The practice of using X-Ray fluorescence analysis as a method in ar-chaeological, forensic and osteological studies have resulted in a vast amount of data. It is time and cost efficient, and the method of µXRF element analysis has been of great use to archaeologists, forensic an-thropologists and osteologists to understand dietary customs, techno-logical trade patterns, understanding of diagenesis, elemental accumu-lation in bone and more. Moreover, the method has been crucial due to its non-destructive nature since bones and ancient artifacts are fragile and thus a nonde-structive method is preferable. This essay will give the reader an intro-duction to the basics of micro X-Ray fluorescence analysis and will explore the possibilities of trace elements in right (dexter) and left (sinister) thighbones (femur) on a medieval population in Visby Got-land, namely Sankt Hans. The reader will also come to know the fun-damental principles, applications, strengths and weaknesses of mi-croX-Ray fluorescence, as well as its limitations. Keywords: µXRF, non-destructive, data, method, left, right, thigh-bone, elements, analysis.

M.Med. (Radiology), Faculty of Health Sciences, University of the Witwatersrand, 2011 / Lymphobronchial tuberculosis (LBTB) is tuberculous lymphadenopathy involving the airways, which is particularly common in children. AIM: To describe the CT findings of LBTB in children, the parenchymal complications and associated abnormalities. METHOD: CT scans of 98 children with LBTB were retrospectively reviewed. Lymphadenopathy, bronchial narrowing, parenchymal complications and associations were documented. RESULTS: Infants comprised 51% of patients. The commonest lymphadenopathy was subcarinal (97% of patients). Bronchial compressions (259 in total) were present in all patients, of which 23% were severe / complete stenoses and 28% affected bronchus intermedius. Parenchymal complications were present in 94% of patients, including consolidation (88%), breakdown (42%), air trapping (38%), expansile pneumonia (28%), collapse (17%) and bronchiectasis (9%), all predominantly right-sided (63%). Associations included oval focal bodies, miliary nodules, pleural disease and intracavitory bodies. CONCLUSIONS: The most important CT finding of children with LBTB is visible airway compression as a result of lymphadenopathy. CT of children with LBTB showed that airway compressions were more severe in infants and most commonly involved bronchus intermedius. Numerous parenchymal complications were documented, all showing rightsided predominance. Several associations were identified.

PhD, Faculty of Engineering and the Built Environment, University of the Witwatersrand, 2010 / Dual Energy X-Ray Transmission (DE-XRT) Imaging is a multi-sensor technique employed to conduct particle-by-particle sorting. The system makes use of a dual energy x-ray line scan sensor, which generates images of the transmitted x-rays, similar to images generated for suitcase inspection in airport security applications. The dual energy x-ray system allows for rapid approximation of atomic number range, which is utilised to evaluate the mineral and maceral content of a variety of minerals, including coal. The process is independent of particle surface condition, and can thus be utilised as a dry process. A unique application of this technology is in the removal of torbanite from a coal deposit located in Mpumalanga, South Africa. The separation of coal from torbanite has been a problem for the coal industry for a long time. The separation of coal and torbanite by conventional gravity separation techniques is difficult, due to the overlapping densities of torbanite and coal. The commercial value of both commodities is significantly compromised if contaminated with the other, thus impacting negatively on the financial viability of mining such a deposit. Preliminary laboratory DE-XRT testwork results on high quality coal and torbanite products were promising. In order to evaluate the separation of typical Run of Mine (ROM) material on pilot scale, a production scale Mikrosort X-Tract Sorter was purchased. This was the first DE-XRT sorter available in South Africa, and was housed at Mintek in Johannesburg. A 150t sample was provided from a box cut adjacent to the coal deposit under investigation in order to conduct bulk and pilot sorting tests, the focus of which was on obtaining coal products of low ash and torbanite content. Clear distinctions between the coal, torbanite and shale fractions were observed using this technique. The sorter feed (-80mm+20mm) could be upgraded from a CV of 22MJ/kg to 28MJ/kg. Ash content could be reduced from 26% to 10%, which meets export quality standards. Petrographic analysis of the coal product indicated that a high purity coal product (in terms of torbanite and ash content) was attainable (91% by volume) at a mass yield of 42.9% to the coal product, with shale and mixed humic/sapropelic coal as contaminants. Under these conditions, torbanite contamination was marginal. It was demonstrated that shale could be removed from the torbanite product via a second sorting stage. This however was not the primary focus of the study, and was not optimised for this investigation. Two major limitations of the sorting process were identified, viz.; poor liberation and limited sorter feed size range. These impacted on the process as follows:- • The effects of poor liberation on coal quality could be counteracted by adjusting the sorting criteria of the algorithm to reject additional material. This would result in a lower coal product mass yield. In addition, interlocked coal/shale particles would report to the torbanite fraction. • A significant proportion of the ROM feed reported to the -20mm size fraction, and therefore did not fall part of the sorter feed. This resulted in a very low coal mass yield as a proportion of the ROM feed. If this process were to be adopted, means of minimizing fines production during mining and crushing would need to be investigated to improve overall yield to coal product. The capability to process coarse materials (-80mm+20mm) allows for throughputs in excess of 40t/hr. Consequently, this technique may be applied in simpler coal upgrading processes, such as coal deshaling in arid regions.

