Global distributions of diazotrophs abundance, biomass and nitrogen fixation rates - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. This is a gridded data product about diazotrophic organisms . There are 6 variables. Each variable is gridded on a dimension of 360 (longitude) * 180 (latitude) * 33 (depth) * 12 (month). The first group of 3 variables are: (1) number of biomass observations, (2) biomass, and (3) special nifH-gene-based biomass. The second group of 3 variables is same as the first group except that it only grids non-zero data. We have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling more than 11,000 direct field measurements including 3 sub-databases: (1) nitrogen fixation rates, (2) cyanobacterial diazotroph abundances from cell counts and (3) cyanobacterial diazotroph abundances from qPCR assays targeting nifH genes. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. Data are assigned to 3 groups including Trichodesmium, unicellular diazotrophic cyanobacteria (group A, B and C when applicable) and heterocystous cyanobacteria (Richelia and Calothrix). Total nitrogen fixation rates and diazotrophic biomass are calculated by summing the values from all the groups. Some of nitrogen fixation rates are whole seawater measurements and are used as total nitrogen fixation rates. Both volumetric and depth-integrated values were reported. Depth-integrated values are also calculated for those vertical profiles with values at 3 or more depths.

Impact of salinity and growth phase on alkenone distributions in coastal haptophytes

Batch cultures of Isochrysis galbana (strain CCMP 1323) and Chrysotila lamellosa (strain CCMP 1307) were grown at salinity ca. 10 to ca. 35 and the alkenone distributions determined for different growth phases. UK'37 values decreased slightly with salinity for C. lamellosa but were largely unaffected for I. galbana except during the decline phase. The values decreased with incubation time in both species. The proportion of C37:4, used as proxy for salinity, increased in both species at 0.16-0.20% per salinity unit, except during the stationary phase for I. galbana. C37:4 was much more abundant in C. lamellosa (30-44%) than in I. galbana (4-12%). Although our results suggest that salinity has a direct effect on alkenone distributions, growth phase and species composition will also have a marked impact, complicating the use of alkenone distributions as a proxy for salinity in the marine environment.

The effects of transients on photospheric and chromospheric power distributions

We have observed a quiet Sun region with the Swedish 1-meter Solar Telescope (SST) equipped with CRISP Imaging SpectroPolarimeter. High-resolution, high-cadence, H-alpha line scanning images were taken to observe different layers of the solar atmosphere from the photosphere to upper chromosphere. We study the distribution of power in different period-bands at different heights. Power maps of the upper photosphere and the lower chromosphere show suppressed power surrounding the magnetic-network elements, known as "magnetic shadows". These also show enhanced power close to the photosphere, traditionally referred to as"power halos". The interaction between acoustic waves and inclined magnetic fields is generally believed to be responsible for these two effects. In this study we explore if small-scale transients can influence the distribution of power at different heights. We show that the presence of transients, like mottles, Rapid Blueshifted Excursions (RBEs) and Rapid Redshifted Excursions (RREs), can strongly influence the power-maps. The short and finite lifetime of these events strongly affects all powermaps, potentially influencing the observed power distribution. We show that Doppler-shifted transients like RBEs and RREs that occur ubiquitously, can have a dominant effect on the formation ofthe power halos in the quiet Sun. For magnetic shadows, transients like mottles do not seem to have a significant effect in the power suppression around 3 minutes and wave interaction may play a key role here. Our high cadence observations reveal that flows, waves and shocks manifest in presence of magnetic fields to form a non-linear magnetohydrodynamic system.

DYNAMICS OF THE SHORT TERM AND LONG TERM AVIAN DISTRIBUTIONS IN NORTH AMERICA - THE ROLES OF VEGETATION HEIGHT HETEROGENEITY AND CLIMATIC FACTORS

Understanding how biodiversity spatially distribute over both the short term and long term, and what factors are affecting the distribution, are critical for modeling the spatial pattern of biodiversity as well as for promoting effective conservation planning and practices. This dissertation aims to examine factors that influence short-term and long-term avian distribution from the geographical sciences perspective. The research develops landscape level habitat metrics to characterize forest height heterogeneity and examines their efficacies in modelling avian richness at the continental scale. Two types of novel vegetation-height-structured habitat metrics are created based on second order texture algorithms and the concepts of patch-based habitat metrics. I correlate the height-structured metrics with the richness of different forest guilds, and also examine their efficacies in multivariate richness models. The results suggest that height heterogeneity, beyond canopy height alone, supplements habitat characterization and richness models of two forest bird guilds. The metrics and models derived in this study demonstrate practical examples of utilizing three-dimensional vegetation data for improved characterization of spatial patterns in species richness. The second and the third projects focus on analyzing centroids of avian distributions, and testing hypotheses regarding the direction and speed of these shifts. I first showcase the usefulness of centroids analysis for characterizing the distribution changes of a few case study species. Applying the centroid method on 57 permanent resident bird species, I show that multi-directional distribution shifts occurred in large number of studied species. I also demonstrate, plain birds are not shifting their distribution faster than mountain birds, contrary to the prediction based on climate change velocity hypothesis. By modelling the abundance change rate at regional level, I show that extreme climate events and precipitation measures associate closely with some of the long-term distribution shifts. This dissertation improves our understanding on bird habitat characterization for species richness modelling, and expands our knowledge on how avian populations shifted their ranges in North America responding to changing environments in the past four decades. The results provide an important scientific foundation for more accurate predictive species distribution modeling in future.

Pore size distributions derived from adsorption isotherms, immersion calorimetry, and isosteric heats: A comparative study

We compare the pore size distribution of a well-characterized activated carbon derived from model-dependent, adsorption integral equation (AIE) methods with those from model-independent, immersion calorimetry and isosteric heat analyses. The AIE approach applied to nitrogen gave a mean pore width of 0.57 nm; the CO2 distribution exhibited wider dispersion. Spherical model application to CO2 and diffusion limitations for nitrogen and argon were proposed as primary reasons for inconsistency. Immersion enthalpy revealed a sharp decrease in available area equivalent to a cut-off due to molecular exclusion when the accessible surface was assessed against probe kinetic diameter. Mean pore width was identified as 0.58 ± 0.02 nm, endorsing the underlying assumptions for the nitrogen-based AIE approach. A comparison of the zero-coverage isosteric heat of adsorption for various non-polar adsorptives by the porous test sample was compared with the same adsorptives in contact with a non-porous reference adsorbent, leading to an energy ratio or adsorption enhancement factor. A linear relationship between the energy ratio and probe kinetic diameter indicated a primary pore size at 0.59 nm. The advantage of this enthalpy, model-independent methods over AIE were due to no assumptions regarding probe molecular shape, and no assumptions for pore shape and/or connectivity.

¬FISH DISTRIBUTIONS IN LAKE ONTARIO’S EASTERN BASIN AND THE UPPER ST. LAWRENCE RIVER: AN ANALYSIS USING GIS AND OCCUPANCY MODELLING TECHNIQUES

Predictive models of species distributions are important tools for fisheries management. Unfortunately, these predictive models can be difficult to perform on large waterbodies where fish are difficult to detect and exhaustive sampling is not possible. In recent years the development of Geographic Information Systems (GIS) and new occupancy modelling techniques has improved our ability to predict distributions across landscapes as well as account for imperfect detection. I surveyed the nearshore fish community at 105 sites between Kingston, Ontario and Rockport, Ontario with the objective of modelling geographic and environmental characteristics associated with littoral fish distributions. Occupancy modelling was performed on Round Goby, Yellow perch, and Lepomis spp. Modelling with geographic and environmental covariates revealed the effect of shoreline exposure on nearshore habitat characteristics and the occupancy of Round Goby. Yellow Perch, and Lepomis spp. occupancy was most strongly associated negatively with distance to a wetland. These results are consistent with past research on large lake systems indicate the importance of wetlands and shoreline exposure in determining the fish community of the littoral zone. By examining 3 species with varying rates of occupancy and detection, this study was also able to demonstrate the variable utility of occupancy modelling.

Distinguishing the distributions of two cryptic frogs (Anura: Discoglossidae) using molecular data and environmental modeling

Currently, the identification of two cryptic Iberian amphibians, Discoglossus galganoi Capula, Nascetti, Lanza, Bullini and Crespo, 1985 and Discoglossus jeanneae Busack, 1986, relies on molecular characterization. To provide a means to discern the distributions of these species, we used 385-base-pair sequences of the cytochrome b gene to identify 54 Spanish populations of Discoglossus. These data and a series of environmental variables were used to build up a logistic regression model capable of probabilistically designating a specimen of Discoglossus found in any Universal Transverse Mercator (UTM) grid cell of 10 km × 10 km to one of the two species. Western longitudes, wide river basins, and semipermeable (mainly siliceous) and sandstone substrates favored the presence of D. galganoi, while eastern longitudes, mountainous areas, severe floodings, and impermeable (mainly clay) or basic (limestone and gypsum) substrates favored D. jeanneae. Fifteen percent of the UTM cells were predicted to be shared by both species, whereas 51% were clearly in favor of D. galganoi and 34% were in favor of D. jeanneae, considering odds of 4:1. These results suggest that these two species have parapatric distributions and allow for preliminary identification of potential secondary contact areas. The method applied here can be generalized and used for other geographic problems posed by cryptic species.

Convergence time to equilibrium distributions of autonomous and periodic non-autonomous graphs

We present some estimates of the time of convergence to the equilibrium distribution in autonomous and periodic non-autonomous graphs, with ergodic stochastic adjacency matrices, using the eigenvalues of these matrices. On this way we generalize previous results from several authors, that only considered reversible matrices.

Modelling and classification with quantile-based distributions

In this work, we explore and demonstrate the potential for modeling and classification using quantile-based distributions, which are random variables defined by their quantile function. In the first part we formalize a least squares estimation framework for the class of linear quantile functions, leading to unbiased and asymptotically normal estimators. Among the distributions with a linear quantile function, we focus on the flattened generalized logistic distribution (fgld), which offers a wide range of distributional shapes. A novel naïve-Bayes classifier is proposed that utilizes the fgld estimated via least squares, and through simulations and applications, we demonstrate its competitiveness against state-of-the-art alternatives. In the second part we consider the Bayesian estimation of quantile-based distributions. We introduce a factor model with independent latent variables, which are distributed according to the fgld. Similar to the independent factor analysis model, this approach accommodates flexible factor distributions while using fewer parameters. The model is presented within a Bayesian framework, an MCMC algorithm for its estimation is developed, and its effectiveness is illustrated with data coming from the European Social Survey. The third part focuses on depth functions, which extend the concept of quantiles to multivariate data by imposing a center-outward ordering in the multivariate space. We investigate the recently introduced integrated rank-weighted (IRW) depth function, which is based on the distribution of random spherical projections of the multivariate data. This depth function proves to be computationally efficient and to increase its flexibility we propose different methods to explicitly model the projected univariate distributions. Its usefulness is shown in classification tasks: the maximum depth classifier based on the IRW depth is proven to be asymptotically optimal under certain conditions, and classifiers based on the IRW depth are shown to perform well in simulated and real data experiments.

Mechanical Properties And Fracture Dynamics Of Silicene Membranes.

As graphene has become one of the most important materials, there is renewed interest in other similar structures. One example is silicene, the silicon analogue of graphene. It shares some of the remarkable graphene properties, such as the Dirac cone, but presents some distinct ones, such as a pronounced structural buckling. We have investigated, through density functional based tight-binding (DFTB), as well as reactive molecular dynamics (using ReaxFF), the mechanical properties of suspended single-layer silicene. We calculated the elastic constants, analyzed the fracture patterns and edge reconstructions. We also addressed the stress distributions, unbuckling mechanisms and the fracture dependence on the temperature. We analysed the differences due to distinct edge morphologies, namely zigzag and armchair.

