Evaluation of fluid transport processes in dental enamel. Methods to assess the relevance of enamel permeability in caries prevention and etching treatments.

This thesis evaluated in vivo and in vitro enamel permeability in different physiological and clinical conditions by means of SEM inspection of replicas of enamel surface obtained from polyvinyl siloxane impressions subsequently later cast in polyether impression ma-terial. This technique, not invasive and risk-free, allows the evaluation of fluid outflow from enamel surface and is able to detect the presence of small quantities of fluid, visu-alized as droplets. Fluid outflow on enamel surface represents enamel permeability. This property has a paramount importance in enamel physiolgy and pathology although its ef-fective role in adhesion, caries pathogenesis and prevention today is still not fully under-stood. The aim of the studies proposed was to evaluate enamel permeability changes in differ-ent conditions and to correlate the findings with the actual knowledge about enamel physiology, caries pathogenesis, fluoride and etchinhg treatments. To obtain confirmed data the replica technique has been supported by others specific techniques such as Ra-man and IR spectroscopy and EDX analysis. The first study carried out visualized fluid movement through dental enamel in vivo con-firmed that enamel is a permeable substrate and demonstrated that age and enamel per-meability are closely related. Examined samples from subjects of different ages showed a decreasing number and size of droplets with increasing age: freshly erupted permanent teeth showed many droplets covering the entire enamel surface. Droplets in permanent teeth were prominent along enamel perikymata. These results obtained through SEM inspection of replicas allowed innovative remarks in enamel physiology. An analogous testing has been developed for evaluation of enamel permeability in primary enamel. The results of this second study showed that primary enamel revealed a substantive permeability with droplets covering the entire enamel sur-face without any specific localization accordingly with histological features, without changes during aging signs of post-eruptive maturation. These results confirmed clinical data that showed a higher caries susceptibility for primary enamel and suggested a strong relationship between this one and enamel permeability. Topical fluoride application represents the gold standard for caries prevention although the mechanism of cariostatic effect of fluoride still needs to be clarified. The effects of topical fluoride application on enamel permeability were evaluated. Particularly two dif-ferent treatments (NaF and APF), with different pH, were examined. The major product of topical fluoride application was the deposition of CaF2-like globules. Replicas inspec-tion before and after both treatments at different times intervals and after specific addi-tional clinical interventions showed that such globule formed in vivo could be removed by professional toothbrushing, sonically and chemically by KOH. The results obtained in relation to enamel permeability showed that fluoride treatments temporarily reduced enamel water permeability when CaF2-like globules were removed. The in vivo perma-nence of decreased enamel permeability after CaF2 globules removal has been demon-strated for 1 h for NaF treated teeth and for at least 7 days for APF treated teeth. Important clinical consideration moved from these results. In fact the caries-preventing action of fluoride application may be due, in part, to its ability to decrease enamel water permeability and CaF2 like-globules seem to be indirectly involved in enamel protection over time maintaining low permeability. Others results obtained by metallographic microscope and SEM/EDX analyses of or-thodontic resins fluoride releasing and not demonstrated the relevance of topical fluo-ride application in decreasing the demineralization marks and modifying the chemical composition of the enamel in the treated area. These data obtained in both the experiments confirmed the efficacy of fluoride in caries prevention and contribute to clarify its mechanism of action. Adhesive dentistry is the gold standard for caries treatment and tooth rehabilitation and is founded on important chemical and physical principles involving both enamel and dentine substrates. Particularly acid etching of dental enamel enamel has usually employed in bonding pro-cedures increasing microscopic roughness. Different acids have been tested in the litera-ture suggesting several etching procedures. The acid-induced structural transformations in enamel after different etching treatments by means of Raman and IR spectroscopy analysis were evaluated and these findings were correlated with enamel permeability. Conventional etching with 37% phosphoric acid gel (H3PO4) for 30 s and etching with 15 % HCl for 120 s were investigated. Raman and IR spectroscopy showed that the treatment with both hydrochloric and phosphoric acids induced a decrease in the carbonate content of the enamel apatite. At the same time, both acids induced the formation of HPO42- ions. After H3PO4 treatment the bands due to the organic component of enamel decreased in intensity, while in-creased after HCl treatment. Replicas of H3PO4 treated enamel showed a strongly reduced permeability while replicas of HCl 15% treated samples showed a maintained permeability. A decrease of the enamel organic component, as resulted after H3PO4 treatment, involves a decrease in enamel permeability, while the increase of the organic matter (achieved by HCl treat-ment) still maintains enamel permeability. These results suggested a correlation between the amount of the organic matter, enamel permeability and caries. The results of the different studies carried out in this thesis contributed to clarify and improve the knowledge about enamel properties with important rebounds in theoretical and clinical aspects of Dentistry.

