Local and global error models to improve uncertainty quantification

In groundwater applications, Monte Carlo methods are employed to model the uncertainty on geological parameters. However, their brute-force application becomes computationally prohibitive for highly detailed geological descriptions, complex physical processes, and a large number of realizations. The Distance Kernel Method (DKM) overcomes this issue by clustering the realizations in a multidimensional space based on the flow responses obtained by means of an approximate (computationally cheaper) model; then, the uncertainty is estimated from the exact responses that are computed only for one representative realization per cluster (the medoid). Usually, DKM is employed to decrease the size of the sample of realizations that are considered to estimate the uncertainty. We propose to use the information from the approximate responses for uncertainty quantification. The subset of exact solutions provided by DKM is then employed to construct an error model and correct the potential bias of the approximate model. Two error models are devised that both employ the difference between approximate and exact medoid solutions, but differ in the way medoid errors are interpolated to correct the whole set of realizations. The Local Error Model rests upon the clustering defined by DKM and can be seen as a natural way to account for intra-cluster variability; the Global Error Model employs a linear interpolation of all medoid errors regardless of the cluster to which the single realization belongs. These error models are evaluated for an idealized pollution problem in which the uncertainty of the breakthrough curve needs to be estimated. For this numerical test case, we demonstrate that the error models improve the uncertainty quantification provided by the DKM algorithm and are effective in correcting the bias of the estimate computed solely from the MsFV results. The framework presented here is not specific to the methods considered and can be applied to other combinations of approximate models and techniques to select a subset of realizations

The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.

DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.

Transcatheter aortic valve replacement for degenerative bioprosthetic surgical valves: results from the global valve-in-valve registry.

BACKGROUND: Transcatheter aortic valve-in-valve implantation is an emerging therapeutic alternative for patients with a failed surgical bioprosthesis and may obviate the need for reoperation. We evaluated the clinical results of this technique using a large, worldwide registry. METHODS AND RESULTS: The Global Valve-in-Valve Registry included 202 patients with degenerated bioprosthetic valves (aged 77.7±10.4 years; 52.5% men) from 38 cardiac centers. Bioprosthesis mode of failure was stenosis (n=85; 42%), regurgitation (n=68; 34%), or combined stenosis and regurgitation (n=49; 24%). Implanted devices included CoreValve (n=124) and Edwards SAPIEN (n=78). Procedural success was achieved in 93.1% of cases. Adverse procedural outcomes included initial device malposition in 15.3% of cases and ostial coronary obstruction in 3.5%. After the procedure, valve maximum/mean gradients were 28.4±14.1/15.9±8.6 mm Hg, and 95% of patients had ≤+1 degree of aortic regurgitation. At 30-day follow-up, all-cause mortality was 8.4%, and 84.1% of patients were at New York Heart Association functional class I/II. One-year follow-up was obtained in 87 patients, with 85.8% survival of treated patients. CONCLUSIONS: The valve-in-valve procedure is clinically effective in the vast majority of patients with degenerated bioprosthetic valves. Safety and efficacy concerns include device malposition, ostial coronary obstruction, and high gradients after the procedure.

Promoter recognition and activation by the global response regulator CbrB in Pseudomonas aeruginosa.

In Pseudomonas aeruginosa, the CbrA/CbrB two-component system is instrumental in the maintenance of the carbon-nitrogen balance and for growth on carbon sources that are energetically less favorable than the preferred dicarboxylate substrates. The CbrA/CbrB system drives the expression of the small RNA CrcZ, which antagonizes the repressing effects of the catabolite repression control protein Crc, an RNA-binding protein. Dicarboxylates appear to cause carbon catabolite repression by inhibiting the activity of the CbrA/CbrB system, resulting in reduced crcZ expression. Here we have identified a conserved palindromic nucleotide sequence that is present in upstream activating sequences (UASs) of promoters under positive control by CbrB and σ(54) RNA polymerase, especially in the UAS of the crcZ promoter. Evidence for recognition of this palindromic sequence by CbrB was obtained in vivo from mutational analysis of the crcZ promoter and in vitro from electrophoretic mobility shift assays using crcZ promoter fragments and purified CbrB protein truncated at the N terminus. Integration host factor (IHF) was required for crcZ expression. CbrB also activated the lipA (lipase) promoter, albeit less effectively, apparently by interacting with a similar but less conserved palindromic sequence in the UAS of lipA. As expected, succinate caused CbrB-dependent catabolite repression of the lipA promoter. Based on these results and previously published data, a consensus CbrB recognition sequence is proposed. This sequence has similarity to the consensus NtrC recognition sequence, which is relevant for nitrogen control.

