Canonical correspondence analysis

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A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

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MULTIVARIATE-ANALYSIS OF THE VEGETATION OF THE VOLCANOS TLALOC AND PELADO, MEXICO

MULTIVARIATE-ANALYSIS OF THE VEGETATION OF THE VOLCANOS TLALOC AND PELADO, MEXICO

Direct Gradient Analysis (DGA) was used to find a linear combination of explanatory variables maximiz- ing the dispersal of samples and species along axes. For this purpose Canonical Correspondence Analysis (CCA, no transformation of species data, no species and sam- ple weights, and downweighting of rare species; ter Braak 1990) was used. The inertia of the most important explanatory variables to the total variance in the floristic data was calculated by invoking the forward selection option. A Monte Carlo permutation test was used to test the significance of the eigenvalue of the first axis, and to test the significance of the effect on the species of the explanatory variables. In all tests, 99 permutations were invoked (ter Braak 1990). Relations were considered significant at P < 0.05 throughout the analysis. The final results obtained by DCA and CCA were compared to see whether environmental variables had been over- looked, i.e. which could have explained a large part of the variation in the species data (ter Braak 1990). All analyses were performed with the help of the program package CANOCO version 3.10 (ter Braak 1990).

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speciated for ecological reasons. Our results indicate that M. nesus inhabits waterbodies in Belize, Campeche, Quintana Roo and Yucatán, as reported by Elías-Gutiérrez et al. (2008). The present distribution of this taxon could be a remnant of the original Mastigodiaptomus fauna in the Yucatán Peninsula and may reflect recent, post-Pliocene dispersal and Holocene climatic fluctuations (Suárez-Morales 2003). We identified P. marshi in aquatic ecosystems in the lowlands of Belize (Lagoons Progreso and Almond Hill) in the Eastern lowlands of Guatemala (Lake Izabal) and Southern Yucatán (Bacalar). Pseudodiaptomid copepods mainly inhabit marine and brackish water environ- ments, although recent studies (Suárez-Morales 2003) suggest that P. marshi is a species that is starting to colonize freshwater environments. Canonical Correspondence Analysis indicated that the ions sodium and chloride affect the distribution of this species. But the fact that we collected this copepod species in freshwater Lake Izabal supports the idea that is starting to colonize freshwater environments. Lake Izabal is connected with the Caribbean Sea via the Río Dulce and El Golfete. Similar to cladocerans, few copepods were found in rivers, probably because they are not well adapted to inhabit running waters, avoiding such environments and preferring the littoral zones of lakes (Casa- nova & Henry 2004).

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Análisis de la pertinencia de las plantaciones forestales en Oaxaca

Análisis de la pertinencia de las plantaciones forestales en Oaxaca

The assessment of large-scale vegetation cover is a complicated and expensive task; however, remote sensing has facilitated the study of its dynamics and spatial distribution, based on the biomass estimator, Normalized Difference Vegetation Index (NDVI). The need to know the success of the forest plantations established in the tropical and temperate region of southern Oaxaca during the 2014-2016 period, as well as the complexity and high costs implicit in the traditional evaluation of large-scale vegetation cover, motivated the use of NDVI and other geomatic techniques to estimate biomass and determine the environmental factors that influence its development. For this, the biomass was obtained by processing three series of satellite images: two from the Landsat 8 OLI sensor and one from the Sentinel-2. Through a canonical correspondence analysis, the variables that affected its dynamics were defined. And, from an analysis with time series it was determined that the plantations of the tropical and temperate zones present good development, but of different behavior between both. The environmental variables that affect its dynamics are altitude, precipitation, temperature, evapotranspiration, humidity and pH. Therefore, it is important to consider the environmental factors and the ecological requirements of the species before their establishment.

