Effect of surface restoring on subsurface variability in a climate model during 1949–2005

Initializing the ocean for decadal predictability studies is a challenge, as it requires reconstructing the little observed subsurface trajectory of ocean variability. In this study we explore to what extent surface nudging using well-observed sea surface temperature (SST) can reconstruct the deeper ocean variations for the 1949–2005 period. An ensemble made with a nudged version of the IPSLCM5A model and compared to ocean reanalyses and reconstructed datasets. The SST is restored to observations using a physically-based relaxation coefficient, in contrast to earlier studies, which use a much larger value. The assessment is restricted to the regions where the ocean reanalyses agree, i.e. in the upper 500 m of the ocean, although this can be latitude and basin dependent. Significant reconstruction of the subsurface is achieved in specific regions, namely region of subduction in the subtropical Atlantic, below the thermocline in the equatorial Pacific and, in some cases, in the North Atlantic deep convection regions. Beyond the mean correlations, ocean integrals are used to explore the time evolution of the correlation over 20-year windows. Classical fixed depth heat content diagnostics do not exhibit any significant reconstruction between the different existing bservation-based references and can therefore not be used to assess global average time-varying correlations in the nudged simulations. Using the physically based average temperature above an isotherm (14°C) alleviates this issue in the tropics and subtropics and shows significant reconstruction of these quantities in the nudged simulations for several decades. This skill is attributed to the wind stress reconstruction in the tropics, as already demonstrated in a perfect model study using the same model. Thus, we also show here the robustness of this result in an historical and observational context.

Variability of daily winter wind speed distribution over Northern Europe during the past millennium in regional and global climate simulations

We analyse the variability of the probability distribution of daily wind speed in wintertime over Northern and Central Europe in a series of global and regional climate simulations covering the last centuries, and in reanalysis products covering approximately the last 60 years. The focus of the study lies on identifying the link of the variations in the wind speed distribution to the regional near-surface temperature, to the meridional temperature gradient and to the North Atlantic Oscillation. Our main result is that the link between the daily wind distribution and the regional climate drivers is strongly model dependent. The global models tend to behave similarly, although they show some discrepancies. The two regional models also tend to behave similarly to each other, but surprisingly the results derived from each regional model strongly deviates from the results derived from its driving global model. In addition, considering multi-centennial timescales, we find in two global simulations a long-term tendency for the probability distribution of daily wind speed to widen through the last centuries. The cause for this widening is likely the effect of the deforestation prescribed in these simulations. We conclude that no clear systematic relationship between the mean temperature, the temperature gradient and/or the North Atlantic Oscillation, with the daily wind speed statistics can be inferred from these simulations. The understand- ing of past and future changes in the distribution of wind speeds, and thus of wind speed extremes, will require a detailed analysis of the representation of the interaction between large-scale and small-scale dynamics.

Is there any imprint of the wind variability on the Atlantic Water circulation within the Arctic Basin?

The Atlantic Water (AW) layer in the Arctic Basin is isolated from the atmosphere by the overlaying surface layer, yet observations have revealed that the velocities in this layer exhibit significant variations. Here analysis of a global ocean/sea ice model hindcast, complemented by experiments performed with an idealized process model, is used to investigate what controls the variability of AW circulation, with a focus on the role of wind forcing. The AW circulation carries the imprint of wind variations, both remotely over the Nordic and Barents Seas where they force the AW inflow variability, and locally over the Arctic Basin through the forcing of the wind-driven Beaufort Gyre, which modulates and transfers the wind variability to the AW layer. The strong interplay between the circulation within the surface and AW layers suggests that both layers must be considered to understand variability in either.

Temporal and spatial variability of fin whale's (Balaenoptera physalus) distribution in the Pelagos Sanctuary: Northwestern Mediterranean Sea

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 20 de Março de 2014, Universidade dos Açores.

