Integrated landmark and outline-based morphometric methods efficiently distinguish species of Euglossa (Hymenoptera, Apidae, Euglossini)

Morphometric methods permit identification of insect species and are an aid for taxonomy. Quantitative wing traits were used to identify male euglossine bees. Landmark- and outline-based methods have been primarily used independently. Here, we combine the two methods using five Euglossa. Landmark-based methods correctly classified 84% and outline-based 77%, but an integrated analysis correctly classified 91% of samples. Some species presented significantly high reclassification percentages when only wing cell contour was considered, and correct identification of specimens with damaged wings was also obtained using this methodology.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions: Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposonscIvana_1 (similar to 60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e. g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Mid- to late-Holocene paleoceanographic changes on the southeastern Brazilian shelf based on grain size records

; High-resolution grain size analyses of three AMS (14)C-dated cores from the Southeastern Brazilian shelf provide a detailed record of mid- to late-Holocene environmental changes in the Southwestern Atlantic Margin. The cores exhibit millennial variability that we associate with the previously described southward shift of the Inter Tropical Convergence Zone (ITCZ) average latitudinal position over the South American continent during the Holocene climatic maximum. This generated changes in the wind-driven current system of the SW Atlantic margin and modified the grain size characteristics of the sediments deposited there. Centennial variations in the grain size are associated with a previously described late-Holocene enhancement of the El Nino-Southern Oscillation (ENSO) amplitude, which led to stronger NNE trade winds off eastern Brazil, favouring SW transport of sediments from the Paraiba do Sul River. This is recorded in a core from off Cabo Frio as a coarsening trend from 3000 cal. BP onwards. The ENSO enhancement also caused changes in precipitation and wind pattern in southern Brazil, allowing high discharge events and northward extensions of the low-saline water plume from Rio de la Plata. We propose that this resulted in a net increase in northward alongshore transport of fine sediments, seen as a prominent fine-shift at 2000 cal. BP in a core from similar to 24 degrees S on the Brazilian shelf. Wavelet-and spectral analysis of the sortable silt records show a significant similar to 1000-yr periodicity, which we attribute to solar forcing. If correct, this is one of the first indications of solar forcing of this timescale on the Southwestern Atlantic margin.

Multidecadal climate variability in Brazil's Nordeste during the last 3000 years based on speleothem isotope records

We present the first high resolution, approximately similar to 4 years sample spacing, precipitation record from northeastern Brazil (hereafter referred to as 'Nordeste') covering the last similar to 3000 yrs from Th-230-dated stalagmites oxygen isotope records. Our record shows abrupt fluctuations in rainfall tied to variations in the intensity of the South American summer monsoon (SASM), including the periods corresponding to the Little Ice Age (LIA), the Medieval Climate Anomaly (MCA) and an event around 2800 yr B.P. Unlike other monsoon records in southern tropical South America, dry conditions prevailed during the LIA in the Nordeste. Our record suggests that the region is currently undergoing drought conditions that are unprecedented over the past 3 millennia, rivaled only by the LIA period. Using spectral, wavelet and cross-wavelet analyses we show that changes in SASM activity in the region are mainly associated with variations of the Atlantic Multidecadal Oscillation (AMO) and to a lesser degree caused by fluctuations in tropical Pacific SST. Our record also shows a distinct periodicity around 210 years, which has been linked to solar variability. Citation: Novello, V. F., et al. (2012), Multidecadal climate variability in Brazil's Nordeste during the last 3000 years based on speleothem isotope records, Geophys. Res. Lett., 39, L23706, doi: 10.1029/2012GL053936.

Collaborative fuzzy clustering algorithms: some refinements and design guidelines

There are some variants of the widely used Fuzzy C-Means (FCM) algorithm that support clustering data distributed across different sites. Those methods have been studied under different names, like collaborative and parallel fuzzy clustering. In this study, we offer some augmentation of the two FCM-based clustering algorithms used to cluster distributed data by arriving at some constructive ways of determining essential parameters of the algorithms (including the number of clusters) and forming a set of systematically structured guidelines such as a selection of the specific algorithm depending on the nature of the data environment and the assumptions being made about the number of clusters. A thorough complexity analysis, including space, time, and communication aspects, is reported. A series of detailed numeric experiments is used to illustrate the main ideas discussed in the study.

