Scaling of semivariograms and the kriging estimation of field-measured properties

Two methods were evaluated for scaling a set of semivariograms into a unified function for kriging estimation of field-measured properties. Scaling is performed using sample variances and sills of individual semivariograms as scale factors. Theoretical developments show that kriging weights are independent of the scaling factor which appears simply as a constant multiplying both sides of the kriging equations. The scaling techniques were applied to four sets of semivariograms representing spatial scales of 30 x 30 m to 600 x 900 km. Experimental semivariograms in each set successfully coalesced into a single curve by variances and sills of individual semivariograms. To evaluate the scaling techniques, kriged estimates derived from scaled semivariogram models were compared with those derived from unscaled models. Differences in kriged estimates of the order of 5% were found for the cases in which the scaling technique was not successful in coalescing the individual semivariograms, which also means that the spatial variability of these properties is different. The proposed scaling techniques enhance interpretation of semivariograms when a variety of measurements are made at the same location. They also reduce computational times for kriging estimations because kriging weights only need to be calculated for one variable. Weights remain unchanged for all other variables in the data set whose semivariograms are scaled.

Numerical simulation of ambient seismic wavefield modification caused by pore-fluid effects in an oil reservoir

We have modeled numerically the seismic response of a poroelastic inclusion with properties applicable to an oil reservoir that interacts with an ambient wavefield. The model includes wave-induced fluid flow caused by pressure differences between mesoscopic-scale (i.e., in the order of centimeters to meters) heterogeneities. We used a viscoelastic approximation on the macroscopic scale to implement the attenuation and dispersion resulting from this mesoscopic-scale theory in numerical simulations of wave propagation on the kilometer scale. This upscaling method includes finite-element modeling of wave-induced fluid flow to determine effective seismic properties of the poroelastic media, such as attenuation of P- and S-waves. The fitted, equivalent, viscoelastic behavior is implemented in finite-difference wave propagation simulations. With this two-stage process, we model numerically the quasi-poroelastic wave-propagation on the kilometer scale and study the impact of fluid properties and fluid saturation on the modeled seismic amplitudes. In particular, we addressed the question of whether poroelastic effects within an oil reservoir may be a plausible explanation for low-frequency ambient wavefield modifications observed at oil fields in recent years. Our results indicate that ambient wavefield modification is expected to occur for oil reservoirs exhibiting high attenuation. Whether or not such modifications can be detected in surface recordings, however, will depend on acquisition design and noise mitigation processing as well as site-specific conditions, such as the geologic complexity of the subsurface, the nature of the ambient wavefield, and the amount of surface noise.

Defining new criteria for selection of cell-based intestinal models using publicly available databases.

BACKGROUND: The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. RESULTS: We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. CONCLUSIONS: This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected features may allow selecting model cell lines that are more adapted and pertinent to the addressed biological question.

The situation of open access institutional repositories in Spain: 2009 report

Introduction. The DRIVER I project drew up a detailed report of European repositories based on data gathered in a survey in which Spain's participation was very low. This created a highly distorted image of the implementation of repositories in Spain. This study aims to analyse the current state of Spanish open-access institutional repositories and to describe their characteristics. Method. The data were gathered through a Web survey. The questionnaire was based on that used by DRIVER I: coverage; technical infrastructure and technical issues; institutional policies; services created; and stimulators and inhibitors for establishing, filling and maintaining their digital institutional repositories. Analysis. Data were tabulated and analysed systematically according responses obtained from the questionnaire and grouped by coverage. Results. Responses were obtained from 38 of the 104 institutions contacted, which had 29 institutional repositories. This represents 78.3% of the Spanish repositories according to the BuscaRepositorios directory. Spanish repositories contained mainly full-text materials (journal articles and doctoral theses) together with metadata. The software most used was DSpace, followed by EPrints. The metadata standard most used was Dublin Core. Spanish repositories offered more usage statistics and fewer author-oriented services than the European average. The priorities for the future development of the repositories are the need for clear policies on access to scientific production based on public funding and the need for quality control indicators. Conclusions.This is the first detailed study of Spanish institutional repositories. The key stimulants for establishing, filling and maintaining were, in order of importance, the increase of visibility and citation, the interest of decision-makers, simplicity of use and search services. On the other hand the main inhibitors identified were the absence of policies, the lack of integration with other national and international systems and the lack of awareness efforts among academia.

