A biophysical model of Sugarcane growth

Scientists predict that global agricultural lands will expand over the next few decades due to increasing demands for food production and an exponential increase in crop-based biofuel production. These changes in land use will greatly impact biogeochemical and biogeophysical cycles across the globe. It is therefore important to develop models that can accurately simulate the interactions between the atmosphere and important crops. In this study, we develop and validate a new process-based sugarcane model (included as a module within the Agro-IBIS dynamic agro-ecosystem model) which can be applied at multiple spatial scales. At site level, the model systematically under/overestimated the daily sensible/latent heat flux (by -10.5% and 14.8%, H and E, respectively) when compared against the micrometeorological observations from southeast Brazil. The model underestimated ET (relative bias between -10.1% and 12.5%) when compared against an agro-meteorological field experiment from northeast Australia. At the regional level, the model accurately simulated average yield for the four largest mesoregions (clusters of municipalities) in the state of Sao Paulo, Brazil, over a period of 16 years, with a yield relative bias of -0.68% to 1.08%. Finally, the simulated annual average sugarcane yield over 31 years for the state of Louisiana (US) had a low relative bias (-2.67%), but exhibited a lower interannual variability than the observed yields.

Identification of literary movements using complex networks to represent texts

The use of statistical methods to analyze large databases of text has been useful in unveiling patterns of human behavior and establishing historical links between cultures and languages. In this study, we identified literary movements by treating books published from 1590 to 1922 as complex networks, whose metrics were analyzed with multivariate techniques to generate six clusters of books. The latter correspond to time periods coinciding with relevant literary movements over the last five centuries. The most important factor contributing to the distinctions between different literary styles was the average shortest path length, in particular the asymmetry of its distribution. Furthermore, over time there has emerged a trend toward larger average shortest path lengths, which is correlated with increased syntactic complexity, and a more uniform use of the words reflected in a smaller power-law coefficient for the distribution of word frequency. Changes in literary style were also found to be driven by opposition to earlier writing styles, as revealed by the analysis performed with geometrical concepts. The approaches adopted here are generic and may be extended to analyze a number of features of languages and cultures.

First-principles studies of complex magnetism in Mn nanostructures on the Fe(001) surface

The magnetic properties of Mn nanostructures on the Fe(001) surface have been studied using the noncollinear first-principles real space-linear muffin-tin orbital-atomic sphere approximation method within density-functional theory. We have considered a variety of nanostructures such as adsorbed wires, pyramids, and flat and intermixed clusters of sizes varying from two to nine atoms. Our calculations of interatomic exchange interactions reveal the long-range nature of exchange interactions between Mn-Mn and Mn-Fe atoms. We have found that the strong dependence of these interactions on the local environment, the magnetic frustration, and the effect of spin-orbit coupling lead to the possibility of realizing complex noncollinear magnetic structures such as helical spin spiral and half-skyrmion.

The dynamical state of galaxy groups and their luminosity content

We analyse the dependence of the luminosity function (LF) of galaxies in groups on group dynamical state. We use the Gaussianity of the velocity distribution of galaxy members as a measurement of the dynamical equilibrium of groups identified in the Sloan Digital Sky Survey Data Release 7 by Zandivarez & Martinez. We apply the Anderson-Darling goodness-of-fit test to distinguish between groups according to whether they have Gaussian or non-Gaussian velocity distributions, i.e. whether they are relaxed or not. For these two subsamples, we compute the (0.1)r-band LF as a function of group virial mass and group total luminosity. For massive groups, , we find statistically significant differences between the LF of the two subsamples: the LFs of groups that have Gaussian velocity distributions have a brighter characteristic absolute magnitude (similar to 0.3 mag) and a steeper faint-end slope (similar to 0.25). We detect a similar effect when comparing the LF of bright [M-0.1r(group) - 5log(h) < -23.5] Gaussian and non-Gaussian groups. Our results indicate that, for massive/luminous groups, the dynamical state of the system is directly related to the luminosity of its galaxy members.

GALAXIES BEHIND THE GALACTIC PLANE: FIRST RESULTS AND PERSPECTIVES FROM THE VVV SURVEY

VISTA Variables in the Via Lactea (VVV) is an ESO variability survey that is performing observations in near-infrared bands (ZY JHK(s)) toward the Galactic bulge and part of the disk with the completeness limits at least 3 mag deeper than Two Micron All Sky Survey. In the present work, we searched in the VVV survey data for background galaxies near the Galactic plane using ZY JHK(s) photometry that covers 1.636 deg(2). We identified 204 new galaxy candidates by analyzing colors, sizes, and visual inspection of multi-band (ZY JHK(s)) images. The galaxy candidate colors were also compared with the predicted ones by star count models considering a more realistic extinction model at the same completeness limits observed by VVV. A comparison of the galaxy candidates with the expected one by Millennium simulations is also presented. Our results increase the number density of known galaxies behind the Milky Way by more than one order of magnitude. A catalog with galaxy properties including ellipticity, Petrosian radii, and ZY JHK(s) magnitudes is provided, as well as comparisons of the results with other surveys of galaxies toward the Galactic plane.

