Direct Determination of Sugar Cane Quality Parameters by X-ray Spectrometry and Multivariate Analysis

Current methods for quality control of sugar cane are performed in extracted juice using several methodologies, often requiring appreciable time and chemicals (eventually toxic), making the methods not green and expensive. The present study proposes the use of X-ray spectrometry together with chemometric methods as an innovative and alternative technique for determining sugar cane quality parameters, specifically sucrose concentration, POL, and fiber content. Measurements in stem, leaf, and juice were performed, and those applied directly in stem provided the best results. Prediction models for sugar cane stem determinations with a single 60 s irradiation using portable X-ray fluorescence equipment allows estimating the % sucrose, % fiber, and POL simultaneously. Average relative deviations in the prediction step of around 8% are acceptable if considering that field measurements were done. These results may indicate the best period to cut a particular crop as well as for evaluating the quality of sugar cane for the sugar and alcohol industries.

A tellurium-based cathepsin B inhibitor: Molecular structure, modelling, molecular docking and biological evaluation

The crystallographically determined structure of biologically active 4,4-dichloro-1,3-diphenyl-4-telluraoct-2-en-1-one, 3, shows the coordination geometry for Te to be distorted psi-pentagonal bipyramidal based on a C2OCl3(lone pair) donor set. Notable is the presence of an intramolecular axial Te center dot center dot center dot O (carbonyl) interaction, a design element included to reduce hydrolysis. Raman and molecular modelling studies indicate the persistence of the Te center dot center dot center dot O(carbonyl) interaction in the solution (CHCl3) and gasphases, respectively. Docking studies of 3' (i.e. original 3 less one chloride) with Cathepsin B reveals a change in the configuration about the vinyl C = C bond. i.e. to E from Z (crystal structure). This isomerism allows the optimisation of interactions in the complex which features a covalent Te-SGCys29 bond. Crucially, the E configuration observed for 3' allows for the formation of a hypervalent Te center dot center dot center dot O interaction as well as an O center dot center dot center dot H-O hydrogen bond with the Gly27 and Glu122 residues, respectively. Additional stabilisation is afforded by a combination of interactions spanning the S1, S2, S1' and S2' sub-sites of Cathepsin B. The greater experimental inhibitory activity of 3 compared with analogues is rationalised by the additional interactions formed between 3' and the His110 and His111 residues in the occluding loop, which serve to hinder the entrance to the active site. (C) 2012 Elsevier B.V. All rights reserved.

Trace elements as tumor biomarkers and prognostic factors in breast cancer: a study through energy dispersive x-ray fluorescence

Abstract Background The application and better understanding of traditional and new breast tumor biomarkers and prognostic factors are increasing due to the fact that they are able to identify individuals at high risk of breast cancer, who may benefit from preventive interventions. Also, biomarkers can make possible for physicians to design an individualized treatment for each patient. Previous studies showed that trace elements (TEs) determined by X-Ray Fluorescence (XRF) techniques are found in significantly higher concentrations in neoplastic breast tissues (malignant and benign) when compared with normal tissues. The aim of this work was to evaluate the potential of TEs, determined by the use of the Energy Dispersive X-Ray Fluorescence (EDXRF) technique, as biomarkers and prognostic factors in breast cancer. Methods By using EDXRF, we determined Ca, Fe, Cu, and Zn trace elements concentrations in 106 samples of normal and breast cancer tissues. Cut-off values for each TE were determined through Receiver Operating Characteristic (ROC) analysis from the TEs distributions. These values were used to set the positive or negative expression. This expression was subsequently correlated with clinical prognostic factors through Fisher’s exact test and chi-square test. Kaplan Meier survival curves were also evaluated to assess the effect of the expression of TEs in the overall patient survival. Results Concentrations of TEs are higher in neoplastic tissues (malignant and benign) when compared with normal tissues. Results from ROC analysis showed that TEs can be considered a tumor biomarker because, after establishing a cut-off value, it was possible to classify different tissues as normal or neoplastic, as well as different types of cancer. The expression of TEs was found statistically correlated with age and menstrual status. The survival curves estimated by the Kaplan-Meier method showed that patients with positive expression for Cu presented a poor overall survival (p < 0.001). Conclusions This study suggests that TEs expression has a great potential of application as a tumor biomarker, once it was revealed to be an effective tool to distinguish different types of breast tissues and to identify the difference between malignant and benign tumors. The expressions of all TEs were found statistically correlated with well-known prognostic factors for breast cancer. The element copper also showed statistical correlation with overall survival.

