Comparison of Experimental and Theoretical Structures of a Transition State Analogue Used for the Induction of Anti-Cocaine Catalytic Antibodies

Comparison of the crystal structure of a transition state analogue that was used to raise catalytic antibodies for the benzoyl ester hydrolysis of cocaine with structures calculated by ab initio, semiempirical, and solvation semiempirical methods reveals that modeling of solvation is crucial for replicating the crystal structure geometry. Both SM3 and SM2 calculations, starting from the crystal structure TSA I, converged on structures similar to the crystal structure. The 3-21G(*)/HF, 6-31G*/HF, PM3, and AM1 calculations converged on structures similar to each other, but these gas-phase structures were significantly extended relative to the condensed phase structures. Two transition states for the hydrolysis of the benzoyl ester of cocaine were located with the SM3 method. The gas phase calculations failed to locate reasonable transition state structures for this reaction. These results imply that accurate modeling of the potential energy surfaces for the hydrolysis of cocaine requires solvation methods.

NONLINEAR TUBE-FITTING FOR THE ANALYSIS OF ANATOMICAL AND FUNCTIONAL STRUCTURES

We are concerned with the estimation of the exterior surface of tube-shaped anatomical structures. This interest is motivated by two distinct scientific goals, one dealing with the distribution of HIV microbicide in the colon and the other with measuring degradation in white-matter tracts in the brain. Our problem is posed as the estimation of the support of a distribution in three dimensions from a sample from that distribution, possibly measured with error. We propose a novel tube-fitting algorithm to construct such estimators. Further, we conduct a simulation study to aid in the choice of a key parameter of the algorithm, and we test our algorithm with validation study tailored to the motivating data sets. Finally, we apply the tube-fitting algorithm to a colon image produced by single photon emission computed tomography (SPECT)and to a white-matter tract image produced using diffusion tensor `imaging (DTI).

Metal-oxide film and photonic structures for integrated device applications

The application of photonic crystal technology on metal-oxide film is a very promising field for future optical telecommunication systems. Band gap and polarization effects in lithium niobate (LiNbO3) photonic crystals and bismuth-substituted iron garnets (BiYIG) photonic crystals are investigated in this work reported here. The design and fabrication process are similar for these two materials while the applications are different, involving Bragg filtering in lithium niobate and polarization rotation in nonreciprocal iron garnets. The research of photonic structures in LiNbO3 is of high interest for integrated device application due to its remarkable electro-optical characteristics. This work investigated the photonic band gap in high quality LiNbO3 single crystalline thin film by ion implantation to realize high efficiency narrow bandwidth filters. LiNbO3 thin film detachment by bonding is also demonstrated for optical device integration. One-dimensional Bragg BiYIG waveguides in gyrotropic system are found to have multiple stopbands and evince enhancement of polarization rotation efficiency. Previous photon trapping theory cannot explain the phenomena because of the presence of linear birefringence. This work is aimed at investigating the mechanism with the support of experiments. The results we obtained show that selective suppression of Bloch states in gyrotropic bandgaps is the key mechanism for the observed phenomena. Finally, the research of ferroelectric single crystal PMN-PT with ultra high piezoelectric coefficient as a biosensor is also reported. This work presents an investigation and results on higher sensitivity effects than conventional materials such as quartz and lithium niobate.

Syntheses, characterization and crystal structures of a new functionalised TTF derivative and its Ni(II) complex

The new ligand 4,5-bis (2-pyridylmethylsulfanyl)-4',5'-bis(cyanoethylthio)tetrathiafulvalene (BPM-BCET-TTF) and its nickel(II) complex have been prepared and crystallographically characterized. The Ni(II) complex shows octahedral geometry around the metal ion with the coordination site occupied by the pyridyl nitrogen atoms, the thioether sulfur atoms of the ligand and cis coordination of the halide ions.

Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa revealed by cryo-electron microscopy of vitreous sections.

