Quantitative Mapping of Waterways Characteristics at Bridge Sites, TR-569, 2008

Iowa state, county, and city engineering offices expend considerable effort monitoring the state’s approximately 25,000 bridges, most of which span small waterways. In fact, the need for monitoring is actually greater for bridges over small waterways because scour processes are exacerbated by the close proximity of abutments, piers, channel banks, approach embankments, and other local obstructions. The bridges are customarily inspected biennially by the county’s road department bridge inspectors. It is extremely time consuming and difficult to obtain consistent, reliable, and timely information on bridge-waterway conditions for so many bridges. Moreover, the current approaches to gather survey information is not uniform, complete, and quantitative. The methodology and associated software (DIGIMAP) developed through the present project enable a non-intrusive means to conduct fast, efficient, and accurate inspection of the waterways in the vicinity of the bridges and culverts using one technique. The technique combines algorithms image of registration and velocimetry using images acquired with conventional devices at the inspection site. The comparison of the current bridge inspection and monitoring methods with the DIGIMAP methodology enables to conclude that the new procedure assembles quantitative information on the waterway hydrodynamic and morphologic features with considerable reduced effort, time, and cost. It also improves the safety of the bridge and culvert inspections conducted during normal and extreme hydrologic events. The data and information are recorded in a digital format, enabling immediate and convenient tracking of the waterway changes over short or long time intervals.

Quantitative genetics of learning ability and resistance to stress in Drosophila melanogaster.

Even though laboratory evolution experiments have demonstrated genetic variation for learning ability, we know little about the underlying genetic architecture and genetic relationships with other ecologically relevant traits. With a full diallel cross among twelve inbred lines of Drosophila melanogaster originating from a natural population (0.75 < F < 0.93), we investigated the genetic architecture of olfactory learning ability and compared it to that for another behavioral trait (unconditional preference for odors), as well as three traits quantifying the ability to deal with environmental challenges: egg-to-adult survival and developmental rate on a low-quality food, and resistance to a bacterial pathogen. Substantial additive genetic variation was detected for each trait, highlighting their potential to evolve. Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage: learning, odorant perception, and resistance to infection. In contrast, the two traits quantifying larval tolerance to low-quality food were more strongly affected by parental effects. We found no evidence for genetic correlations between traits, suggesting that these traits could evolve at least to some degree independently of one another. Finally, inbreeding adversely affected all traits.

Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics.

Following the success of the first round table in 2001, the Swiss Proteomic Society has organized two additional specific events during its last two meetings: a proteomic application exercise in 2002 and a round table in 2003. Such events have as their main objective to bring together, around a challenging topic in mass spectrometry, two groups of specialists, those who develop and commercialize mass spectrometry equipment and software, and expert MS users for peptidomics and proteomics studies. The first round table (Geneva, 2001) entitled "Challenges in Mass Spectrometry" was supported by brief oral presentations that stressed critical questions in the field of MS development or applications (Stöcklin and Binz, Proteomics 2002, 2, 825-827). Topics such as (i) direct analysis of complex biological samples, (ii) status and perspectives for MS investigations of noncovalent peptide-ligant interactions; (iii) is it more appropriate to have complementary instruments rather than a universal equipment, (iv) standardization and improvement of the MS signals for protein identification, (v) what would be the new generation of equipment and finally (vi) how to keep hardware and software adapted to MS up-to-date and accessible to all. For the SPS'02 meeting (Lausanne, 2002), a full session alternative event "Proteomic Application Exercise" was proposed. Two different samples were prepared and sent to the different participants: 100 micro g of snake venom (a complex mixture of peptides and proteins) and 10-20 micro g of almost pure recombinant polypeptide derived from the shrimp Penaeus vannamei carrying an heterogeneous post-translational modification (PTM). Among the 15 participants that received the samples blind, eight returned results and most of them were asked to present their results emphasizing the strategy, the manpower and the instrumentation used during the congress (Binz et. al., Proteomics 2003, 3, 1562-1566). It appeared that for the snake venom extract, the quality of the results was not particularly dependant on the strategy used, as all approaches allowed Lication of identification of a certain number of protein families. The genus of the snake was identified in most cases, but the species was ambiguous. Surprisingly, the precise identification of the recombinant almost pure polypeptides appeared to be much more complicated than expected as only one group reported the full sequence. Finally the SPS'03 meeting reported here included a round table on the difficult and challenging task of "Quantification by Mass Spectrometry", a discussion sustained by four selected oral presentations on the use of stable isotopes, electrospray ionization versus matrix-assisted laser desorption/ionization approaches to quantify peptides and proteins in biological fluids, the handling of differential two-dimensional liquid chromatography tandem mass spectrometry data resulting from high throughput experiments, and the quantitative analysis of PTMs. During these three events at the SPS meetings, the impressive quality and quantity of exchanges between the developers and providers of mass spectrometry equipment and software, expert users and the audience, were a key element for the success of these fruitful events and will have definitively paved the way for future round tables and challenging exercises at SPS meetings.

