Influence of configurational atomic order on the relative stability of bcc and close-packed structures in Cu-based alloys

We present a study of the influence of atomic order on the relative stability of the bcc and the 18R martensitic structures in a Cu2.96Al0.92Be0.12 crystal. Calorimetric measurements have shown that disorder increases the stability of the 18R phase, contrary to what happens in Cu-Zn-Al alloys for which it is the bcc phase that is stabilized by disordering the system. This different behavior has been explained in terms of a model recently reported. We have also proved that the entropy change at the martensitic transition is independent of the state of atomic order of the crystal, as predicted theoretically. Our results suggest that differences in the vibrational spectrum of the crystal due to different states of atomic order must be equal in the bcc and in the close-packed phases.

Quantification of the local heartwall motion by magnetic resonance myocardial tagging.

Sophisticated magnetic resonance tagging techniques provide powerful tools for the non-invasive assessment of the local heartwall motion towards a deeper fundamental understanding of local heart function. For the extraction of motion data from the time series of magnetic resonance tagged images and for the visualization of the local heartwall motion a new image analysis procedure has been developed. New parameters have been derived which allows quantification of the motion patterns and are highly sensitive to any changes in these patterns. The new procedure has been applied for heart motion analysis in healthy volunteers and in patient collectives with different heart diseases. The achieved results are summarized and discussed.

ANIBAL, stable isotope-based quantitative proteomics by aniline and benzoic acid labeling of amino and carboxylic groups

Identification and relative quantification of hundreds to thousands of proteins within complex biological samples have become realistic with the emergence of stable isotope labeling in combination with high throughput mass spectrometry. However, all current chemical approaches target a single amino acid functionality (most often lysine or cysteine) despite the fact that addressing two or more amino acid side chains would drastically increase quantifiable information as shown by in silico analysis in this study. Although the combination of existing approaches, e.g. ICAT with isotope-coded protein labeling, is analytically feasible, it implies high costs, and the combined application of two different chemistries (kits) may not be straightforward. Therefore, we describe here the development and validation of a new stable isotope-based quantitative proteomics approach, termed aniline benzoic acid labeling (ANIBAL), using a twin chemistry approach targeting two frequent amino acid functionalities, the carboxylic and amino groups. Two simple and inexpensive reagents, aniline and benzoic acid, in their (12)C and (13)C form with convenient mass peak spacing (6 Da) and without chromatographic discrimination or modification in fragmentation behavior, are used to modify carboxylic and amino groups at the protein level, resulting in an identical peptide bond-linked benzoyl modification for both reactions. The ANIBAL chemistry is simple and straightforward and is the first method that uses a (13)C-reagent for a general stable isotope labeling approach of carboxylic groups. In silico as well as in vitro analyses clearly revealed the increase in available quantifiable information using such a twin approach. ANIBAL was validated by means of model peptides and proteins with regard to the quality of the chemistry as well as the ionization behavior of the derivatized peptides. A milk fraction was used for dynamic range assessment of protein quantification, and a bacterial lysate was used for the evaluation of relative protein quantification in a complex sample in two different biological states

Simultaneous quantification of selective serotonin reuptake inhibitors and metabolites in human plasma by liquid chromatography-electrospray mass spectrometry for therapeutic drug monitoring.