High-resolution structural information on optimally preserved bacterial cells can be obtained with cryo-electron microscopy of vitreous sections. With the help of this technique, the existence of a periplasmic space between the plasma membrane and the thick peptidoglycan layer of the gram-positive bacteria Bacillus subtilis and Staphylococcus aureus was recently shown. This raises questions about the mode of polymerization of peptidoglycan. In the present study, we report the structure of the cell envelope of three gram-positive bacteria (B. subtilis, Streptococcus gordonii, and Enterococcus gallinarum). In the three cases, a previously undescribed granular layer adjacent to the plasma membrane is found in the periplasmic space. In order to better understand how nascent peptidoglycan is incorporated into the mature peptidoglycan, we investigated cellular regions known to represent the sites of cell wall production. Each of these sites possesses a specific structure. We propose a hypothetic model of peptidoglycan polymerization that accommodates these differences: peptidoglycan precursors could be exported from the cytoplasm to the periplasmic space, where they could diffuse until they would interact with the interface between the granular layer and the thick peptidoglycan layer. They could then polymerize with mature peptidoglycan. We report cytoplasmic structures at the E. gallinarum septum that could be interpreted as cytoskeletal elements driving cell division (FtsZ ring). Although immunoelectron microscopy and fluorescence microscopy studies have demonstrated the septal and cytoplasmic localization of FtsZ, direct visualization of in situ FtsZ filaments has not been obtained in any electron microscopy study of fixed and dehydrated bacteria.

Variables affecting the stability of multiple cloning sites and hairpin structures in retroviral vectors

Retroviruses are RNA viruses that replicate through a double-stranded DNA intermediate. The viral enzyme reverse transcriptase copies the retroviral genomic RNA into this DNA intermediate through the process of reverse transcription. Many variables can affect the fidelity of reverse transcriptase during reverse transcription, including specific sequences within the retroviral genome. ^ Previous studies have observed that multiple cloning sites (MCS) and sequences predicted to form stable hairpin structures are hotspots for deletion during retroviral replication. The studies described in this dissertation were performed to elucidate the variables that affect the stability of MCS and hairpin structures in retroviral vectors. Two series of retroviral vectors were constructed and characterized in these studies. ^ Spleen necrosis virus-based vectors were constructed containing separate MCS insertions of varying length, orientation, and symmetry. The only MCS that was a hotspot for deletion formed a stable hairpin structure. Upon more detailed study, the MCS previously reported as a hotspot for deletion was found to contain a tandem linker insertion that formed a hairpin structure. Murine leukemia virus-based vectors were constructed containing separate sequence insertions of either inverted repeat symmetry (122IR) that could form a hairpin structure, or little symmetry (122c) that would form a less stable structure. These insertions were made into either the neomycin resistance marker ( neo) or the hygromycin resistance marker (hyg) of the vector. 122c was stable in both neo and hyg, while 122IR was preferentially deleted in neo and was remarkably unstable in hyg. ^ These results suggest that MCS are hotspots for deletion in retroviral vectors if they can form hairpin structures, and that hairpin structures can be highly unstable at certain locations in retroviral vectors. This information may contribute to improved design of retroviral vectors for such uses as human gene therapy, and will contribute to a greater understanding of the basic science of retroviral reverse transcription. ^

Abundance and community structures of heterotrophic and oligotrophic bacteria from the Sierra Leone Abbyssal Plain

Colony counts on high and low-nutrient agar media incubated at 2 and 20 °C, Acridine Orange Direct Counts and biomasses are reported for sediments of the Sierra Leone Abyssal Plain. All isolates from low-nutrient agars also grew in nutrient-rich seawater broth (100 % SWB). However, a greater proportion of the 2 °C than of the 20 °C isolates grew in 2.5% SWB, containing 125 mg/l peptone and 25 mg/l yeast extract. Only 14 strains or 12.7% of the 2 °C isolates, but none of the 20 °C isolates, grew in 0.25 % SWB. Psychrophilic bacteria with maximum growth temperatures below 12 °C, isolated at 2 °C, were predominant among the cultivable bacteria from the surface layer. They required seawater for growth and belonged mainly to the Gram-negative genera Alteromonas and Vibrio. In contrast to the earlier view that psychrophily is connected with the Gram-negative cell type, it was found that cold-adapted bacteria of the Gram-positive genus Bacillus predominated in the 4 to 6 cm layer. The 20 °C isolates, however, were mostly Gram-positive, mesophilic, not dependent on seawater for growth, not able to utilize organic substrates at 4 °C, and belonged mainly to the genus Bacillus and to the Gram-positive cocci. The majority of the mesophilic bacilli most likely evolved from dormant spores, but not from actively metabolizing cells. It can be concluded that only the strains isolated at 2 °C can be regarded as indigenous to the deep-sea.