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.

Milky Way demographics with the VVV survey I. The 84-million star colour-magnitude diagram of the Galactic bulge

Context. The Milky Way (MW) bulge is a fundamental Galactic component for understanding the formation and evolution of galaxies, in particular our own. The ESO Public Survey VISTA Variables in the Via Lactea is a deep near-IR survey mapping the Galactic bulge and southern plane. Particularly for the bulge area, VVV is covering similar to 315 deg(2). Data taken during 2010 and 2011 covered the entire bulge area in the JHKs bands. Aims. We used VVV data for the whole bulge area as a single and homogeneous data set to build for the first time a single colour-magnitude diagram (CMD) for the entire Galactic bulge. Methods. Photometric data in the JHK(s) bands were combined to produce a single and huge data set containing 173 150 467 sources in the three bands, for the similar to 315 deg(2) covered by VVV in the bulge. Selecting only the data points flagged as stellar, the total number of sources is 84 095 284. Results. We built the largest colour-magnitude diagrams published up to date, containing 173.1+ million sources for all data points, and more than 84.0 million sources accounting for the stellar sources only. The CMD has a complex shape, mostly owing to the complexity of the stellar population and the effects of extinction and reddening towards the Galactic centre. The red clump (RC) giants are seen double in magnitude at b similar to -8 degrees-10 degrees, while in the inner part (b similar to -3 degrees) they appear to be spreading in colour, or even splitting into a secondary peak. Stellar population models show the predominance of main-sequence and giant stars. The analysis of the outermost bulge area reveals a well-defined sequence of late K and M dwarfs, seen at (J - K-s) similar to 0.7-0.9 mag and K-s greater than or similar to 14 mag. Conclusions. The interpretation of the CMD yields important information about the MW bulge, showing the fingerprint of its structure and content. We report a well-defined red dwarf sequence in the outermost bulge, which is important for the planetary transit searches of VVV. The double RC in magnitude seen in the outer bulge is the signature of the X-shaped MW bulge, while the spreading of the RC in colour, and even its splitting into a secondary peak, are caused by reddening effects. The region around the Galactic centre is harder to interpret because it is strongly affected by reddening and extinction.

Spatial analysis of leprosy incidence and associated socioeconomic factors

OBJECTIVE: To identify clusters of the major occurrences of leprosy and their associated socioeconomic and demographic factors. METHODS: Cases of leprosy that occurred between 1998 and 2007 in Sao Jose do Rio Preto (southeastern Brazil) were geocodified and the incidence rates were calculated by census tract. A socioeconomic classification score was obtained using principal component analysis of socioeconomic variables. Thematic maps to visualize the spatial distribution of the incidence of leprosy with respect to socioeconomic levels and demographic density were constructed using geostatistics. RESULTS: While the incidence rate for the entire city was 10.4 cases per 100,000 inhabitants annually between 1998 and 2007, the incidence rates of individual census tracts were heterogeneous, with values that ranged from 0 to 26.9 cases per 100,000 inhabitants per year. Areas with a high leprosy incidence were associated with lower socioeconomic levels. There were identified clusters of leprosy cases, however there was no association between disease incidence and demographic density. There was a disparity between the places where the majority of ill people lived and the location of healthcare services. CONCLUSIONS: The spatial analysis techniques utilized identified the poorer neighborhoods of the city as the areas with the highest risk for the disease. These data show that health departments must prioritize politico-administrative policies to minimize the effects of social inequality and improve the standards of living, hygiene, and education of the population in order to reduce the incidence of leprosy.

Star formation in H I tails: HCG 92, HCG 100 and six interacting systems

We present new Gemini spectra of 14 new objects found within the H?i tails of Hickson Compact Groups (HCGs) 92 and 100. Nine of them are Galaxy Evolution Explorer (GALEX) far-ultraviolet (FUV) and near-ultraviolet (NUV) sources. The spectra confirm that these objects are members of the compact groups and have metallicities close to solar, with an average value of 12+log(O/H) similar to 8.5. They have average FUV luminosities 7 x 10(40)?erg?s-1 and very young ages (<100?Myr), and two of them resemble tidal dwarf galaxy (TDG) candidates. We suggest that they were created within gas clouds that were ejected during galaxygalaxy interactions into the intergalactic medium, which would explain the high metallicities of the objects, inherited from the parent galaxies from which the gas originated. We conduct a search for similar objects in six interacting systems with extended H?i tails: NGC 2623, NGC 3079, NGC 3359, NGC 3627, NGC 3718 and NGC 4656. We found 35 ultraviolet (UV) sources with ages < 100?Myr; however, most of them are on average less luminous/massive than the UV sources found around HCG 92 and HCG 100. We speculate that this might be an environmental effect and that compact groups of galaxies are more favourable to TDG formation than other interacting systems.