A simple and sensitive liquid chromatography-electrospray ionization mass spectrometry method was developed for the simultaneous quantification in human plasma of all selective serotonin reuptake inhibitors (citalopram, fluoxetine, fluvoxamine, paroxetine and sertraline) and their main active metabolites (desmethyl-citalopram and norfluoxetine). A stable isotope-labeled internal standard was used for each analyte to compensate for the global method variability, including extraction and ionization variations. After sample (250μl) pre-treatment with acetonitrile (500μl) to precipitate proteins, a fast solid-phase extraction procedure was performed using mixed mode Oasis MCX 96-well plate. Chromatographic separation was achieved in less than 9.0min on a XBridge C18 column (2.1×100mm; 3.5μm) using a gradient of ammonium acetate (pH 8.1; 50mM) and acetonitrile as mobile phase at a flow rate of 0.3ml/min. The method was fully validated according to Société Française des Sciences et Techniques Pharmaceutiques protocols and the latest Food and Drug Administration guidelines. Six point calibration curves were used to cover a large concentration range of 1-500ng/ml for citalopram, desmethyl-citalopram, paroxetine and sertraline, 1-1000ng/ml for fluoxetine and fluvoxamine, and 2-1000ng/ml for norfluoxetine. Good quantitative performances were achieved in terms of trueness (84.2-109.6%), repeatability (0.9-14.6%) and intermediate precision (1.8-18.0%) in the entire assay range including the lower limit of quantification. Internal standard-normalized matrix effects were lower than 13%. The accuracy profiles (total error) were mainly included in the acceptance limits of ±30% for biological samples. The method was successfully applied for routine therapeutic drug monitoring of more than 1600 patient plasma samples over 9 months. The β-expectation tolerance intervals determined during the validation phase were coherent with the results of quality control samples analyzed during routine use. This method is therefore precise and suitable both for therapeutic drug monitoring and pharmacokinetic studies in most clinical laboratories.

Spectroscopic quantification of soil phosphorus forms by 31p-nmr after nine years of organic or mineral fertilization

Long-standing applications of mineral fertilizers or types of organic wastes such as manure can cause phosphorus (P) accumulation and changes in the accumulated P forms in the soil. The objective of this research was to evaluate the forms of P accumulated in soils treated with mineral fertilizer or different types of manure in a long-term experiment. Soil was sampled from the 0-5 cm layer of plots fertilized with five different nutrient sources for nine years: 1) control without fertilizer; 2) mineral fertilizer at recommended rates for local conditions; 3) 5 t ha-1 year-1 of moist poultry litter; 4) 60 m³ ha-1 year-1 of liquid cattle manure and 5) 40 m³ ha-1 year-1 of liquid swine manure. The 31P-NMR spectra of soil extracts detected the following P compounds: orthophosphate, pyrophosphate, inositol phosphate, glycerophosphate, and DNA. The use of organic or mineral fertilizer over nine years did not change the soil P forms but influenced their concentration. Fertilization with mineral or organic fertilizers stimulated P accumulation in inorganic forms. Highest inositol phosphate levels were observed after fertilization with any kind of manure and highest organic P concentration in glycerophosphate form in after mineral or no fertilization.

Quantification of aluminium in soil of the Solimões Formation, Acre State, Brazil

The variety of soils in the State of Acre is wide and their chemical profiles are still not fully understood. The nature of the material of origin of these soils is indicated by the high aluminium (Al) content, commonly associated with high calcium (Ca) and magnesium (Mg) contents. The study objective was to use different methods to quantify Al in soils from toposequences formed from material of a sedimentary nature originating from the Solimões Formation, in Acre, Brazil. Trenches were opened at three distinct points in the landscape: shoulder, backslope and footslope positions. Soil samples were collected for physical, chemical, mineralogical analyses. The Al content was quantified using different methods. High Al contents were found in most of these horizons, associated with high Ca and Mg levels, representing the predominant cations in the sum of exchangeable bases. The mineralogy indicates that the soils are still in a low weathering phase, with the presence of significant quantities of 2:1 minerals. Similar Al contents were determined by the methods of NaOH titration, xylenol orange spectrometry and inductively coupled plasma optical emission spectrometry. However, no consistent data were obtained by the pyrocatechol violet method. Extraction with KCl overestimated the exchangeable Al content due to its ability to extract the non-exchangeable Al present in the smectite interlayers. It was observed that high Al contents are related to the instability of the hydroxyl-Al smectite interlayers.