X-Ray analysis to assess mechanical damage in sweet corn seeds

The X-ray test is a precise, fast and non-destructive method to detect mechanical damage in seeds. In the present study, the efficiency of X-ray analysis in identifying the extent of mechanical damage in sweet corn seeds and its relationship with germination and vigor was evaluated. Hybrid 'SWB 551' (sh2) seeds with round (R) and flat (F) shapes were classified as large (L), medium (M1, M2 and M3) and small (S), using sieves with round and oblong screens. After artificial exposure to different levels of damage (0, 1, 3, 5 and 7 impacts), seeds were X-rayed (15 kV, 5 min) and submitted to germination (25 °C/5 days) and cold (10 °C/7 days) tests. Digital images of normal and abnormal seedlings and ungerminated seeds from germination and cold tests were jointly analyzed with the seed X-ray images. Results showed that damage affecting the embryonic axis resulted in abnormal seedlings or dead seeds in the germination and cold tests. The X-ray analysis is efficient for identifying mechanical damage in sweet corn seeds, allowing damage severity to be associated with losses in germination and vigor.

Time lags of the kilohertz quasi-periodic oscillations in the low-mass X-ray binaries 4U 1608−52 and 4U 1636−53

We studied the energy and frequency dependence of the Fourier time lags and intrinsic coherence of the kilohertz quasi-periodic oscillations (kHz QPOs) in the neutron-star lowmass X-ray binaries 4U 1608−52 and 4U 1636−53, using a large data set obtained with the Rossi X-ray Timing Explorer. We confirmed that, in both sources, the time lags of the lower kHz QPO are soft and their magnitude increases with energy. We also found that: (i) In 4U 1636−53, the soft lags of the lower kHz QPO remain constant at∼30 μs in the QPO frequency range 500–850 Hz, and decrease to ∼10 μs when the QPO frequency increases further. In 4U 1608−52, the soft lags of the lower kHz QPO remain constant at 40 μs up to 800 Hz, the highest frequency reached by this QPO in our data. (ii) In both sources, the time lags of the upper kHz QPO are hard, independent of energy or frequency and inconsistent with the soft lags of the lower kHz QPO. (iii) In both sources the intrinsic coherence of the lower kHz QPO remains constant at ∼0.6 between 5 and 12 keV, and drops to zero above that energy. The intrinsic coherence of the upper kHz QPO is consistent with being zero across the full energy range. (iv) In 4U 1636−53, the intrinsic coherence of the lower kHz QPO increases from ∼0 at ∼600 Hz to ∼1, and it decreases to ∼0.5 at 920 Hz; in 4U 1608−52, the intrinsic coherence is consistent with the same trend. (v) In both sources the intrinsic coherence of the upper kHz QPO is consistent with zero over the full frequency range of the QPO, except in 4U 1636−53 between 700 and 900 Hz where the intrinsic coherence marginally increases. We discuss our results in the context of scenarios in which the soft lags are either due to reflection off the accretion disc or up-/down-scattering in a hot medium close to the neutron star. We finally explore the connection between, on one hand the time lags and the intrinsic coherence of the kHz QPOs, and on the other the QPOs’ amplitude and quality factor in these two sources.

Monte Carlo Semi-Empirical Model for Si(Li) X-Ray Detector: Differences between Nominal and Fitted Parameters.

A detailed characterization of a X-ray Si(Li) detector was performed to obtain the energy dependence of efficiency in the photon energy range of 6.4 - 59.5 keV. which was measured and reproduced by Monte Carlo (MC) simulations. Significant discrepancies between MC and experimental values were found when lhe manufacturer parameters of lhe detector were used in lhe simulation. A complete Computerized Tomagraphy (CT) detector scan allowed to find the correct crystal dimensions and position inside the capsule. The computed efficiencies with the resulting detector model differed with the measured values no more than 10% in most of the energy range.

