Systematic Management of Variability in UML-based Software Product Lines

This paper presents SMarty, a variability management approach for UML-based software product lines (PL). SMarty is supported by a UML profile, the SMartyProfile, and a process for managing variabilities, the SMartyProcess. SMartyProfile aims at representing variabilities, variation points, and variants in UML models by applying a set of stereotypes. SMartyProcess consists of a set of activities that is systematically executed to trace, identify, and control variabilities in a PL based on SMarty. It also identifies variability implementation mechanisms and analyzes specific product configurations. In addition, a more comprehensive application of SMarty is presented using SEI's Arcade Game Maker PL. An evaluation of SMarty and related work are discussed.

Cold Nuclear Matter Effects on J/psi Yields as a Function of Rapidity and Nuclear Geometry in d plus A Collisions at root S(NN)=200 GeV

We present measurements of J/psi yields in d + Au collisions at root S(NN) = 200 GeV recorded by the PHENIX experiment and compare them with yields in p + p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/psi rapidity (-2.2 < y < 2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.

Nuclear modification factors of phi mesons in d plus Au, Cu plus Cu, and Au plus Au collisions at root s(NN)=200 GeV

The PHENIX experiment at the Relativistic Heavy Ion Collider has performed systematic measurements of phi meson production in the K(+)K(-) decay channel at midrapidity in p + p, d + Au, Cu + Cu, and Au + Au collisions at root s(NN) = 200 GeV. Results are presented on the phi invariant yield and the nuclear modification factor R(AA) for Au + Au and Cu + Cu, and R(dA) for d + Au collisions, studied as a function of transverse momentum (1 < p(T) < 7 GeV/c) and centrality. In central and midcentral Au + Au collisions, the R(AA) of phi exhibits a suppression relative to expectations from binary scaled p + p results. The amount of suppression is smaller than that of the pi(0) and the. in the intermediate p(T) range (2-5 GeV/c), whereas, at higher p(T), the phi, pi(0), and. show similar suppression. The baryon (proton and antiproton) excess observed in central Au + Au collisions at intermediate p(T) is not observed for the phi meson despite the similar masses of the proton and the phi. This suggests that the excess is linked to the number of valence quarks in the hadron rather than its mass. The difference gradually disappears with decreasing centrality, and, for peripheral collisions, the R(AA) values for both particle species are consistent with binary scaling. Cu + Cu collisions show the same yield and suppression as Au + Au collisions for the same number of N(part). The R(dA) of phi shows no evidence for cold nuclear effects within uncertainties.

Systematic studies of elliptic flow measurements in Au plus Au collisions at s(NN)=200 GeV

We present inclusive charged hadron elliptic flow (v(2)) measured over the pseudorapidity range vertical bar eta vertical bar < 0.35 in Au+Au collisions at s(NN)=200 GeV. Results for v(2) are presented over a broad range of transverse momentum (p(T)=0.2-8.0 GeV/c) and centrality (0-60%). To study nonflow effects that are correlations other than collective flow, as well as the fluctuations of v(2), we compare two different analysis methods: (1) the event-plane method from two independent subdetectors at forward (vertical bar eta vertical bar=3.1-3.9) and beam (vertical bar eta vertical bar>6.5) pseudorapidities and (2) the two-particle cumulant method extracted using correlations between particles detected at midrapidity. The two event-plane results are consistent within systematic uncertainties over the measured p(T) and in centrality 0-40%. There is at most a 20% difference in the v(2) between the two event-plane methods in peripheral (40-60%) collisions. The comparisons between the two-particle cumulant results and the standard event-plane measurements are discussed.