Evolution of mRNA expression levels of autosomal and sex-linked genes in amniotes

In addition to differences in protein-coding gene sequences, changes in expression resulting from mutations in regulatory sequences have long been hypothesized to be responsible for phenotypic differences between species. However, unlike comparison of genome sequences, few studies, generally restricted to pairwise comparisons of closely related mammalian species, have assessed between-species differences at the transcriptome level. They reported that gene expression evolves at different rates in various organs and in a pattern that is overall consistent with neutral models of evolution. In the first part of my thesis, I investigated the evolution of gene expression in therian mammals (i.e.7 placental and marsupials), based on microarray data from human, mouse and the gray short-tailed opossum (Monodelphis domestica). In addition to autosomal genes, a special focus was given to the evolution of X-linked genes. The therian X chromosome was recently shown to be younger than previously thought and to harbor a specific gene content (e.g., genes involved in brain or reproductive functions) that is thought to have been shaped by specific sex-related evolutionary forces. Sex chromosomes derive from ordinary autosomes and their differentiation led to the degeneration of the Y chromosome (in mammals) or W chromosome (in birds). Consequently, X- or Z-linked genes differ in gene dose between males and females such that the heterogametic sex has half the X/Z gene dose compared to the ancestral state. To cope with this dosage imbalance, mammals have been reported to have evolved mechanisms of dosage compensation.¦In the first project, I could first show that transcriptomes evolve at different rates in different organs. Out of the five tissues I investigated, the testis is the most rapidly evolving organ at the gene expression level while the brain has the most conserved transcriptome. Second, my analyses revealed that mammalian gene expression evolution is compatible with a neutral model, where the rates of change in gene expression levels is linked to the efficiency of purifying selection in a given lineage, which, in turn, is determined by the long-term effective population size in that lineage. Thus, the rate of DNA sequence evolution, which could be expected to determine the rate of regulatory sequence change, does not seem to be a major determinant of the rate of gene expression evolution. Thus, most gene expression changes seem to be (slightly) deleterious. Finally, X-linked genes seem to have experienced elevated rates of gene expression change during the early stage of X evolution. To further investigate the evolution of mammalian gene expression, we generated an extensive RNA-Seq gene expression dataset for nine mammalian species and a bird. The analyses of this dataset confirmed the patterns previously observed with microarrays and helped to significantly deepen our view on gene expression evolution.¦In a specific project based on these data, I sought to assess in detail patterns of evolution of dosage compensation in amniotes. My analyses revealed the absence of male to female dosage compensation in monotremes and its presence in marsupials and, in addition, confirmed patterns previously described for placental mammals and birds. I then assessed the global level of expression of X/Z chromosomes and contrasted this with its ancestral gene expression levels estimated from orthologous autosomal genes in species with non-homologous sex chromosomes. This analysis revealed a lack of up-regulation for placental mammals, the level of expression of X-linked genes being proportional to gene dose. Interestingly, the ancestral gene expression level was at least partially restored in marsupials as well as in the heterogametic sex of monotremes and birds. Finally, I investigated alternative mechanisms of dosage compensation and found that gene duplication did not seem to be a widespread mechanism to restore the ancestral gene dose. However, I could show that placental mammals have preferentially down-regulated autosomal genes interacting with X-linked genes which underwent gene expression decrease, and thus identified a novel alternative mechanism of dosage compensation.

Quantification of permanent and variable charges in reference soils of the State of Pernambuco, Brazil

The electrical charges in soil particles are divided into structural or permanent charges and variable charges. Permanent charges develop on the soil particle surface by isomorphic substitution. Variable charges arise from dissociation and association of protons (H+), protonation or deprotonation, and specific adsorption of cations and anions. The aim of this study was to quantify the permanent charges and variable charges of Reference Soils of the State of Pernambuco, Brazil. To do so, 24 subsurface profiles from different regions (nine in the Zona da Mata, eight in the Agreste, and seven in the Sertão) were sampled, representing approximately 80 % of the total area of the state. Measurements were performed using cesium chloride solution. Determination was made of the permanent charges and the charges in regard to the hydroxyl functional groups through selective ion exchange of Cs+ by Li+ and Cs+ by NH4+, respectively. All the soils analyzed exhibited variable cation exchange capacity, with proportions from 0.16 to 0.60 and an average of 0.40 when related to total cation exchange capacity.

