Spectroscopic analysis of C80 doping with group III and group V elements using semiempirical PM3 molecular modelling technique

Semiempirical calculations at the level of PM3 of theory were carried out to study the structural and electronic properties of C80 and some of its doped derivatives with the elements of group III and V at the level of PM3 of theory. We have selected these elements to be substituted in the fullerene-C80 cage in order to show the effect of such structural change on the electronic properties of the molecules studied. The theoretical IR spectra, some of physical and chemical properties of the molecules studied are obtained and discussed.

HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Structural aspects of the ribosome evolution and function

Les résultats ont été obtenus avec le logiciel "Insight-2" de Accelris (San Diego, CA)

Investigations on Structural response of Water Backed Perforated plates

The study envisaged herein contains the numerical investigations on Perforated Plate (PP) as well as numerical and experimental investigations on Perforated Plate with Lining (PPL) which has a variety of applications in underwater engineering especially related to defence applications. Finite element method has been adopted as the tool for analysis of PP and PPL. The commercial software ANSYS has been used for static and free vibration response evaluation, whereas ANSYS LS-DYNA has been used for shock analysis. SHELL63, SHELL93, SOLID45, SOLSH190, BEAM188 and FLUID30 finite elements available in the ANSYS library as well as SHELL193 and SOLID194 available in the ANSYS LS-DYNA library have been made use of. Unit cell of the PP and PPL which is a miniature of the original plate with 16 perforations have been used. Based upon the convergence characteristics, the utility of SHELL63 element for the analysis of PP and PPL, and the required mesh density are brought out. The effect of perforation, geometry and orientation of perforation, boundary conditions and lining plate are investigated for various configurations. Stress concentration and deflection factor are also studied. Based on these investigations, stadium geometry perforation with horizontal orientation is recommended for further analysis.Linear and nonlinear static analysis of PP and PPL subjected to unit normal pressure has been carried out besides the free vibration analysis. Shock analysis has also been carried out on these structural components. The analytical model measures 0.9m x 0.9m with stiffener of 0.3m interval. The influence of finite element, boundary conditions, and lining plate on linear static response has been estimated and presented. Comparison of behavior of PP and PPL in the nonlinear strain regime has been made using geometric nonlinear analysis. Free vibration analysis of the PP and PPL has been carried out ‘in vacuum’ condition and in water backed condition, and the influence of water backed condition and effect of perforation on natural frequency have been investigated.Based upon the studies on the vibration characteristics of NPP, PP and PPL in water backed condition and ‘in vacuum’ condition, the reduction in the natural frequency of the plate in immersed condition has been rightly brought out. The necessity to introduce the effect of water medium in the analysis of water backed underwater structure has been highlighted.Shock analysis of PP and PPL for three explosives viz., PEK, TNT and C4 has been carried out and deflection and stresses on plate as well as free field pressure have been estimated using ANSYS LS-DYNA. The effect of perforations and the effect of lining plate have been predicted. Experimental investigations of the measurement of free field pressure using PPL have been conducted in a shock tank. Free field pressure has been measured and has been validated with finite element analysis results. Besides, an experiment has been carried out on PPL, for the comparison of the static deflection predicted by finite element analysis.The distribution of the free field pressure and the estimation of differential pressure from experimentation and the provision for treating the differential pressure as the resistance, as a part of the design load for PPL, has been brought out.

Ions of the superheavy elements in vacuum and in solution

The extension of the Periodic Table into the range of unknown atomic numbers of above one hundred requires relativistic calculations. The results of the latter are used to indicate probable values for X-ray transition lines which will be useful for identification of the atomic species formed during collision between accelerated ions and the target. If the half-lives of the isotopes are long, then the chemistry of these new species becomes an important question which is reviewed for E110, E 111 and E112. The possible structural chemistry of the elements E108 to E112 is suggested. Finally the effects of solvation on ions of the actinide and superheavy elements have been studied.