Coarse-graining methods and polymer dynamics

This thesis studies molecular dynamics simulations on two levels of resolution: the detailed level of atomistic simulations, where the motion of explicit atoms in a many-particle system is considered, and the coarse-grained level, where the motion of superatoms composed of up to 10 atoms is modeled. While atomistic models are capable of describing material specific effects on small scales, the time and length scales they can cover are limited due to their computational costs. Polymer systems are typically characterized by effects on a broad range of length and time scales. Therefore it is often impossible to atomistically simulate processes, which determine macroscopic properties in polymer systems. Coarse-grained (CG) simulations extend the range of accessible time and length scales by three to four orders of magnitude. However, no standardized coarse-graining procedure has been established yet. Following the ideas of structure-based coarse-graining, a coarse-grained model for polystyrene is presented. Structure-based methods parameterize CG models to reproduce static properties of atomistic melts such as radial distribution functions between superatoms or other probability distributions for coarse-grained degrees of freedom. Two enhancements of the coarse-graining methodology are suggested. Correlations between local degrees of freedom are implicitly taken into account by additional potentials acting between neighboring superatoms in the polymer chain. This improves the reproduction of local chain conformations and allows the study of different tacticities of polystyrene. It also gives better control of the chain stiffness, which agrees perfectly with the atomistic model, and leads to a reproduction of experimental results for overall chain dimensions, such as the characteristic ratio, for all different tacticities. The second new aspect is the computationally cheap development of nonbonded CG potentials based on the sampling of pairs of oligomers in vacuum. Static properties of polymer melts are obtained as predictions of the CG model in contrast to other structure-based CG models, which are iteratively refined to reproduce reference melt structures. The dynamics of simulations at the two levels of resolution are compared. The time scales of dynamical processes in atomistic and coarse-grained simulations can be connected by a time scaling factor, which depends on several specific system properties as molecular weight, density, temperature, and other components in mixtures. In this thesis the influence of molecular weight in systems of oligomers and the situation in two-component mixtures is studied. For a system of small additives in a melt of long polymer chains the temperature dependence of the additive diffusion is predicted and compared to experiments.

