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Gene regulation lies at the heart of most biological processes and transcription factors are the key molecules that control tissues specific gene expression. In higher eukaryotes transcription factors control gene expression by binding regulatory DNA segments called cis-regulatory modules (CRMs). The increasing number of sequenced genomes of multicellular eukaryotes along with high-throughput methods such as whole genome microarray expression data allows for systematic characterization of the CRMs that control gene expression. A first step towards understanding gene regulation is the identification of the regulatory elements present in the genome. We take advantage of the large database of spatio-temporal patterns of gene expression in D. melanogaster embryogenesis to identify sets of developmentally co-expressed genes. We developed a computational method that identifies DNA binding sites for transcription factors from families of co-regulated genes that are expressed during Drosophila embryo development. This method discovers over-represented motifs in a set of co-regulated genes using the exhaustive motif enumeration technique. Clustering the predicted motifs identifies the CRMs, which assist in translating a combinatorial code of TF inputs into a specific gene expression output. The predicted CRMs were verified experimentally by searching the whole genome for the predicted CRMs and establishing expression pattern of the genes that are associated with these CRMs. It is well know that the gene expression is substantially controlled through CRMs and those key regulatory sequences are conserved in related species. The conservation of CRMs can be studied by comparing the related genomes and alignment methods are widely used computational tools for comparing the sequences. However, in distantly related species the CRM sequences are simply not align able. To identify the similar CRMs in distantly related species we developed a non-alignment based method for discovering similar CRMs in related species. This method is based on word frequencies where the given sequences are compared using Poisson based metric. When starting with a set of CRMs involved in Drosophila early embryo development, we show here that our non-alignment method successfully detects similar CRMs in distantly related species ( D. ananassae, D. pseudoobscura, D. willisoni, D. mojavensis, D. virilis, D. grimshawi ). This method proved efficient in discriminating the functional CRMs from the non-functional ones.

Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 19, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Thesis advisor: Dr. John D. Robertson. Includes bibliographical references.