‘Boots for my Sancho’: structural vulnerability among Latin American day labourers in Berkeley, California

This paper addresses the structural vulnerability of Latin American undocumented day labourers in Northern California, as it is expressed in conversations on street corners where they wait for work. The intimate aspects of migrant experience become exemplified in jokes about the Sancho – a hypothetical character who has moved in on a day labourer's family and who enjoys the money he sends home. Joking turns to more serious topics of nostalgia and tensions with family far away, elements that come together with the fears and threats of labour on the corner and affect the way day labourers see themselves. Sexuality is rearticulated in the absence of women and masculinity becomes enmeshed in the contingencies of unregulated work and long-term separation from the people the men support. Together, these elements result in the articulation of threat to the immigrant body itself, which is exemplified by anxieties over homosexual propositions on the corner. Cet article aborde la vulnérabilité structurelle des travailleurs journaliers latino-américains sans papiers dans le Nord de la Californie, telle qu'ils l'expriment dans leurs conversations en attendant du travail aux coins des rues. Les aspects intimes de l'expérience de la migration sont exemplifiés à travers des blagues sur le Sancho – un personnage hypothétique qui, au pays natal, s'est installé dans la famille d'un journalier pour profiter de l'argent qu'elle reçoit de ce dernier. Les blagues deviennent alors des sujets de conversation plus sérieux, sur un fond de nostalgie et de tensions qui résulte de l'éloignement vis-à-vis de la famille – des éléments qui accompagnent les peurs et les menaces liées aux embauches des coins de rue et ont un impact sur la manière dont les journaliers se perçoivent. La sexualité est articulée par rapport à l'absence des femmes et la virilité s'empêtre dans les contingences du travail illégal et de la séparation sur le long terme d'avec les êtres que ces hommes soutiennent financièrement. Ensemble, tous ces éléments ont pour résultat une articulation de la menace vis-à-vis du corps de l'immigré lui-même, qui est exemplifiée par les angoisses dues aux propositions d'homosexuels aux coins des rues.

A hybrid approach of knowledge-based reasoning for structural assessment

La idea básica de detección de defectos basada en vibraciones en Monitorización de la Salud Estructural (SHM), es que el defecto altera las propiedades de rigidez, masa o disipación de energía de un sistema, el cual, altera la respuesta dinámica del mismo. Dentro del contexto de reconocimiento de patrones, esta tesis presenta una metodología híbrida de razonamiento para evaluar los defectos en las estructuras, combinando el uso de un modelo de la estructura y/o experimentos previos con el esquema de razonamiento basado en el conocimiento para evaluar si el defecto está presente, su gravedad y su localización. La metodología involucra algunos elementos relacionados con análisis de vibraciones, matemáticas (wavelets, control de procesos estadístico), análisis y procesamiento de señales y/o patrones (razonamiento basado en casos, redes auto-organizativas), estructuras inteligentes y detección de defectos. Las técnicas son validadas numérica y experimentalmente considerando corrosión, pérdida de masa, acumulación de masa e impactos. Las estructuras usadas durante este trabajo son: una estructura tipo cercha voladiza, una viga de aluminio, dos secciones de tubería y una parte del ala de un avión comercial.

Effective elements of cognitive behaviour therapy for psychosis: results of a novel type of subgroup analysis based on principal stratification

Background. Meta-analyses show that cognitive behaviour therapy for psychosis (CBT-P) improves distressing positive symptoms. However, it is a complex intervention involving a range of techniques. No previous study has assessed the delivery of the different elements of treatment and their effect on outcome. Our aim was to assess the differential effect of type of treatment delivered on the effectiveness of CBT-P, using novel statistical methodology. Method. The Psychological Prevention of Relapse in Psychosis (PRP) trial was a multi-centre randomized controlled trial (RCT) that compared CBT-P with treatment as usual (TAU). Therapy was manualized, and detailed evaluations of therapy delivery and client engagement were made. Follow-up assessments were made at 12 and 24 months. In a planned analysis, we applied principal stratification (involving structural equation modelling with finite mixtures) to estimate intention-to-treat (ITT) effects for subgroups of participants, defined by qualitative and quantitative differences in receipt of therapy, while maintaining the constraints of randomization. Results. Consistent delivery of full therapy, including specific cognitive and behavioural techniques, was associated with clinically and statistically significant increases in months in remission, and decreases in psychotic and affective symptoms. Delivery of partial therapy involving engagement and assessment was not effective. Conclusions. Our analyses suggest that CBT-P is of significant benefit on multiple outcomes to patients able to engage in the full range of therapy procedures. The novel statistical methods illustrated in this report have general application to the evaluation of heterogeneity in the effects of treatment.