Potential impact of climate change on vegetation in the European Alps: a review

Based on conclusions drawn from general climatic impact assessment in mountain regions, the review synthesizes results relevant to the European Alps published mainly from 1994 onward in the fields of population genetics, ecophysiology, phenology, phytogeography, modeling, paleoecology and vegetation dynamics. Other important factors of global change interacting synergistically with climatic factors are also mentioned, such as atmospheric CO2 concentration, eutrophication, ozone or changes in land-use. Topics addressed are general species distribution and populations (persistence, acclimation, genetic variability, dispersal, fragmentation, plant/animal interaction, species richness, conservation), potential response of vegetation (ecotonal shift - area, physiography - changes in the composition, structural changes), phenology, growth and productivity, and landscape. In conclusion, the European Alps appear to have a natural inertia and thus to tolerate an increase of 1-2 K of mean air temperature as far as plant species and ecosystems are concerned in general. However, the impact of land-use is very likely to negate this buffer in many areas. For a change of the order of 3 K or more, profound changes may be expected.

Psychometric characteristics of the Spanish version of instruments to measure neck pain disability

Background: The NDI, COM and NPQ are evaluation instruments for disability due to NP. There was no Spanish version of NDI or COM for which psychometric characteristics were known. The objectives of this study were to translate and culturally adapt the Spanish version of the Neck Disability Index Questionnaire (NDI), and the Core Outcome Measure (COM), to validate its use in Spanish speaking patients with non-specific neck pain (NP), and to compare their psychometric characteristics with those of the Spanish version of the Northwick Pain Questionnaire (NPQ).Methods: Translation/re-translation of the English versions of the NDI and the COM was done blindly and independently by a multidisciplinary team. The study was done in 9 primary care Centers and 12 specialty services from 9 regions in Spain, with 221 acute, subacute and chronic patients who visited their physician for NP: 54 in the pilot phase and 167 in the validation phase. Neck pain (VAS), referred pain (VAS), disability (NDI, COM and NPQ), catastrophizing (CSQ) and quality of life (SF-12) were measured on their first visit and 14 days later. Patients' self-assessment was used as the external criterion for pain and disability. In the pilot phase, patients' understanding of each item in the NDI and COM was assessed, and on day 1 test-retest reliability was estimated by giving a second NDI and COM in which the name of the questionnaires and the order of the items had been changed.Results: Comprehensibility of NDI and COM were good. Minutes needed to fill out the questionnaires [median, (P25, P75)]: NDI. 4 (2.2, 10.0), COM: 2.1 (1.0, 4.9). Reliability: [ICC, (95%CI)]: NDI: 0.88 (0.80, 0.93). COM: 0.85 (0.75,0.91). Sensitivity to change: Effect size for patients having worsened, not changed and improved between days 1 and 15, according to the external criterion for disability: NDI: -0.24, 0.15, 0.66; NPQ: -0.14, 0.06, 0.67; COM: 0.05, 0.19, 0.92. Validity: Results of NDI, NPQ and COM were consistent with the external criterion for disability, whereas only those from NDI were consistent with the one for pain. Correlations with VAS, CSQ and SF-12 were similar for NDI and NPQ (absolute values between 0.36 and 0.50 on day 1, between 0.38 and 0.70 on day 15), and slightly lower for COM (between 0.36 and 0.48 on day 1, and between 0.33 and 0.61 on day 15). Correlation between NDI and NPQ: r = 0.84 on day 1, r = 0.91 on day 15. Correlation between COM and NPQ: r = 0.63 on day 1, r = 0.71 on day 15.Conclusion: Although most psychometric characteristics of NDI, NPQ and COM are similar, those from the latter one are worse and its use may lead to patients' evolution seeming more positive than it actually is. NDI seems to be the best instrument for measuring NP-related disability, since its results are the most consistent with patient's assessment of their own clinical status and evolution. It takes two more minutes to answer the NDI than to answer the COM, but it can be reliably filled out by the patient without assistance.

