbulk values in each depositional environment and the consistently low δ15N values from Mesoproterozoic units compared to the Paleoproterozoic and Neoproterozoic suggest that nitrate concentrations in the global ocean were likely low. This trend is now seen in all three Mesoproterozoic basins so far examined, and contrasts with the Paleoproterozoic and Neoproterozoic where nearly all δ15Nbulk data plot above the N2 fixation window. Thus, we propose that the Mesoproterozoic ocean was characterized by a nitrate minimum between the Paleo- and Neoproterozoic, with the lowest concentrations in offshore environments. This inference is consistent with a Mesoproterozoic O2 decline following a temporary Paleoproterozoic O2 peak, and it further supports the idea that nitrate limitation offshore may have contributed to the restriction of photosynthetic eukaryotes to near-shore environments, delaying their rise to ecological dominance until the Neoproterozoic Era.PostprintPeer reviewe

Simulation of human factors for material safety

The D-1 (Statistical Sciences) and D-2 (Stockpile Complex Modeling and Analysis) groups frequently collaborate to analyze production capabilities at Los Alamos National Laboratory. The facilities in question run the gamut from traditional machining to the fabrication of Plutonium components. This paper documents our efforts to extend our modeling capabilities from traditional discrete event simulation modeling to include agent based models

A portal of educational resources: providing evidence for matching pedagogy with technology

The TPACK (Technology, Pedagogy and Content Knowledge) model presents the three types of knowledge that are necessary to implement a successful technology-based educational activity. It highlights how the intersections between TPK (Technological Pedagogical Knowledge), PCK (Pedagogical Content Knowledge) and TCK (Technological Content Knowledge) are not a sheer sum up of their components but new types of knowledge. This paper focuses on TPK, the intersection between technology knowledge and pedagogy knowledge – a crucial field of investigation. Actually, technology in education is not just an add-on but is literally reshaping teaching/learning paradigms. Technology modifies pedagogy and pedagogy dictates requirements to technology. In order to pursue this research, an empirical approach was taken, building a repository (back-end) and a portal (front-end) of about 300 real-life educational experiences run at school. Educational portals are not new, but they generally emphasise content. Instead, in our portal, technology and pedagogy take centre stage. Experiences are classified according to more than 30 categories (‘facets’) and more than 200 facet values, all revolving around the pedagogical implementation and the technology used. The portal (an innovative piece of technology) supports sophisticated ‘exploratory’ sessions of use, targeted at researchers (investigating the TPK intersection), teachers (looking for inspiration in their daily jobs) and decision makers (making decisions about the introduction of technology into schools)

The DEEP Groth Strip Survey VI. Spectroscopic, Variability, and X-ray Detection of AGN

We identify active galactic nuclei (AGN) in the Groth-Westphal Survey Strip (GSS) using the independent and complementary selection techniques of optical spectroscopy and photometric variability. We discuss the X-ray properties of these AGN using Chandra/XMM data for this region. From a sample of 576 galaxies with high quality spectra we identify 31 galaxies with AGN signatures. Seven of these have broad emission lines (Type 1 AGNs). We also identify 26 galaxies displaying nuclear variability in HST WFPC2 images of the GSS separated by ~7 years. The primary overlap of the two selected AGN samples is the set of broad-line AGNs, of which 80% appear as variable. Only a few narrow-line AGNs approach the variability threshold. The broad-line AGNs have an average redshift of z~1.1 while the other spectroscopic AGNs have redshifts closer to the mean of the general galaxy population (z~0.7). Eighty percent of the identified broad-line AGNs are detected in X-rays and these are among the most luminous X-ray sources in the GSS. Only one narrow-line AGN is X-ray detected. Of the variable nuclei galaxies within the X-ray survey, 27% are X-ray detected. We find that 1.9+/-0.6% of GSS galaxies to V=24 are broad-line AGNs, 1.4+/-0.5% are narrow-line AGNs, and 4.5+/-1.4% contain variable nuclei. The fraction of spectroscopically identified BLAGNs and NLAGNs at z~1 reveals a marginally significant increase of 1.3+/-0.9% when compared to the local population.Comment: 29 pages, 8 figures, accepted for publication in ApJ

Comparing the effects of calibration and climate errors on a statistical crop model and a process-based crop model

Understanding the relationship between climate and crop productivity is a key component of projections of future food production, and hence assessments of food security. Climate models and crop yield datasets have errors, but the effects of these errors on regional scale crop models is not well categorized and understood. In this study we compare the effect of synthetic errors in temperature and precipitation observations on the hindcast skill of a process-based crop model and a statistical crop model. We find that errors in temperature data have a significantly stronger influence on both models than errors in precipitation. We also identify key differences in the responses of these models to different types of input data error. Statistical and process-based model responses differ depending on whether synthetic errors are overestimates or underestimates. We also investigate the impact of crop yield calibration data on model skill for both models, using datasets of yield at three different spatial scales. Whilst important for both models, the statistical model is more strongly influenced by crop yield scale than the process-based crop model. However, our results question the value of high resolution yield data for improving the skill of crop models; we find a focus on accuracy to be more likely to be valuable. For both crop models, and for all three spatial scales of yield calibration data, we found that model skill is greatest where growing area is above 10-15 %. Thus information on area harvested would appear to be a priority for data collection efforts. These results are important for three reasons. First, understanding how different crop models rely on different characteristics of temperature, precipitation and crop yield data allows us to match the model type to the available data. Second, we can prioritize where improvements in climate and crop yield data should be directed. Third, as better climate and crop yield data becomes available, we can predict how crop model skill should improve

Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients

On September 14–15, 2015, a meeting of clinicians and investigators in the fields of veterinary and human neuro-oncology, clinical trials, neuropathology, and drug development was convened at the National Institutes of Health campus in Bethesda, Maryland. This meeting served as the inaugural event launching a new consortium focused on improving the knowledge, development of, and access to naturally occurring canine brain cancer, specifically glioma, as a model for human disease. Within the meeting, a SWOT (strengths, weaknesses, opportunities, and threats) assessment was undertaken to critically evaluate the role that naturally occurring canine brain tumors could have in advancing this aspect of comparative oncology aimed at improving outcomes for dogs and human beings. A summary of this meeting and subsequent discussion are provided to inform the scientific and clinical community of the potential for this initiative. Canine and human comparisons represent an unprecedented opportunity to complement conventional brain tumor research paradigms, addressing a devastating disease for which innovative diagnostic and treatment strategies are clearly needed

Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites.

Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy