Multimodal species abundance distributions: a deconstruction approach reveals the processes behind the pattern

Copyright © 2014 The Authors. Oikos © 2014 Nordic Society Oikos.

The gambin model provides a superior fit to species abundance distributions with a single free parameter : evidence, implementation and interpretation

The species abundance distribution (SAD) has been a central focus of community ecology for over fifty years, and is currently the subject of widespread renewed interest. The gambin model has recently been proposed as a model that provides a superior fit to commonly preferred SAD models. It has also been argued that the model's single parameter (α) presents a potentially informative ecological diversity metric, because it summarises the shape of the SAD in a single number. Despite this potential, few empirical tests of the model have been undertaken, perhaps because the necessary methods and software for fitting the model have not existed. Here, we derive a maximum likelihood method to fit the model, and use it to undertake a comprehensive comparative analysis of the fit of the gambin model. The functions and computational code to fit the model are incorporated in a newly developed free-to-download R package (gambin). We test the gambin model using a variety of datasets and compare the fit of the gambin model to fits obtained using the Poisson lognormal, logseries and zero-sum multinomial distributions. We found that gambin almost universally provided a better fit to the data and that the fit was consistent for a variety of sample grain sizes. We demonstrate how α can be used to differentiate intelligibly between community structures of Azorean arthropods sampled in different land use types. We conclude that gambin presents a flexible model capable of fitting a wide variety of observed SAD data, while providing a useful index of SAD form in its single fitted parameter. As such, gambin has wide potential applicability in the study of SADs, and ecology more generally.

Polycyclic aromatic hydrocarbons in gas and particulate phases of indoor environments influenced by tobacco smoke: levels, phase distributions, and health risks

As polycyclic aromatic hydrocarbons (PAHs) have a negative impact on human health due to their mutagenic and/or carcinogenic properties, the objective of this work was to study the influence of tobacco smoke on levels and phase distribution of PAHs and to evaluate the associated health risks. The air samples were collected at two homes; 18 PAHs (the 16 PAHs considered by U.S. EPA as priority pollutants, dibenzo[a,l]pyrene and benzo[j]fluoranthene) were determined in gas phase and associated with thoracic (PM10) and respirable (PM2.5) particles. At home influenced by tobacco smoke the total concentrations of 18 PAHs in air ranged from 28.3 to 106 ngm 3 (mean of 66.7 25.4 ngm 3),∑PAHs being 95% higher than at the non-smoking one where the values ranged from 17.9 to 62.0 ngm 3 (mean of 34.5 16.5 ngm 3). On average 74% and 78% of ∑PAHs were present in gas phase at the smoking and non-smoking homes, respectively, demonstrating that adequate assessment of PAHs in air requires evaluation of PAHs in both gas and particulate phases. When influenced by tobacco smoke the health risks values were 3.5e3.6 times higher due to the exposure of PM10. The values of lifetime lung cancer risks were 4.1 10 3 and 1.7 10 3 for the smoking and nonsmoking homes, considerably exceeding the health-based guideline level at both homes also due to the contribution of outdoor traffic emissions. The results showed that evaluation of benzo[a]pyrene alone would probably underestimate the carcinogenic potential of the studied PAH mixtures; in total ten carcinogenic PAHs represented 36% and 32% of the gaseous ∑PAHs and in particulate phase they accounted for 75% and 71% of ∑PAHs at the smoking and non-smoking homes, respectively.

Equilibrium distributions of discrete non-autonomous graphs

We introduce the notions of equilibrium distribution and time of convergence in discrete non-autonomous graphs. Under some conditions we give an estimate to the convergence time to the equilibrium distribution using the second largest eigenvalue of some matrices associated with the system.

Angular distributions in t(t)over-barH(H -> b(b)over-bar) reconstructed events at the LHC

The associated production of a Higgs boson and a top-quark pair, t (t) over barH, in proton-proton collisions is addressed in this paper for a center of mass energy of 13 TeV at the LHC. Dileptonic final states of t (t) over barH events with two oppositely charged leptons and four jets from the decays t -> bW(+) -> bl(+)v(l), (t) over bar -> (b) over barW(-) -> (b) over barl(-)(v) over bar (l) and h -> b (b) over bar are used. Signal events, generated with MadGraph5_aMC@NLO, are fully reconstructed by applying a kinematic fit. New angular distributions of the decay products as well as angular asymmetries are explored in order to improve discrimination of t (t) over barH signal events over the dominant irreducible background contribution, t (t) over barb (b) over bar. Even after the full kinematic fit reconstruction of the events, the proposed angular distributions and asymmetries are still quite different in the t (t) over barH signal and the dominant background (t (t) over barb (b) over bar).

