Compositional data analysis of Holocene sediments from the West Bengal Sundarbans, India: Geochemical proxies for grain-size variability in a delta environment

This paper is part of a special issue of Applied Geochemistry focusing on reliable applications of compositional multivariate statistical methods. This study outlines the application of compositional data analysis (CoDa) to calibration of geochemical data and multivariate statistical modelling of geochemistry and grain-size data from a set of Holocene sedimentary cores from the Ganges-Brahmaputra (G-B) delta. Over the last two decades, understanding near-continuous records of sedimentary sequences has required the use of core-scanning X-ray fluorescence (XRF) spectrometry, for both terrestrial and marine sedimentary sequences. Initial XRF data are generally unusable in ‘raw-format’, requiring data processing in order to remove instrument bias, as well as informed sequence interpretation. The applicability of these conventional calibration equations to core-scanning XRF data are further limited by the constraints posed by unknown measurement geometry and specimen homogeneity, as well as matrix effects. Log-ratio based calibration schemes have been developed and applied to clastic sedimentary sequences focusing mainly on energy dispersive-XRF (ED-XRF) core-scanning. This study has applied high resolution core-scanning XRF to Holocene sedimentary sequences from the tidal-dominated Indian Sundarbans, (Ganges-Brahmaputra delta plain). The Log-Ratio Calibration Equation (LRCE) was applied to a sub-set of core-scan and conventional ED-XRF data to quantify elemental composition. This provides a robust calibration scheme using reduced major axis regression of log-ratio transformed geochemical data. Through partial least squares (PLS) modelling of geochemical and grain-size data, it is possible to derive robust proxy information for the Sundarbans depositional environment. The application of these techniques to Holocene sedimentary data offers an improved methodological framework for unravelling Holocene sedimentation patterns.

Tooth replacement for partially dentate elders: a willingness-to-pay analysis

Objectives: The primary aim of this study was to investigate partially dentate elders' willingness-to-pay (WTP) for two different tooth replacement strategies: Removable Partial Dentures (RPDs) and, functionally orientated treatment according to the principles of the Shortened Dental Arch (SDA). The secondary aim was to measure the same patient groups' WTP for dental implant treatment.Methods: 55 patients who had completed a previous RCT comparing two tooth replacement strategies (RPDs (n=27) and SDA (n=28)) were recruited (Trial Registration no. ISRCTN26302774). Patients were asked to indicate their WTP for treatment to replace missing teeth in a number of hypothetical scenarios using the payment card method of contingency evaluation coupled to different costs. Data were collected on patients' social class, income levels and other social circumstances. A Mann-Whitney U Test was used to compare differences in WTP between the two treatment groups. To investigate predictive factors for WTP, multiple linear regression analyses were conducted.Results: The median age for the patient sample was 72.0 years (IQR: 71-75 years). Patients who had been provided with RPDs indicated that their WTP for this treatment strategy was significantly higher (€550; IQR: 500-650) than those patients who had received SDA treatment (€500; IQR: 450-550) (p=0.003). However patients provided with RPDs indicated that their WTP for SDA treatment (€650; IQR: 600-650) was also significantly higher than those patients who had actually received functionally orientated treatment (€550; IQR: 500-600) (p<0.001). The results indicated that both current income levels and previous treatment allocation were significantly correlated to WTP for both the RPD and the SDA groups. Patients in both treatment groups exhibited little WTP for dental implant treatment with a median value recorded which was half the market value for this treatment (€1000; IQR: 500-1000).Conclusions: Amongst this patient cohort previous treatment experience had a strong influence on WTP as did current income levels. Both treatment groups indicated a very strong WTP for simpler, functionally orientated care using adhesive fixed prostheses (SDA) over conventional RPDs. Clinical significance: Partially dentate older patients expressed a strong preference for functionally orientated tooth replacement as an alternative to conventional RPDs.