Systematic investigation of a family of gradient-dependent functionals for solids

Eleven density functionals are compared with regard to their performance for the lattice constants of solids. We consider standard functionals, such as the local-density approximation and the Perdew-Burke-Ernzerhof (PBE) generalized-gradient approximation (GGA), as well as variations of PBE GGA, such as PBEsol and similar functionals, PBE-type functionals employing a tighter Lieb-Oxford bound, and combinations thereof. On a test set of 60 solids, we perform a system-by-system analysis for selected functionals and a full statistical analysis for all of them. The impact of restoring the gradient expansion and of tightening the Lieb-Oxford bound is discussed, and confronted with previous results obtained from other codes, functionals or test sets. No functional is uniformly good for all investigated systems, but surprisingly, and pleasingly, the simplest possible modifications to PBE turn out to have the most beneficial effect on its performance. The atomization energy of molecules was also considered and on a testing set of six molecules, we found that the PBE functional is clearly the best, the others leading to strong overbinding.

Development and validation of a fast RP-HPLC method to determine the analogue of the thyroid hormone, 3,5,3 '-triiodothyroacetic acid (TRIAC), in polymeric nanoparticles

The objective of this work was to develop and validate a rapid Reversed-Phase High-Performance Liquid Chromatography method for the quantification of 3,5,3 '-triiodothyroacetic acid (TRIAC) in nanoparticles delivery system prepared in different polymeric matrices. Special attention was given to developing a reliable reproductive technique for the pretreatment of the samples. Chromatographic runs were performed on an Agilent 1200 Series HPLC with a RP Phenomenex (R) Gemini C18 (150 x 4, 6 mm i.d., 5 mu m) column using acetonitrile and triethylamine buffer 0.1% (TEA) (40 : 60 v/v) as a mobile phase in an isocratic elution, pH 5.6 at a flow rate of 1 ml min(-1). TRIAC was detected at a wavelength of 220 nm. The injection volume was 20 mu l and the column temperature was maintained at 35 degrees C. The validation characteristics included accuracy, precision, specificity, linearity, recovery, and robustness. The standard curve was found to have a linear relationship (r(2) - 0.9996) over the analytical range of 5-100 mu g ml(-1) . The detection and quantitation limits were 1.3 and 3.8 mu g ml(-1), respectively. The recovery and loaded TRIAC in colloidal system delivery was nearly 100% and 98%, respectively. The method was successfully applied in polycaprolactone, polyhydroxybutyrate, and polymethylmethacrylate nanoparticles.

Placebo Response of Non-Pharmacological and Pharmacological Trials in Major Depression: A Systematic Review and Meta-Analysis

Background: Although meta-analyses have shown that placebo responses are large in Major Depressive Disorder (MDD) trials; the placebo response of devices such as repetitive transcranial magnetic stimulation (rTMS) has not been systematically assessed. We proposed to assess placebo responses in two categories of MDD trials: pharmacological (antidepressant drugs) and non-pharmacological (device-rTMS) trials. Methodology/Principal Findings: We performed a systematic review and meta-analysis of the literature from April 2002 to April 2008, searching MEDLINE, Cochrane, Scielo and CRISP electronic databases and reference lists from retrieved studies and conference abstracts. We used the keywords placebo and depression and escitalopram for pharmacological studies; and transcranial magnetic stimulation and depression and sham for non-pharmacological studies. All randomized, double-blinded, placebo-controlled, parallel articles on major depressive disorder were included. Forty-one studies met our inclusion criteria-29 in the rTMS arm and 12 in the escitalopram arm. We extracted the mean and standard values of depression scores in the placebo group of each study. Then, we calculated the pooled effect size for escitalopram and rTMS arm separately, using Cohen's d as the measure of effect size. We found that placebo response are large for both escitalopram (Cohen's d-random-effects model-1.48; 95% C.I. 1.26 to 1.6) and rTMS studies (0.82; 95% C.I. 0.63 to 1). Exploratory analyses show that sham response is associated with refractoriness and with the use of rTMS as an add-on therapy, but not with age, gender and sham method utilized. Conclusions/Significance: We confirmed that placebo response in MDD is large regardless of the intervention and is associated with depression refractoriness and treatment combination (add-on rTMS studies). The magnitude of the placebo response seems to be related with study population and study design rather than the intervention itself.