A Review on the Characterization of Signals and Systems by Power Law Distributions

Power laws, also known as Pareto-like laws or Zipf-like laws, are commonly used to explain a variety of real world distinct phenomena, often described merely by the produced signals. In this paper, we study twelve cases, namely worldwide technological accidents, the annual revenue of America׳s largest private companies, the number of inhabitants in America׳s largest cities, the magnitude of earthquakes with minimum moment magnitude equal to 4, the total burned area in forest fires occurred in Portugal, the net worth of the richer people in America, the frequency of occurrence of words in the novel Ulysses, by James Joyce, the total number of deaths in worldwide terrorist attacks, the number of linking root domains of the top internet domains, the number of linking root domains of the top internet pages, the total number of human victims of tornadoes occurred in the U.S., and the number of inhabitants in the 60 most populated countries. The results demonstrate the emergence of statistical characteristics, very close to a power law behavior. Furthermore, the parametric characterization reveals complex relationships present at higher level of description.

Polycyclic aromatic hydrocarbons: levels and phase distributions in preschool microenvironment

This work aims to characterize levels and phase distribution of polycyclic aromatic hydrocarbons (PAHs) in indoor air of preschool environment and to assess the impact of outdoor PAH emissions to indoor environment. Gaseous and particulate (PM1 and PM2.5) PAHs (16 USEPA priority pollutants, plus dibenzo[a,l]pyrene, and benzo[j]fluoranthene) were concurrently sampled indoors and outdoors in one urban preschool located in north of Portugal for 35 days. The total concentration of 18 PAHs (ΣPAHs) in indoor air ranged from 19.5 to 82.0 ng/m3; gaseous compounds (range of 14.1–66.1 ng/m3) accounted for 85% ΣPAHs. Particulate PAHs (range 0.7–15.9 ng/m3) were predominantly associated with PM1 (76% particulate ΣPAHs) with 5-ring PAHs being the most abundant. Mean indoor/outdoor ratios (I/O) of individual PAHs indicated that outdoor emissions significantly contributed to PAH indoors; emissions from motor vehicles and fuel burning were the major sources.

Extracting temporal and spatial distributions information about marine mucilage phenomenon based on Modis satellite images; a case study of the Tyrrhenian and the Adriatic Sea, 2010-2012

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Using epidemiological survey data to infer geographic distributions of leishmaniasis vector species

An important aspect of tropical medicine is analysis of geographic aspects of risk of disease transmission, which for lack of detailed public health data must often be reduced to an understanding of the distributions of critical species such as vectors and reservoirs. We examine the applicability of a new technique, ecological niche modeling, to the challenge of understanding distributions of such species based on municipalities in the state of São Paulo in which a group of 5 Lutzomyia sandfly species have been recorded. The technique, when tested based on independent occurrence data, yielded highly significant predictions of species' distributions; minimum sample sizes for effective predictions were around 40 municipalities.

Analysis of metabolic flux distributions in relation to the extracellular environment in Avian cells

Continuous cell lines that proliferate in chemically defined and simple media have been highly regarded as suitable alternatives for vaccine production. One such cell line is the AG1.CR.pIX avian cell line developed by PROBIOGEN. This cell line can be cultivated in a fully scalable suspension culture and adapted to grow in chemically defined, calf serum free, medium [1]–[5]. The medium composition and cultivation strategy are important factors for reaching high virus titers. In this project, a series of computational methods was used to simulate the cell’s response to different environments. The study is based on the metabolic model of the central metabolism proposed in [1]. In a first step, Metabolic Flux Analysis (MFA) was used along with measured uptake and secretion fluxes to estimate intracellular flux values. The network and data were found to be consistent. In a second step, Flux Balance Analysis (FBA) was performed to access the cell’s biological objective. The objective that resulted in the best predicted results fit to the experimental data was the minimization of oxidative phosphorylation. Employing this objective, in the next step Flux Variability Analysis (FVA) was used to characterize the flux solution space. Furthermore, various scenarios, where a reaction deletion (elimination of the compound from the media) was simulated, were performed and the flux solution space for each scenario was calculated. Growth restrictions caused by essential and non-essential amino acids were accurately predicted. Fluxes related to the essential amino acids uptake and catabolism, the lipid synthesis and ATP production via TCA were found to be essential to exponential growth. Finally, the data gathered during the previous steps were analyzed using principal component analysis (PCA), in order to assess potential changes in the physiological state of the cell. Three metabolic states were found, which correspond to zero, partial and maximum biomass growth rate. Elimination of non-essential amino acids or pyruvate from the media showed no impact on the cell’s assumed normal metabolic state.