Contrasting Genomic Variability between Clones from Field Isolates and Laboratory Populations of Schistosoma mansoni

The extent of genomic variability of clones of Schistosoma mansoni obtained from field isolates was compared with that of strains that have been laboratory maintained. Analysis was undertaken using randomly amplified polymorphic dNAs (RAPDs) generated with three primers. Phenograms showing the similarity among the clones were constructed. The data showed that while the laboratory strain is highly homogeneous the clones derived from the field populations were highly variable with 43% of RAPDs exhibiting polymorphisms among 23 clones. Clones isolated from the same infected individual were always more closely grouped than clones from different individuals. The data clearly demonstrated that earlier analyses of the genomic variability in S. mansoni have underestimated this phenomenon due to the failure to examine field isolates

VARIABILITY OF PHENOTYPIC, PROTEOMIC AND TRANSCRIPTOMIC EXPRESSION OF STAPHYLOCOCCUS AUREUS SURFACE ADHESINS

Staphylococcus aureus is a highly successful pathogen responsible of a wide variety of diseases, from minor skin infection to life-threatening sepsis or infective endocarditis, as well as food poisoning and toxic shock syndrome. This heterogeneity of infections and the ability of S. aureus to develop antibiotic-resistance to virtually any available drugs reflect its extraordinary capacity to adapt and survive in a great variety of environments. The pathogenesis of S. aureus infection involves a wide range of cell wall-associated adhesins and extracellular toxins that promote host colonization and invasion. In addition, S. aureus is extremely well equipped with regulatory systems that sense environmental conditions and respond by fine tuning the expression of metabolic and virulence determinants. Surface adhesins referred to MSCRAMMs - for Microbial Surface Component Recognizing Adherence Matrix Molecules - mediate binding to the host extracellular matrix or serum components, including fibrinogen, fibronectin, collagen and elastin, and promote tissue colonization and invasion. Major MSCRAMMs include a family of surface-attached proteins covalently bound to the cell wall peptidoglycan via a conserved LPXTG motif. Genomic analyses indicate that S. aureus contain up to 22 LPXTG surface proteins, which could potentially act individually or in synergy to promote infection. In the first part of this study we determined the range of adherence phenotypes to fibrinogen and fibronectin among 30 carriage isolates of S. aureus and compared it to the adherence phenotypes of 30 infective endocarditis and 30 blood culture isolates. Overall there were great variations in in vitro adherence, but no differences were observed between carriage and infection strains. We further determined the relation between in vitro adherence and in vivo infectivity in a rat model of experimental endocarditis, using 4 isolates that displayed either extremely low or high adherence phenotypes. Unexpectedly, no differences were observed between the in vivo infectivity of isolates that were poorly and highly adherent in vitro. We concluded that the natural variability of in vitro adherence to fibrinogen and fibronectin did not correlate with in vivo infectivity, and thus that pathogenic differences between various strains might only be expressed in in vivo conditions, but not in vitro. Therefore, considering the importance of adhesins expression for infection, direct measurement of those adhesins present on the bacterial surface were made by proteomic approach. 5 In the second series of experiments we assessed the physical presence of the LPXTG species at the staphylococcal surface, as measured at various time points during growth in different culture media. S. aureus Newman was grown in either tryptic soy broth (TSB) or in Roswell Park Memorial Institute (RPMI) culture medium, and samples were removed from early exponential growth phase to late stationary phase. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa) and clumping factor A (ClfA). Peptides of surface proteins were recovered by "trypsin-shaving" of live bacteria, and semi-quantitative proteomic analysis was performed by tandem liquid-chromatography and mass-spectrometry (LC-MS). We also determined in parallel the mRNA expression by microarrays analysis, as well as the phenotypic adherence of the bacteria to fibrinogen in vitro. The surface proteome was highly complex and contained numerous proteins theoretically not belonging to the bacterial envelope, including ribosomal proteins and metabolic enzymes. Sixteen of the 21 known LPXTG species were detected, but were differentially expressed. As expected, 9 known agr-regulated proteins (e.g. including Spa, FnBPA, ClfA, IsdA, IsdB, SasH, SasD, SasG and FmtB) increased up to the late exponential growth phase, and were abrogated in agr-negative mutants. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr negative mutant, while all other LPXTG proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in in vitro fibrinogen adherence tests during late growth (24h), whereas it remained poorly detected by proteomics. Differential expression was also detected in iron-rich TSB versus iron-poor RPMI. Proteins from the iron-regulated surface determinant (isd) system, including IsdA, IsdB and IsdH were barely expressed in iron-rich TSB, whereas they increased their expression by >10 time in iron-poor RPMI. We conclude that semi-quantitative proteomic analysis of specific protein species is feasible in S. aureus and that proteomic, transcriptomic and adherence phenotypes demonstrated differential profiles in S. aureus. Furthermore, peptide signatures released by trypsin shaving suggested differential protein domain exposures in various environments, which might be relevant for antiadhesins vaccines. A comprehensive understanding of the S. aureus physiology should integrate all these approaches.