KeaA, a Dictyostelium kelch-domain protein that regulates the response to stress and development

Background: The protein kinase YakA is responsible for the growth arrest and induction of developmental processes that occur upon starvation of Dictyostelium cells. yakA-cells are aggregation deficient, have a faster cell cycle and are hypersensitive to oxidative and nitrosoative stress. With the aim of isolating members of the YakA pathway, suppressors of the death induced by nitrosoative stress in the yakA-cells were identified. One of the suppressor mutations occurred in keaA, a gene identical to DG1106 and similar to Keap1 from mice and the Kelch protein from Drosophila, among others that contain Kelch domains. Results: A mutation in keaA suppresses the hypersensitivity to oxidative and nitrosoative stresses but not the faster growth phenotype of yakA-cells. The growth profile of keaA deficient cells indicates that this gene is necessary for growth. keaA deficient cells are more resistant to nitrosoative and oxidative stress and keaA is necessary for the production and detection of cAMP. A morphological analysis of keaA deficient cells during multicellular development indicated that, although the mutant is not absolutely deficient in aggregation, cells do not efficiently participate in the process. Gene expression analysis using cDNA microarrays of wild-type and keaA deficient cells indicated a role for KeaA in the regulation of the cell cycle and pre-starvation responses. Conclusions: KeaA is required for cAMP signaling following stress. Our studies indicate a role for kelch proteins in the signaling that regulates the cell cycle and development in response to changes in the environmental conditions.

The P450 oxidoreductase, RedA, controls development beyond the mound stage in Dictyostelium discoideum

Background: NADPH-cytochrome- P450 oxidoreductase (CPR) is a ubiquitous enzyme that belongs to a family of diflavin oxidoreductases and is required for activity of the microsomal cytochrome-P450 monooxygenase system. CPR gene-disruption experiments have demonstrated that absence of this enzyme causes developmental defects both in mouse and insect. Results: Annotation of the sequenced genome of D. discoideum revealed the presence of three genes (redA, redB and redC) that encode putative members of the diflavin oxidoreductase protein family. redA transcripts are present during growth and early development but then decline, reaching undetectable levels after the mound stage. redB transcripts are present in the same levels during growth and development while redC expression was detected only in vegetative growing cells. We isolated a mutant strain of Dictyostelium discoideum following restriction enzyme-mediated integration (REMI) mutagenesis in which redA was disrupted. This mutant develops only to the mound stage and accumulates a bright yellow pigment. The mound-arrest phenotype is cell-autonomous suggesting that the defect occurs within the cells rather than in intercellular signaling. Conclusion: The developmental arrest due to disruption of redA implicates CPR in the metabolism of compounds that control cell differentiation.

Nitrogen dynamics during ecosystem development in tropical forest restoration

We considered whether ecological restoration using high diversity of native tree species serves to restore nitrogen dynamics in the Brazilian Atlantic Forest. We measured delta(15)N and N content in green foliage and soil; vegetation N:P ratio; and soil N mineralization in a preserved natural forest and restored forests of ages 21 and 52 years. Green foliage delta(15)N values, N content, N:P ratio, inorganic N and net mineralization and nitrification rates were all higher, the older the forest. Our findings indicate that the recuperation of N cycling has not been achieved yet in the restored forests even after 52 years, but show that they are following a trajectory of development that is characterized by their N cycling intensity becoming similar to a natural mature forest of the same original forest formation. This study demonstrated that some young restored forests are more limited by N compared to mature natural forests. We document that the recuperation of N cycling in tropical forests can be achieved through ecological restoration actions. (C) 2011 Elsevier B.V. All rights reserved.

Development of novel microsatellites from Moniliophthora perniciosa, causal agent of the witches` broom disease of Theobroma cacao

Moniliophthora perniciosa is the causal agent of the witches` broom disease of cacao. Based on available genomic sequences, we identified 30 new microsatellite loci, which were analysed using 50 isolates from four populations sampled over a wide geographical area in Brazil, including three populations from the Amazon, the fungal putative centre of diversity, plus one from Bahia. Nine loci were polymorphic, with an average of 2.9 alleles per locus. The level of polymorphism observed was low, but these markers may allow the evaluation of pathogen diversity and the establishment of molecular standards for isolate fingerprinting to support cacao breeding.