Partial Cooperation in Location Choice: Salop’s Model with Three Firms

We consider how three firms compete in a Salop location model and how cooperation in location choice by two of these firms affects the outcomes. We con- sider the classical case of linear transportation costs as a two-stage game in which the firms select first a location on a unit circle along which consumers are dispersed evenly, followed by the competitive selection of a price. Standard analysis restricts itself to purely competitive selection of location; instead, we focus on the situation in which two firms collectively decide about location, but price their products competitively after the location choice has been effectuated. We show that such partial coordination of location is beneficial to all firms, since it reduces the number of equilibria significantly and, thereby, the resulting coordination problem. Subsequently, we show that the case of quadratic transportation costs changes the main conclusions only marginally.

Analysis of the Market Potential of Syrian Organic Fruit and Vegetables for Exports to Germany

Syria has been a major producer and exporter of fresh fruit and vegetables (FFV) in the Arabic region. Prior to 2011, Syrian FFV were mainly exported to the neighbouring countries, the Gulf States and Northern Africa as well as to Eastern European countries. Although the EU is potentially one of the most profitable markets of high quality FFV (such as organic ones) in the world, Syrian exports of FFV to Western European countries like Germany have been small. It could be a lucrative opportunity for Syrian growers and exporters of FFV to export organic products to markets such as Germany, where national production is limited to a few months due to climatic conditions. Yet, the organic sector in Syria is comparatively young and only a very small area of FFV is certified according to EU organic regulations. Up to the author’s knowledge, little was known about Syrian farmers’ attitudes towards organic FFV production. There was also no study so far that explored and analysed the determining factors for organic FFV adoption among Syrian farmers as well as the exports of these products to the EU markets. The overarching aim of the present dissertation focused on exploring and identifying the market potential of Syrian exports of organic FFV to Germany. The dissertation was therefore concerned with three main objectives: (i) to explore if German importers and wholesalers of organic FFV see market opportunities for Syrian organic products and what requirements in terms of quality and quantity they have, (ii) to determine the obstacles Syrian producers and exporters face when exporting agricultural products to Germany, and (iii) to investigate whether Syrian farmers of FFV can imagine converting their farms to organic production as well as the underlying reasons why they do so or not. A twofold methodological approach with expert interviews and a farmer survey were used in this dissertation to address the abovementioned objectives. While expert interviews were conducted with German and Syrian wholesalers of (organic) FFV in 2011 (9 interviews each), the farmer survey was administrated with 266 Syrian farmers of FFV in the main region for the production of FFV (i.e. the coastal region) from November 2012 till May 2013. For modelling farmers’ decisions to adopt organic farming, the Theory of Planned Behaviour as theoretical framework and Partial Least Squares Structural Equation Modelling as the main method for data analysis were used in this study. The findings of this dissertation yield implications for the different stakeholders (governmental institutions and NGOs, farmers, exporters, wholesalers, etc.) who are interested in prompting the Syrian export of organic products. Based on the empirical results and a literature review, an action plan to promote Syrian production and export of organic products was developed which can help in the post-war period in Syria at improving the organic sector.

Analysis of a socio-professional group underestimated: officials of notaries in Southern Spain according to the cadastre of Ensenada.

This paper tries to show the reality of one of the trades more important for historians, the officials of the notaries. The work of these officials has allowed us to have great historical sources; we refer to the notarial documentation and documenta-tion of the City Council. They were the executive arm of the pub-lic notaries. Nevertheless, the approach to this figure seems diffi-cult, since we do not find lavish allusions of them or any of their obligations in the documentation preserved. However, we have one of the most important historical sources by middle of Eight-eenth century; this is known as the Cadastre of Ensenada. We have been able to approach this type of job through analysis and study of the Cadastre, so we know who were those men who did this huge undertaking and what was his salary for performing their tasks. In addition, we proceeded to the consultation of doc-umentation kept in local files to have a more accurate understand-ing of the real situation of those officials.

