Evaluation of the sonically induced narrowing of nuclear magnetic resonance spectra of solids

The Nuclear Magnetic Resonance (NMR) spectra of liquids contain a wealth of quantitative information that may be derived, for instance, from chemical shifts and spin-spin couplings. The available information depends on the incoherent rapid molecular motion that causes complicating effects present in the solid state to average to zero. Whereas liquid state NMR spectra show narrow lines, the corresponding NMR spectra from the solid state are normally composed of exceedingly broad resonance lines due to highly restricted molecular motion. It is, therefore, difficult to obtain directly as detailed information from the spectra of solids as from those derived from the liquid state. Studies on a new technique (SINNMR, the sonically induced narrowing of the NMR spectra of solids) to remove line broadening effects in the NMR spectra of the solid state are reported within this thesis. SINNMR involves narrowing the NMR absorptions from solid particles by irradiating them with ultrasound when they are suspended in a support liquid. It is proposed that ultrasound induces incoherent motion of the suspended particles, producing motional characteristics of the particles similar to those of rather large molecules. The first report of apparently successful experiments involving SINNMR[1] emphasised both the irreproducibility of the technique and the uncertainty regarding its true origin. If SINNMR can be made reproducible and the effect definitively attributed to the sonically induced incoherent motional averaging of particles, the technique could offer a simple alternative to the now classical magic-angle spinning (MAS) NMR[2] and the recently reported dynamic angle spinning (DAS)[3] and double rotation (DOR)[4] techniques. Evidence is presented in this thesis to support the proposal that ultrasound may be used to narrow the NMR spectral resonances from solids by inducing incoherent motion of particles suspended in support liquids and, additionally, for some solids, by inducing rotational motion of molecular constituents in the lattices of solids. Successful SINNMR line narrowing using 20 kHz ultrasound is reported for a variety of samples: including trisodium orthophosphate, polytetrafluoroethylene and aluminium alloys. Investigations of SINNMR line narrowing in trisodium phosphate have revealed the relationship between ultrasonic power, particle size and support liquid density for the production of optimum SINNMR conditions. It is also proposed that the incoherent motion of particles induced by 20 kHz ultrasound can originate from interactions between acoustically induced cavitation microjets and particles.

From detection of complex motion to descriptions of moving surfaces in human vision

A preliminary study by Freeman et al (1996b) has suggested that when complex patterns of motion elicit impressions of 2-dimensionality, odd-item-out detection improves given targets can be differentiated on the basis of surface properties. Their results can be accounted for, it if is supposed that observers are permitted efficient access to 3-D surface descriptions but access to 2-D motion descriptions is restricted. To test the hypothesis, a standard search technique was employed, in which targets could be discussed on the basis of slant sign. In one experiment, slant impressions were induced through the summing of deformation and translation components. In a second theory were induced through the summing of shear and translation components. Neither showed any evidence of efficient access. A third experiment explored the possibility that access to these representations may have been hindered by a lack of grouping between the stimuli. Attempts to improve grouping failed to produce convincing evidence in support of life. An alternative explanation is that complex patterns of motion are simply not processed simultaneously. Psychophysical and physiological studies have, however, suggested that multiple mechanisms selective for complex motion do exist. Using a subthreshold summation technique I found evidence supporting the notion that complex motions are processed in parallel. Furthermore, in a spatial summation experiment, coherence thresholds were measured for displays containing different numbers of complex motion patches. Consistent with the idea that complex motion processing proceeds in parallel, increases in the number of motion patches were seen to decrease thresholds, both for expansion and rotation. Moreover, the rates of decrease were higher than those typically expected from probability summation, thus implying mechanisms are available, which can pool signals from spatially distinct complex motion flows.