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A one-way ANOVA was used to examine differences among sites in relation to veg- etation variables. Soil variables were analyzed using a randomized nested ANOVA, where the factors were the species (P. laevigata and M. biuncifera) and the microenvironments (under the canopy of the legumes, and open area) nested within the sites (Site one-Bingu, Site 2-González and Site 3-Rincón). In all the cases, when the ANOVA indicated a significant factor, means were compared with a Tukey post-hoc test. Normality test was examined for all data, and when a normal distribution and homogeneity of variance were not found, the data were log-transformed to meet ANOVA assumptions (Sokal & Rohlf 1995), but report- ed in their original scale of measurement. All statistical analyses were performed with Statistica 6 software (StatSoft 2000), and in all cases p≤0.05 was taken to be significant. A Canonical Correspondence Analysis (CCA) was used to search differences in the floristic composition patterns among sites, legume spe- cies and microenvironments. In this analysis,

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How the Wnt signaling pathway protects from neurodegeneration: the mitochondrial scenario

How the Wnt signaling pathway protects from neurodegeneration: the mitochondrial scenario

2010). By contrast, the Wnt/β-catenin pathway is activated by the binding of a Wnt ligand to its Fz receptor and to the co- receptor LRP5/6 (Willert and Nusse, 2012; Liu et al., 2014). This interaction activates Dvl and causes the dissociation of the destruction complex to inhibit the glycogen synthase kinase- 3β (GSK-3β) and to prevent β-catenin degradation through the proteasome, inducing its accumulation into the cytoplasm, which finally translocates to the nucleus and triggers the expression of Wnt target genes (Arrázola et al., 2009; Clevers and Nusse, 2012). Canonical Wnt signaling has been implicated in neuroprotection against Aβ-induced neuronal damage (Cerpa et al., 2009). In fact, its activation protects hippocampal neurons from Aβ-induced cell death (Alvarez et al., 2004), and also prevents the intracellular calcium increase generated by Aβ in neurons, which directly affects mitochondrial calcium levels (Quintanilla et al., 2005; Dinamarca et al., 2010). In addition, we have demonstrated that the non-canonical Wnt pathway, through its ligand Wnt5a, also has a neuroprotective response against Aβ exposition through the modulation of mitochondrial dynamics (Silva-Alvarez et al., 2013). However, the mechanism by which this protection occurs is unknown. Recently, our lab explored whether Wnt signaling could exert its neuroprotective role against Aβ-induced toxicity through the protection of the mitochondria (Arrázola and Inestrosa, 2013).

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Canonical Wnt signaling protects hippocampal neurons from A beta oligomers: role of non canonical Wnt 5a/Ca2+ in mitochondrial dynamics

Canonical Wnt signaling protects hippocampal neurons from A beta oligomers: role of non canonical Wnt 5a/Ca2+ in mitochondrial dynamics

pathway with either Wnt-3a or Wnt-7a in hippocampal neurons prevents the neurotoxicity triggered by A β aggregates formed by amyloid fibrils. In the present study, we assessed the capacity of canonical Wnt signaling activation to prevent the neurodegen- erative effects of Aβ oligomers. In these experiments, to activate the canonical Wnt signaling pathway, we used 6-BIO an inhibitor of GSK-3 β at low concentrations (10 nM) (Meijer et al., 2004; Polychronopoulos et al., 2004). In cultured neurons we evaluated the integrity of neuronal branching with β III-tubulin and β - catenin levels under treatment of 5 μM Aβ oligomers plus 10 nM 6-BIO. This compound prevented almost all the Aβ oligomer- induced neurotoxicity and also recovered β -catenin levels in the neuritic branches and particularly at the soma, as shown in the graph (Figure 2A, graph: b). In addition, we also stud- ied the effect of Aβ oligomers and 6-BIO on apoptosis, using Hoechst staining. In hippocampal neurons treated with 5 μM of A β oligomers, several picnotic nuclei were observed (Figure 2Ba), however, the apoptotic nuclei were not observed when 6-BIO was

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Gold–palladium core@shell nanoalloys: experiments and simulations

Gold–palladium core@shell nanoalloys: experiments and simulations

to study the metallic deposition phenomenon on crystalline planar surfaces (electrodes). Now, the method has been extended to non-planar systems, like clusters, nanowires and bimetallic nanoparticles (NPs). Langevin dynamics is a method that extends molecular dynamics to represent the effect of perturba- tions caused by friction and eventual collisions occurring due to the presence of a solvent (the molecules in real systems hardly are under vacuum). For doing so, it makes use of stochastic differential equations, adding two terms to Newton’s second law to approximate the effects of neglected degrees of freedom. On the other hand, temperature can be controlled, approximating the canonical ensemble. Although it does not fully represent an implicit solvent (electrostatic screening and hydrophobicity), it mimics the viscosity of the medium.