An analysis of inflation rates in the European Union using wavelets : strong evidence against unit roots

In this paper we assume inflation rates in European Union countries may in fact be fractionally integrated. Given this assumption, we obtain estimations of the order of integration by means a method based on wavelets coefficients. Finally, results obtained allow reject the unit root hypothesis on inflation rates. It means that a random shock on the rate of inflation in these countries has transitory effects that gradually diminish with the passage of time, that this, said shock hasn¿t a permanent effect on future values of inflation rates

Polarization strategies to improve the emission of a Si-based light source emitting at 1.55 um

We present a electroluminescence (EL) study of the Si-rich silicon oxide (SRSO) LEDs with and without Er3+ ions under different polarization schemes: direct current (DC) and pulsed voltage (PV). The power efficiency of the devices and their main optical limitations are presented. We show that under PV polarization scheme, the devices achieve one order of magnitude superior performance in comparison with DC. Time-resolved measurements have shown that this enhancement is met only for active layers in which annealing temperature is high enough (>1000 ◦C) for silicon nanocrystal (Si-nc) formation. Modeling of the system with rate equations has been done and excitation cross-sections for both Si-nc and Er3+ ions have been extracted.

The efficacy of a protective cream in a real-world apprentice hairdresser environment.

The object of this study was to compare the protective action of a new barrier cream (Excipial Protect, Spirig Pharma AG, Egerkingen, Switzerland) to its vehicle in the context of hand irritation of apprentice hairdressers caused by repeated shampooing and exposure to hair-care products. This was a double-blind cross-over comparing Excipial Protect (containing aluminium chlorohydrate 5% as active ingredient) against its vehicle alone. The efficacy of the creams was evaluated taking into account: (1) clinical scores by researchers, (2) biometric measurements, (3) subjective opinions of the subjects. An analysis of variance was performed considering order of application, degree of atopy, and reported number of shampoos. We observed very little difference in efficacy between the protective cream and its vehicle. The presence, however, of aluminium chlorhydrate in the protective cream was shown to have a positive effect against work-related irritation. The cosmetic qualities of the creams seemed, to the participants, to be as important as their real protective and hydrating properties, an important factor in compliance issues.

An analysis of inflation rates in the European Union using wavelets : strong evidence against unit roots

In this paper we assume inflation rates in European Union countries may in fact be fractionally integrated. Given this assumption, we obtain estimations of the order of integration by means a method based on wavelets coefficients. Finally, results obtained allow reject the unit root hypothesis on inflation rates. It means that a random shock on the rate of inflation in these countries has transitory effects that gradually diminish with the passage of time, that this, said shock hasn¿t a permanent effect on future values of inflation rates

What trees tell us: dendrochronological and statistical analysis of the data

Trees are a great bank of data, named sometimes for this reason as the "silentwitnesses" of the past. Due to annual formation of rings, which is normally influenced directly by of climate parameters (generally changes in temperature and moisture or precipitation) and other environmental factors; these changes, occurred in the past, are"written" in the tree "archives" and can be "decoded" in order to interpret what hadhappened before, mainly applied for the past climate reconstruction.Using dendrochronological methods for obtaining samples of Pinus nigra fromthe Catalonian PrePirineous region, the cores of 15 trees with total time spine of about 100 - 250 years were analyzed for the tree ring width (TRW) patterns and had quite high correlation between them (0.71 ¿ 0.84), corresponding to a common behaviour for the environmental changes in their annual growth.After different trials with raw TRW data for standardization in order to take outthe negative exponential growth curve dependency, the best method of doubledetrending (power transformation and smoothing line of 32 years) were selected for obtaining the indexes for further analysis.Analyzing the cross-correlations between obtained tree ring width indexes andclimate data, significant correlations (p<0.05) were observed in some lags, as forexample, annual precipitation in lag -1 (previous year) had negative correlation with TRW growth in the Pallars region. Significant correlation coefficients are between 0.27- 0.51 (with positive or negative signs) for many cases; as for recent (but very short period) climate data of Seu d¿Urgell meteorological station, some significant correlation coefficients were observed, of the order of 0.9.These results confirm the hypothesis of using dendrochronological data as aclimate signal for further analysis, such as reconstruction of climate in the past orprediction in the future for the same locality.