Easy preoperative planning of deeply located brain lesions using external skin reference and 3-Dimensional surface MRI

Open skull surgery of deeply located intracerebral lesions requires precise determination of the treatment area in 3-dimensional (3-D) space. 3-D MRI can give important additional information in presurgical determination of the surgical approach to the target, taking into account highly functional brain areas and important vascular structures. The day before surgery, a grid composed of 9 tubings intersecting at 90° at 1 cm intervals and filled with a Q1SO4 solution is firmly attached to the skin of the patient’s head in the presumed region of the craniotomy. A 3-D turbo-FLASH sequence is then performed in the sagittal plane after intravenous Gd-DOTA injection on a IT Magnetom. 3-D surface reconstruction of the cortical gyri and sulci is performed. Once the gyri are identified, the 3-D program is then implemented in order to perform a color display of the cortical veins and of the tumor boundaries. The surgical access is then chosen by the surgeon, taking into account highly functional areas. Finally, the boundaries of the tumor are projected on the cortex reconstruction and on the external reference placed on the skin. The entry place for surgery as well as the size of craniotomy are drawn on the skin and the tubed grid is removed. The accuracy of this method tested in 9 patients with deeply located brain tumors or arteriovenous malformations was very satisfactory. In daily practice, this method is a valuable technique providing important clinical information in determining the shortest and safest way through the brain tissue, decreasing possible functional deficit and reducing craniotomy size in cases of difficult to access deep brain areas. Our method does not require a stereotactic frame permanently fixed to the head of the patient during surgery. © 1994 S. Karger AG, Basel.

STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain cap-independent translation elements (CITEs) within their 3´ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (kl-TSS) can simultaneously bind to ribosomes and associate with the 5´ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3´ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques.

Proposição, validação e aplicação de um novo metodo para analise cinematica tridimensional da movimentação da caixa toracica durante a respiração

Universidade Estadual de Campinas . Faculdade de Educação Física

Reprodutibilidade das mensurações da espessura das tábuas ósseas na tomografia computadorizada Cone-Beam utilizando diferentes protocolos de aquisição de imagem

INTRODUÇÃO: quanto menor a dimensão do voxel, maior a nitidez da imagem de tomografia computadorizada Cone-Beam (TCCB), porém, maior a dose de radiação emitida. OBJETIVOS: avaliar e comparar a reprodutibilidade da mensuração da espessura das tábuas ósseas vestibular e lingual em imagens de TCCB, utilizando diferentes protocolos de aquisição de imagem com variação da dimensão do voxel. MÉTODOS: exames de TCCB foram tomados de 12 mandíbulas humanas secas, com dimensão do voxel de 0,2; 0,3 e 0,4mm, no aparelho i-CAT Cone-Beam 3-D Dental Imaging System. No software i-CAT Viewer, foi mensurada a espessura das tábuas ósseas vestibular e lingual, em um corte axial passando 12mm acima do forame mentoniano do lado direito. A reprodutibilidade intraexaminador foi avaliada por meio da aplicação do teste t pareado. Para a comparação interexaminadores, foi utilizado o teste t independente. Os resultados foram considerados com o nível de significância de 5%. RESULTADOS: observou-se uma excelente reprodutibilidade interexaminadores para os três protocolos avaliados. A reprodutibilidade intraexaminadores foi muito boa, com exceção de algumas regiões dos dentes anteriores, que mostraram diferenças estatisticamente significativas, independentemente da dimensão do voxel. CONCLUSÃO: a mensuração da espessura das tábuas ósseas vestibular e lingual em imagens de TCCB mostrou boa precisão para exames obtidos com voxel de 0,2; 0,3 ou 0,4mm. A reprodutibilidade das mensurações na região anterior da mandíbula foi mais crítica do que na região posterior.