A complex networks approach for data clustering

This work proposes a method for data clustering based on complex networks theory. A data set is represented as a network by considering different metrics to establish the connection between each pair of objects. The clusters are obtained by taking into account five community detection algorithms. The network-based clustering approach is applied in two real-world databases and two sets of artificially generated data. The obtained results suggest that the exponential of the Minkowski distance is the most suitable metric to quantify the similarities between pairs of objects. In addition, the community identification method based on the greedy optimization provides the best cluster solution. We compare the network-based clustering approach with some traditional clustering algorithms and verify that it provides the lowest classification error rate. (C) 2012 Elsevier B.V. All rights reserved.

Optimal Code Set Selection and Security Issues in Spectral Phase-Encoded Time Spreading (SPECTS) OCDMA Systems

In this paper, we perform a thorough analysis of a spectral phase-encoded time spreading optical code division multiple access (SPECTS-OCDMA) system based on Walsh-Hadamard (W-H) codes aiming not only at finding optimal code-set selections but also at assessing its loss of security due to crosstalk. We prove that an inadequate choice of codes can make the crosstalk between active users to become large enough so as to cause the data from the user of interest to be detected by other user. The proposed algorithm for code optimization targets code sets that produce minimum bit error rate (BER) among all codes for a specific number of simultaneous users. This methodology allows us to find optimal code sets for any OCDMA system, regardless the code family used and the number of active users. This procedure is crucial for circumventing the unexpected lack of security due to crosstalk. We also show that a SPECTS-OCDMA system based on W-H 32(64) fundamentally limits the number of simultaneous users to 4(8) with no security violation due to crosstalk. More importantly, we prove that only a small fraction of the available code sets is actually immune to crosstalk with acceptable BER (<10(-9)) i.e., approximately 0.5% for W-H 32 with four simultaneous users, and about 1 x 10(-4)% for W-H 64 with eight simultaneous users.

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

Solid electrolytes for electrochromic devices based on reversible metal electrodeposition

Air conditioning and lighting costs can be reduced substantially by changing the optical properties of "intelligent windows." The electrochromic devices studied to date have used copper as an additive. Copper, used here as an electrochromic material, was dissolved in an aqueous animal protein-derived gel electrolyte. This combination constitutes the electrochromic system for reversible electrodeposition. Cyclic voltammetry, chronoamperometric and chromogenic analyses indicated that were obtained good conditions of transparency (initial transmittance of 70%), optical reversibility, small potential window (2.1 V), variation of transmittance in visible light (63.6%) and near infrared (20%) spectral regions. Permanence in the darkened state was achieved by maintaining a lower pulse potential (-0.16 V) than the deposition potential (-1.0 V). Increasing the number of deposition and dissolution cycles favored the transmittance and photoelectrochemical reversibility of the device. The conductivity of the electrolyte (10(-3) S/cm) at several concentrations of CuCl2 was determined by electrochemical impedance spectroscopy. A thermogravimetric analysis confirmed the good thermal stability of the electrolyte, since the mass loss detected up to 100 degrees C corresponded to water evaporation and decomposition of the gel started only at 200 degrees C. Micrographic and small angle X-ray scattering analyses indicated the formation of a persistent deposit of copper particles on the ITO. (C) 2012 Elsevier B.V. All rights reserved.

Evaluating links through spectral decomposition

Spectral decomposition has rarely been used to investigate complex networks. In this work we apply this concept in order to define two kinds of link-directed attacks while quantifying their respective effects on the topology. Several other kinds of more traditional attacks are also adopted and compared. These attacks had substantially diverse effects, depending on each specific network (models and real-world structures). It is also shown that the spectrally based attacks have special effects in affecting the transitivity of the networks.