The processing of number and gender agreement in Spanish: an event related potential investigation of the effects of structural distance

Previous research suggests that the processing of agreement is affected by the distance between the agreeing elements. However, the unique contribution of structural distance (number of intervening syntactic phrases) to the processing of agreement remains an open question, since previous investigations do not tease apart structural and linear distance (number of intervening words). We used event related potentials (ERPs) to examine the extent to which structural distance impacts the processing of Spanish number and gender agreement. Violations were realized both within the phrase and across the phrase. Across both levels of structural distance, linear distance was kept constant, as was the syntactic category of the agreeing elements. Number and gender agreement violations elicited a robust P600 between 400 and 900ms, a component associated with morphosyntactic processing. No amplitude differences were observed between number and gender violations, suggesting that the two features are processed similarly at the brain level. Within-phrase agreement yielded more positive waveforms than across-phrase agreement, both for agreement violations and for grammatical sentences (no agreement by distance interaction). These effects can be interpreted as evidence that structural distance impacts the establishment of agreement overall, consistent with sentence processing models which predict that hierarchical structure impacts the processing of syntactic dependencies. However, due to the lack of an agreement by distance interaction, the possibility cannot be ruled out that these effects are driven by differences in syntactic predictability between the within-phrase and across-phrase configurations, notably the fact that the syntactic category of the critical word was more predictable in the within-phrase conditions.

Morphosyntactic processing in advanced second language (L2) learners: An event-related potential investigation of the effects of L1-L2 similarity and structural distance

Different theoretical accounts of second language (L2) acquisition differ with respect to whether or not advanced learners are predicted to show native like processing for features not instantiated in the native language (L1). We examined how native speakers of English, a language with number but not gender agreement, process number and gender agreement in Spanish. We compare agreement within a determiner phrase (órgano muy complejo “[DP organ-MASC-SG very complex-MASC-SG]”) and across a verb phrase (cuadro es auténtico “painting-MASC-SG [VP is authentic-MASC-SG]”) in order to investigate whether native like processing is limited to local domains (e.g. within the phrase), in line with Clahsen and Felser (2006). We also examine whether morphological differences in how the L1 and L2 realize a shared feature impact processing by comparing number agreement between nouns and adjectives, where only Spanish instantiates agreement, and between demonstratives and nouns, where English also instantiates agreement. Similar to Spanish natives, advanced learners showed a P600 for both number and gender violations overall, in line with the Full Transfer/Full Access Hypothesis (Schwartz and Sprouse, 1996), which predicts that learners can show native-like processing for novel features. Results also show that learners can establish syntactic dependencies outside of local domains, as suggested by the presence of a P600 for both within and across phrase violations. Moreover, similar to native speakers, learners were impacted by the structural distance (number of intervening phrases) between the agreeing elements, as suggested by the more positive waveforms for within than across-phrase agreement overall. These results are consistent with the proposal that learners are sensitive to hierarchical structure.

The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria

The rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site-specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR-II virulence region of genomic island PAGI-5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

Structural and electrochemical characteristics of Mg((55-x))Ti(x)Ni((45-y))Pt(y) metal hydride electrodes

In recent years, Mg-Ni-based metastable alloys have been attracting attention due to their large hydrogen sorption capacities, low weight, low cost, and high availability. Despite the large discharge capacity and high activity of these alloys, the accelerated degradation of the discharge capacity after only few cycles of charge and discharge is the main shortcoming against their commercial use in batteries. The addition of alloying elements showed to be an effective way of improving the electrode performance of Mg-Ni-based alloys. In the present work, the effect of Ti and Pt alloying elements on the structure and electrode performance of a binary Mg-Ni alloy was investigated. The XRD and HRTEM revealed that all the investigated alloy compositions had multi-phase nanostructures, with crystallite size in the range of 6 nm. Moreover, the investigated alloying elements demonstrated remarkable improvements of both maximum discharge capacity and cycling life. Simultaneous addition of Ti and Pd demonstrated a synergetic effect on the electrochemical properties of the alloy electrodes. Among the investigated alloys, the best electrochemical performance was obtained for the Mg(51)Ti(4)Ni(43)Pt(2) composition (in at.%), which achieved 448 mAh g(-1) of maximum discharge capacity and retained almost 66% of this capacity after 10 cycles. In contrast, the binary Mg(55)Ni(45) alloy achieved only 248 mAh g(-1) and retained 11% of this capacity after 10 cycles. (C) 2010 Elsevier By. All rights reserved.

Synthesis and structural characterization of Eu(III)-doped Zn7Sb2O12

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Modeling of interfaces in two-dimensional problems using solid finite elements with high aspect ratio

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Histological aspects and structural characteristics of the testes of Dendropsophus minutus (Anura, Hylidae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)