Genotype by environment interaction for birth and weaning weights of composite beef cattle in different regions of Brazil

The objectives of the present study were to characterize and define homogenous production environments of composite beef cattle in Brazil in terms of climatic and geographic variables using multivariate exploratory techniques and to use them to assess the presence of G x E for birth weight (BW) and weaning weight (WW). Data from animals born between 1995 and 2008 on 36 farms located in 27 municipalities of the Brazilian states were used. Fifteen years of climate observations (mean minimum and maximum annual temperature and mean annual rainfall) and geographic (latitude, longitude and altitude) data were obtained for each municipality where the farms were located for characterization of the production environments. Hierarchical and nonhierarchical cluster analysis was used to group farms located in regions with similar environmental variables into clusters. Six clusters of farms were formed. The effect of sire-cluster interaction was tested by single-trait analysis using deviance information criterion (DIC). Genetic parameters were estimated by multi-trait analysis considering the same trait to be different in each cluster. According to the values of DIC, the inclusion of sire-cluster effect did not improve the fit of the genetic evaluation model for BW and WW. Estimates of genetic correlations among clusters ranged from -0.02 to 0.92. The low genetic correlation among the most studied regions permits us to suggest that a separate genetic evaluation for some regions should be undertaken. (C) 2012 Elsevier B.V. All rights reserved.

Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

Abstract Background In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown. Results By using cDNA microarray analyses of >6,000 Apis mellifera ESTs, we found 240 differentially expressed genes (DEGs) between developing queens and workers. Many genes recorded as up-regulated in prospective workers appear to be unique to A. mellifera, suggesting that the workers' developmental pathway involves the participation of novel genes. Workers up-regulate more developmental genes than queens, whereas queens up-regulate a greater proportion of physiometabolic genes, including genes coding for metabolic enzymes and genes whose products are known to regulate the rate of mass-transforming processes and the general growth of the organism (e.g., tor). Many DEGs are likely to be involved in processes favoring the development of caste-biased structures, like brain, legs and ovaries, as well as genes that code for cytoskeleton constituents. Treatment of developing worker larvae with juvenile hormone (JH) revealed 52 JH responsive genes, specifically during the critical period of caste development. Using Gibbs sampling and Expectation Maximization algorithms, we discovered eight overrepresented cis-elements from four gene groups. Graph theory and complex networks concepts were adopted to attain powerful graphical representations of the interrelation between cis-elements and genes and objectively quantify the degree of relationship between these entities. Conclusion We suggest that clusters of functionally related DEGs are co-regulated during caste development in honeybees. This network of interactions is activated by nutrition-driven stimuli in early larval stages. Our data are consistent with the hypothesis that JH is a key component of the developmental determination of queen-like characters. Finally, we propose a conceptual model of caste differentiation in A. mellifera based on gene-regulatory networks.

The subplacenta of the red-rumped agouti (Dasyprocta leporina L)

Background: Hystricognath rodents have a lobed placenta, comprising labyrinthine exchange areas and interlobular trophoblast. These correspond to the labyrinthine and spongy zones of other rodent placentae. Beneath them, however, is a structure unique to hystricognath rodents called the subplacenta. We here describe the subplacenta of the red-rumped agouti and examine the possible functional correlates of this structure. Methods: Placentae were collected from early in midgestation to near term of pregnancy and examined by standard histological techniques, immunohistochemistry and transmission electron microscopy. In addition, to study the microvasculature of the subplacenta, vessel casts were inspected by scanning electron microscopy. Results: In the subplacenta, lamellae of connective tissue support a layer of mononuclear cytotrophoblast cells. Beneath this is found syncytiotrophoblast. Clusters of multinuclear giant cells occur in the transition zone between the subplacenta and decidua. There are prominent intercellular spaces between the cytotrophoblast cells. The basal membrane of these cells is often close to fetal blood vessels. The syncytiotrophoblast surrounds an extensive system of lacunae. Microvilli project into these lacunae from the plasma membrane of the syncytiotrophoblast. The syncytial cytoplasm contains electron-dense granules. This is probably the amylase-resistant PAS-positive material identified by histochemistry. The subplacenta is supplied entirely from the fetal circulation. Within it the vessels pursue a tortuous course with sinusoidal dilatations and constrictions. Conclusion: The functions that have been attributed to the subplacenta include hormone production. Our findings are consistent with this interpretation, but suggest that hormone secretion is directed towards the fetal circulation rather than the maternal tissues.