FAculty of SCience School of Cheistry 9910913j messai@auvum.chem.wits.ac.za / The monodentate phosphine complexes bui3PMX (2a: M = Cu, X = Cl, 2b: M = Cu, X = I, 2c: M = Ag, X = Cl, 2d: M = Au, X = Cl) were synthesised in high yields from bui3P and MX. Their reaction with [Li{μ-N(R)C(but)C(H)R}]2 (R = SiMe3) gave the monomeric complexes bui3PCuN(R)C(but)=C(H)R (3a) and bui3PMC(H)RC(but)=NR (3b: M = Ag, 3c: M = Au) in moderate to high yields. The bonding mode in the 1-aza-allyl complexes 3a-c was found to depend strongly on the metal ion, with 3a being an enamide complex and 3b and 3c iminoalkyl complexes. The reaction of bidentate ligand dpmaaH2 (2,3-bis(diphenylphosphino)maleic acid) with R2Sn-precursors led to novel dialkyl tin dpmaa complexes (R2Sn)(O,O dpmaa) (6) (where 6a, R = Me; 6b, R = Bu) were synthesized. Complexation of the tin/phosphine complexes led to the heterobimetallic complexes {Au[(dpmaaO,O)(SnR2)]2}Cl (7a and 8a) {Au[(dpmaaO,O)(SnR2)][dpmaaH2]}Cl (7b and 8b) (where 7a and 8a, R = Me; 7b and 8b, R = Bu) and the mixed metal complexes {Au[(dpmaaO,O)(RuCl)]2}Cl (9a) {Au[(dpmaaO,O)(SnBu2)(dpmaaO,O)RuCl)]}Cl (9b) and {Au[(dpmaaO,O)(RuCl)][dpmaa]}Cl (9c). All compounds were fully characterised by multinuclear NMR spectroscopy and microanalysis (not 3a, 3b, 4 and 5) solid state IR spectroscopy (KBr-pellets) (4-9) and mass spectrometry (6-8). The solid state structures of complexes 2c, 2d, 3c, 6a and 6b (two polymorphs) have been determined by X-ray crystallography revealing the presence of rare trimeric macrocycles in the case of 6a and 6b. The anti-tumour activity of the metal complexes (6b and 7-9) was tested on a single cell-line (except 7a and 8a which were on eight cell-lines) and their activity was compared to cisplatin.

A estrutura da florencita foi refinada pelo método de mínimos quadrados, utilizando dados experimentais obtidos através do método de Debye-Scherrer. A coleta dos dados das intensidades integradas foi feita através da leitura do difratograma de pó por um microdensitômetro óptico automático, e empregando métodos de análise numérica para fazer a integração da função (2&#952,Y), tabelada a pontos eqüidistantes. Foram observados 14 picos de difração e as reflexões que se superpunham contribuindo para as intensidades dos picos foram identificadas e suas contribuições levadas em conta através de seus fatores de multiplicidade. O refinamento foi feito com o programa POWLS (Powder Least Squares) e inicialmente foram fornecidos os parâmetros posicionais dos átomos da Goyazita, que é isomorfa com a florencita. As intensidades observadas foram corrigidas pelos fatores de Lorentz-polarização e adsorção. O índice de discordância R atingido para os 14 picos de difração observados foi de 0.097. A fórmula molecular da florencita é CeAl3(PO4)2(OH)6. O composto cristaliza no sistema hexagonal com parâmetros de rede ao=6.96Å co=16.33Å &#945= &#946 = 90° &#947=120° V=685.07&#1973. O grupo espacial é R3m com Z=3 e densidade calculada igual a 3.67g.cm-3. / The crystal structure of the florencita was refined by least squares using experimental data obtained with the Debye-Scherrer method. An automatic optical microdensitometer was used for the data collection from powder difractogram and numerical analysis methods for the integration of the function (2&#952,Y) which is tabulated at equidistant points. 14 diffraction peaks were observed, reflections which superpose contributing to the same peak were identified and their contributions were taken in account using multiplicity factors. The program POWLS (Powder Least Squares) was used for the refinement and initially the positional parameters of the atoms of the Goyazite, which is isomorfous with the florencita were used. Intensities were corrected for the Lorentz, polarization and absorption factors. The final R factor for the 14 peaks was of 0.097. The molecular formula of the florencitais CeAl3(PO4)2(OH)6. It crystallizes in the hexagonal system, space group R3m with cell ao=6.96Å co=16.33Å &#945= &#946 = 90° &#947=120° V=685.07&#1973.