Kinetic study of neuropeptide Y (NPY) proteolysis in blood and identification of NPY3-35: a new peptide generated by plasma kallikrein.

There is little information on how neuropeptide Y (NPY) proteolysis by peptidases occurs in serum, in part because reliable techniques are lacking to distinguish different NPY immunoreactive forms and also because the factors affecting the expression of these enzymes have been poorly studied. In the present study, LC-MS/MS was used to identify and quantify NPY fragments resulting from peptidolytic cleavage of NPY(1-36) upon incubation with human serum. Kinetic studies indicated that NPY(1-36) is rapidly cleaved in serum into 3 main fragments with the following order of efficacy: NPY(3-36) &gt;&gt; NPY(3-35) &gt; NPY(2-36). Trace amounts of additional NPY forms were identified by accurate mass spectrometry. Specific inhibitors of dipeptidyl peptidase IV, kallikrein, and aminopeptidase P prevented the production of NPY(3-36), NPY(3-35), and NPY(2-36), respectively. Plasma kallikrein at physiological concentrations converted NPY(3-36) into NPY(3-35). Receptor binding assays revealed that NPY(3-35) is unable to bind to NPY Y1, Y2, and Y5 receptors; thus NPY(3-35) may represent the major metabolic clearance product of the Y2/Y5 agonist, NPY(3-36).

Molecular genetic approaches to the biology of the moss "Physcomitrella patens"