Characterization of unisexual flower development in the endangered mahogany tree Swietenia macrophylla King. (Meliaceae)

The selection of candidate plus trees of desirable phenotypes from tropical forest trees and the rapid devastation of the natural environments in which these trees are found have created the need for a more detailed knowledge of the floral and reproductive biology of tropical tree species. In this article, the organogenic processes related to unisexual flower development in tropical mahogany, Swietenia macrophylla, are described. Mahogany inflorescences at different developmental stages were evaluated using scanning electron microscopy or optical microscopy of histological sections. The unisexual flowers of S. macrophylla are usually formed in a thyrse, in which the positions of the female and male flowers are not random. Differences between male and female flowers arise late during development. Both female and male flowers can only be structurally distinguished after stage 9, where ovule primordia development is arrested in male flowers and microspore development is aborted in female flower anthers. After this stage, male and female flowers can be distinguished by the naked eye as a result of differences in the dimensions of the gynoecium. The floral characteristics of S. macrophylla (distribution of male and female flowers within the inflorescence, and the relative number of male to female flowers) have practical implications for conservation strategies of this endangered species. (c) 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 156, 529-535.

Floral development in the tribe Cedreleae (Meliaceae, sub-family Swietenioideae): Cedrela and Toona

Background and Aims Floral development of Cedrela and Toona, the genera comprising the basal tribe Cedreleae of the sub-family Swietenioideae of Meliaceae, is described. The focus was on three endangered, ecologically and economically important species: Cedrela fissilis, Cedrela odorata and Toona ciliata. The aims of the study were to characterize the patterns of floral development in the tribe and to establish apomorphic and plesiomorphic floral characters in relation to other taxa within the family based on the current molecular phylogeny of Meliaceae. Methods A detailed floral structural and developmental study was completed using both scanning electron microscopy and visualization of microtome sections with a light microscope. Key Results Twelve floral developmental stages were identified. The initial development of the pentamerous flowers of both Toona and Cedrela is strikingly similar. The morphological differences observed between them are due to differential patterns of organ elongation and adnation/connation occurring late in development. Additionally, the formation of functionally male and female flowers was found to occur at specific positions within the inflorescence. Conclusions Due to the basal position of the tribe Cedreleae in the phylogeny of Meliaceae, functionally either male or female pentamerous flowers and the presence of (at least partially) free stamens may be considered plesiomorphic traits within the family. In contrast, sympetaly and the absence of nectaries in Cedrela species are synapomorphies.

Biofuels and Sustainable Energy Development in Brazil

Through the assessment of three decades of the Alcohol Program in Brazil, the paper shows that adequate public policies regarding biomass production can deliver direct benefits like energy security improvement, foreign exchange savings, and local employment generation, reduced urban air pollution and avoided CO(2) emissions. Moreover, the paper shows that Brazilian produced ethanol has faced economies of scale, technical progress and productivity gains and is no longer dependent on subsidies to be competitive. The paper also examines the potential in Brazil for fostering other biofuels, namely biodiesel obtained from vegetable oils, as well as their implications on sustainable energy development. (C) 2011 Elsevier Ltd. All rights reserved.

Systematic review and cladistic analysis of the genus Eusarcus Perty 1833 (Arachnida, Opiliones, Gonyleptidae)