Psychometric validation of the Portuguese version of the Neuropathic Pain Symptoms Inventory

Backgroud: It has been shown that different symptoms or symptom combinations of neuropathic pain (NeP) may correspond to different mechanistic backgrounds and respond differently to treatment. The Neuropathic Pain Symptom Inventory (NPSI) is able to detect distinct clusters of symptoms (i.e. dimensions) with a putative common mechanistic background. The present study described the psychometric validation of the Portuguese version (PV) of the NPSI. Methods: Patients were seen in two consecutive visits, three to four weeks apart. They were asked to: (i) rate their mean pain intensity in the last 24 hours on an 11-point (0-10) numerical scale; (ii) complete the PV-NPSI; (iii) provide the list of pain medications and doses currently in use. VAS and Global Impression of Change (GIC) were filled out in the second visit. Results: PV-NPSI underwent test-retest reliability, factor analysis, analysis of sensitivity to changes between both visits. The PV-NPSI was reliable in this setting, with a good intra-class correlation for all items. The factorial analysis showed that the PV-NPSI inventory assessed different components of neuropathic pain. Five different factors were found. The PV-NPSI was adequate to evaluate patients with neuropathic pain and to detect clusters of NeP symptoms. Conclusions: The psychometric properties of the PV-NPSI rendered it adequate to evaluate patients with both central and peripheral neuropathic pain syndromes and to detect clusters of NeP symptoms.

Galaxy triplets in Sloan Digital Sky Survey Data Release 7: II. A connection with compact groups?

We analyse a sample of 71 triplets of luminous galaxies derived from the work of O’Mill et al. We compare the properties of triplets and their members with those of control samples of compact groups, the 10 brightest members of rich clusters and galaxies in pairs. The triplets are restricted to have members with spectroscopic redshifts in the range 0.01 ≤ z ≤ 0.14 and absolute r-band luminosities brighter than Mr = −20.5. For these member galaxies, we analyse the stellar mass content, the star formation rates, the Dn(4000) parameter and (Mg − Mr) colour index. Since galaxies in triplets may finally merge in a single system, we analyse different global properties of these systems. We calculate the probability that the properties of galaxies in triplets are strongly correlated. We also study total star formation activity and global colours, and define the triplet compactness as a measure of the percentage of the system total area that is filled by the light of member galaxies. We concentrate in the comparison of our results with those of compact groups to assess how the triplets are a natural extension of these compact systems. Our analysis suggests that triplet galaxy members behave similarly to compact group members and galaxies in rich clusters. We also find that systems comprising three blue, star-forming, young stellar population galaxies (blue triplets) are most probably real systems and not a chance configuration of interloping galaxies. The same holds for triplets composed of three red, non-star-forming galaxies, showing the correlation of galaxy properties in these systems. From the analysis of the triplet as a whole, we conclude that, at a given total stellar mass content, triplets show a total star formation activity and global colours similar to compact groups. However, blue triplets show a high total star formation activity with a lower stellar mass content. From an analysis of the compactness parameter of the systems we find that light is even more concentrated in triplets than in compact groups. We propose that triplets composed of three luminous galaxies, should not be considered as an analogous of galaxy pairs with a third extra member, but rather they are a natural extension of compact groups.

Analysis of genetic lineages and their correlation with virulence genes in enterococcus faecalis clinical isolates from root canal and systemic infections

Introduction: Enterococcus faecalis is a member of the mammalian gastrointestinal microbiota but has been considered a leading cause of hospital-acquired infections. In the oral cavity, it is commonly detected from root canals of teeth with failed endodontic treatment. However, little is known about the virulence and genetic relatedness among E. faecalis isolates from different clinical sources. This study compared the presence of enterococcal virulence factors among root canal strains and clinical isolates from hospitalized patients to identify virulent clusters of E. faecalis. Methods: Multilocus sequence typing analysis was used to determine genetic lineages of 40 E. faecalis clinical isolates from different sources. Virulence clusters were determined by evaluating capsule (cps) locus polymorphisms, pathogenicity island gene content, and antibiotic resistance genes by polymerase chain reaction. Results: The clinical isolates from hospitalized patients formed a phylogenetically separate group and were mostly grouped in the clonal complex 2, which is a known virulent cluster of E. faecalis that has caused infection outbreaks globally. The clonal complex 2 group comprised capsule-producing strains harboring multiple antibiotic resistance and pathogenicity island genes. On the other hand, the endodontic isolates were more diverse and harbored few virulence and antibiotic resistance genes. In particular, although more closely related to isolates from hospitalized patients, capsuleproducing E. faecalis strains from root canals did not carry more virulence/antibiotic genes than other endodontic isolates. Conclusions: E. faecalis isolates from endodontic infections have a genetic and virulence profile different from pathogenic clusters of hospitalized patients’ isolates, which is most likely due to niche specialization conferred mainly by variable regions in the genome.