Methods and strategies to identify the mode of action of phytoactive compounds

Small molecules affecting biological processes in plants are widely used in agricultural practice as herbicides or plant growth regulators and in basic plant sciences as probes to study the physiology of plants. Most of the compounds were identified in large screens by the agrochemical industry, as phytoactive natural products and more recently, novel phytoactive compounds originated from academic research by chemical screens performed to induce specific phenotypes of interest. The aim of the present PhD thesis is to evaluate different approaches used for the identification of the primary mode of action (MoA) of a phytoactive compound. Based on the methodologies used for MoA identification, three approaches are discerned: a phenotyping approach, an approach based on a genetic screen and a biochemical screening approach.rnFour scientific publications resulting from my work are presented as examples of how a phenotyping approach can successfully be applied to describe the plant MoA of different compounds in detail.rnI. A subgroup of cyanoacrylates has been discovered as plant growth inhibitors. A set of bioassays indicated a specific effect on cell division. Cytological investigations of the cell division process in plant cell cultures, studies of microtubule assembly with green fluorescent protein marker lines in vivo and cross resistant studies with Eleusine indica plants harbouring a mutation in alpha-tubulin, led to the description of alpha-tubulin as a target site of cyanoacrylates (Tresch et al., 2005).rnII. The MoA of the herbicide flamprop-m-methyl was not known so far. The studies described in Tresch et al. (2008) indicate a primary effect on cell division. Detailed studies unravelled a specific effect on mitotic microtubule figures, causing a block in cell division. In contrast to other inhibitors of microtubule rearrangement such as dinitroanilines, flamprop-m-methyl did not influence microtubule assembly in vitro. An influence of flamprop-m-methyl on a target within the cytoskeleton signalling network could be proposed (Tresch et al., 2008).rnIII. The herbicide endothall is a protein phosphatase inhibitor structurally related to the natural product cantharidin. Bioassay studies indicated a dominant effect on dark-growing cells that was unrelated to effects observed in the light. Cytological characterisation of the microtubule cytoskeleton in corn tissue and heterotrophic tobacco cells showed a specific effect of endothall on mitotic spindle formation and ultrastructure of the nucleus in combination with a decrease of the proliferation index. The observed effects are similar to those of other protein phosphatase inhibitors such as cantharidin and the structurally different okadaic acid. Additionally, the observed effects show similarities to knock-out lines of the TON1 pathway, a protein phosphatase-regulated signalling pathway. The data presented in Tresch et al. (2011) associate endothall’s known in vitro inhibition of protein phosphatases with in vivo-effects and suggest an interaction between endothall and the TON1 pathway.rnIV. Mefluidide as a plant growth regulator induces growth retardation and a specific phenotype indicating an inhibition of fatty acid biosynthesis. A test of the cuticle functionality suggested a defect in the biosynthesis of very-long-chain fatty acids (VLCFA) or waxes. Metabolic profiling studies showed similarities with different groups of VLCFA synthesis inhibitors. Detailed analyses of VLCFA composition in tissues of duckweed (Lemna paucicostata) indicated a specific inhibition of the known herbicide target 3 ketoacyl-CoA synthase (KCS). Inhibitor studies using a yeast expression system established for plant KCS proteins verified the potency of mefluidide as an inhibitor of plant KCS enzymes. It could be shown that the strength of inhibition varied for different KCS homologues. The Arabidopsis Cer6 protein, which induces a plant growth phenotype similar to mefluidide when knocked out, was one of the most sensitive KCS enzymes (Tresch et al., 2012).rnThe findings of my own work were combined with other publications reporting a successful identification of the MoA and primary target proteins of different compounds or compound classes.rnA revised three-tier approach for the MoA identification of phytoactive compounds is proposed. The approach consists of a 1st level aiming to address compound stability, uniformity of effects in different species, general cytotoxicity and the effect on common processes like transcription and translation. Based on these findings advanced studies can be defined to start the 2nd level of MoA characterisation, either with further phenotypic characterisation, starting a genetic screen or establishing a biochemical screen. At the 3rd level, enzyme assays or protein affinity studies should show the activity of the compound on the hypothesized target and should associate the in vitro effects with the in vivo profile of the compound.

New methods can extend the use of minimal important difference units in meta-analyses of continuous outcome measures

For continuous outcomes measured using instruments with an established minimally important difference (MID), pooled estimates can be usefully reported in MID units. Approaches suggested thus far omit studies that used instruments without an established MID. We describe an approach that addresses this limitation.

STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

Methods of Determining Porosity and Spatter Losses of Arc Welds

The original objective of this project was to determine the effect of varying current intensity and electrode coating composition upon the spatter losses and porosity of arc welds made by alternating current. This subject was suggested by the Welding Research Council of the Engineering Foundation, which is a clearing house for welding research in order to avoid du­plication of work.

Training Volume and Methods of Athletes Competing at a Mixed Martial Arts Events

This study surveyed 32 athletes competing at a mixed martial arts (MMA) event held in Butte, Montana. The survey attempted to gather information regarding overall training volume, supplement use, volume change and specific exercises used. The survey return rate was 100 percent (32/32). Twenty-five of 32 athletes supplemented their training with strength training. Overall frequency of strength training ranged from one to six sessions/week, and overall frequency of fighting-specific training sessions/weel ranged from two to 10. Two of the 32 athletes used/had used anabolic-androgenic steroids. Sixteen MMA athletes performed exercises specifically for the neck musculature, and eight use the power clean within their strength-training program. Results suggested that strength and conditioning speciialists should educate the importance of, volume variation and periodization, balanced training, effective exercises, and the side effects of anabolic steroid use.

Comparison of several wood smoke markers and source apportionment methods for wood burning particulate mass

Residential wood combustion has only recently been recognized as a major contributor to air pollution in Switzerland and in other European countries. A source apportionment method using the aethalometer light absorption parameters was applied to five winter campaigns at three sites in Switzerland: a village with high wood combustion activity in winter, an urban background site and a highway site. The particulate mass from traffic (PMtraffic) and wood burning (PMwb) emissions obtained with this model compared fairly well with results from the 14C source apportionment method. PMwb from the model was also compared to well known wood smoke markers such as anhydrosugars (levoglucosan and mannosan) and fine mode potassium, as well as to a marker recently suggested from the Aerodyne aerosol mass spectrometer (mass fragment m/z 60). Additionally the anhydrosugars were compared to the 14C results and were shown to be comparable to literature values from wood burning emission studies using different types of wood (hardwood, softwood). The levoglucosan to PMwb ratios varied much more strongly between the different campaigns (4–13%) compared to mannosan to PMwb with a range of 1–1.5%. Possible uncertainty aspects for the various methods and markers are discussed.