Variability of apparently homogeneous soilscapes in São Paulo state, Brazil: I. spatial analysis

The spatial variability of strongly weathered soils under sugarcane and soybean/wheat rotation was quantitatively assessed on 33 fields in two regions in São Paulo State, Brazil: Araras (15 fields with sugarcane) and Assis (11 fields with sugarcane and seven fields with soybean/wheat rotation). Statistical methods used were: nested analysis of variance (for 11 fields), semivariance analysis and analysis of variance within and between fields. Spatial levels from 50 m to several km were analyzed. Results are discussed with reference to a previously published study carried out in the surroundings of Passo Fundo (RS). Similar variability patterns were found for clay content, organic C content and cation exchange capacity. The fields studied are quite homogeneous with respect to these relatively stable soil characteristics. Spatial variability of other characteristics (resin extractable P, pH, base- and Al-saturation and also soil colour), varies with region and, or land use management. Soil management for sugarcane seems to have induced modifications to greater depths than for soybean/wheat rotation. Surface layers of soils under soybean/wheat present relatively little variation, apparently as a result of very intensive soil management. The major part of within-field variation occurs at short distances (< 50 m) in all study areas. Hence, little extra information would be gained by increasing sampling density from, say, 1/km² to 1/50 m². For many purposes, the soils in the study regions can be mapped with the same observation density, but residual variance will not be the same in all areas. Bulk sampling may help to reveal spatial patterns between 50 and 1.000 m.

Variability of apparently homogeneous soilscapes in São Paulo state, Brazil: II. quality of soil maps

The quality of semi-detailed (scale 1:100.000) soil maps and the utility of a taxonomically based legend were assessed by studying 33 apparently homogeneous fields with strongly weathered soils in two regions in São Paulo State: Araras and Assis. An independent data set of 395 auger sites was used to determine purity of soil mapping units and analysis of variance within and between mapping units and soil classification units. Twenty three soil profiles were studied in detail. The studied soil maps have a high purity for some legend criteria, such as B horizon type (> 90%) and soil texture class (> 80%). The purity for the "trophic character" (eutrophic, dystrophic, allic) was only 55% in Assis. It was 88% in Araras, where many soil units had been mapped as associations. In both regions, the base status of clay-textured soils was generally better than suggested by the maps. Analysis of variance showed that mapping was successful for "durable" soil characteristics such as clay content (> 80% of variance explained) and cation exchange capacity (≥ 50% of variance explained) of 0-20 and 60-80 cm layers. For soil characteristics that are easily modified by management, such as base saturation of the 0-20 cm layer, the maps had explained very little (< 15%) of the total variance in the study areas. Intermediate results were obtained for base saturation of the 60-80 cm layer (56% in Assis; 42% in Araras). Variance explained by taxonomic groupings that formed the basis for the legend of the soil maps was similar to, often even smaller than, variance explained by mapping units. The conclusion is that map boundaries have been very carefully located, but descriptions of mapping units could be improved. In future mappings, this could possibly be done at low cost by (a) bulk sampling to remove short range variation and enhance visualization of spatial patterns at distances > 100 m; (b) taking advantage of correlations between easily measured soil characteristics and chemical soil properties and, (c) unbending the link between legend criteria and a taxonomic system. The maps are well suited to obtain an impression of land suitability for high-input farming. Additional field work and data on former land use/management are necessary for the evaluation of chemical properties of surface horizons.