Influence of specimens' design and manufacturing process on microtensile bond strength to enamel: laboratory and FEA comparison

This study evaluated the effect of specimens' design and manufacturing process on microtensile bond strength, internal stress distributions (Finite Element Analysis - FEA) and specimens' integrity by means of Scanning Electron Microscopy (SEM) and Laser Scanning Confocal Microscopy (LCM). Excite was applied to flat enamel surface and a resin composite build-ups were made incrementally with 1-mm increments of Tetric Ceram. Teeth were cut using a diamond disc or a diamond wire, obtaining 0.8 mm² stick-shaped specimens, or were shaped with a Micro Specimen Former, obtaining dumbbell-shaped specimens (n = 10). Samples were randomly selected for SEM and LCM analysis. Remaining samples underwent microtensile test, and results were analyzed with ANOVA and Tukey test. FEA dumbbell-shaped model resulted in a more homogeneous stress distribution. Nonetheless, they failed under lower bond strengths (21.83 ± 5.44 MPa)c than stick-shaped specimens (sectioned with wire: 42.93 ± 4.77 MPaª; sectioned with disc: 36.62 ± 3.63 MPa b), due to geometric irregularities related to manufacturing process, as noted in microscopic analyzes. It could be concluded that stick-shaped, nontrimmed specimens, sectioned with diamond wire, are preferred for enamel specimens as they can be prepared in a less destructive, easier, and more precise way.

Revision of the species of the genus Cathorops (Siluriformes: Ariidae) from Mesoamerica and the Central American Caribbean, with description of three new species

The ariid genus Cathorops includes species that occur mainly in estuarine and freshwater habitats of the eastern and western coasts of southern Mexico, Central and South America. The species of Cathorops from the Mesoamerica (Atlantic slope) and Caribbean Central America are revised, and three new species are described: C. belizensis from mangrove areas in Belize; C. higuchii from shallow coastal areas and coastal rivers in the Central American Caribbean, from Honduras to Panama; and C. kailolae from río Usumacinta and lago Izabal basins in Mexico and Guatemala. Additionally, C. aguadulce, from the río Papaloapan basin in Mexico, and C. melanopus from the río Motagua basin in Guatemala and Honduras, are redescribed and their geographic distributions are revised.

New species of thorny catfish, genus Leptodoras Boulenger (Siluriformes: Doradidae), from Tapajós and Xingu basins, Brazil

A new species of thorny catfish (family Doradidae) is described as a member of genus Leptodoras Boulenger by having a modified oral hood and first gill arch with enlarged accessory lamellae extending well onto medial face of gill filaments. The new species is distinguished by three characteristics unique within Leptodoras: gas bladder moderately sized (not reduced) with simple walls (diverticula absent), and paired bony capsules on anteriormost vertebrae reduced to paired cup-like laminar ossifications separated by triangular septum. The new species was discovered from material recently collected in the Tapajós basin at Serra do Cachimbo and in the headwaters of rio Xingu. The species description is supplemented by a detailed osteological description, discussion on its placement among congeners, and a re-evaluation of the diagnosis of Leptodoras and its relationships with sister taxon Anduzedoras oxyrhynchus. In addition, the distributions of several species of Leptodoras are expanded based on recent collecting efforts and identification of museum specimens not previously studied.

Minor and Unsystematic Cortical Topographic Changes of Attention Correlates between Modalities

In this study we analyzed the topography of induced cortical oscillations in 20 healthy individuals performing simple attention tasks. We were interested in qualitatively replicating our recent findings on the localization of attention-induced beta bands during a visual task [1], and verifying whether significant topographic changes would follow the change of attention to the auditory modality. We computed corrected latency averaging of each induced frequency bands, and modeled their generators by current density reconstruction with Lp-norm minimization. We quantified topographic similarity between conditions by an analysis of correlations, whereas the inter-modality significant differences in attention correlates were illustrated in each individual case. We replicated the qualitative result of highly idiosyncratic topography of attention-related activity to individuals, manifested both in the beta bands, and previously studied slow potential distributions [2]. Visual inspection of both scalp potentials and distribution of cortical currents showed minor changes in attention-related bands with respect to modality, as compared to the theta and delta bands, known to be major contributors to the sensory-related potentials. Quantitative results agreed with visual inspection, supporting to the conclusion that attention-related activity does not change much between modalities, and whatever individual changes do occur, they are not systematic in cortical localization across subjects. We discuss our results, combined with results from other studies that present individual data, with respect to the function of cortical association areas.