Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions

Patterns of substitution in chloroplast encoded trnL_F regions were compared between species of Actaea (Ranunculales), Digitalis (Scrophulariales), Drosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lycopodiales). In total, the study included 265 taxa, each with > 900-bp sequences, totaling 0.24 Mb. Both pairwise and phylogeny-based comparisons were used to assess nucleotide substitution patterns. In all six groups, we found that transition/transversion ratios, as estimated by maximum likelihood on most-parsimonious trees, ranged between 0.8 and 1.0 for ingroups. These values occurred both at low sequence divergences, where substitutional saturation, i.e., multiple substitutions having occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL-F regions evolve in a pattern different from that generally observed for nuclear and animal mtDNA (transitional/transversion ratio > or = 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the regions were highly similar in all six groups. A>-C transversions were significantly less frequent than the other four substitution types. This correlates with results from studies on fidelity mechanisms in DNA replication that predict A<->T and G<->C transversions to be least likely to occur. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees, and concomitantly, in the neutrality of nucleotide substitutions as phylogenetic markers.

Complex history of a chromosomal paralogy region: insights from amphioxus aromatic amino acid hydroxylase genes and insulin-related genes

Aromatic amino acid hydroxylase (AAAH) genes and insulin-like genes form part of an extensive paralogy region shared by human chromosomes 11 and 12, thought to have arisen by tetraploidy in early vertebrate evolution. Cloning of a complementary DNA (cDNA) for an amphioxus (Branchiostoma floridae) hydroxylase gene (AmphiPAH) allowed us to investigate the ancestry of the human chromosome 11/12 paralogy region. Molecular phylogenetic evidence reveals that AmphiPAH is orthologous to vertebrate phenylalanine (PAH) genes; the implication is that all three vertebrate AAAH genes arose early in metazoan evolution, predating vertebrates. In contrast, our phylogenetic analysis of amphioxus and vertebrate insulin-related gene sequences is consistent with duplication of these genes during early chordate ancestry. The conclusion is that two tightly linked gene families on human chromosomes 11 and 12 were not duplicated coincidentally. We rationalize this paradox by invoking gene loss in the AAAH gene family and conclude that paralogous genes shared by paralogous chromosomes need not have identical evolutionary histories.

Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae

Root nodule symbiosis (RNS) is one of the most efficient biological systems for nitrogen fixation and it occurs in 90% of genera in the Papilionoideae, the largest subfamily of legumes. Most papilionoid species show evidence of a polyploidy event occurred approximately 58 million years ago. Although polyploidy is considered to be an important evolutionary force in plants, the role of this papilionoid polyploidy event, especially its association with RNS, is not understood. In this study, we explored this role using an integrated comparative genomic approach and conducted gene expression comparisons and gene ontology enrichment analyses. The results show the following: (1) approximately a quarter of the papilionoid-polyploidy-derived duplicate genes are retained; (2) there is a striking divergence in the level of expression of gene duplicate pairs derived from the polyploidy event; and (3) the retained duplicates are frequently involved in the processes crucial for RNS establishment, such as symbiotic signalling, nodule organogenesis, rhizobial infection and nutrient exchange and transport. Thus, we conclude that the papilionoid polyploidy event might have further refined RNS and induced a more robust and enhanced symbiotic system. This conclusion partly explains the widespread occurrence of the Papilionoideae.

The Mid-Brunhes Event and West Antarctic ice sheet stability

The complex cyclical nature of Pleistocene climate, driven by the evolving orbital configuration of the Earth, is well known but not well understood. A major climatic transition took place at the Mid-Brunhes Event (MBE), ca. 430 ka ago after which the amplitude of the ca.100 ka climate oscillations increased, with substantially warmer interglacials, including periods warmer than present. Recent modelling has indicated that while the timing of these warmer-than-present transient (WPT) events is consistent with southern warming due to a deglaciation-forced slowdown of the Atlantic Meridional Overturning Circulation, the magnitude of warming requires a local amplification, for which a candidate is the feedback of significant West Antarctic Ice Sheet (WAIS) retreat. We here extend this argument, based on the absence of WPTs in the early ice core record (450–800 ka ago), to hypothesize that the MBE could be a manifestation of decreased WAIS stability, triggered by ongoing subglacial erosion.