Atlas of cancer mortality in the United Arab Emirates aided by application of geographic information system methods

The aim of this study was to determine cancer mortality rates for the United Arab Emirates (UAE) and to create an atlas of cancer mortality for the UAE. This atlas is the first of its kind in the Gulf country and the Middle East. Death certificates were reviewed for a period from January 1, 1990 to December 31, 1999 and cancer deaths were identified. Cancer mortality cases were verified by comparing with medical records. Age-adjusted cancer mortality rates were calculated by gender, emirate/medical district and nationality (UAE nationals and overall UAE population). Individual rates for each emirate were compared to the overall rate of the corresponding population for the same cancer site and gender. Age-adjusted rates were mapped using MapInfo software. High rates for liver, lung and stomach cancer were observed in Abu Dhabi, Dubai and the northern emirates, respectively. Rates for UAE nationals were greater compared to the overall UAE population. Several factors were suggested that may account for high rates of specific cancers observed in certain emirates. It is hoped that this atlas will provide leads that will guide further epidemiologic and public health activities aimed at preventing cancer. ^

A systematic review of the methods used to assess race and racial disparities in uterine fibroid research

Context: Black women are reported to have a higher prevalence of uterine fibroids, and a threefold higher incidence rate and relative risk for clinical uterine fibroid development as compared to women of other races. Uterine fibroid research has reported that black women experience greater uterine fibroid morbidity and disproportionate uterine fibroid disease burden. With increased interest in understanding uterine fibroid development, and race being a critical component of uterine fibroid assessment, it is imperative that the methods used to determine the race of research participants is defined and the operational definition of the use of race as a variable is reported for methodological guidance, and to enable the research community to compare statistical data and replicate studies. ^ Objectives: To systematically review and evaluate the methods used to assess race and racial disparities in uterine fibroid research. ^ Data Sources: Databases searched for this review include: OVID Medline, NML PubMed, Ebscohost Cumulative Index to Nursing and Allied Health Plus with Full Text, and Elsevier Scopus. ^ Review Methods: Articles published in English were retrieved from data sources between January 2011 and March 2011. Broad search terms, uterine fibroids and race, were employed to retrieve a comprehensive list of citations for review screening. The initial database yield included 947 articles, after duplicate extraction 485 articles remained. In addition, 771 bibliographic citations were reviewed to identify additional articles not found through the primary database search, of which 17 new articles were included. In the first screening, 502 titles and abstracts were screened against eligibility questions to determine citations of exclusion and to retrieve full text articles for review. In the second screening, 197 full texted articles were screened against eligibility questions to determine whether or not they met full inclusion/exclusion criteria. ^ Results: 100 articles met inclusion criteria and were used in the results of this systematic review. The evidence suggested that black women have a higher prevalence of uterine fibroids when compared to white women. None of the 14 studies reporting data on prevalence reported an operational definition or conceptual framework for the use of race. There were a limited number of studies reporting on the prevalence of risk factors among racial subgroups. Of the 3 studies, 2 studies reported prevalence of risk factors lower for black women than other races, which was contrary to hypothesis. And, of the three studies reporting on prevalence of risk factors among racial subgroups, none of them reported a conceptual framework for the use of race. ^ Conclusion: In the 100 uterine fibroid studies included in this review over half, 66%, reported a specific objective to assess and recruit study participants based upon their race and/or ethnicity, but most, 51%, failed to report a method of determining the actual race of the participants, and far fewer, 4% (only four South American studies), reported a conceptual framework and/or operational definition of race as a variable. However, most, 95%, of all studies reported race-based health outcomes. The inadequate methodological guidance on the use of race in uterine fibroid studies, purporting to assess race and racial disparities, may be a primary reason that uterine fibroid research continues to report racial disparities, but fails to understand the high prevalence and increased exposures among African-American women. A standardized method of assessing race throughout uterine fibroid research would appear to be helpful in elucidating what race is actually measuring, and the risk of exposures for that measurement. ^