Neste trabalho apresenta-se inicialmente algumas considerações sobre a difração de raios-X, suas principais leis, fatores de correção dos dados experimentais, uma revisão sobre os principais Métodos Diretos de resolução da estrutura, e considerações sobre o refinamento da estrutura obtida. A seguir descreve-se a determinação da estrutura cristalina do produto natural 5,4\'-Dihidroxi-3\', 5\' -dimetoxi- 6,7 -(2\",2\" -dimetilpirano) flavona de fórmula molecular C22H20O<sub<7, isolado de plantas da espécie Neoraputia paraensis, que cristaliza-se no sistema monoclínico, grupo espacial C2/c, com os seguintes parâmetros de cela unitária: a = 13,651(1), b= 23,428(2),c= 13,725(1) &#197; &#946= 119,528(4)&#176, V=3819,6(5)A&#9463 , Dc = 1,366g cm-3 e Z =8 moléculas por cela unitária. A estrutura foi resolvida através da aplicação de Métodos Diretos. Os índices de discordância finais são: R= 0,0509, Rw = 0,0530 para 1743 reflexões com I &#8805 3&#963(I) e Ra11=0,157. A estrutura foi refinada fazendo uso dos cálculos de Fourier Diferença e pelo método de mínimos quadrados usando matriz completa. A molécula apresenta duas ligações de hidrogênio intramoleculares, de força média (distâncias O-O 2,558(3) e 2,674(4) &#946). O empacotamento cristalino apresenta duas outras ligações de hidrogênio intermoleculares, mais fracas, sendo feitas com as moléculas geradas pelo espelho c (distâncias O-O 2,830(3) e 2,992(3) &#946). O efeito destas ligações intermoleculares é o da formação de cadeias ao longo da direção [101]. / Initially, some considerations about X-ray diffraction, its laws, the factors for the correction of experimental data, a revision of the main Direct Methods for structure resolution, and comments on the refinement of the resulting structure are presented. Next, the structure determination of the compound 5,4\' -dihydroxy-3\'-5\'- dimethoxy-6,7(2\",2\' \')dimethylpyran)flavone is described The compound is isolated from plants of the species Neuroputia paraenesis and has the molecular formula C22H20O<sub<7. It crystallizes in the monoclinic system, space group C2/c, with the following unit cell parameters: a = 13.651(1), b= 23.428(2), c= 13.725(1) &#197; &#946= 119,528(4)&#176, V=3819,6(5)A&#9463 , Dc = 1,366g cm-3 e Z =8molecules per unit cell. The structure was solved applying Direct Methods. The final disagreement indices are: R= 0.0509, Rw= 0.0530 for 1743 reflections with &#8805 3&#963(I) and Ra11=0,157. The structure was refined applying Fourier difference calculations and full matrix least squares methods. The molecule shows two intramolecular hydrogen bonds of medium strength (distances O-O 2.558(3) and 2.674(4) &#946). The crystal packing shows also two weaker hydrogen bonds; these are formed between the molecules generated by the c mirror (distances O-O 2.830(3) and 2.992(3) &#946). The result of these intermolecular hydrogen bonds is the formation of chains in [10 1] direction.

