Analysis Of Multiple Datasets Research Articles

Phylogenetic relationships of class II fumarase genes from trichomonad species.

Class II fumarase sequences were obtained by polymerase chain reaction from five trichomonad species. All residues known to be highly conserved in this enzyme were present. Nuclear run-on assays showed that one of the two genes identified in Tritrichomonas foetus was expressed, whereas no fumarase transcripts were detected in the related species Trichomonas vaginalis. These findings corroborate previous biochemical data. Fumarase genes were also expressed in Monocercomonas sp. and Tetratrichomonas gallinarum but not in Pentatrichomonas hominis, Trichomonas gallinae, Trichomonas tenax, and Trichomitus batrachorum under the culture conditions used. Molecular trees inferred by likelihood methods reveal that trichomonad sequences have no affinity to described class II fumarase genes from other eukaryotes. The absence of functional mitochondria in protists such as trichomonads suggests that they diverged from other eukaryotes prior to the alpha-proteobacterial symbiosis that led to mitochondria. Furthermore, they are basal to other eukaryotes in rRNA analyses. However, support for the early-branching status of trichomonads and other amitochondriate protists based on phylogenetic analyses of multiple data sets has been equivocal. Although the presence of hydrogenosomes suggests that trichomonads once had mitochondria, their class II iron-independent fumarase sequences differ markedly from those of other mitochondriate eukaryotes. All of the class II fumarase genes described from other eukaryotes are of apparent alpha-proteobacterial origin and hence a marker of mitochondrial evolution. In contrast, the class II fumarase from trichomonads emerges among other eubacterial homologs. This is intriguing evidence for an independent acquisition of these genes in trichomonads apart from the mitochondrial endosymbiosis event that gave rise to the form present in other eukaryotes. The ancestral trichomonad class II fumarase may represent a prokaryotic form that was replaced in other eukaryotes after the divergence of trichomonads with the movement of endosymbiont genes into the nucleus. Alternatively, it may have been acquired via a separate endosymbiotic event or lateral gene transfer.

Quantifying Uncertainties in Determining SW Cloud Radiative Forcing and Cloud Absorption due to Variability in Atmospheric Conditions

The concept of cloud radiative forcing (CRF) has been widely employed in studying the effects of clouds on the earth’s radiation budget and climate. CRF denotes, in principle, the net influence of cloud alone on the radiation budget of a system. In practice, however, observational determination of CRF is fraught with uncertainties due to factors other than cloud that induce changes in atmospheric background conditions. The most notable variables include aerosol, water vapor, and the data sampling scheme. The impact of these factors on the derivation of CRF and cloud absorption is investigated here by means of modeling and analysis of multiple datasets. Improved estimation of CRF is attempted at the top of the atmosphere (TOA) and at the surface from spatially and temporally collocated ground and satellite measurements for broadband shortwave fluxes. Satellite data employed include pixel measurements from ERBE (1988–90), ScaRaB (1994–95), and CERES (1998), as well as surface data acquired across the Canadian radiation network, the ARM Central Facility site in Oklahoma, the US/NOAA SURFRAD networks, and the world BSRN (WMO) networks. It is found that surface CRF is much more susceptible to the variability in background conditions than TOA CRF. Selection of overly clear sky conditions often leads to significant overestimation of surface CRF, but TOA CRF remains intact or only slightly affected. As a result, the ratio of CRF at the surface and TOA is prone to overestimation. With careful treatments of these effects, the CRF ratio turns out to vary mostly between 0.9 and 1.1, implying approximately the same magnitude of atmospheric absorption under clear-sky and cloudy-sky conditions.

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

The phylogenetic relationships among the loliginid squids, a species-rich group of shallow-water muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis), and a clade of several east Atlantic species (Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d»Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus. TheSepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo (Alloteuthis) also varied across analyses. A new loliginid classification is proposed based on these findings.

Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets

Abstract The phylogenetic relationships among the loliginid squids, a species-rich group of shallow-water muscular squids, have been investigated recently using several approaches, including allozyme electrophoresis and analyses of morphological and DNA sequence data, yet no consensus has been reached. This study examines the effects of combining multiple data sets (morphology, allozymes and DNA sequence data from two mitochondrial genes) on estimates of loliginid phylogeny. Various data combinations were analysed under three maximum parsimony weighting schemes: equal weights for all characters, successive approximations and implicit weights parsimony. When feasible, support for branches within trees was assessed with nonparametric bootstrapping and decay analysis. Some ingroup relationships were consistent across all analyses, but relationships among outgroup taxa and basal ingroup taxa varied. Combining data increased bootstrap support for several nodes. Methods that downweight highly variable characters (i.e. successive approximations and implicit weights parsimony) produced very similar trees which included two major clades: a clade consisting of all species sampled from American waters (except Sepioteuthis ), and a clade of several east Atlantic species ( Loligo forbesi Steenstrup, Loligo vulgaris Lamarck and Loligo reynaudi d»Orbigny) plus several Indo-West Pacific species in the genera Uroteuthis and Loliolus . The Sepioteuthis species occupied a basal position within Loliginidae, but Sepioteuthis itself was not always monophyletic. The position of a clade of a few Lolliguncula species and Loligo ( Alloteuthis ) also varied across analyses. A new loliginid classification is proposed based on these findings.

Affinities among Anostracan (Crustacea: Branchiopoda) Families Inferred from Phylogenetic Analyses of Multiple Gene Sequences

To gain insights into the relationships among anostracan families, molecular phylogenetic analyses were performed on nuclear (28S D1–D3 ribosomal DNA) and mitochondrial (16S rDNA, COI) gene regions for representatives of seven families and an outgroup. Data matrices used in the analyses included 951 base pairs (bp) of aligned sequences for 28S, 465 bp for 16S, and 658 bp (219 amino acids) for COI. Maximum-parsimony and maximum-likelihood methods were used to construct phylogenetic trees, enabling the evaluation of both previous hypotheses of taxonomic relationships among families based on morphology, and of the relative merits of independent versus simultaneous analyses of multiple data sets for phylogeny construction. Data from various combinations of the gene regions produced relatively congruent patterns of phylogenetic affinity. In most analyses, two monophyletic groups were resolved: one cluster included the families Polyartemiidae, Chirocephalidae, Branchinectidae, Streptocephalidae, and Thamnocephalidae, while the other contained the Artemiidae and Branchipodidae. Comparative analyses showed that combining gene regions in a single matrix generally resulted in increased resolution and support for each cluster relative to those obtained from single-gene analyses. Statistical tests demonstrated that morphology-based hypotheses of relationships among families had poorer support than those determined from molecular data, reflecting the homoplasy in characters used to differentiate families.

In-situ control of temperature and alloy composition of Cd1−xZnxTe grown by molecular beam epitaxy

In this work in-situ spectroscopic ellipsometry (SE) has been applied for the simultaneous determination of the growth temperature and alloy composition for the epitaxial Cd1−xZnxTe(211)/Si(211) structure. The optical dielectric functions of CdTe and Cd0.96Zn0.04Te (CZT) epilayers were studied as a function of temperature both ex-situ and in-situ in the range from 1.6 eV to 4.5 eV. We employed parametric models for the simulation of the optical properties of CZT at and between the critical points (CP) E0, E0 + Δ0, E1, E1 + Δ1, E2(Σ) and E2(Σ). Critical point energies and line widths for Cd1−xZnxTe were obtained through the fitting process, which included both zero order and higher order derivatives of the SE pseudo dielectric function. The dependence of the different critical points on Zn concentration x is discussed. It has been demonstrated that the energy of the weak E0 + Δ0 transition can be used to measure composition, while the E1 energy can be used as a real-time temperature measure. The model parameters were optimized through the simultaneous analysis of multiple data sets, and the temperature dependent model was developed for in-situ application. Our analysis is estimated to produce uncertainties of only ±0.5°C in measuring the temperature and ±0.5% in measuring the composition of only the zero order dielectric function is being fitted. The effects of a surface overlayer, of reflected beam deflections, and of other experimental problems on the overall accuracy, are discussed as well as ways to improve the in-situ SE data quality.