Comparison between a high-resolution single-stage Orbitrap and a triple quadrupole mass spectrometer for quantitative analyses of drugs.

The capabilities of a high-resolution (HR), accurate mass spectrometer (Exactive-MS) operating in full scan MS mode was investigated for the quantitative LC/MS analysis of drugs in patients' plasma samples. A mass resolution of 50,000 (FWHM) at m/z 200 and a mass extracted window of 5 ppm around the theoretical m/z of each analyte were used to construct chromatograms for quantitation. The quantitative performance of the Exactive-MS was compared with that of a triple quadrupole mass spectrometer (TQ-MS), TSQ Quantum Discovery or Quantum Ultra, operating in the conventional selected reaction monitoring (SRM) mode. The study consisted of 17 therapeutic drugs including 8 antifungal agents (anidulafungin, caspofungin, fluconazole, itraconazole, hydroxyitraconazole posaconazole, voriconazole and voriconazole-N-oxide), 4 immunosuppressants (ciclosporine, everolimus, sirolimus and tacrolimus) and 5 protein kinase inhibitors (dasatinib, imatinib, nilotinib, sorafenib and sunitinib). The quantitative results obtained with HR-MS acquisition show comparable detection specificity, assay precision, accuracy, linearity and sensitivity to SRM acquisition. Importantly, HR-MS offers several benefits over TQ-MS technology: absence of SRM optimization, time saving when changing the analysis from one MS to another, more complete information of what is in the samples and easier troubleshooting. Our work demonstrates that U/HPLC coupled to Exactive HR-MS delivers comparable results to TQ-MS in routine quantitative drug analyses. Considering the advantages of HR-MS, these results suggest that, in the near future, there should be a shift in how routine quantitative analyses of small molecules, particularly for therapeutic drugs, are performed.

Heritability and quantitative genetic divergence of serotiny, a fire-persistence plant trait.

BACKGROUND AND AIMS: Although it is well known that fire acts as a selective pressure shaping plant phenotypes, there are no quantitative estimates of the heritability of any trait related to plant persistence under recurrent fires, such as serotiny. In this study, the heritability of serotiny in Pinus halepensis is calculated, and an evaluation is made as to whether fire has left a selection signature on the level of serotiny among populations by comparing the genetic divergence of serotiny with the expected divergence of neutral molecular markers (QST-FST comparison). METHODS: A common garden of P. halepensis was used, located in inland Spain and composed of 145 open-pollinated families from 29 provenances covering the entire natural range of P. halepensis in the Iberian Peninsula and Balearic Islands. Narrow-sense heritability (h(2)) and quantitative genetic differentiation among populations for serotiny (QST) were estimated by means of an 'animal model' fitted by Bayesian inference. In order to determine whether genetic differentiation for serotiny is the result of differential natural selection, QST estimates for serotiny were compared with FST estimates obtained from allozyme data. Finally, a test was made of whether levels of serotiny in the different provenances were related to different fire regimes, using summer rainfall as a proxy for fire regime in each provenance. KEY RESULTS: Serotiny showed a significant narrow-sense heritability (h(2)) of 0·20 (credible interval 0·09-0·40). Quantitative genetic differentiation among provenances for serotiny (QST = 0·44) was significantly higher than expected under a neutral process (FST = 0·12), suggesting adaptive differentiation. A significant negative relationship was found between the serotiny level of trees in the common garden and summer rainfall of their provenance sites. CONCLUSIONS: Serotiny is a heritable trait in P. halepensis, and selection acts on it, giving rise to contrasting serotiny levels among populations depending on the fire regime, and supporting the role of fire in generating genetic divergence for adaptive traits.