Eusarcus Perty 1833 is one of the oldest described genera of Pachylinae, comprising 36 species distributed from northeastern to southern Brazil (including the central west region), northeastern Argentina, eastern Paraguay and Uruguay. The genus is reviewed and a new classification is proposed based on a cladistic analysis. A cladistic analysis was performed with the 34 valid species of Eusarcus and 11 species belonging to certain Gonyleptidae subfamilies. The data matrix has 67 characters: 14 from dorsal scutum and pedipalp, 38 from male legs and 15 from male genitalia. Two equally parsimonious trees were found (L=319; C. I.=0.26, R. I.=0.61). Pygophalangodus gemignanii uruguayensis Ringuelet 1955a and Pygophalangodus gemignanii gemignanii Mello-Leitao 1931b are here elevated to the category of species, and the following new combinations are proposed: E. catharinensis (Mello-Leitao 1927); E. berlae (Mello-Leitao 1932); E. gemignanii (Mello-Leitao 1931b); E. signatus(Roewer 1949); E. sooretamae (Soares & Soares 1946a); E. uruguayensis (Ringuelet 1955a). The following generic synonymies are proposed: Eusarcus Perty 1833 (type species E. armatus Perty 1833) = Metagraphinotus Mello-Leitao 1927 (type species M. catharinensis Mello-Leitao 1927), Pareusarcus Roewer 1929 (type species P. corniculatus Roewer 1929), Pygophalangodus Mello-Leitao 1931b (type species P. gemignanii-gemignanii Mello-Leitao 1931b) and Antetriceras Roewer 1949 (type species A. signatus Roewer 1949). The following specific synonymies are proposed: Eusarcus hastatus Sorensen 1884 = Pucrolioides argentina Roewer 1913, E. guimaraensi H. Soares 1945, Jacarepaguana pectinifemur Piza 1943, Canestrinia canalsi Mello-Leitao 1931a, and E. maquinensis H. Soares 1966b; E. armatus Perty 1833 = E. curvispinosus Mello-Leitao 1923b, and Enantiocentron montis Mello-Leitao 1936; Eusarcus catharinensis (Mello-Leitao 1927) = E. antoninae Mello-Leitao 1936, E. perpusillus Mello-Leitao 1945, E. tripos Mello-Leitao 1940, and Metagraphinotus trochanterspinosus Soares & Soares 1947b; E. nigrimaculatus Mello-Leitao 1924 = Pareusarcus centromelos Mello-Leitao 1935a, E. furcatus Roewer 1929, Orguesia armata Roewer 1913, and Pareusarcus corniculatus Roewer 1929; E. oxyacanthus Kollar in Koch 1839a = Enantiocentron doriphorus Mello-Leitao 1932, and E. spinimanu Mello-Leitao 1932; E. pusillus Sorensen 1884 = E. vervloeti B. Soares 1944c; E. berlae Mello-Leitao 1932 = Metagraphinotus arlei Mello-Leitao 1935a. Metapucrolia armata (Sorensen 1895) is revalidated, transferred to Eusarcus and considered as a species inquirenda. A new name, Eusarcus metapucrolia is proposed for this species to avoid homonymy with the type species of Eusarcus, E. armatus Perty 1833. Eusarcus aberrans Mello-Leitao 1939a is considered as a species inquirenda. The male of E. teresincola Soares & Soares 1946a is described. Female of the following species are described: E. bifidus Roewer 1929; E. dubius B. Soares 1943b; E. insperatus B. Soares 1944a; E. schubarti Soares & Soares 1946a; E. sooretamae (Soares & Soares 1946a). The following new species are described from Brazil: E. acrophthalmus (type locality: Bahia, Ilheus, Parataquice); E. alpinus (Rio de Janeiro, Santa Maria Madalena, Parque Estadual do Desengano); E. caparaoensis (Minas Gerais, Alto Caparao, Parque Nacional do Caparao); E. cavernicola (Goias, Sao Domingos, Parque Estadual de Terra Ronca, Lapa da Angelica); E. didactylus (Rio de Janeiro, Teresopolis, Parque Nacional Serra dos Orgaos); E. garibaldiae (Santa Catarina, Itajai); E. geometricus (Rio de Janeiro, Teresopolis, Parque Nacional Serra dos Orgaos); E. manero (Rio de Janeiro, Marica, Itaipuacu); E. matogrossensis (Mato Grosso, Chapada dos Guimaraes); E. mirabilis (Minas Gerais, Marlieria, Parque Estadual Rio Doce); E. sergipanus (Sergipe, Itabaiana, Parque Nacional de Itabaiana) and E. tripectinatus (Minas Gerais, Rio Preto). The holotype of E. curvispinosus is proposed as the neotype of E. armatus Perty 1833, the type material of which has been lost. Lectotypes for the following species were designated: E. aduncus; E. hastatus; E. oxyacanthus.