Early branching eukaryotes?

Recent phylogenetic analyses suggest that Giardia, Trichomonas and Microsporidia contain genes of mitochondrial origin and are thus unlikely to be primitively amitochondriate as previously thought. Furthermore, phylogenetic analyses of multiple data sets suggest that Microsporidia are related to Fungi rather than being deep branching as depicted in trees based upon SSUrRNA analyses. There is also room for doubt, on the basis of a lack of consistent support from analyses of other genes, whether Giardia or Trichomonas branch before other eukaryotes. So, at present, we cannot be sure which eukaryotes are descendants of the earliest-branching organisms in the eukaryote tree. Future resolution of the order of emergence of eukaryotes will depend upon a more critical phylogenetic analysis of new and existing data than hitherto. Hypotheses of branching order should preferably be based upon congruence between independent data sets, rather than on single gene trees.

Epidemiologic studies of ionizing radiation and cancer: past successes and future challenges.

The health effects of radiation have been a focus for research since early in the 20th century. As the century ends, extensive experimental and epidemiologic evidence has been accumulated that addresses the adverse consequences of radiation exposure; epidemiologic studies of radiation-exposed groups from the general population and specific occupational groups provide quantitative estimates of the cancer risks associated with exposure. This report provides a perspective on the extensive epidemiologic evidence on the health effects of ionizing radiation and on likely needs for further epidemiologic research on radiation and health. Epidemiologic studies have proved informative on the quantitative risks of radiation-caused cancer but we now face the challenges of more precisely characterizing risks at lower levels of exposure and also of assessing modifiers of the risks, including dose rate, genetic susceptibility, and other environmental exposures. This report considers investigative approaches, such as pooled analysis of multiple data sets, that can be used to address these complex questions and the limitations of these approaches for addressing societal concerns about the risks of radiation exposure.

Bipolar disorder and chromosome 18: an analysis of multiple data sets.

There have been conflicting reports of linkage between bipolar disorder and chromosome 18. We have analyzed five separate data sets using the two-point affected sib-pair method and family based association methods. We have found evidence of linkage in multiple data sets and differences in maternal and paternal allele sharing. Suggestive, though nonsignificant, evidence of linkage disequilibrium of two tightly linked markers has also been demonstrated in multiple data sets.

ON SIMULTANEOUS ANALYSIS

Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow “secondary signals” to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are discussed.

ON SIMULTANEOUS ANALYSIS.

- Arguments for and against combined analysis of multiple data sets in phylogenetic inference are reviewed. Simultaneous analysis of combined data better maximizes cladistic parsimony than separate analyses, hence is to be preferred. Simultaneous analysis can allow "secondary signals" to emerge because it measures strength of evidence supporting disparate results. Separate analyses are useful and of interest to understanding the differences among data sets, but simultaneous analysis provides the greatest possible explanatory power, and should always be evaluated when possible. The mechanics of simultaneous analysis are discussed.

Modeling Survival and Testing Biological Hypotheses Using Marked Animals: A Unified Approach with Case Studies