Investigation of the accuracy of historical irradiance products and interannual variability of solar irradiance using Met Office ground data

Met Office station data from 1980 to 2012 has been used to characterise the interannual variability of incident solar irradiance across the UK. The same data are used to evaluate four popular historical irradiance products to determine which are most suitable for use by the UK PV industry for site selection and system design. The study confirmed previous findings that interannual variability is typically 3–6% and weighted average probability of a particular percentage deviation from the mean at an average site in the UK was calculated. This weighted average showed that fewer than 2% of site-years could be expected to fall below 90% of the long-term site mean. The historical irradiance products were compared against Met Office station data from the input years of each product. This investigation has found that all products perform well. No products have a strong spatial trend. Meteonorm 7 is most conservative (MBE = −2.5%), CMSAF is most optimistic (MBE = +3.4%) and an average of all four products performs better than any one individual product (MBE = 0.3%)

Engineering of 3D self-directed quantum dot ordering in multilayer InGaAs/GaAs nanostructures by means of flux gas composition

Lateral ordering of InGaAs quantum dots on the GaAs (001) surface has been achieved in earlier reports, resembling an anisotropic pattern. In this work, we present a method of breaking the anisotropy of ordered quantum dots (QDs) by changing the growth environment. We show experimentally that using As(2) molecules instead of As(4) as a background flux is efficient in controlling the diffusion of distant Ga adatoms to make it possible to produce isotropic ordering of InGaAs QDs over GaAs (001). The control of the lateral ordering of QDs under As(2) flux has enabled us to improve their optical properties. Our results are consistent with reported experimental and theoretical data for structure and diffusion on the GaAs surface.

Discrepancies in solar irradiation data for Stockholm and Athens

The aim of this study is to evaluate the variation of solar radiation data between different data sources that will be free and available at the Solar Energy Research Center (SERC). The comparison between data sources will be carried out for two locations: Stockholm, Sweden and Athens, Greece. For the desired locations, data is gathered for different tilt angles: 0°, 30°, 45°, 60° facing south. The full dataset is available in two excel files: “Stockholm annual irradiation” and “Athens annual irradiation”. The World Radiation Data Center (WRDC) is defined as a reference for the comparison with other dtaasets, because it has the highest time span recorded for Stockholm (1964–2010) and Athens (1964–1986), in form of average monthly irradiation, expressed in kWh/m2. The indicator defined for the data comparison is the estimated standard deviation. The mean biased error (MBE) and the root mean square error (RMSE) were also used as statistical indicators for the horizontal solar irradiation data. The variation in solar irradiation data is categorized in two categories: natural or inter-annual variability, due to different data sources and lastly due to different calculation models. The inter-annual variation for Stockholm is 140.4kWh/m2 or 14.4% and 124.3kWh/m2 or 8.0% for Athens. The estimated deviation for horizontal solar irradiation is 3.7% for Stockholm and 4.4% Athens. This estimated deviation is respectively equal to 4.5% and 3.6% for Stockholm and Athens at 30° tilt, 5.2% and 4.5% at 45° tilt, 5.9% and 7.0% at 60°. NASA’s SSE, SAM and RETScreen (respectively Satel-light) exhibited the highest deviation from WRDC’s data for Stockholm (respectively Athens). The essential source for variation is notably the difference in horizontal solar irradiation. The variation increases by 1-2% per degree of tilt, using different calculation models, as used in PVSYST and Meteonorm. The location and altitude of the data source did not directly influence the variation with the WRDC data. Further examination is suggested in order to improve the methodology of selecting the location; Examining the functional dependence of ground reflected radiation with ambient temperature; variation of ambient temperature and its impact on different solar energy systems; Im pact of variation in solar irradiation and ambient temperature on system output.

Revisão sistemática e meta-análise do uso de antidepressivos no transtorno de ansiedade generalizada

Revisão da Literatura: O Transtorno de Ansiedade Generalizada (TAG) é caracterizado por preocupação excessiva, persistente e incontrolável sobre diversos aspectos da vida do paciente. Tem prevalência entre 1,6% e 5,1% e índice de comorbidades de até 90,4%. As principais comorbidades são depressão maior (64%) e distimia (37%). Os antidepressivos podem ser eficazes no tratamento do TAG. A Medicina Baseada em Evidências (MBE) busca reunir a melhor evidência disponível com experiência clínica e conhecimentos de fisiopatologia. A melhor maneira disponível de síntese das evidências é a revisão sistemática e a meta-análise. Objetivos: Investigar a eficácia e tolerabilidade dos antidepressivos no tratamento do TAG através de uma revisão sistemática da literatura e meta-análise. Sumário do artigo científico: A revisão sistemática incluiu ensaios clínicos randomizados e controlados e excluiu estudos não-randomizados, estudos com pacientes com TAG e outro transtorno de eixo I. Os dados foram extraídos por dois revisores independentes e risco relativo, diferença da média ponderada e número necessário para tratamento (NNT) foram calculados. Antidepressivos (imipramina, paroxetina e venlafaxina) foram superiores ao placebo. O NNT calculado foi de 5,5. A evidência disponível sugere que os antidepressivos são superiores ao placebo no tratamento do TAG e bem tolerados pelos pacientes.