Where and how family members spend time at home? A quantitative analysis of the observational tracking on the everyday lives of Italian families

This paper examines a dataset that derives from an observational tracking, in order to analyze where and how middle-class working families spend time at home. We use an ethnographic approach to study the everyday lives of Italian dual-income middle-class families, with the aim to analyze quantitatively the use of home spaces and the types of activities of family members on weekday afternoons and evenings. The different analyses (multiple correspondence analysis, agglomerative hierarchical cluster, discriminant analysis) show how particular spaces and activities in these spaces are dominated by certain family members. We suggest a combination of qualitative and quantitative methodologies as useful tools to explore in detail the everyday lives of families, and to understand how family members use the domestic spaces. In particular, we consider relevant the use of quantitative analyses to examine ethnographic data, especially in connection with the methodological reflexivity among researchers

Quantitative genetic analysis of methylxanthines and phenolic compounds in mate progenies

The objective of this work was to determine the contents of methylxanthines, caffeine and theobromine, and phenolic compounds, chlorogenic and caffeic acids, in 51 mate progenies (half-sib families) and estimate the heritability of genetic parameters. Mate progenies were from five Brazilian municipalities: Pinhão, Ivaí, Barão de Cotegipe, Quedas do Iguaçu, and Cascavel. The progenies were grown in the Ivaí locality. The contents of the compounds were obtained by high performance liquid chromatography (HPLC). The estimation of genetic parameters by the restricted maximum likelihood (REML) and the prediction of genotypic values via best linear unbiased prediction (BLUP) were obtained by the Selegen - REML/BLUP software. Caffeine (0.248-1.663%) and theobromine (0.106-0.807%) contents were significantly different (p<0.05) depending on the region of origin, with high individual heritability (ĥ²>0.5). The two different progeny groups determined for chlorogenic (1.365-2.281%) and caffeic (0.027-0.037%) acid contents were not significantly different (p<0.05) depending on the locality of origin. Individual heritability values were low to medium for chlorogenic (ĥ²<0.4) and caffeic acid (ĥ²<0.3). The content of the compounds and the values of genetic parameters could support breeding programs for mate.

Aggregate Costs of Gender Gaps in the Labor Market: A Quantitative Estimate

[eng] This paper examines the quantitative effects of gender gaps in entrepreneurship and labor force participation on aggregate productivity and income per capita. We simulate an occupational choice model with heterogeneous agents in entrepreneurial ability, where agents choose to be workers, self-employed or employers. The model assumes that men and women have the same talent distribution, but we impose several frictions on women's opportunities and pay in the labor market. In particular, we restrict the fraction of women participating in the labor market.

Aggregate Costs of Gender Gaps in the Labor Market: A Quantitative Estimate

This paper examines the quantitative effects of gender gaps in entrepreneurship and labor force participation on aggregate productivity and income per capita. We simulate an occupational choice model with heterogeneous agents in entrepreneurial ability, where agents choose to be workers, self-employed or employers. The model assumes that men and women have the same talent distribution, but we impose several frictions on women's opportunities and pay in the labor market. In particular, we restrict the fraction of women participating in the labor market.

Aggregate Costs of Gender Gaps in the Labor Market: A Quantitative Estimate

This paper examines the quantitative effects of gender gaps in entrepreneurship and labor force participation on aggregate productivity and income per capita. We simulate an occupational choice model with heterogeneous agents in entrepreneurial ability, where agents choose to be workers, self-employed or employers. The model assumes that men and women have the same talent distribution, but we impose several frictions on women's opportunities and pay in the labor market. In particular, we restrict the fraction of women participating in the labor market.

Statistical significance of quantitative PCR.

BACKGROUND: PCR has the potential to detect and precisely quantify specific DNA sequences, but it is not yet often used as a fully quantitative method. A number of data collection and processing strategies have been described for the implementation of quantitative PCR. However, they can be experimentally cumbersome, their relative performances have not been evaluated systematically, and they often remain poorly validated statistically and/or experimentally. In this study, we evaluated the performance of known methods, and compared them with newly developed data processing strategies in terms of resolution, precision and robustness. RESULTS: Our results indicate that simple methods that do not rely on the estimation of the efficiency of the PCR amplification may provide reproducible and sensitive data, but that they do not quantify DNA with precision. Other evaluated methods based on sigmoidal or exponential curve fitting were generally of both poor resolution and precision. A statistical analysis of the parameters that influence efficiency indicated that it depends mostly on the selected amplicon and to a lesser extent on the particular biological sample analyzed. Thus, we devised various strategies based on individual or averaged efficiency values, which were used to assess the regulated expression of several genes in response to a growth factor. CONCLUSION: Overall, qPCR data analysis methods differ significantly in their performance, and this analysis identifies methods that provide DNA quantification estimates of high precision, robustness and reliability. These methods allow reliable estimations of relative expression ratio of two-fold or higher, and our analysis provides an estimation of the number of biological samples that have to be analyzed to achieve a given precision.