Temporal variability of soil water content under different surface conditions in the semiarid region of the Pernambuco state

Rainfall in the semiarid region of Pernambuco is characterized by irregular distribution in time and space, which significantly hinders the rainfed agriculture in the region. This work aims to evaluate the temporal profile of soil moisture in the semiarid region of the Pernambuco State (Brazil) and the effect of different soil surface conditions on soil water content variation and the yield of rainfed beans. To monitor soil water content, five plots 4.5 m wide by 11 m long were installed in a Yellow Argisol (Ultisol). The following treatments were adopted in the experimental plots: natural vegetation, bean intercropped with cactus, beans planted down the slope, beans planted along contour lines with mulch and rock barriers, and bare soil. In each plot, eight PVC access tubes were installed for monitoring the soil water content profile at depths of 0.20 and 0.40 m using a neutron probe device. The surface condition significantly influenced the soil water content variation, both in the dry and rainy seasons. The use of mulch, associated with rock barriers, provided higher soil water content levels than the other treatments and increased the rainfed beans production.

The data treatment dependent variability of U-Pb zircon ages obtained using mono-collector, sector field, laser ablation ICP-MS

U-Pb dating of zircons by laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) is a widely used analytical technique in Earth Sciences. For U-Pb ages below 1 billion years (1 Ga), Pb-206/U-238 dates are usually used, showing the least bias by external parameters such as the presence of initial lead and its isotopic composition in the analysed mineral. Precision and accuracy of the Pb/U ratio are thus of highest importance in LA-ICPMS geochronology. We consider the evaluation of the statistical distribution of the sweep intensities based on goodness-of-fit tests in order to find a model probability distribution fitting the data to apply an appropriate formulation for the standard deviation. We then discuss three main methods to calculate the Pb/U intensity ratio and its uncertainty in the LA-ICPMS: (1) ratio-of-the-mean intensities method, (2) mean-of-the-intensity-ratios method and (3) intercept method. These methods apply different functions to the same raw intensity vs. time data to calculate the mean Pb/U intensity ratio. Thus, the calculated intensity ratio and its uncertainty depend on the method applied. We demonstrate that the accuracy and, conditionally, the precision of the ratio-of-the-mean intensities method are invariant to the intensity fluctuations and averaging related to the dwell time selection and off-line data transformation (averaging of several sweeps); we present a statistical approach how to calculate the uncertainty of this method for transient signals. We also show that the accuracy of methods (2) and (3) is influenced by the intensity fluctuations and averaging, and the extent of this influence can amount to tens of percentage points; we show that the uncertainty of these methods also depends on how the signal is averaged. Each of the above methods imposes requirements to the instrumentation. The ratio-of-the-mean intensities method is sufficiently accurate provided the laser induced fractionation between the beginning and the end of the signal is kept low and linear. We show, based on a comprehensive series of analyses with different ablation pit sizes, energy densities and repetition rates for a 193 nm ns-ablation system that such a fractionation behaviour requires using a low ablation speed (low energy density and low repetition rate). Overall, we conclude that the ratio-of-the-mean intensities method combined with low sampling rates is the most mathematically accurate among the existing data treatment methods for U-Pb zircon dating by sensitive sector field ICPMS.

A model of the wind direction signature in the Stokes emission vector from the ocean surface at microwave frequencies

This paper presents a model of the Stokes emission vector from the ocean surface. The ocean surface is described as an ensemble of facets with Cox and Munk's (1954) Gram-Charlier slope distribution. The study discusses the impact of different up-wind and cross-wind rms slopes, skewness, peakedness, foam cover models and atmospheric effects on the azimuthal variation of the Stokes vector, as well as the limitations of the model. Simulation results compare favorably, both in mean value and azimuthal dependence, with SSM/I data at 53° incidence angle and with JPL's WINDRAD measurements at incidence angles from 30° to 65°, and at wind speeds from 2.5 to 11 m/s.