The understanding of the dynamics of animal populations and of related ecological and evolutionary issues frequently depends on a direct analysis of life history parameters. For instance, examination of trade—offs between reproduction and survival usually rely on individually marked animals, for which the exact time of death is most often unknown, because marked individuals cannot be followed closely through time. Thus, the quantitative analysis of survival studies and experiments must be based on capture—recapture (or resighting) models which consider, besides the parameters of primary interest, recapture or resighting rates that are nuisance parameters. Capture—recapture models oriented to estimation of survival rates are the result of a recent change in emphasis from earlier approaches in which population size was the most important parameter, survival rates having been first introduced as nuisance parameters. This emphasis on survival rates in capture—recapture models developed rapidly in the 1980s and used as a basic structure the Cormack—Jolly—Seber survival model applied to an homogeneous group of animals, with various kinds of constraints on the model parameters. These approaches are conditional on first captures; hence they do not attempt to model the initial capture of unmarked animals as functions of population abundance in addition to survival and capture probabilities. This paper synthesizes, using a common framework, these recent developments together with new ones, with an emphasis on flexibility in modeling, model selection, and the analysis of multiple data sets. The effects on survival and capture rates of time, age, and categorical variables characterizing the individuals (e.g., sex) can be considered, as well as interactions between such effects. This "analysis of variance" philosophy emphasizes the structure of the survival and capture process rather than the technical characteristics of any particular model. The flexible array of models encompassed in this synthesis uses a common notation. As a result of the great level of flexibility and relevance achieved, the focus is changed from fitting a particular model to model building and model selection. The following procedure is recommended: (1) start from a global model compatible with the biology of the species studied and with the design of the study, and assess its fit; (2) select a more parsimonious model using Akaike's Information Criterion to limit the number of formal tests; (3) test for the most important biological questions by comparing this model with neighboring ones using likelihood ratio tests; and (4) obtain maximum likelihood estimates of model parameters with estimates of precision. Computer software is critical, as few of the models now available have parameter estimators that are in closed form. A comprehensive table of existing computer software is provided. We used RELEASE for data summary and goodness—of—fit tests and SURGE for iterative model fitting and the computation of likelihood ratio tests. Five increasingly complex examples are given to illustrate the theory. The first, using two data sets on the European Dipper (Cinclus cinclus), tests for sex—specific parameters, explores a model with time—dependent survival rates, and finally uses a priori information to model survival allowing for an environmental variable. The second uses data on two colonies of the Swift (Apus apus), and shows how interaction terms can be modeled and assessed and how survival and recapture rates sometimes partly counterbalance each other. The third shows complex variation in survival rates across sexes and age classes in the roe deer (Capreolus capreolus), with a test of density dependence in annual survival rates. The fourth is an example of experimental density manipulation using the common lizard (Lacerta vivipara). The last example attempts to examine a large and complex data set on the Greater Flamingo (Phoenicopterus ruber), where parameters are age specific, survival is a function of an environmental variable, and an age × year interaction term is important. Heterogeneity seems present in this example and cannot be adequately modeled with existing theory. The discussion presents a summary of the paradigm we recommend and details issues in model selection and design, and foreseeable future developments.

Developments in digital map production and data integration within the British Geological Survey

AbstractDigital techniques for cartographic data capture and high quality map production have been developed and applied over some 18 years to the mapping of the geoscientific datasets of the British Geological Survey, in particular to the geochemical dataset. Over this period, technological advances and developments in both vector and raster data processing techniques have facilitated high quality map production and the integration and display of multiple datasets. This paper reviews the developments in high quality map production and interpretation of survey information, with particular regard to the Regional Geochemical Atlas Series, through the application of image processing techniques on the display and analysis of multiple datasets.

Analysis of fluorescence decay kinetics measured in the frequency domain using distributions of decay times

We describe the theoretical and practical aspects of analyzing complex fluorescence decay kinetics using continuous distributions of decay times. Our analysis uses frequency-domain data, provides for global analysis of multiple data sets and includes the possibility of excited-state processes. Simulated data were used to estimate the types of distributions which can be reasonably recovered from the measurements. Additionally, we describe a variety of distributions recovered from experimental data. For mixtures of one, two or three exponentially decaying fluorophores we recovered narrow lifetime distributions, which are essentially identical to a multi-exponential decay. Similarly, a two-state excited-state reaction also yielded a narrow distribution with negative preexponential factors. The presence of time-dependent spectral relaxation of labeled lipids results in a wide distribution of decay times, which becomes narrower for faster relaxation rates at higher temperatures. Hence, the decay-time distributions appear to be sensitive to the dynamics of the environment surrounding the fluorophore. Additionally, distributions of decay times were observed to result from transient effects in collisional quenching, from energy transfer in the presence of a range of donor-to-acceptor distances, and for several single-tryptophan proteins.