La mousse haplobiontique Physcomitrella patens est utilisée comme système génétique modèle pour l'étude du développement des plantes. Cependant, l'absence d'un protocole efficace de transformation a constitué jusqu'à présent un gros désavantage méthodologique pour le développement futur de ce système expérimental. Les résultats présentés dans le premier chapitre relatent la mise au point d'un protocole de transformation basé sur la technique de transfert direct de gènes dans des protoplastes par précipitation au PEG. Un essai d'expression transitoire de gènes a été mis au point. Ce protocole a été adapté afin de permettre l'introduction in vivo d'anticorps dans des protoplastes. Le protocole modifié permet d'introduire simultanément du DNA et des IgG dans les cellules, et nous avons démontré que ces anticorps peuvent inactiver spécifiquement le produit d'un gène co-introduit (GUS), ainsi que certaines protéines impliquées dans des processus cellulaires (tubuline). Cet essai, baptisé "essai transitoire d'immuno-inactivation in vivo", devrait être directement applicable à d'autres protoplastes végétaux, et permettre l'élaboration de nouvelles stratégies dans l'étude de processus cellulaires. Le second chapitre est consacré aux expériences de transformation de la mousse avec des gènes conférant une résistance à des antibiotiques. Nos résultats démontrent que l'intégration de gènes de résistance dans le génome de P. patens est possible, mais que cet événement est rare. Il s'agit là néanmoins de la première démonstration d'une transformation génétique réussie de cet organisme. L'introduction de gènes de résistance aux antibiotiques dans les protoplastes de P. patens génère à haute fréquence des clones résistants instables. Deux classes de clones instables ont été identifiés. La caractérisation phénotypique, génétique et moléculaire de ces clones suggère fortement que les séquences transformantes sont concaténées pour former des structures de haut poids moléculaire, et que ces structures sont efficacement répliquées et maintenues dans les cellules résistantes en tant qu'éléments génétiques extrachromosomaux. Ce type de transformation nous permet d'envisager des expériences permettant l'identification des séquences génomiques impliquées dans la replication de l'ADN de mousse. Plusieurs lignées transgéniques ont été retransformées avec des plasmides portant des séquences homologues aux séquences intégrées dans le génome, mais conférant une résistance à un autre antibiotique. Les résultats présentés dans le troisième chapitre montrent que les fréquences de transformation intégrative dans les lignées transgéniques sont 10 fois plus élevées que dans la lignée sauvage, et que cette augmentation est associée à une coségrégation des gènes de résistance dans la plupart des clones testés. Ces résultats génétiques indiquent que l'intégration de séquences d'ADN étranger dans le génome de P. patens a lieu en moyenne 10 fois plus fréquemment par recombinaison homologue que par intégration aléatoire. Ce rapport homologue/aléatoire est 10000 fois supérieur aux rapports obtenus avec d'autres plantes, et fournit l'outil indispensable à la réalisation d'expériences de génétique inverse dans cet organisme à haplophase dominante. THESIS SUMMARY The moss Physcomitrella patens is used as a model genetic system to study plant development, taking advantage of the fact that the haploid gametophyte dominates in its life cycle. But further development of this model system was hampered by the lack of a protocol allowing the genetic transformation of this plant. We have developed a transformation protocol based on PEG-mediated direct gene transfer to protoplasts. Our data demonstrate that this procedure leads to the establishment of an efficient transient gene expression assay. A slightly modified protocol has been developed allowing the in vivo introduction of antibodies in moss protoplasts. Both DNA and IgGs can be loaded simultaneously, and specific antibodies can immunodeplete the product of an expression cassette (GUS) as well as proteins involved in cellular processes (tubulins). This assay, named transient in vivo immunodepletion assay, should be applicable to other plant protoplasts, and offers new approaches to study cellular processes. Transformations have been performed with bacterial plasmids carrying antibiotic resistance expression cassette. Our data demonstrate that integrative transformation occurs, but at low frequencies. This is the first demonstration of a successful genetic transformation of mosses. Resistant unstable colonies are recovered at high frequencies following transformation, and two different classes of unstable clones have been identified. Phenotypical, genetic and molecular characterisation of these clones strongly suggests that bacterial plasmids are concatenated to form high molecular arrays which are efficiently replicated and maintained as extrachromosomal elements in the resistant cells. Replicative transformation in P. patens should allow the design of experiments aimed at the identification of genomic sequences involved in moss DNA replication. Transgenic strains have been retransformed with bacterial plasmids carrying sequences homologous to the integrated transloci, but conferring resistance to another antibiotic. Our results demonstrate an order of magnitude increase of integrative transformation frequencies in transgenic strains as compared to wild-type, associated with cosegregation of the resistance genes in most of these double resistant transgenic strains. These observations provide strong genetic evidence that gene targeting occurs about ten times more often than random integration in the genome of P. patens. Such ratio of targeted to random integration is about 10 000 times higher than previous reports of gene targeting in plants, and provides the essential requirement for the development of efficient reverse genetics in the haplodiplobiontic P. patens.

Critical behavior of a system with orientational and positional degrees of freedom: A Monte Carlo simulation study

The critical behavior of a system constituted by molecules with a preferred symmetry axis is studied by means of a Monte Carlo simulation of a simplified two-dimensional model. The system exhibits two phase transitions, associated with the vanishing of the positional order of the center of mass of the molecules and with the orientational order of the symmetry axis. The evolution of the order parameters and the specific heat is also studied. The transition associated with the positional degrees of freedom is found to change from a second-order to a first-order behavior when the two phase transitions are close enough, due to the coupling with the orientational degrees of freedom. This fact is qualitatively compared with similar results found in pure liquid crystals and liquid-crystal mixtures.

Pharmacodynamic and humoral effects of single intravenous doses of captopril in normal subjects.

The blood pressure, heart rate and humoral responses to single intravenous doses of the angiotensin converting enzyme inhibitor captopril were evaluated in 5 volunteers on a free salt intake. Each subject was given at one-week intervals a 1, 5 and 25 mg intravenous dose of captopril as well as the vehicle of captopril. The study was conducted in a single-blind fashion and the order of treatment phases was randomized. Captopril was found to inhibit the renin-angiotensin system in a dose-dependent fashion. A fall in circulating angiotensin II was observed with doses of 1 and 5 mg. Plasma angiotensin II was not detectable 15 min after the 25 mg dose. Acute inhibition of angiotensin converting enzyme with intravenous captopril had no effect on blood pressure and heart rate.