Reactive sputter magnetron reactor for preparation of thin films and simultaneous in-situ structural study by X-ray diffraction.

Reactive Sputter Magnetron (RSM) is a widely used technique to thin films growing of compounds both, in research laboratories and in industrial processes. The nature of the deposited compound will depend then on the nature of the magnetron target and the nature of the ions generated in the plasma. One important aspect of the problem is the knowledge of the evolution of the film during the process of growing itself. In this work, we present the design, construction of a chamber to be installed in the Huber goniometer in the XRD2 line of LNLS in Campinas, which allows in situ growing kinetic studies of thin films.

Crystallization and preliminary X-ray diffraction analysis of selenophosphate synthetases from Trypanosoma brucei and Leishmania major

Selenophosphate synthetase (SPS) plays an indispensable role in selenium metabolism, being responsible for catalyzing the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential selenium donor for selenocysteine synthesis. Recombinant full-length Leishmania major SPS (LmSPS2) was recalcitrant to crystallization. Therefore, a limited proteolysis technique was used and a stable N-terminal truncated construct (ΔN-LmSPS2) yielded suitable crystals. The Trypanosoma brucei SPS orthologue (TbSPS2) was crystallized by the microbatch method using paraffin oil. X-ray diffraction data were collected to resolutions of 1.9 Å for ΔN-LmSPS2 and 3.4 Å for TbSPS2.

Properties of gas and dark matter in X-ray galaxy clusters with Sunyaev Zel'dovich measurements

I have studied entropy profiles obtained in a sample of 24 X-ray objects at high redshift retrieved from the Chandra archive. I have discussed the scaling properties of the entropy S, the correlation between metallicity Z and S, the profiles of the temperature of the gas, Tgas, and performed a comparison between the dark matter 'temperature' and Tgas in order to constrain the non-gravitational processes which affect the thermal history of the gas. Furthermore I have studied the scaling relations between the X-ray quantities and Sunyaev Zel'dovich measurements. I have observed that X-ray laws are steeper than the relations predicted from the adiabatic model. These deviations from expectations based on self-similarity are usually interpreted in terms of feedback processes leading to non-gravitational gas heating, and suggesting a scenario in which the ICM at higher redshift has lower both X-ray luminosity and pressure in the central regions than the expectations from self-similar model. I have also investigated a Bayesian X-ray and Sunyaev Zel'dovich analysis, which allows to study the external regions of the clusters well beyond the volumes resolved with X-ray observations (1/3-1/2 of the virial radius), to measure the deprojected physical cluster properties, like temperature, density, entropy, gas mass and total mass up to the virial radius.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

X-Ray studies of the physics of matter around super-massive black-holes in nearby Seyfert galaxies