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Canonical Correlation Analysis for Interpreting Airborne Laser Scanning Metrics along the Lorenz Curve of Tree Size Inequality

Canonical Correlation Analysis for Interpreting Airborne Laser Scanning Metrics along the Lorenz Curve of Tree Size Inequality

In this study, we explored the explanatory capac- ity of ALS remote sensing for describing the tree size inequality properties of the forest. Valbuena et al. (2013b) analyzed the relation of ALS metrics to spe- cific indicators, which are descriptors about the am- plitude and symmetry of the Lorenz curve. A natural step forward was to focus on a more profound analy- sis of the relations observed along the whole curve. The analysis of the entire Lorenz curve was chosen in order to observe the effect that relations of rela- tive dominance among trees has in the return cloud rendered from an ALS survey. The aim of this research is to acquire a more profound knowledge of the effects that ALS metrics have at different segments of the Lorenz curve.

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Are there population differences in minutiae frequencies? A comparative study of two Argentinian population samples and one Spanish sample

Are there population differences in minutiae frequencies? A comparative study of two Argentinian population samples and one Spanish sample

Recent challenges to fingerprint evidence in court have strengthened the need for statistical research to underpin the fingerprint identification process. The problem of the uniqueness of fingerprint impressions was earlier addressed [16], and since then, various models have been proposed for establishing this unique identity, a critical analysis of the models proposed has been made by Stoney and Thornton [19], Stoney [20] and Srihari and Srinivasan [21]. These models have been based on very heteroge- neous, and generally very small, samples and very disparate approaches (studying different types of minutiae, different finger- print patterns, different fingers and different finger areas) see [17,18]. Recently, Neumann et al. [22–24] and Egli et al. [25] reported on the use of likelihood ratios as a means of objectively assessing the evidential weight of corresponding minutiae between a fingermark and a fingerprint.

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The translator as mediator in researcher/referee correspondence

The translator as mediator in researcher/referee correspondence

Introspective publications have generally begun with an analysis of the contexts arising as a result of the peer review process in which the authors of a scientific publication can face one of four different scenarios: (1) the unqualified acceptance of their article; (2) the acceptance of their article subject to minor revisions; (3) the suggestion that the article should undergo substantial revision with no guarantee that it will be accepted for publication even if the revision is carried out to the letter; and (4) outright rejection. The authors of these studies are often former or current editors and/or referees of academic journals and they consider that the peer review process in itself constitutes “mediation” through which editors/referees and authors negotiate the production of a final document “worthy” of publication. To achieve this, Williams (2004) suggests authors need to follow a set of “Golden rules” when making their responses. He recommends they respond promptly, putting their emotions aside despite the all-too-natural sense of injury at having their work criticized. Furthermore, he suggests authors read the reviews carefully and respond to them point by point, enumerating the reviewers’ comments if necessary. The authors’ replies should always by complete, polite, and supported by the appropriate evidence.

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Computation of the canonical lifting via division polynomials

Computation of the canonical lifting via division polynomials

This theorem was proved in [3] in a computational way using Greenberg trans- forms and elliptic Teichm¨ uller lift. Also a similar result for separably closed K using fppf-cohomology theory has been given in [1]. Here we give another proof based on a simple fact which is directly used in the proof of the Serre–Tate theorem in [5]. Naively we can state the idea of the proof as follows: the canonical lifting is the unique lifting which has “lots of” nontrivial p-th power torsion points and the existence of these points force the existence of the desired Weierstrass model.