Dynamic Studies of Shell and Spatial Structures

For the past 20 years, dynamic analysis of shells has been one of the most fascinating fields for research. Using the new light materials the building engineer soon discovered that the subsequent reduction of gravity forces produced not only the desired shape freedom but the appearance of ecologic loads as the first factor of design; loads which present strong random properties and marked dynamic influence. On the other hand, the technological advance in the aeronautical and astronautical field placed the engineers in front of shell structures of nonconventional shape and able to sustain substantialy dynamic loads. The response to the increasingly challenger problems of the last two decades has been very bright; new forms, new materials and new methods of analysis have arosen in the design of off-shore platforms, nuclear vessels, space crafts, etc. Thanks to the intensity of the lived years we have at our disposition a coherent and homogeneous amount of knowledge which enable us to face problems of inconceivable complexity when IASS was founded. The open minded approach to classical problems and the impact of the computer are, probably, important factors in the Renaissance we have enjoyed these years, and a good proof of this are the papers presented to the previous IASS meetings as well as that we are going to consider in this one. Particularly striking is the great number of papers based on a mathematical modeling in front of the meagerness of those treating laboratory experiments on physical models. The universal entering of the computer into almost every phase of our lifes, and the cost of physical models, are –may be- reasons for this lack of experimental methods. Nevertheless they continue offering useful results as are those obtained with the shaking-table in which the computer plays an essential role in the application of loads as well as in the instantaneous treatment of control data. Plates 1 and 2 record the papers presented under dynamic heading, 40% of them are from Japan in good correlation with the relevance that Japanese research has traditionally showed in this area. Also interesting is to find old friends as profesors Tanaka, Nishimura and Kostem who presented valuable papers in previous IASS conferences. As we see there are papers representative of all tendencies, even purely analytical! Better than discuss them in detail, which can be done after the authors presentation, I think we can comment in the general pattern of the dynamical approach are summarized in plate 3.

Condicionantes de la adherencia y anclaje en el refuerzo de muros de fábrica con elementos de fibras