Οι συνεχώς αυξανόμενες απαιτήσεις για στιβαρότερες και ελαφρύτερες κατασκευές οδήγησαν στην ανάπτυξη νέων υλικών. Η αύξηση της αντοχής με την ταυτόχρονη μείωση του βάρους έχουν σαν συνέπεια τη μείωση του κόστους, όχι όμως εναντίον της αξιοπιστίας και λειτουργικότητας. Τα νέα υλικά έχουν υψηλότερες τιμές του λόγου αντοχής/βάρος σε σύγκριση με εκείνες των συμβατικών υλικών. Σαν αποτέλεσμα, χρησιμοποιούνται στη δημιουργία προηγμένων και ευφυών κατασκευών, οι οποίες ανταποκρίνονται στα πρότυπα αξιοπιστίας και λειτουργικότητας για τα οποία έχουν σχεδιαστεί. Το πεδίο εφαρμογής των προηγμένων υλικών εκτείνεται σε ένα ευρύ φάσμα κατασκευών, όπως στη βιομηχανία των αυτοκινήτων, στην αεροδιαστημική, καθώς και σε μια πληθώρα προϊόντων καθημερινής χρήσης. Η ανά χείρας διατριβή ασχολείται με την προσομοίωση και τη μελέτη των φαινομένων που σχετίζονται με τις αστοχίες και ειδικότερα με τις διαδικασίες διάρρηξης δεσμού πρόσφυσης σε υλικά με ανομοιογένειες, που κατά κύριο λόγο είναι σύνθετα υλικά. Με την εισαγωγή αντιπροσωπευτικών όγκων αναφοράς που περιγράφουν την επαναληψιμότητα της γεωμετρίας, είναι δυνατόν να επιτευχθεί μια αντικειμενική προσομοίωση, με ανεξάρτητες μεταβλητές τη διάταξη των ενισχύσεων και την κατ’ όγκο περιεκτικότητα. Διερευνώνται οι εστίες συγκέντρωσης τάσεων και παραμορφώσεων, καθώς και η αλληλεξάρτησή τους από τις ανεξάρτητες μεταβλητές του προβλήματος, όπως μεταξύ άλλων είναι η παρουσία ενδιάμεσης φάσης, η ατελής πρόσφυση κλπ. Προσομοιώνεται η αποκόλληση κατά μήκος της ενδιάμεσης φάσης, ο θρυμματισμός των ινών και αναλύεται ο τρόπος με τον οποίο αλληλεπιδρά μια θραυσμένη ίνα στις ΠΡΟΛΟΓΟΣ iii γειτονικές της. Οι προσομοιώσεις και οι αναλύσεις που πραγματοποιήθηκαν, αφορούν υλικά τα οποία έχουν εκτεταμένες ή συγκεντρωμένες ενισχύσεις και χαρακτηρίζονται από ανομοιογένειες στην περιοχή μεταξύ των ενισχύσεων και της μήτρας. Το ένα υλικό διακρίνεται από το άλλο και κατά συνέπεια η μία φάση από την άλλη, διαμέσου της διεπιφάνειας. Η τυχαία ή συστηματική διάταξη των ενισχύσεων επιβάλλει την υιοθέτηση ενός αντιπροσωπευτικού στοιχείου όγκου, το οποίο να περιλαμβάνει δύο ή και περισσότερες ομογενείς φάσεις, που διαχωρίζονται μεταξύ τους με διεπιφάνειες, οι οποίες δεν είναι τίποτα περισσότερο από ανομοιογενείς στρώσεις ενδιάμεσων φάσεων, των οποίων οι ιδιότητες μεταβάλλονται κατά την έννοια του πάχους αυτών. Οι αστοχίες υλικών όπως τα παραπάνω αποτελούν δημοφιλέστατο αντικείμενο μελέτης εξαιτίας των ιδιαίτερα καταστροφικών τους αποτελεσμάτων. Η μείωση ή και η ολοκληρωτική απώλεια της ικανότητάς του να επιτελούν το σκοπό για τον οποίο σχεδιάστηκαν, μειώνουν την αξιοπιστία τους και οδηγούν σε απροσδόκητες αστοχίες με ολέθριες συνέπειες σε ότι αφορά την ασφάλεια, τη λειτουργικότητα και το κόστος του εξοπλισμού. Η κύρια αιτία που οδηγεί σε αστοχία ένα υλικό (εκτός από τη φθορά και τη διάβρωση) είναι η παραμόρφωση, με την οποία εννοούμε τη μεταβολή στο σχήμα ενός υλικού και αφορά κυρίως τις μηχανικές αστοχίες, οι οποίες είναι και το αντικείμενο μελέτης αυτής της διατριβής. Η παραμόρφωση ως επί το πλείστον οφείλεται σε εξωτερικά φορτία και μπορεί να είναι ελαστική ή πλαστική. Η τελευταία είναι δυνατόν να οδηγήσει σε θραύση. Ένα νέο είδος μηχανικής αστοχίας είναι η αποκόλληση, η οποία εμφανίζεται στις διεπιφάνειες των προηγμένων υλικών. Σαν αποτέλεσμα, όταν τα υλικά αυτά βρεθούν κάτω από κρίσιμο συνδυασμό εντατικών καταστάσεων να εγείρεται η διάρρηξη του δεσμού πρόσφυσής και κατά συνέπεια να αποτελούν εστίες εκκίνησης ρωγμών. Όλοι οι παραπάνω λόγοι επέβαλλαν τη μελέτη της αριθμητικής προσομοίωσης διάρρηξης δεσμού πρόσφυσης σε ανομοιογενή υλικά, καταλαβαίνοντας τη σημαντικότατη συμβολή που θα έχουν τα αποτελέσματα και τα συμπεράσματα που θα προκύψουν από αυτή. Αρχικά ο αναγνώστης, στο πρώτο κεφάλαιο, έρχεται σε μια πρώτη επαφή με τα σύνθετα υλικά, τα χαρακτηριστικά τους, τις αστοχίες που εκδηλώνονται σε αυτά, τον τρόπο με τον οποίο θεωρούνται από απλά ολιγοφασικά σε πολυφασικά υλικά, ενώ εισάγεται η έννοια της ενδιάμεσης φάσης, παρουσιάζονται οι ιδιότητες της και εν συνεχεία γίνεται μια σύντομη βιβλιογραφική ανασκόπηση. Έπειτα περιγράφεται το αντικείμενο των κεφαλαίων της παρούσας διατριβής. Στο δεύτερο κεφάλαιο αναπτύσσεται η μοντελοποίηση των iv φάσεων των σύνθετων υλικών και παρουσιάζονται τα διάφορα μοντέλα της ενδιάμεσης φάσης. Στο τρίτο κεφάλαιο επεξηγείτε ο τρόπος με τον οποίο επιτυγχάνεται η τμηματική ομοιογένεια της ενδιάμεσης φάσης, πραγματοποιείται ο αντικειμενικός ορισμός του μοντέλου, εφαρμόζεται μια ημιαναλυτική διαδικασία προσέγγισης της ανομοιογένειας της ενδιάμεσης φάσης και περιγράφονται τα λεγόμενα διεπιφανειακά στοιχεία, που χρησιμεύουν στην εκκίνηση της διάρρηξης του δεσμού πρόσφυσης. Στο τέταρτο κεφάλαιο παρουσιάζονται επιλεκτικά αποτελέσματα που ελήφθησαν από τις προσομοιώσεις που πραγματοποιήθηκαν, ενώ τέλος στο πέμπτο κεφάλαιο παραθέτονται τα συνολικά συμπεράσματα αυτής της προσπάθειας και οι προοπτικές που διανοίγονται από αυτήν. / The increasing demands for the development of improved and intelligent constructions, that will meet the desired reliability and functional standards, have led to new materials of higher strength/weight ratio comparing to those of the traditional materials. The present work is focused on the study -through simulation- of phenomena related to material failures and specifically to adhesion bond breaking of inhomogeneous materials. Through the introduction of representative reference volumes describing the repetitiveness of geometry, a realistic simulation can be evaluated, in which fibers packing dimensions and volumetric composition are the independent parameters. The areas of stress and strain accumulation, as well as their dependence on the problem independent variables (as weak interphase, imperfect adhesion etc), are discussed. The debonding along interphase and fiber fragmentation are simulated, while the reaction mechanism of a broken fiber near it is analysed. The materials under study include short and long reinforcements, while presenting inhomogenities among reinforcements and fibers (interphase area). Fibers packing demand the use of a representative volume element, which is consisted of two or more homogeneous phases, separated by interfaces. Those interfaces are inhomogeneous interphase layers, whose properties vary with their thickness. The validity of the proposed simulation method is established through the accuracy, the repetitiveness and the convergence of its results. The innovations of this work are the following:  For the first time, a study of the interphase and imperfect adhesion affection to the side debonding of fiber composite materials with FEA takes place.  A parametric model is developed, contributing to the realistic solution of this kind of problems.  For the first time, the development of hybrid interphase and its introduction to FEA analysis, take place.  For the first time, the simulation of fiber fragmentation and the use of interphase elements, to this analysis, take place.  Realistic simulation is improved, as well as the result process through modern computation tools. This general model for the prediction and the failure analysis of bonds breaking can be applied to other kinds of failure problems as well, for future research.