Quantification of the least limiting water range in an oxisol using two methodological strategies

The least limiting water range (LLWR) has been used as an indicator of soil physical quality as it represents, in a single parameter, the soil physical properties directly linked to plant growth, with the exception of temperature. The usual procedure for obtaining the LLWR involves determination of the water retention curve (WRC) and the soil resistance to penetration curve (SRC) in soil samples with undisturbed structure in the laboratory. Determination of the WRC and SRC using field measurements (in situ ) is preferable, but requires appropriate instrumentation. The objective of this study was to determine the LLWR from the data collected for determination of WRC and SRC in situ using portable electronic instruments, and to compare those determinations with the ones made in the laboratory. Samples were taken from the 0.0-0.1 m layer of a Latossolo Vermelho distrófico (Oxisol). Two methods were used for quantification of the LLWR: the traditional, with measurements made in soil samples with undisturbed structure; and in situ , with measurements of water content (θ), soil water potential (Ψ), and soil resistance to penetration (SR) through the use of sensors. The in situ measurements of θ, Ψ and SR were taken over a period of four days of soil drying. At the same time, samples with undisturbed structure were collected for determination of bulk density (BD). Due to the limitations of measurement of Ψ by tensiometer, additional determinations of θ were made with a psychrometer (in the laboratory) at the Ψ of -1500 kPa. The results show that it is possible to determine the LLWR by the θ, Ψ and SR measurements using the suggested approach and instrumentation. The quality of fit of the SRC was similar in both strategies. In contrast, the θ and Ψ in situ measurements, associated with those measured with a psychrometer, produced a better WRC description. The estimates of the LLWR were similar in both methodological strategies. The quantification of LLWR in situ can be achieved in 10 % of the time required for the traditional method.

Growth decrease in Alpine whitefish: investigating the relative contribution of fishing induced selection and environmental change and its implication for conservation measures

La pression exercée par les activités humaines menace pratiquement tous les écosystèmes aquatiques du globe. Ainsi, sous l'effet de divers facteurs tels que la pollution, le réchauffement climatique ou encore la pêche industrielle, de nombreuses populations de poissons ont vu leurs effectifs chuter et divers changements morphologiques ont été observés. Dans cette étude, nous nous sommes intéressés à une menace particulière: la sélection induite par la pêche sur la croissance des poissons. En effet, la génétique des populations prédit que la soustraction régulière des individus les plus gros peut entraîner des modifications rapides de certains traits physiques comme la croissance individuelle. Cela a par ailleurs été observé dans de nombreuses populations marines ou lacustres, dont les populations de féras, bondelles et autres corégones des lacs suisses. Toutefois, malgré un nombre croissant d'études décrivant ce phénomène, peu de plans de gestion en tiennent compte, car l'importance des effets génétiques liés à la pêche est le plus souvent négligée par rapport à l'impact des changements environnementaux. Le but premier de cette étude a donc été de quantifier l'importance des facteurs génétiques et environnementaux. Dans le premier chapitre, nous avons étudié la population de palée du lac de Joux (Coregonus palaea). Nous avons déterminé les différentiels de sélection dus à la pêche, c'est-à-dire l'intensité de la sélection sur le taux de croissance, ainsi que les changements nets de croissance au cours du temps. Nous avons observé une baisse marquée de croissance et un différentiel de sélection important indiquant qu'au moins 30% de la diminution de croissance observée était due à la pression de sélection induite par la pêche. Dans le deuxième chapitre, nous avons effectué les mêmes analyses sur deux espèces proches du lac de Brienz (C. albellus et C. fatioi) et avons observé des effets similaires dont l'intensité était spécifique à chaque espèce. Dans le troisième chapitre, nous avons analysé deux autres espèces : C. palaea et C. confusus du lac de Bienne, et avons constaté que le lien entre la pression de sélection et la diminution de croissance était influencé par des facteurs environnementaux. Finalement, dans le dernier chapitre, nous avons étudié les effets potentiels de différentes modifications de la taille des mailles des filets utilisés pour la pêche à l'aide de modèles mathématiques. Nous concluons que la pêche a un effet génétique non négligeable (et donc peu réversible) sur la croissance individuelle dans les populations observée, que cet effet est lié à la compétition pour la nourriture et à la qualité de l'environnement, et que certaines modifications simples de la taille des mailles des filets de pêche pourraient nettement diminuer l'effet de sélection et ainsi ralentir, voir même renverser la diminution de croissance observée.