Développement de l'interprétation quantitative de la sismique réflexion lacustre : application de l'AVO aux sédiments quaternaires dans le lac Léman

Résumé Des développements antérieurs, au sein de l'Institut de Géophysique de Lausanne, ont permis de développer des techniques d'acquisition sismique et de réaliser l'interprétation des données sismique 2D et 3D pour étudier la géologie de la région et notamment les différentes séquences sédimentaires du Lac Léman. Pour permettre un interprétation quantitative de la sismique en déterminant des paramètres physiques des sédiments la méthode AVO (Amplitude Versus Offset) a été appliquée. Deux campagnes sismiques lacustres, 2D et 3D, ont été acquises afin de tester la méthode AVO dans le Grand Lac sur les deltas des rivières. La géométrie d'acquisition a été repensée afin de pouvoir enregistrer les données à grands déports. Les flûtes sismiques, mises bout à bout, ont permis d'atteindre des angles d'incidence d'environ 40˚ . Des récepteurs GPS spécialement développés à cet effet, et disposés le long de la flûte, ont permis, après post-traitement des données, de déterminer la position de la flûte avec précision (± 0.5 m). L'étalonnage de nos hydrophones, réalisé dans une chambre anéchoïque, a permis de connaître leur réponse en amplitude en fonction de la fréquence. Une variation maximale de 10 dB a été mis en évidence entre les capteurs des flûtes et le signal de référence. Un traitement sismique dont l'amplitude a été conservée a été appliqué sur les données du lac. L'utilisation de l'algorithme en surface en consistante a permis de corriger les variations d'amplitude des tirs du canon à air. Les sections interceptes et gradients obtenues sur les deltas de l'Aubonne et de la Dranse ont permis de produire des cross-plots. Cette représentation permet de classer les anomalies d'amplitude en fonction du type de sédiments et de leur contenu potentiel en gaz. L'un des attributs qui peut être extrait des données 3D, est l'amplitude de la réflectivité d'une interface sismique. Ceci ajoute une composante quantitative à l'interprétation géologique d'une interface. Le fond d'eau sur le delta de l'Aubonne présente des anomalies en amplitude qui caractérisent les chenaux. L'inversion de l'équation de Zoeppritz par l'algorithme de Levenberg-Marquardt a été programmée afin d'extraire les paramètres physiques des sédiments sur ce delta. Une étude statistique des résultats de l'inversion permet de simuler la variation de l'amplitude en fonction du déport. On a obtenu un modèle dont la première couche est l'eau et dont la seconde est une couche pour laquelle V P = 1461 m∕s, ρ = 1182 kg∕m3 et V S = 383 m∕s. Abstract A system to record very high resolution (VHR) seismic data on lakes in 2D and 3D was developed at the Institute of Geophysics, University of Lausanne. Several seismic surveys carried out on Lake Geneva helped us to better understand the geology of the area and to identify sedimentary sequences. However, more sophisticated analysis of the data such as the AVO (Amplitude Versus Offset) method provides means of deciphering the detailed structure of the complex Quaternary sedimentary fill of the Lake Geneva trough. To study the physical parameters we applied the AVO method at some selected places of sediments. These areas are the Aubonne and Dranse River deltas where the configurations of the strata are relatively smooth and the discontinuities between them easy to pick. A specific layout was developed to acquire large incidence angle. 2D and 3D seismic data were acquired with streamers, deployed end to end, providing incidence angle up to 40˚ . One or more GPS antennas attached to the streamer enabled us to calculate individual hydrophone positions with an accuracy of 50 cm after post-processing of the navigation data. To ensure that our system provides correct amplitude information, our streamer sensors were calibrated in an anechoic chamber using a loudspeaker as a source. Amplitude variations between the each hydrophone were of the order of 10 dB. An amplitude correction for each hydrophone was computed and applied before processing. Amplitude preserving processing was then carried out. Intercept vs. gradient cross-plots enable us to determine that both geological discontinuities (lacustrine sediments/moraine and moraine/molasse) have well defined trends. A 3D volume collected on the Aubonne river delta was processed in order ro obtain AVO attributes. Quantitative interpretation using amplitude maps were produced and amplitude maps revealed high reflectivity in channels. Inversion of the water bottom of the Zoeppritz equation using the Levenberg-Marquadt algorithm was carried out to estimate V P , V S and ρ of sediments immediately under the lake bottom. Real-data inversion gave, under the water layer, a mud layer with V P = 1461 m∕s, ρ = 1182 kg∕m3 et V S = 383 m∕s.