Some Inverse Problems in Analysis and Geometry

Thesis (Ph.D.)--University of Washington, 2016-08

Building monitoring during the partial implosion stage

The partial collapse of a building in Colombia caused severe damage to its structural components -- An implosion was realized to induce the collapse of 50% of the deteriorated building -- To evaluate the influence of the implosion on the remaining structure, a monitoring survey was realized using triaxial accelerometers -- Time signals associated with ambient, seismic and forced vibration were obtained -- A study of the records in the time and the frequency domain was made -- The analysis of the information allowed determining some structural properties that were useful to calibrate the analytical model of the structure

The mosaic of habitats of the Seine estuary: Insights from food-web modelling and network analysis

Ecological network analysis was applied in the Seine estuary ecosystem, northern France, integrating ecological data from the years 1996 to 2002. The Ecopath with Ecosim (EwE) approach was used to model the trophic flows in 6 spatial compartments leading to 6 distinct EwE models: the navigation channel and the two channel flanks in the estuary proper, and 3 marine habitats in the eastern Seine Bay. Each model included 12 consumer groups, 2 primary producers, and one detritus group. Ecological network analysis was performed, including a set of indices, keystoneness, and trophic spectrum analysis to describe the contribution of the 6 habitats to the Seine estuary ecosystem functioning. Results showed that the two habitats with a functioning most related to a stressed state were the northern and central navigation channels, where building works and constant maritime traffic are considered major anthropogenic stressors. The strong top-down control highlighted in the other 4 habitats was not present in the central channel, showing instead (i) a change in keystone roles in the ecosystem towards sediment-based, lower trophic levels, and (ii) a higher system omnivory. The southern channel evidenced the highest system activity (total system throughput), the higher trophic specialisation (low system omnivory), and the lowest indication of stress (low cycling and relative redundancy). Marine habitats showed higher fish biomass proportions and higher transfer efficiencies per trophic levels than the estuarine habitats, with a transition area between the two that presented intermediate ecosystem structure. The modelling of separate habitats permitted disclosing each one's response to the different pressures, based on their a priori knowledge. Network indices, although non-monotonously, responded to these differences and seem a promising operational tool to define the ecological status of transitional water ecosystems.

A Posteriori Error Analysis of hp-Version Discontinuous Galerkin Finite Element Methods for Second-Order Quasilinear Elliptic Problems

We develop the a-posteriori error analysis of hp-version interior-penalty discontinuous Galerkin finite element methods for a class of second-order quasilinear elliptic partial differential equations. Computable upper and lower bounds on the error are derived in terms of a natural (mesh-dependent) energy norm. The bounds are explicit in the local mesh size and the local degree of the approximating polynomial. The performance of the proposed estimators within an automatic hp-adaptive refinement procedure is studied through numerical experiments.

Discontinuous Galerkin Methods on hp-Anisotropic Meshes I: A Priori Error Analysis

We consider the a priori error analysis of hp-version interior penalty discontinuous Galerkin methods for second-order partial differential equations with nonnegative characteristic form under weak assumptions on the mesh design and the local finite element spaces employed. In particular, we prove a priori hp-error bounds for linear target functionals of the solution, on (possibly) anisotropic computational meshes with anisotropic tensor-product polynomial basis functions. The theoretical results are illustrated by a numerical experiment.

Transcriptome, carbohydrate, and phytohormone analysis of Petunia hybrida reveals a complex disturbance of plant functional integrity under mild chilling stress