Seyfert galaxies are the closest active galactic nuclei. As such, we can use them to test the physical properties of the entire class of objects. To investigate their general properties, I took advantage of different methods of data analysis. In particular I used three different samples of objects, that, despite frequent overlaps, have been chosen to best tackle different topics: the heterogeneous BeppoS AX sample was thought to be optimized to test the average hard X-ray (E above 10 keV) properties of nearby Seyfert galaxies; the X-CfA was thought the be optimized to compare the properties of low-luminosity sources to the ones of higher luminosity and, thus, it was also used to test the emission mechanism models; finally, the XMM–Newton sample was extracted from the X-CfA sample so as to ensure a truly unbiased and well defined sample of objects to define the average properties of Seyfert galaxies. Taking advantage of the broad-band coverage of the BeppoS AX MECS and PDS instruments (between ~2-100 keV), I infer the average X-ray spectral propertiesof nearby Seyfert galaxies and in particular the photon index (~1.8), the high-energy cut-off (~290 keV), and the relative amount of cold reflection (~1.0). Moreover the unified scheme for active galactic nuclei was positively tested. The distribution of isotropic indicators used here (photon index, relative amount of reflection, high-energy cut-off and narrow FeK energy centroid) are similar in type I and type II objects while the absorbing column and the iron line equivalent width significantly differ between the two classes of sources with type II objects displaying larger absorbing columns. Taking advantage of the XMM–Newton and X–CfA samples I also deduced from measurements that 30 to 50% of type II Seyfert galaxies are Compton thick. Confirming previous results, the narrow FeK line is consistent, in Seyfert 2 galaxies, with being produced in the same matter responsible for the observed obscuration. These results support the basic picture of the unified model. Moreover, the presence of a X-ray Baldwin effect in type I sources has been measured using for the first time the 20-100 keV luminosity (EW proportional to L(20-100)^(−0.22±0.05)). This finding suggests that the torus covering factor may be a function of source luminosity, thereby suggesting a refinement of the baseline version of the unifed model itself. Using the BeppoSAX sample, it has been also recorded a possible correlation between the photon index and the amount of cold reflection in both type I and II sources. At a first glance this confirms the thermal Comptonization as the most likely origin of the high energy emission for the active galactic nuclei. This relation, in fact, naturally emerges supposing that the accretion disk penetrates, depending to the accretion rate, the central corona at different depths (Merloni et al. 2006): the higher accreting systems hosting disks down to the last stable orbit while the lower accreting systems hosting truncated disks. On the contrary, the study of the well defined X–C f A sample of Seyfert galaxies has proved that the intrinsic X-ray luminosity of nearby Seyfert galaxies can span values between 10^(38−43) erg s^−1, i.e. covering a huge range of accretion rates. The less efficient systems have been supposed to host ADAF systems without accretion disk. However, the study of the X–CfA sample has also proved the existence of correlations between optical emission lines and X-ray luminosity in the entire range of L_(X) covered by the sample. These relations are similar to the ones obtained if high-L objects are considered. Thus the emission mechanism must be similar in luminous and weak systems. A possible scenario to reconcile these somehow opposite indications is assuming that the ADAF and the two phase mechanism co-exist with different relative importance moving from low-to-high accretion systems (as suggested by the Gamma vs. R relation). The present data require that no abrupt transition between the two regimes is present. As mentioned above, the possible presence of an accretion disk has been tested using samples of nearby Seyfert galaxies. Here, to deeply investigate the flow patterns close to super-massive black-holes, three case study objects for which enough counts statistics is available have been analysed using deep X-ray observations taken with XMM–Newton. The obtained results have shown that the accretion flow can significantly differ between the objects when it is analyzed with the appropriate detail. For instance the accretion disk is well established down to the last stable orbit in a Kerr system for IRAS 13197-1627 where strong light bending effect have been measured. The accretion disk seems to be formed spiraling in the inner ~10-30 gravitational radii in NGC 3783 where time dependent and recursive modulation have been measured both in the continuum emission and in the broad emission line component. Finally, the accretion disk seems to be only weakly detectable in rk 509, with its weak broad emission line component. Finally, blueshifted resonant absorption lines have been detected in all three objects. This seems to demonstrate that, around super-massive black-holes, there is matter which is not confined in the accretion disk and moves along the line of sight with velocities as large as v~0.01-0.4c (whre c is the speed of light). Wether this matter forms winds or blobs is still matter of debate together with the assessment of the real statistical significance of the measured absorption lines. Nonetheless, if confirmed, these phenomena are of outstanding interest because they offer new potential probes for the dynamics of the innermost regions of accretion flows, to tackle the formation of ejecta/jets and to place constraints on the rate of kinetic energy injected by AGNs into the ISM and IGM. Future high energy missions (such as the planned Simbol-X and IXO) will likely allow an exciting step forward in our understanding of the flow dynamics around black holes and the formation of the highest velocity outflows.

X-ray and lensing mass estimates in galaxy clusters

In this Thesis we have presented our work on the analysis of galaxy clusters through their X-ray emission and the gravitational lensing effect that they induce. Our research work was mainly finalised to verify and possibly explain the observed mismatch between the galaxy cluster mass distributions estimated through two of the most promising techniques, i.e. the X-ray and the gravitational lensing analyses. Moreover, it is an established evidence that combined, multi-wavelength analyses are extremely effective in addressing and explaining the open issues in astronomy: however, in order to follow this approach, it is crucial to test the reliability and the limitations of the individual analysis techniques. In this Thesis we also assessed the impact of some factors that could affect both the X-ray and the strong lensing analyses.