This work analyses orientation and assembly methods for not cylindrical elements. Models of two assembly elements was created using Auto Cad 2004 software. Taking advantages and disadvantages of assembly methods into consideration, it was chosen to assemble components with industrial robot, because it is high speed, programmable device. Trajectory of robot movement was calculated using vector algebra and homogenous coordinates methods to ensure control reliability. The program was developed for robot control, using Delphi 7. The program can bee applied not only for these two components.

Risk assessment of trace-metal contamination in soils requires predictive models that can accurately describe the complex uptake processes at the soil-plant interface, which are usually characterized by the coexistence of and interaction between multiple components. Competing cations such as Ca and H can affect metal availability to plants and subsequent rhizotoxicity. The biotic ligand model (BLM) has been proposed as a promising approach to model these interactive processes. Under the BLM assumption, we designed experiments to investigate how the solution chemistry is correlated with metal uptake and rhizotoxicity. Our first goal is to acquire a set of BLM parameters that can accurately represent the experimental data over varied solution conditions and parameters that are easy to integrate with general speciation models. The second objective is to get insight into the physical nature of the interactions. Our titration experiments revealed three types of biotic ligands in the pea roots with defined site densities and stability constants with H. Our ion sorption experiments estimated the surface-adsorption stability constants of Ca, Mg, Cd, Cu, Ni, and Zn with excised fresh pea roots. Our 48-h root growth tests have established the formation constants (KMe's) of living pea roots with Ca, Cd, Cu, Ni, and Zn. In these studies, we hypothesized and confirmed that the concentration of the metal-root complexes correlated with observed rhizotoxicity and that Ca, H, and trace metals competed for root absorption where lower solution pH decreased both Ca and metal uptake. Root elongation was found to be highly sensitive to root Ca content rather than merely to the direct toxic effects of the trace metals. It is shown that the physiological complexity arising from a living root affected our modeling so that adjustable KMe values, as a function of solution and root chemistry, are required for good model fits. The established model parameters were tested in hydroponic mixture solutions for their ability to predict the uptake of multiple metals simultaneously. The joint effects of Cd, Cu, and Ni in mixtures on root growth were studied and the potential interactions between these ions were also investigated.