Embryonic, Larval, and Juvenile Development of the Sea Biscuit Clypeaster subdepressus (Echinodermata: Clypeasteroida)

Sea biscuits and sand dollars diverged from other irregular echinoids approximately 55 million years ago and rapidly dispersed to oceans worldwide. A series of morphological changes were associated with the occupation of sand beds such as flattening of the body, shortening of primary spines, multiplication of podia, and retention of the lantern of Aristotle into adulthood. To investigate the developmental basis of such morphological changes we documented the ontogeny of Clypeaster subdepressus. We obtained gametes from adult specimens by KCl injection and raised the embryos at 26 degrees C. Ciliated blastulae hatched 7.5 h after sperm entry. During gastrulation the archenteron elongated continuously while ectodermal red-pigmented cells migrated synchronously to the apical plate. Pluteus larvae began to feed in 3 d and were similar to 20 d old at metamorphosis; starved larvae died 17 d after fertilization. Postlarval juveniles had neither mouth nor anus nor plates on the aboral side, except for the remnants of larval spicules, but their bilateral symmetry became evident after the resorption of larval tissues. Ossicles of the lantern were present and organized in 5 groups. Each group had 1 tooth, 2 demipyramids, and 2 epiphyses with a rotula in between. Early appendages consisted of 15 spines, 15 podia (2 types), and 5 sphaeridia. Podial types were distributed in accordance to Loven's rule and the first podium of each ambulacrum was not encircled by the skeleton. Seven days after metamorphosis juveniles began to feed by rasping sand grains with the lantern. Juveniles survived in laboratory cultures for similar to 9 months and died with <500 mu m wide, a single open sphaeridium per ambulacrum, aboral anus, and no differentiated food grooves or petaloids. Tracking the morphogenesis of early juveniles is a necessary step to elucidate the developmental mechanisms of echinoid growth and important groundwork to clarify homologies between irregular urchins.

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

Background: Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBP(II)), which is the most variable segment of the protein. Methods: To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBP(II) in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBP(II), and T-and B-cell epitopes were localized on the 3-D structure. Results: The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBP(II), and (ii) PvDBP(II) appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions: This study shows that some polymorphisms of PvDBP(II) are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.

Three-dimensional visualization of human hemoglobin phenotypes with HPLC

Hemoglobinopathies were included in the Brazilian Neonatal Screening Program on June 6, 2001. Automated high-performance liquid chromatography (HPLC) was indicated as one of the diagnostic methods. The amount of information generated by these systems is immense, and the behavior of groups cannot always be observed in individual analyses. Three-dimensional (3-D) visualization techniques can be applied to extract this information, for extracting patterns, trends or relations from the results stored in databases. We applied the 3-D visualization tool to analyze patterns in the results of hemoglobinopathy based on neonatal diagnosis by HPLC. The laboratory results of 2520 newborn analyses carried out in 2001 and 2002 were used. The ""Fast"", ""F1"", ""F"" and ""A"" peaks, which were detected by the analytical system, were chosen as attributes for mapping. To establish a behavior pattern, the results were classified into groups according to hemoglobin phenotype: normal (N = 2169), variant (N = 73) and thalassemia (N = 279). 3-D visualization was made with the FastMap DB tool; there were two distribution patterns in the normal group, due to variation in the amplitude of the values obtained by HPLC for the F1 window. It allowed separation of the samples with normal Hb from those with alpha thalassemia, based on a significant difference (P < 0.05) between the mean values of the ""Fast"" and ""A"" peaks, demonstrating the need for better evaluation of chromatograms; this method could be used to help diagnose alpha thalassemia in newborns.

Programmable diagnostic devices made from paper and tape

This paper describes three-dimensional microfluidic paper-based analytical devices (3-D mu PADs) that can be programmed (postfabrication) by the user to generate multiple patterns of flow through them. These devices are programmed by pressing single-use 'on' buttons, using a stylus or a ballpoint pen. Pressing a button closes a small space (gap) between two vertically aligned microfluidic channels, and allows fluids to wick from one channel to the other. These devices are simple to fabricate, and are made entirely out of paper and double-sided adhesive tape. Programmable devices expand the capabilities of mu PADs and provide a simple method for controlling the movement of fluids in paper-based channels. They are the conceptual equivalent of field-programmable gate arrays (FPGAs) widely used in electronics.