Spatial variability of apparent electrical conductivity and soil properties in a coffee production field

Precision agriculture based on the physical and chemical properties of soil requires dense sampling to determine the spatial variability of these properties. This dense sampling is often expensive and time-consuming. One technique used to reduce sample numbers involves defining management zones based on information collected in the field. Some researchers have demonstrated the importance of soil electrical variables in defining management zones. The objective of this study was to evaluate the relationship between the spatial variability of the apparent electrical conductivity and the soil properties in the coffee production of mountain regions. Spatial variability maps were generated using a geostatistical method. Based on the spatial variability results, a correlation analysis, using bivariate Moran's index, was done to evaluate the relationship between the apparent electrical conductivity and soil properties. The maps of potassium (K) and remaining phosphorus (P-rem) were the closest to the spatial variability pattern of the apparent electrical conductivity.

Phytosociological variability of weeds in soybean field

Understanding spatial distribution of weeds in the crop enables to perform localized herbicide applications, increasing the technical and economic efficiency of operations and reducing environmental impacts. This work aimed to characterize the spatial and phytosociological variability of weeds occurring in soybean commercial field. It was conducted in an agricultural area located at the municipality of Boa Vista das Missões - RS, during the 2010/2011 harvest season. The area, that had been managed under no-tillage with soybean monoculture (summer) for five years, was divided in regular squares of 50 x 50 m (0.25 ha), totalizing 356 points. For species identification, 0.5 x 0.5 m sample squares were used. During the survey, 1,739 individuals were identified, distributed in 19 species of 13 families. The weed species Cardiospermum halicacabum, Digitaria horizontalis, Urochloa plantaginea and Raphanus raphanistrum showed the highest population variation in the area; however, only C. halicacabum, U. plantaginea and R. raphanistrum stood out based on the Importance Index Value (IVI). Localized management strategies considering the spatial variability of weed species placed in the Magnoliopsidas and Liliopsidas group show a high potential for use in soybean crop. The results show that the sampling method through regular grid was capable of characterizing the occurrence, population density and spatial variability of weed species in soybean crop.

Uniform decrease of alpha-global field power induced by intermittent photic stimulation of healthy subjects

Nineteen-channel EEGs were recorded from the scalp surface of 30 healthy subjects (16 males and 14 females, mean age: 34 years, SD: 11.7 years) at rest and under trains of intermittent photic stimulation (IPS) at rates of 5, 10 and 20 Hz. Digitalized data were submitted to spectral analysis with fast fourier transformation providing the basis for the computation of global field power (GFP). For quantification, GFP values in the frequency ranges of 5, 10 and 20 Hz at rest were divided by the corresponding data obtained under IPS. All subjects showed a photic driving effect at each rate of stimulation. GFP data were normally distributed, whereas ratios from photic driving effect data showed no uniform behavior due to high interindividual variability. Suppression of alpha-power after IPS with 10 Hz was observed in about 70% of the volunteers. In contrast, ratios of alpha-power were unequivocal in all subjects: IPS at 20 Hz always led to a suppression of alpha-power. Dividing alpha-GFP with 20-Hz IPS by alpha-GFP at rest (R = alpha-GFP IPS/alpha-GFPrest) thus resulted in ratios lower than 1. We conclude that ratios from GFP data with 20-Hz IPS may provide a suitable paradigm for further investigations.

Spatial and Temporal Variability of some Meteorological Parameters over Tropical Indian Ocean

The objective of the present study is to understand the spatial and temporal variability of sea surface temperature(SST), precipitable water, zonal and meridional components of wind stress over the tropical Indian Ocean to understand the different scales of variability of these features of Indian Ocean. Empirical Orthogonal Function (EOF) and wavelet analysis techniques are utilized to understand the standing oscillations and multi scale oscillations respectively. The study has been carried out over Indian Ocean and South Indian Ocean. For the present study, NCEP/NCAR(National Center for Environmental Prediction National Center for Atmospheric Research) reanalyzed daily fields of sea surface temperature, zonal and meridional surface wind components and precipitable water amount during 1960-1998 are used. The principle of EOF analysis and the methodology used for the analysis of spatial and temporal variance modes.