Identification of protein expression signatures in gastric carcinomas using clustering analysis

Background and Aim: The identification of gastric carcinomas (GC) has traditionally been based on histomorphology. Recently, DNA microarrays have successfully been used to identify tumors through clustering of the expression profiles. Random forest clustering is widely used for tissue microarrays and other immunohistochemical data, because it handles highly-skewed tumor marker expressions well, and weighs the contribution of each marker according to its relatedness with other tumor markers. In the present study, we e identified biologically- and clinically-meaningful groups of GC by hierarchical clustering analysis of immunohistochemical protein expression. Methods: We selected 28 proteins (p16, p27, p21, cyclin D1, cyclin A, cyclin B1, pRb, p53, c-met, c-erbB-2, vascular endothelial growth factor, transforming growth factor [TGF]-beta I, TGF-beta II, MutS homolog-2, bcl-2, bax, bak, bcl-x, adenomatous polyposis coli, clathrin, E-cadherin, beta-catenin, mucin (MUC) 1, MUC2, MUC5AC, MUC6, matrix metalloproteinase [ MMP]-2, and MMP-9) to be investigated by immunohistochemistry in 482 GC. The analyses of the data were done using a random forest-clustering method. Results: Proteins related to cell cycle, growth factor, cell motility, cell adhesion, apoptosis, and matrix remodeling were highly expressed in GC. We identified protein expressions associated with poor survival in diffuse-type GC. Conclusions: Based on the expression analysis of 28 proteins, we identified two groups of GC that could not be explained by any clinicopathological variables, and a subgroup of long-surviving diffuse-type GC patients with a distinct molecular profile. These results provide not only a new molecular basis for understanding the biological properties of GC, but also better prediction of survival than the classic pathological grouping.

Multivariate analyses of UV-Vis absorption spectral data from cachaca wood extracts: a model to classify aged Brazilian cachacas according to the wood species used

Multivariate analyses of UV-Vis spectral data from cachaca wood extracts provide a simple and robust model to classify aged Brazilian cachacas according to the wood species used in the maturation barrels. The model is based on inspection of 93 extracts of oak and different Brazilian wood species by a non-aged cachaca used as an extraction solvent. Application of PCA (Principal Components Analysis) and HCA (Hierarchical Cluster Analysis) leads to identification of 6 clusters of cachaca wood extracts (amburana, amendoim, balsamo, castanheira, jatoba, and oak). LDA (Linear Discriminant Analysis) affords classification of 10 different wood species used in the cachaca extracts (amburana, amendoim, balsamo, cabreuva-parda, canela-sassafras, castanheira, jatoba, jequitiba-rosa, louro-canela, and oak) with an accuracy ranging from 80% (amendoim and castanheira) to 100% (balsamo and jequitiba-rosa). The methodology provides a low-cost alternative to methods based on liquid chromatography and mass spectrometry to classify cachacas aged in barrels that are composed of different wood species.

Simcluster: clustering enumeration gene expression data on the simplex space

Abstract Background Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space. Results Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster. Conclusion Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data.

Functional clustering of time series gene expression data by Granger causality

Background: A common approach for time series gene expression data analysis includes the clustering of genes with similar expression patterns throughout time. Clustered gene expression profiles point to the joint contribution of groups of genes to a particular cellular process. However, since genes belong to intricate networks, other features, besides comparable expression patterns, should provide additional information for the identification of functionally similar genes. Results: In this study we perform gene clustering through the identification of Granger causality between and within sets of time series gene expression data. Granger causality is based on the idea that the cause of an event cannot come after its consequence. Conclusions: This kind of analysis can be used as a complementary approach for functional clustering, wherein genes would be clustered not solely based on their expression similarity but on their topological proximity built according to the intensity of Granger causality among them.

Spectral characteristics of the hippocampal LFP during contextual fear conditioning

OBJECTIVE: The hippocampus has an important role in the acquisition and recall of aversive memories. The objective of this study was to investigate the relationship among hippocampal rhythms. METHODS: Microeletrodes arrays were implanted in the hippocampus of Wistar rats. The animals were trained and tested in a contextual fear conditioning task. The training consisted in applying shocks in the legs. The memory test was performed 1 day (recent memory) or 18 days (remote memory) after training. We proposed a measure based on the FFT power spectrum, denominated "delta-theta ratio", to characterize the different behaviors (active exploration and freezing) and the memories types. RESULTS: The delta-theta ratio was able to distinguish recent and remote memories. In this study, the ratio for the 18-day group was smaller than for the 1-day group. Moreover, this measure was useful to distinguish the different behavior states active exploration and freezing. CONCLUSIONS: The results suggest delta-theta oscillations could reflect the demands on information processing during recent and remote memory recalls.