A novel aerobic-anoxic biological filter for nitrogen removal from UASB effluent using biogas compounds as electron donors for denitrification

The performance of a new trickling filter (TF) configuration composed of an upper compartment for nitrification and a lower compartment for denitrification of effluent from a UASB reactor treating domestic sewage was evaluated. The TF was packed with new plastic material characterized by its durability and high percentage of void spaces. The feasibility of using the reduced compounds present in the biogas produced by a UASB reactor as electron donor for denitrification was also evaluated. Efficient nitrification and denitrification was achieved for the mean hydraulic (5.6 m(3) m(-2) d(-1)) organic (0.26 kg COD m(-3) d(-1)) and ammonia-N (0.08 kg m(-3) d(-1)) loading rates applied, resulting in ammonia-N removal ranging from 60 to 74%. The final effluent presented ammonia-N lower than 13 mg L(-1). Despite the presence of dissolved oxygen (DO) in the denitrification compartment, its performance was considered quite satisfactory and final nitrate concentrations were lower than 10 mg L(-1). The results indicate that methane was the main electron donor used for denitrification. Additionally, denitrification can probably be improved by avoiding high DO concentration in the denitrification compartment and by enhancing biogas transfer in the anoxic zone.

Harmonic Distortion of Unstrained and Strained FinFETs Operating in Saturation

The harmonic distortion (HD) exhibited by un-strained and biaxially strained fin-shaped field-effect transistors operating in saturation as single-transistor amplifiers has been investigated for devices with different channel lengths L and fin widths W(fin). The study has been performed through device characterization, 3-D device simulations, and modeling. Nonlinearity has been evaluated in terms of second- and third-order HDs (HD2 and HD3, respectively), and a discussion on its physical sources has been carried out. Also, the influence of the open-loop voltage gain AV in HD has been observed.

Using Reverberation to Improve Range and Elevation Discrimination for Small Array Sound Source Localization

Sound source localization (SSL) is an essential task in many applications involving speech capture and enhancement. As such, speaker localization with microphone arrays has received significant research attention. Nevertheless, existing SSL algorithms for small arrays still have two significant limitations: lack of range resolution, and accuracy degradation with increasing reverberation. The latter is natural and expected, given that strong reflections can have amplitudes similar to that of the direct signal, but different directions of arrival. Therefore, correctly modeling the room and compensating for the reflections should reduce the degradation due to reverberation. In this paper, we show a stronger result. If modeled correctly, early reflections can be used to provide more information about the source location than would have been available in an anechoic scenario. The modeling not only compensates for the reverberation, but also significantly increases resolution for range and elevation. Thus, we show that under certain conditions and limitations, reverberation can be used to improve SSL performance. Prior attempts to compensate for reverberation tried to model the room impulse response (RIR). However, RIRs change quickly with speaker position, and are nearly impossible to track accurately. Instead, we build a 3-D model of the room, which we use to predict early reflections, which are then incorporated into the SSL estimation. Simulation results with real and synthetic data show that even a simplistic room model is sufficient to produce significant improvements in range and elevation estimation, tasks which would be very difficult when relying only on direct path signal components.

Junctionless Multiple-Gate Transistors for Analog Applications

This paper presents the evaluation of the analog properties of nMOS junctionless (JL) multigate transistors, comparing their performance with those exhibited by inversion-mode (IM) trigate devices of similar dimensions. The study has been performed for devices operating in saturation as single-transistor amplifiers, and we have considered the dependence of the analog properties on fin width W(fin) and temperature T. Furthermore, this paper aims at providing a physical insight into the analog parameters of JL transistors. For that, in addition to device characterization, 3-D device simulations were performed. It is shown that, depending on gate voltage, JL devices can present both larger Early voltage V(EA) and larger intrinsic voltage gain A(V) than IM devices of similar dimensions. In addition, V(EA) and A(V) are always improved in JL devices when the temperature is increased, whereas they present a maximum value around room temperature for IM transistors.