Quantification of human adenoviruses in European recreational waters

The presence of human adenoviruses in recreational water might cause disease in the population upon exposure. Human adenoviruses detected by PCR could also serve as indicators of the virological water quality. In order to assess the applicability of human adenoviruses to the evaluation of the faecal contamination in European bathing waters, a real-time quantitative PCR assay was developed for the quantification of human adenoviruses in 132 samples collected from 24 different recreational marine and freshwater sites in nine European countries.Selected samples presenting positive nested-PCR results for human adenoviruses were analyzed using quantitative PCR and 80 samples from a total of 132 produced quantitative results with mean values of 3.2x102 10 per 100 ml of water, human adenovirus 41 being the most prevalent serotype. Human adenoviruses were quantified in samples from all 15 surveillance laboratories. Statistical analysis showed no homogeneous linear relation between humanadenoviruses and E. coli, intestinal enterococci or somatic coliphages concentrations in the tested samples when considering all the data together. Significant correlations between human adenoviruses and at least one of the other indicators were observed only when data from individual Laboratories were considered. The quantification of human adenoviruses may provide complementary information in relation to the use of bacterial standards in the control of water quality in bathing water.

Feasibility Study for Detection and Quantification of Corrosion in Bridge Barrier Rails, RB11-012, 2013

"Technical challenges exist with infrastructure that can be addressed by nondestructive evaluation (NDE) methods, such as detecting corrosion damage to reinforcing steel that anchor concrete bridge railings to bridge road decks. Moisture and chloride ions reach the anchors along the cold joint between the rails and deck, causing corrosion that weakens the anchors and ultimately the barriers. The Center for Nondestructive Evaluation at Iowa State University has experience in development of measurement techniques and new sensors using a variety of interrogating energies. This research evaluated feasibility of three technologies — x-ray radiation, ground-penetrating radar (GPR), and magnetic flux leakage (MFL) — for detection and quantification of corrosion of embedded reinforcing steel. Controlled samples containing pristine reinforcing steel with and without epoxy and reinforcing steel with 25 percent and 50 percent section reduction were embedded in concrete at 2.5 in. deep for laboratory evaluation. Two of the techniques, GPR and MFL, were used in a limited field test on the Iowa Highway 210 Bridge over Interstate 35 in Story County. The methods provide useful and complementary information. GPR provides a rapid approach to identify reinforcing steel that has anomalous responses. MFL provides similar detection responses but could be optimized to provide more quantitative correlation to actual condition. Full implementation could use either GPR or MFL methods to identify areas of concern, followed by radiography to give a visual image of the actual condition, providing the final guidance for maintenance actions." The full 103 page report and the 2 page Tech Transfer Summary are included in this link.

Calibration of a desktop scanner and digital image analysis procedure for quantification of a root morphology

Selostus: Tasoskannerin ja digitaalisen kuva-analyysimenetelmän kalibrointi juurten morfologian kvantifioimiseksi