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A comprehensive survey of non canonical splice sites in the human transcriptome

A comprehensive survey of non canonical splice sites in the human transcriptome

Alternative splicing could be influenced by RNA editing. In particular, A-to-I editing was found to directly modify three reported cases of non-canonical splice sites (41–43). Because inosine is recognized as guanine by the spliceo- some, alternative 5 -AT or AA-3 can be turned into canon- ical splice sites through A-to-I editing. Since inosine is base- paired with cytosine during reverse transcription, sequenc- ing machines also identify inosine as guanosine. We found three AT–AG and four GT–AA non-canonical splice sites that have consistent A > G mismatches in poly(A)-minus RNA-seq alignments from ENCODE cell lines (Table 2). These splice sites are involved in alternative splicing. For ex- ample, when the GT–AA non-canonical splice site of NRK gene is edited to GT–AI, a 42 nucleotide exon is included, making this an A-to-I editing dependent exon inclusion event (Figure 5).

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Computational study of DNA in non-canonical environment

Computational study of DNA in non-canonical environment

MS experiments cannot determine alone the structure of the triplex in the gas phase. However, low-resolution structural data derived from IMS-MS experiments can help us validate our theoretical models. The triplexes were prepared in neutral or acidic condi- tions. Single stranded d(GA)6, d(GA)9, d(TC)6, and d(TC)9 were bought from either Sigma-Aldrich or Eurogentec. For the neutral conditions, the strands were mixed in suitable stoichiometry and resuspended in 150 mM ammonium acetate (pH = 5.5) to a final 2 µsM concentration. Samples were heated at 90 degrees and annealed overnight to form 12- and 18-mer d(TC)d(GA)d(TC) triplexes, which were easily detected in 20% polyacrylamide gels. Melting curves revealed clear triplex signatures with melting tem- peratures around 50 (12-mer) and 65 (18-mer) degrees in UV-melting experiments (data not shown). Triplex samples were lyophilized before use and resuspended for MS anal- ysis in water and mixed 1:1 (v/v) with solution A to a final concentration of 150 µM (solution A: 100 mM NH4OAc neutralized with triethylamine (pH 7.11)/isopropanol (9:1)) immediately prior to the IMS-MS analysis. Neutral pH and 5% isopropanol fa- vored ionization in the negative mode and significantly improved signal-to-noise ratio with chip-based nanoelectrospray in the negative mode (Turner, Hagan et al. 2006). For acidic conditions, strands were dissolved in water, and triplexes were prepared by annealing in solution B to a final concentration of 100 µM (solution B: 150 mM NH4OAc

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Evaluation of a Caries Detecting Software System

Evaluation of a Caries Detecting Software System

The diagnostic accuracy of caries detecting software that assesses density in digital radiographs was questioned. Analysis of radiographs of extracted teeth using Logicon revealed a deviation in specificity for caries from visual examination of the teeth as well as from their radiographic images. Subsequent preparation of teeth similar to a clinical preparation for a restoration revealed a marked deviation from the Logicon analysis. Radiographic interpretation of early caries and resultant treatment decisions are a multifaceted complex process that is not simplified by desired but unreliable current computerized technique.

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Imposed Deformations Measured on a Real Integral Structure: New Airport Terminal Barajas, Madrid, Spain

Imposed Deformations Measured on a Real Integral Structure: New Airport Terminal Barajas, Madrid, Spain

The study described here deals with the effects of imposed deformations in an integral structure: the Satellite Building of the New Airport Terminal Barajas, which has been monitored through- out a period of five years from construction into service. The building is shown during construction in Fig. 1. Its overall length is approximately 1 km with a substructure consisting of post-tensioned concrete frames evenly divided approximately every 80 m by ex- pansion joints. A symmetrical frame, which forms part of this sub- structure, was selected and instrumented in its extremes over three stories. It was, furthermore, the aim of this research to find out whether the structure's behavior can be efficiently predicted with common methods of analysis such as those used in daily practice.