Foram realizadas medidas das seçõesde choque de produção de raios X L, L e L bem como medidas das seções de choque de ionização das subcamadas L1, L2 e L3 para os elementos Au e Ta com o Acelerador de elétrons Microtron de São Paulo, do Instituto de Física da Universidade de São Paulo. Os alvos foram produzidos no Laboratório de Alvos do Pelletron por evaporação desses elementos sobre substratos finos de carbono. Eles foram posicionados no centro da câmara de irradiação, de modo que o feixe incidia perpendicularmente à sua superfície. Os raios X decorrentes da ionização do alvo de tântalo foram observados com um detetor de Si(Li), enquanto que para o alvo de ouro usou-se um detetor HPGe, ambos posicionados a 120 graus em relação ao feixe. As curvas de eficiência de ambos os detetores foram levantadas usando as fontes de calibração e ajustando os pontos obtidos com um modelo analítico. Para cada energia de feixe, a seção de choque foi determinada a partir das áreas dos picos dos raios X característicos, da corrente incidente no alvo, da eficiência de deteção no pico e da espessura do alvo. As áreas dos picos foram determinadas pelo ajuste de uma forma gaussiana, a corrente incidente no alvo foi medida com um copo de Faraday e corrigida para a dispersão dos elétrons ao passarem pelo alvo, e as medidas de espessura dos alvos foram realizadas pelo método de retro-espalhamento de Rutherford (RBS). Os resultados experimentais obtidos ficaram acima do calculado com a aproximação de Born de ondas distorcidas para as medidas de seção de choque de produção de raios X L, L do Au e para os multipletos L e L do Ta. Para o grupo L do Au e do Ta as medidas foram consistentes com o modelo teórico. Os dados encontrados na literatura para ambos os elementos referem-se todos a energias próximas do limiar de ionização da camada L e nessa faixa são consistentes com o modelo teórico, embora em alguns casos afetados por incertezas superiores a 20%. Este trabalho traz as primeiras medidas para a seção de choque de produção de raios X L do Ta para energias superiores a 50 keV. / Measurements were made of the L, L and L x-rays production cross section and also of the ionization cross section of subshell L1 , L_2 and L3 for the elements Au and Ta in the electron accelerator Microtron of São Paulo, located at the Institute of Physics of the University of São Paulo. The targets used were produced in the Pelletron Targets Laboratory and consisted of fine targets evaporated on thin carbon substrates. These targets were positioned in the center of the Microtrons irradiation chamber, so that the focused beam perpendicular to the surface. The x-ray originated from the ionization of the Ta target were obtained with a Si(Li), for the Au target it was used a HPGe detector, both positioned at 120 degrees relative to the electrons beam. The efficiency curve for both detectors was made by using calibration sources and by adjusting the points with a analytical model. For every beam energy the x-rays production cross section were obtained by an accurate knowledge of the peak areas, of the current incident on the target, of the absolute efficiency, and of the thickness of the target. The peak areas were determined by fitting a Gaussian shape, the measurements of the current were made with a Faraday cup and it were corrected for the electrons\' dispersion when they pass through the target, and the measurements of the thickness were performed with the method of Rutherford Back Scattering (RBS). The experimental results were above the Born approximation of distorted waves for measurements of L and L x-rays production cross sections of Au and for the multiplets L and L and of Ta. The measurements of L group of Au and Ta were consistent with the theoretical model. The data founded in literature for both elements are all near to the region of the threshold ionization energy of the shell L, on that energy range they are consistent with the theoretical model, although in some instances they are affected by uncertainties greater than 20%. This work presents the first measurements of Ta L x-rays production cross section to energies above 50 keV.

Este trabalho apresenta uma parte introdutória que descreve os conceitos básicos da determinação de estruturas cristalinas e, na parte experimental, a determinação da estrutura cristalina e molecular, por difração de raios-X, de dois compostos de coordenação contendo cobre: catena-tri-µ-cloro-µ-[trans-1,2-bis(4-piridil)eteno]cobre(I): Sistema cristalino monoclínico; grupo espacial P21/c; a=3,7819(1); b=15,0582(9); c=10,8742(6) Å; B=96,284(4)º; Z= 4 moléculas por cela unitária; V=615,55(5) Å3; Dc=2,040 Mg.m-3. Os índices de discordância finais são: Robs=0,0465 ; Rall=0,1367 com GOF=1,13 para 1243 reflexões observadas (I>2Sigma(I)) e 83 parâmetros refinados. µ-oxalato-µ-[trans-1,2-bis(piridil)eteno]cobre(II): Sistema cristalino triclínico; grupo espacial P ; a=8,7948(5); b=9,0228(5); c=5,5172(3) Å; Alfa=108,860(3), Beta=109,895(3), Gama=97,572(3)º; Z= 2 