Transpiração e crescimento foliar de clones de batata em resposta à fração de água transpirável no solo

A água é vital para as plantas. Uma redução na disponibilidade de água pode afetar a transpiração e o crescimento foliar das culturas. O objetivo deste trabalho foi determinar a resposta da transpiração e do crescimento foliar ao conteúdo de água disponível no solo, representado pela fração de água transpirável no solo (FATS), em dois clones de batata (um antigo e um recente) adaptados ao Sul do Brasil. Foram realizados três experimentos em ambiente protegido por abrigo telado em Santa Maria, RS, dois deles na primavera (cultivo de safra), com plantios em 20/08/2008 (E1) e 20/10/2008 (E2), e um experimento no outono (cultivo de safrinha), com plantio em 25/03/2009 (E3), usando-se dois clones de batata: um antigo ('Macaca') e um recente ('SMINIA793101-3'). A água disponível, representada pela FATS, a transpiração e o crescimento foliar foram medidos diariamente durante o período de imposição da deficiência hídrica. A FATS crítica que começa a alterar a transpiração, indicativo do início do fechamento estomático, foi de 0,39, 0,47 e 0,28 no clone 'Macaca' e de 0,47, 0,49 e 0,33 no clone 'SMINIA793101-3', para os experimentos E1, E2 e E3, respectivamente, enquanto o crescimento foliar começou a ser reduzido, com valor de FATS crítica maior para o clone 'Macaca', indicando que o clone 'SMINIA793101-3' é mais tolerante ao déficit hídrico no solo que o clone 'Macaca'.

Northern agriculture : constraints and responses to global climate change

Selostus: Maatalous pohjoisilla äärialueilla: ilmastolliset rajoitukset ja ilmaston muutosten vaikutukset viljelyyn

Evaluation of the susceptibility of pathogenic Candida species to fluconazole. Fluconazole Global Susceptibility Study Group.

A fluconazole 25 microg disk diffusion test was used to test 2230 consecutively isolated Candida strains from 42 different hospital laboratories in 23 countries. Ninety seven percent of 1634 Candida albicans isolates and 83.4% of 596 non-Candida albicans isolates were susceptible to fluconazole, applying the proposed breakpoints (> or = 26 mm for susceptible strains and 18-25 mm for dose-dependent susceptible strains). This is the first hospital laboratory study to evaluate a large number and wide range of sequential Candida isolates from patients with all types of hospital infections. The fluconazole disk diffusion test appears to be a low-cost, reproducible, and accurate means of assessing the in vitro susceptibility of Candida isolates.

Comportamento dos óxidos de ferro da fração argila e do fósforo adsorvido, em diferentes sistemas de colheita de cana-de-açúcar

Na agricultura, a obtenção de maiores produtividades das culturas com base no manejo sustentável do solo tem levado a uma busca gradativa do conhecimento das variáveis envolvidas nos sistemas de produção. Determinar as causas da variabilidade dos atributos passa a ser uma etapa do planejamento estratégico no setor sucroenergético. Este trabalho teve por objetivo estudar a variabilidade espacial dos óxidos de ferro da fração argila e sua relação com atributos físicos e químicos do solo, em diferentes sistemas de colheita de cana-de-açúcar na Região de Ribeirão Preto, SP. Duas parcelas de 1 ha foram delimitadas em áreas com sistema de colheitas mecanizada e manual. Foram retiradas, em cada área, amostras de solos em 126 pontos, na profundidade de 0,00-0,25 m. Os resultados das análises mineralógicas e químicas foram submetidos às análises geoestatísticas, obtendo-se a dependência espacial, os semivariogramas e os mapas de krigagem dos atributos estudados. Para analisar a correlação espacial entre os atributos estudados, foram construídos semivariogramas cruzados. A variabilidade espacial dos atributos químicos é maior em áreas com colheita de cana crua, quando comparada com áreas de colheita de cana queimada, ao contrário dos atributos mineralógicos, que apresentaram os maiores alcances na área de cana crua. Os atributos matéria orgânica, diâmetro médio do cristal da goethita apresentaram correlação espacial negativa, enquanto a argila apresentou correlação positiva com a adsorção de fósforo nos dois sistemas de colheita de cana-de-açúcar avaliados.

Use of information on the manufacture of samples for the optical characterization of multilayers through a global optimization

We present a procedure for the optical characterization of thin-film stacks from spectrophotometric data. The procedure overcomes the intrinsic limitations arising in the numerical determination of manyparameters from reflectance or transmittance spectra measurements. The key point is to use all theinformation available from the manufacturing process in a single global optimization process. The method is illustrated by a case study of solgel applications.