There are two main components to the research: the theoretical and the experimental. Chapter 2 contains an analysis of the state of soil quality guidelines and the scientific methods used to determine them. A number of recommendations to improve soil quality criteria for trace metals are offered including the importance of considering bioavailability and the need to use realistic conditions, trace metal sources and organisms. / A critical review of the literature dealing with predicting the availability of trace metals to plants is presented in Chapter 3. We found little agreement among hundreds of similar studies which relate plant metal uptake to the amount of metal extracted by selective chemical dissolution procedures. An extensive summary of the data shows clearly that the extraction methods are not widely applicable. Differences between individual soils, their metal retention capacities, as well as plant factors and environmental conditions contribute to the variability of the results. Alternative ways of assessing bioavailability are suggested. / The experimental component of the thesis focuses on the availability of trace metals to plants. In Chapter 4 the uptake of Cu from different soil pools was examined and the free metal ion (Cu2+) was found to be the best predictor of uptake by lettuce (Latuca sativa cv. Buttercrunch), ryegrass (Lolium perenne cv. Barmultra) and radish (Raphanus sativus cv. Cherry Belle). / In Chapters 5 and 6 we examined the effect of low-cost in-situ treatments on the availability of metals to plants in greenhouse and field experiments. Synthetic zeolites, P amendments, organic matter and clean soil were used and their effect on the bioavailability of Cd, Cu, Pb, Ni and Zn evaluated. The plants for the experimental work were lettuce and perennial ryegrass. Only the clean soil treatment was consistently effective in reducing the concentration of metals in the plant. We also wanted to determine whether the trace metals in the plant tissue came from the soil or from direct deposition of pollutants on the leaf surfaces. We found little evidence that metals in plants were a result of atmospheric fallout. / A method for the accurate analysis of total metal concentrations in a range of contaminated soils including those containing oil and grease was developed (Chapter 7). For this research the trace metals of concern are Cd, Cu, Ni, Pb and Zn---all commonly found in urban/industrial soils. The proposed method using HNO3/HClO4 has several advantages over the common HNO3/H2O2 procedure. We were able to digest larger soil samples and hence the final concentration of trace metals was usually in the range for analysis by inductively coupled plasma atomic absorption spectrometry or flame atomic absorption spectrometry.

Soil quality guidelines are currently based on total trace metal loads. There is a need to define indices of bioavailability to allow reasonable predictions for plant metal uptake and toxicity in soils. Trace metal toxicities to plants often correlate best with free metal ion activities. The first objective was to develop a plant bioassay that is sensitive to trace metals at concentrations realistic for soils. The root elongation of lettuce Lactuca sativa 'Buttercrunch' was used as toxicological endpoint. This endpoint was sensitive and reproducible to environmentally relevant concentrations of Cd, Cu, Ni, Pb and Zn. The second objective was to test whether free metal ion activities are constant predictors of metal toxicities in synthetic solutions and in soil extracts that differ in their concentrations of cations and ligands. The root elongation assay was used to test this hypothesis. In synthetic solutions, the rhizotoxicity of Cd, Cu, Ni, Pb and Zn decreased with increasing Ca and H concentrations. This could not be explained with the effect of higher cationic concentrations on root growth or on solution speciation. It was concluded that Ca and H inhibited the rhizotoxicity of all metals tested. The rhizotoxicity of Cu and Cd was further examined in soil extracts. Both metals became less rhizotoxic at higher H and dissolved organic matter concentrations. The rhizotoxicity endpoints from the experiments in synthetic solution were used to develop parameters for a Biotic Ligand Model (BLM) for Cd, Cu, Ni, Pb and Zn. The BLM accounts for solution speciation and interprets cationic inhibition of rhizotoxicity as competition of metals with Ca and H for potential sites of rhizotoxicity. The BLM predicted metal rhizotoxicity better than the free metal ion activity in synthetic solutions and in soil extracts. Different models were tested against literature rhizotoxicity data for metals at different Ca and H concentrations. Predictions for metal rhizotoxicity given by BLM, Gouy-Chapman-Stern model and Freundlich equation model were compared with predictions based on free metal ion activities in solution. The BLM predicted rhizotoxicity most accurately. The BLM seems promising for predictions of metal toxicity and metal bioavailability in soils to support site-specific environmental risk assessments.

This creative project is a textbook which has only one objective: to improve the Spanish vocabulary.The method consists of showing a group of Greek and Latin elements such as roots, prefixes and suffixes. It will be possible with this list to derive a large quantity of Spanish words and special terminology. It will be possible also to study some linguistic phenomena concerning semantic changes.The exercices are systematized in order to present words which are necessary for the students to learn. They will have to recognize these elements in different sentences and, at the same time, they will have to deduce their meaning from the context.

Thesis (M.S. - Hydrology)--University of Arizona, 1984. / Includes bibliographical references (leaves 68-72).