Search for New Phenomena in Dijet Angular Distributions in Proton-Proton Collisions at s√=8 TeV Measured with the ATLAS Detector

A search for new phenomena in LHC proton-proton collisions at a center-of-mass energy of s√=8 TeV was performed with the ATLAS detector using an integrated luminosity of 17.3 fb−1. The angular distributions are studied in events with at least two jets; the highest dijet mass observed is 5.5 TeV. All angular distributions are consistent with the predictions of the Standard Model. In a benchmark model of quark contact interactions, a compositeness scale below 8.1 TeV in a destructive interference scenario and 12.0 TeV in a constructive interference scenario is excluded at 95% CL; median expected limits are 8.9 TeV for the destructive interference scenario and 14.1 TeV for the constructive interference scenario.

Angular distributions in tt¯H(H→bb¯) reconstructed events at the LHC

The associated production of a Higgs boson and a top-quark pair, tt¯H, in proton-proton collisions is addressed in this paper for a center of mass energy of 13TeV at the LHC. Dileptonic final states of tt¯H events with two oppositely charged leptons and four jets from the decays t→bW+→bℓ+νℓ, t¯→b¯W−→b¯ℓ−ν¯ℓ and h→bb¯, are used. Signal events, generated with MadGraph5_aMC@NLO, are fully reconstructed by applying a kinematic fit. New angular distributions of the decay products as well as angular asymmetries are explored in order to improve discrimination of tt¯H signal events over the dominant irreducible background contribution, tt¯bb¯. Even after the full kinematic fit reconstruction of the events, the proposed angular distributions and asymmetries are still quite different in the tt¯H signal and the dominant background (tt¯bb¯).

The distributions of the native land mollusks of the Eastern United States / Leslie Hubricht.

n.s. no.24(1985)

Scenario-based assessment of future land use change on butterfly species distributions

Species distribution models (SDMs) are increasingly used to predict environmentally induced range shifts of habitats of plant and animal species. Consequently SDMs are valuable tools for scientifically based conservation decisions. The aims of this paper are (1) to identify important drivers of butterfly species persistence or extinction, and (2) to analyse the responses of endangered butterfly species of dry grasslands and wetlands to likely future landscape changes in Switzerland. Future land use was represented by four scenarios describing: (1) ongoing land use changes as observed at the end of the last century; (2) a liberalisation of the agricultural markets; (3) a slightly lowered agricultural production; and (4) a strongly lowered agricultural production. Two model approaches have been applied. The first (logistic regression with principal components) explains what environmental variables have significant impact on species presence (and absence). The second (predictive SDM) is used to project species distribution under current and likely future land uses. The results of the explanatory analyses reveal that four principal components related to urbanisation, abandonment of open land and intensive agricultural practices as well as two climate parameters are primary drivers of species occurrence (decline). The scenario analyses show that lowered agricultural production is likely to favour dry grassland species due to an increase of non-intensively used land, open canopy forests, and overgrown areas. In the liberalisation scenario dry grassland species show a decrease in abundance due to a strong increase of forested patches. Wetland butterfly species would decrease under all four scenarios as their habitats become overgrown

Comparing population distributions from bin-aggregated sample data: an application to historical height data from France

This paper develops a methodology to estimate the entire population distributions from bin-aggregated sample data. We do this through the estimation of the parameters of mixtures of distributions that allow for maximal parametric flexibility. The statistical approach we develop enables comparisons of the full distributions of height data from potential army conscripts across France's 88 departments for most of the nineteenth century. These comparisons are made by testing for differences-of-means stochastic dominance. Corrections for possible measurement errors are also devised by taking advantage of the richness of the data sets. Our methodology is of interest to researchers working on historical as well as contemporary bin-aggregated or histogram-type data, something that is still widely done since much of the information that is publicly available is in that form, often due to restrictions due to political sensitivity and/or confidentiality concerns.