Cultivation of chilling-tolerant ornamental crops at lower temperature could reduce the energy demands of heated greenhouses. To provide a better understanding of how sub-optimal temperatures (12 degrees C vs. 16 degrees C) affect growth of the sensitive Petunia hybrida cultivar 'SweetSunshine Williams', the transcriptome, carbohydrate metabolism, and phytohormone homeostasis were monitored in aerial plant parts over 4 weeks by use of a microarray, enzymatic assays and GC-MS/MS. The data revealed three consecutive phases of chilling response. The first days were marked by a strong accumulation of sugars, particularly in source leaves, preferential up-regulation of genes in the same tissue and down-regulation of several genes in the shoot apex, especially those involved in the abiotic stress response. The midterm phase featured a partial normalization of carbohydrate levels and gene expression. After 3 weeks of chilling exposure, a new stabilized balance was established. Reduced hexose levels in the shoot apex, reduced ratios of sugar levels between the apex and source leaves and a higher apical sucrose/hexose ratio, associated with decreased activity and expression of cell wall invertase, indicate that prolonged chilling induced sugar accumulation in source leaves at the expense of reduced sugar transport to and reduced sucrose utilization in the shoot. This was associated with reduced levels of indole-3-acetic acid and abscisic acid in the apex and high numbers of differentially, particularly up-regulated genes, especially in the source leaves, including those regulating histones, ethylene action, transcription factors, and a jasmonate-ZIM-domain protein. Transcripts of one Jumonji C domain containing protein and one expansin accumulated in source leaves throughout the chilling period. The results reveal a dynamic and complex disturbance of plant function in response to mild chilling, opening new perspectives for the comparative analysis of differently tolerant cultivars.

Discontinuous Galerkin Methods on hp-Anisotropic Meshes II: A Posteriori Error Analysis and Adaptivity

We consider the a posteriori error analysis and hp-adaptation strategies for hp-version interior penalty discontinuous Galerkin methods for second-order partial differential equations with nonnegative characteristic form on anisotropically refined computational meshes with anisotropically enriched elemental polynomial degrees. In particular, we exploit duality based hp-error estimates for linear target functionals of the solution and design and implement the corresponding adaptive algorithms to ensure reliable and efficient control of the error in the prescribed functional to within a given tolerance. This involves exploiting both local isotropic and anisotropic mesh refinement and isotropic and anisotropic polynomial degree enrichment. The superiority of the proposed algorithm in comparison with standard hp-isotropic mesh refinement algorithms and an h-anisotropic/p-isotropic adaptive procedure is illustrated by a series of numerical experiments.

Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation

Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK). TprK demonstrated remarkable variability and redundancy, intra- and interpatient, suggesting ongoing parallel adaptive diversification during human infection. Some bacterial functions (for example, flagella- and chemotaxis-associated) were systematically targeted by both inter- and intrastrain single nucleotide polymorphisms, as well as by ongoing within-patient phase variation events. Finally, patient-derived genomes possess mutations targeting a penicillin-binding protein coding gene (mrcA) that had never been reported, unveiling it as a candidate target to investigate the impact on the susceptibility to penicillin. Our findings decode the major genetic mechanisms by which T. pallidum promotes immune evasion and survival, and demonstrate the exceptional power of characterizing evolving pathogen subpopulations during human infection.

2-(4-Amino-3-methylphenyl)-5-fluorobenzothiazole is a ligand and shows species-specific partial agonism of the Aryl Hydrocarbon Receptor

2-(4-Amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203) and related compounds are a series of anti-cancer candidate pharmaceuticals (Table 1.), that have been shown to activate the AhR. We show that these compounds are high affinity ligands for the rat AhR, but a quantitative assay for their ability to induce CYP1A1 RNA in H4IIEC3 cells, a measure of activation of the AhR, showed a poor relationship between affinity for the AhR and ability to induce CYP1A1 RNA. 5F 203, an agonist with low potency, was able to antagonise the induction of CYP1A1 RNA by TCDD, while IH 445, a potent agonist, did not antagonise the induction of CYP1A1 RNA by TCDD, and Schild analysis confirmed 5F 203 to be a potent antagonist of the induction of CYP1A1 RNA by TCDD in H4IIEC3 cells. In contrast, several benzothiazoles show potent induction of CYP1A1 RNA in human MCF-7 cells, and 5F 203 is unable to detectably antagonise the induction of CYP1A1 RNA in MCF-7 cells, showing a species difference in antagonism. Evaluation of the antiproliferative activity of benzothiazoles showed that the ability to agonise the AhR correlated with growth inhibition both in H4IIEC3 cells for a variety of benzothiazoles, and between H4IIEC3 and MCF-7 cells for 5F 203, suggesting an important role of agonism of the AhR in the anti-proliferative activity of benzothiazoles.