Operational parameters of soybean seeding in santa fe system

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influência da distribuição espacial do milho e da Brachiaria brizantha consorciados sobre a população de plantas daninhas em sistema plantio direto na palha

O cultivo consorciado de milho com forrageiras tropicais no sistema plantio direto na palha pode diminuir a incidência de plantas daninhas em decorrência da elevada produção de fitomassa e da alelopatia proporcionada pela deposição superficial de palha no solo. Este trabalho objetivou avaliar a influência da distribuição espacial da cultura do milho com Brachiaria brizantha, cultivados em consórcio no sistema plantio direto na palha, sobre a população de plantas daninhas. O experimento foi instalado em condições de campo, nos anos agrícolas 2002/03 e 2003/04, na Fazenda Experimental Lageado, em Botucatu-SP. O delineamento experimental foi o de blocos casualizados em esquema fatorial simples 2 x 4, com quatro repetições. Os tratamentos foram dois espaçamentos entre linhas de milho (E1-45 cm e E2- 90 cm) e quatro modalidades de cultivo (MCS - cultivo do milho solteiro; MBL - cultivo do milho com B. brizantha na linha de semeadura; BEM - cultivo do milho com B. brizantha na entrelinha; e MBLE - cultivo do milho com B. brizantha simultaneamente na linha e na entrelinha). Foram avaliados a produtividade de matéria seca da forrageira, a caracterização fitossociológica, a incidência e o controle de plantas daninhas. O cultivo MBLE a 90 cm foi a modalidade de consorciação que proporcionou maior produção de palhada. A presença de B. brizantha em cultivo consorciado diminuiu a densidade de plantas daninhas. A utilização do cultivo consorciado do milho com B. brizantha na linha+entrelinha proporcionou índice de controle de 95%, independentemente do espaçamento utilizado.

Numerical correction for the diffuse solar irradiance by the melo-escobedo shadowring measuring method

The present paper deals with numerical corrections factors proposed as a function of the clearness index in order to correct the diffuse solar irradiance measured with the Melo-Escobedo Shadowring Measuring Method (ME shadowring). The global irradiance was measured by an Eppley - PSP pyranometer ; direct normal irradiance by an Eppley-NIP pyrheliometer fitted to a ST-3 sun tracking device and the diffuse irradiance by an Eppley-PSP pyranometer fitted to a ME shadowring. The validations were performed by the MBE and RMSE statistical indicators. The results showed that the numerical correction factors were appropriate to correct the shadowring diffuse irradiance.

Mathematical analysis and simulations involving chemotherapy and surgery on large human tumours under a suitable cell-kill functional response

Dosage and frequency of treatment schedules are important for successful chemotherapy. However, in this work we argue that cell-kill response and tumoral growth should not be seen as separate and therefore are essential in a mathematical cancer model. This paper presents a mathematical model for sequencing of cancer chemotherapy and surgery. Our purpose is to investigate treatments for large human tumours considering a suitable cell-kill dynamics. We use some biological and pharmacological data in a numerical approach, where drug administration occurs in cycles (periodic infusion) and surgery is performed instantaneously. Moreover, we also present an analysis of stability for a chemotherapeutic model with continuous drug administration. According to Norton & Simon [22], our results indicate that chemotherapy is less eficient in treating tumours that have reached a plateau level of growing and that a combination with surgical treatment can provide better outcomes.

Estimativas da radiação global incidente em superfícies inclinadas com base na razáo de insolação

Estimating equations of global radiation based on the sunshine duration were proposed for horizontal surface and with inclination of 12.85, 22.85 and 32.85° facing the North in Botucatu, SP, Brazil, in monthly, seasonal and annual groupings of data. Simple linear correlations were applied (for definition of the linear and angular coefficients of Angstrom-Prescott model), in a database measured in all three inclinations in different periods (22.85°: 04/1998 to 07/2001; 12.85°: 08/2011 to 02/2003; and 32.85°: 03/2003 to 12/2007) concomitant with horizontal measures and sunshine duration. The statistical performance of the model was analysed by the means absolute error (MBE), the square root of the mean square error (RMSE) and the index adjustment (d). The minimum global radiation transmissivity varied from 14.35% in August (12.85°) to 27.86% in December (32.85°) and the maximum transmissivity ranged between 62.10% and 78.90%, for June (32.85°) and December (12.85°). Increasing the angle of inclination surface increased the scattering and decreased the index of adjustment and performance. The worst results were found for application of the seasonal and annual models in the months of autumn and winter for 32.85° (RMSE below 42.93% and adjustment superior to 0.4693).

Efeitos estruturais e ópticos da incorporação de Mn em filmes nanocristalinos de 'Ga IND. 1-x Mn IND. xAs' preparados por sputtering

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Efeitos estruturais e ópticos da incorporação de Mn em filmes nanocristalinos de 'GA IND.1-x'MN IND.XN' preparados por sputtering reativo

Pós-graduação em Ciência e Tecnologia de Materiais - FC