Comparison of two statistical methods for rare variant association analysis

Studies have shown that rare genetic variants have stronger effects in predisposing common diseases, and several statistical methods have been developed for association studies involving rare variants. In order to better understand how these statistical methods perform, we seek to compare two recently developed rare variant statistical methods (VT and C-alpha) on 10,000 simulated re-sequencing data sets with disease status and the corresponding 10,000 simulated null data sets. The SLC1A1 gene has been suggested to be associated with diastolic blood pressure (DBP) in previous studies. In the current study, we applied VT and C-alpha methods to the empirical re-sequencing data for the SLC1A1 gene from 300 whites and 200 blacks. We found that VT method obtains higher power and performs better than C-alpha method with the simulated data we used. The type I errors were well-controlled for both methods. In addition, both VT and C-alpha methods suggested no statistical evidence for the association between the SLC1A1 gene and DBP. Overall, our findings provided an important comparison of the two statistical methods for future reference and provided preliminary and pioneer findings on the association between the SLC1A1 gene and blood pressure.^

(Appendix 1-4) Geochemistry, desorption methods, TOC, TC, and mineral content of different settings

Sorption of volatile hydrocarbon gases (VHCs) to marine sediments is a recognized phenomenon that has been investigated in the context of petroleum exploration. However, little is known about the biogeochemistry of sorbed methane and higher VHCs in environments that are not influenced by thermogenic processes. This study evaluated two different extraction protocols for sorbed VHCs, used high pressure equipment to investigate the sorption of methane to pure clay mineral phases, and conducted a geochemical and mineralogical survey of sediment samples from different oceanographic settings and geochemical regimes that are not significantly influenced by thermogenic gas. Extraction of sediments under alkaline conditions yielded higher concentrations of sorbed methane than the established protocol for acidic extraction. Application of alkaline extraction in the environmental survey revealed the presence of substantial amounts of sorbed methane in 374 out of 411 samples (91%). Particularly high amounts, up to 2.1 mmol kg**-1 dry sediment, were recovered from methanogenic sediments. Carbon isotopic compositions of sorbed methane suggested substantial contributions from biogenic sources, both in sulfate-depleted and sulfate-reducing sediments. Carbon isotopic relationships between sorbed and dissolved methane indicate a coupling of the two pools. While our sorption experiments and extraction conditions point to an important role for clay minerals as sorbents, mineralogical analyses of marine sediments suggest that variations in mineral composition are not controlling variations in quantities of sorbed methane. We conclude that the distribution of sorbed methane in sediments is strongly influenced by in situ production.

Remarks on methods for the computation of boundary-element integrals by co-ordinate transformation

It is well known that the evaluation of the influence matrices in the boundary-element method requires the computation of singular integrals. Quadrature formulae exist which are especially tailored to the specific nature of the singularity, i.e. log(*- x0)9 Ijx- JC0), etc. Clearly the nodes and weights of these formulae vary with the location Xo of the singular point. A drawback of this approach is that a given problem usually includes different types of singularities, and therefore a general-purpose code would have to include many alternative formulae to cater for all possible cases. Recently, several authors1"3 have suggested a type independent alternative technique based on the combination of standard Gaussian rules with non-linear co-ordinate transformations. The transformation approach is particularly appealing in connection with the p.adaptive version, where the location of the collocation points varies at each step of the refinement process. The purpose of this paper is to analyse the technique in eference 3. We show that this technique is asymptotically correct as the number of Gauss points increases. However, the method possesses a 'hidden' source of error that is analysed and can easily be removed.

Modern pilgrims: showing the improvements in travel, and the newest methods of reaching the celestial city ...

The plan of the book was suggested by Hawthorne's allegory, "The celestial railroad."

Events in Indonesia: exploring the limits to formal tourism trends forecasting methods in complex crisis situations

The desire to know the future is as old as humanity. For the tourism industry the demand for accurate foretelling of the future course of events is a task that consumes considerable energy and is of great significance to investors. This paper examines the issue of forecasting by comparing forecasts of inbound tourism made prior to the political and economic crises that engulfed Indonesia from 1997 onwards with actual arrival figures. The paper finds that current methods of forecasting are not able to cope with unexpected crises and other disasters and that alternative methods need to be examined including scenarios, political risk and application of chaos theory. The paper outlines a framework for classifying shocks according to a scale of severity, probability, type of event, level of certainty and suggested forecasting tools for each scale of shock. (C) 2003 Elsevier Science Ltd. All rights reserved.