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The ring compression test: Analysis of dimensions and canonical geometry

The ring compression test: Analysis of dimensions and canonical geometry

The set correspondence between the results of the load P necessary to achieve the deformation of the pieces tested, and those obtained from the application of TLS (for the tests discussed have a deviation of about 2%), shows a evidence of the suitability of using the Ring Compression Test for determining the friction existing in the process of shaping by plastic deformation, and analogous forms of employment viability Upper Limit Theorem under their specific development model Rigid Block Triangular

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Variation in the wood anatomical structure of Gmelina arborea (Verbenaceae) trees at different ecological conditions in Costa Rica

Variation in the wood anatomical structure of Gmelina arborea (Verbenaceae) trees at different ecological conditions in Costa Rica

vP, RP, FL, FW, CRW and LD presented some relationship with some ecological param- eters (Table 3, Fig. 4-7). Multivariate analyses confirmed also the variation of vP, RP, FL, FW and LD for ecological conditions, but for CRW was no found any relation in this analysis. Those features were highly correlated with two canonical components (Table 5). Two canoni- cal components obtained from multivariate analyses can be interpreted with the variation of wood structure for conductive water into the trunk for variation the ecological conditions. Anatomical features, vP, vD, RP and fibers dimensions (FL, FW and LD) and ecological conditions (altitude, longitude, latitude and precipitation) were correlated with two canoni- cal components (Table 5). Those anatomi- cal features are important parameters for two vital functions carried out by xylem in living trees, which varied with growing conditions of trees. The resistance to flow is proportional to the fourth power of the vessels radius and to vessels frequency (Zimmermann 1971). The mechanical resistance depends on fiber dimen- sions (van der Oever et al. 1981, Domec and Gartner 2002).

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Aplicació de l’espectroscòpia d’infraroig a l’anàlisi de control a les indústries adobera i paperera

Aplicació de l’espectroscòpia d’infraroig a l’anàlisi de control a les indústries adobera i paperera

The finishing process is one of the crucial steps in the process by which the tanning industry transforms leather into an end-product. Therefore, ensuring the required quality in the product requires careful control of this step. Traditionally, the leather tanning industry has used polluting processes and slow analytical methods involving time-consuming separations and also, frequently, the use of environmentally unfriendly reagents. In this work, we used a large matrix of spectroscopic data obtained from 63 leather specimens (34 from Pielcolor and 29 from the laboratories of the Leather Technology School of Igualada) to develop a method allowing the finishing method used on a leather (viz. a resin, wax/oil or grain correction treatment) to be expeditiously, non-destructively identified with the need for no sample treatment. To this end, Fourier transform infrared (FTIR) spectra were recorded with the aid of an ATR module and near-infrared (NIR) spectra with a fibre-optic probe. Chemometric processing of the FTIR or NIR spectral information thus obtained by Principal Component Analysis (PCA) and Canonical Variate Analysis (CVA) allowed the identification of the finishing treatment used on the studied leather samples. The results for the external prediction set (80% of hits with the FTIR model and 60% with the NIR model) were of the same order of magnitude than those obtained by leave-one-out cross-validation of the calibration set (85% with FTIR and 72% with NIR).

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Detrended correspondence analysis: A useful tool
				to quantify ecological changes from fossil data sets

Detrended correspondence analysis: A useful tool to quantify ecological changes from fossil data sets

Fossil assemblages reflect the parental communities that produced them, and are in turn associated with specific environmental conditions. Thus, climatic and environmental changes are associated with changes in both the biotic communities and the fossil as- semblages they produce. As a consequence, the environmental reconstruction of the past relies on the interpretation of multivariate fossil sequences that are commonly analyzed through dimensional rescaling techniques. Detrended correspondence analysis (DCA) has proven as an excellent technique to summarize ecological changes through time with the advantage of few prior assumptions and results that can be directly interpreted in terms of ecological turnover. In this paper we elaborate on a brief description of the technique and the interpretation of results, using a worked example on pollen and diatom data sets from Lago Verde (Los Tuxtlas, Mexico). With this worked example, we highlight the three basic ways in which DCA can provide useful approaches for a clear and relatively easy interpretation of the fossil data: i) identification of the ecological space through the a priori interpretation of species ordination; ii) localization of time slices within the ecological space defined by species, and quantification of the ecological turnover among samples; and iii) calculation of ecological distances as a means for putting individual samples into the historical context provided by the time frame in question.

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