moléculas por cela unitária; V=374,92(4) Å3; Dc=1,469 Mg.m-3. Os índices de discordância finais são: Robs=0,0567, Rall=0,1544 com GOF=1,08 para 1694 reflexões observadas (I>2Sigma(I)) e 97 parâmetros refinados. Estes complexos são produtos da reação entre oxalato de potássio e cloreto de cobre(II) dihidratado. A síntese foi feita na presença de etanol e água utilizando o trans-1,2-bis(4-piridil)eteno (bpe) como ligante. Os compostos formados são cristalinos e estáveis ao ar. / This work presents a brief description about the basic concepts of X-ray crystallography and the experimental part contains the crystal and molecular structure determination of coordination compounds with copper , by X-ray diffraction. Catena-tri-µ-chloro-µ-[trans-1,2-bis(4-pyridyl)ethene]copper(I): monoclínic system, space group P21/c; a=3.7819(1); b=15.0582(9); c=10.8742(6) Å; B=96.284(4) º; Z=4; V=615.55(5) Å3; Dc=2.040 Mg.m-3. The final disagreement indices are: Robs=0.0465; Rall=0.1367; GOF=1.13 to 1243 observed reflections (I>2Sigma(I)) and NPAR=83. µ-oxalate-µ-[trans-1,2-bis(pyridyl)ethene]copper(II): triclinic system, space group P ; a=8.7948(5); b=9.228(5); c=5.5172(3) Å; Alfa =108.860(3), Beta =109.895(3), Gama=97.572(3) º; Z=2; V=374.92(4) Å3; Dc=1.469 Mg.m-3. The final disagreement indices are: Robs=0.0567; Rall=0.1544; GOF=1.08 to 1694 observed reflections (I>2Sigma(I)) and NPAR=97. These complexes are products in the reaction with potassium oxalate and copper(II) chloride dihydrate. The synthesis was made in presence of ethanol and water, using the trans-1, 2-bis(4-pyridyl)ethene (bpe) as ligand. The obtained compounds they are crystalline and the stable.

Thesis advisor: Daniel A. Kirschner / Reactive oxygen species (ROS) are implicated in a range of degenerative conditions, including aging, neurodegenerative diseases, and neurological disorders such as multiple sclerosis. Myelin is a lipid-rich multilamellar assembly that facilitates rapid nerve conduction in higher animals, and may be intrinsically vulnerable to oxidative damage given the high energetic demands and low antioxidant capacity of myelinating cells. To determine whether ROS can cause structural damage to internodal myelin, whole mouse sciatic and optic nerves were incubated ex vivo with a previously-characterized copper (Cu)/hydrogen peroxide (HP)/o-phenanthroline (OP)-based hydroxyl radical-generating system followed by quantitative determination of myelin packing by x-ray diffraction. Exposure to Cu/OP/HP-mediated ROS caused irreversible myelin decompaction in both sciatic and optic nerves. The addition of the hydroxyl radical scavenger, sodium formate, to the ROS-producing incubation solution significantly prevented sciatic nerve myelin decompaction, implicating hydroxyl radical species in causing the damage. Furthermore, Cu/OP/HP-mediated decompaction could be prevented by the addition of EDTA, which can compete with OP for Cu binding and sequester the metal within the bulk solution. These findings suggest that Cu/OP/HP-dependent myelin decompaction is caused by OP-mediated membrane-targeted hydroxyl radical production. Myelin membranes are particularly enriched in plasmalogen phospholipids, which have been linked to antioxidant activity; this enrichment may constitute an endogenous ROS-defense mechanism that protects ROS-vulnerable myelin tissue from damage. Intriguingly, it was found that sciatic nerve myelin from plasmalogen deficient (Pex7 KO) mice was significantly more susceptible to ROS-mediated decompaction than that from WT mice, supporting the role of plasmalogens as endogenous antioxidants. / Thesis (MS) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Thesis advisor: Mary F. Roberts / Myo-inositol and its phosphorylated derivatives are found across all domains of life, and these molecules play crucial roles in a wide variety of cellular processes. While the biosynthesis of inositol is an evolutionarily conserved pathway, there are a wide variety of enzymes that use inositol and its derivatives as substrates. This thesis explores two such enzymes; a phosphatidylinositol- specific phospholipase C (PI-PLC) produced by <i>Staphylococcus aureus</i>, and AF2372, a dual action inositol monophosphatase/ fructose bisphosphatase produced by the <i>Archaeoglobus fulgidus</i>. At the outset of this work, the structure of the <i>S. aureus</i> PI-PLC was unknown, but some interesting biochemical properties about the enzyme had been observed. The structure of AF2372 had been reported, but a structure had not yet been solved in the presence of osmolytes known to thermoprotect the enzyme. Both the <i>S. aureus</i> PI-PLC and AF2372 catalyze the cleavage of phosphorylated inositol compounds, but share no mechanistic, structural, or taxonomical similarities. Protein crystallography is a powerful tool, and with it I have been able to study these two enzymes at a molecular level, providing insight into complex biological questions about each enzyme. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.