Es cada vez más frecuente la rehabilitación de patrimonio construido, tanto de obras deterioradas como para la adecuación de obras existentes a nuevos usos o solicitaciones. Se ha considerado el estudio del refuerzo de obras de fábrica ya que constituyen un importante número dentro del patrimonio tanto de edificación como de obra civil (sistemas de muros de carga o en estructuras principales porticadas de acero u hormigón empleándose las fábricas como cerramiento o distribución con elementos autoportantes). A la hora de reparar o reforzar una estructura es importante realizar un análisis de las deficiencias, caracterización mecánica del elemento y solicitaciones presentes o posibles; en el apartado 1.3 del presente trabajo se refieren acciones de rehabilitación cuando lo que se precisa no es refuerzo estructural, así como las técnicas tradicionales más habituales para refuerzo de fábricas que suelen clasificarse según se trate de refuerzos exteriores o interiores. En los últimos años se ha adoptado el sistema de refuerzo de FRP, tecnología con origen en los refuerzos de hormigón tanto de elementos a flexión como de soportes. Estos refuerzos pueden ser de láminas adheridas a la fábrica soporte (SM), o de barras incluidas en rozas lineales (NSM). La elección de un sistema u otro depende de la necesidad de refuerzo y tipo de solicitación predominante, del acceso para colocación y de la exigencia de impacto visual. Una de las mayores limitaciones de los sistemas de refuerzo por FRP es que no suele movilizarse la resistencia del material de refuerzo, produciéndose previamente fallo en la interfase con el soporte con el consecuente despegue o deslaminación; dichos fallos pueden tener un origen local y propagarse a partir de una discontinuidad, por lo que es preciso un tratamiento cuidadoso de la superficie soporte, o bien como consecuencia de una insuficiente longitud de anclaje para la transferencia de los esfuerzos en la interfase. Se considera imprescindible una caracterización mecánica del elemento a reforzar. Es por ello que el trabajo presenta en el capítulo 2 métodos de cálculo de la fábrica soporte de distintas normativas y también una formulación alternativa que tiene en cuenta la fábrica histórica ya que su caracterización suele ser más complicada por la heterogeneidad y falta de clasificación de sus materiales, especialmente de los morteros. Una vez conocidos los parámetros resistentes de la fábrica soporte es posible diseñar el refuerzo; hasta la fecha existe escasa normativa de refuerzos de FRP para muros de fábrica, consistente en un protocolo propuesto por la ACI 440 7R-10 que carece de mejoras por tipo de anclaje y aporta valores muy conservadores de la eficacia del refuerzo. Como se ha indicado, la problemática principal de los refuerzos de FRP en muros es el modo de fallo que impide un aprovechamiento óptimo de las propiedades del material. Recientemente se están realizando estudios con distintos métodos de anclaje para estos refuerzos, con lo que se incremente la capacidad última y se mantenga el soporte ligado al refuerzo tras la rotura. Junto con sistemas de anclajes por prolongación del refuerzo (tanto para láminas como para barras) se han ensayado anclajes con llaves de cortante, barras embebidas, o anclajes mecánicos de acero o incluso de FRP. Este texto resume, en el capítulo 4, algunas de las campañas experimentales llevadas a cabo entre los años 2000 y 2013 con distintos anclajes. Se observan los parámetros fundamentales para medir la eficacia del anclajes como son: el modo de fallo, el incremento de resistencia, y los desplazamientos que permite observar la ductilidad del refuerzo; estos datos se analizan en función de la variación de: tipo de refuerzo incluyéndose el tipo de fibra y sistema de colocación, y tipo de anclaje. Existen también parámetros de diseño de los propios anclajes. En el caso de barras embebidas se resumen en diámetro y material de la barra, acabado superficial, dimensiones y forma de la roza, tipo de adhesivo. En el caso de anclajes de FRP tipo pasador la caracterización incluye: tipo de fibra, sistema de fabricación del anclajes y diámetro del mismo, radio de expansión del abanico, espaciamiento longitudinal de anclajes, número de filas de anclajes, número de láminas del refuerzo, longitud adherida tras el anclaje; es compleja la sistematización de resultados de los autores de las campañas expuestas ya que algunos de estos parámetros varían impidiendo la comparación. El capítulo 5 presenta los ensayos empleados para estas campañas de anclajes, distinguiéndose entre ensayos de modo I, tipo tracción directa o arrancamiento, que servirían para sistemas NSM o para cuantificar la resistencia individual de anclajes tipo pasador; ensayos de modo II, tipo corte simple, que se asemeja más a las condiciones de trabajo de los refuerzos. El presente texto se realiza con objeto de abrir una posible investigación sobre los anclajes tipo pasador, considerándose que junto con los sistemas de barra embebida son los que permiten una mayor versatilidad de diseño para los refuerzos de FRP y siendo su eficacia aún difícil de aislar por el número de parámetros de diseño. Rehabilitation of built heritage is becoming increasingly frequent, including repair of damaged works and conditioning for a new use or higher loads. In this work it has been considered the study of masonry wall reinforcement, as most buildings and civil works have load bearing walls or at least infilled masonry walls in concrete and steel structures. Before repairing or reinforcing an structure, it is important to analyse its deficiencies, its mechanical properties and both existing and potential loads; chapter 1, section 4 includes the most common rehabilitation methods when structural reinforcement is not needed, as well as traditional reinforcement techniques (internal and external reinforcement) In the last years the FRP reinforcement system has been adopted for masonry walls. FRP materials for reinforcement were initially used for concrete pillars and beams. FRP reinforcement includes two main techniques: surface mounted laminates (SM) and near surface mounted bars (NSM); one of them may be more accurate according to the need for reinforcement and main load, accessibility for installation and aesthetic requirements. One of the main constraints of FRP systems is not reaching maximum load for material due to premature debonding failure, which can be caused by surface irregularities so surface preparation is necessary. But debonding (or delamination for SM techniques) can also be a consequence of insufficient anchorage length or stress concentration. In order to provide an accurate mechanical characterisation of walls, chapter 2 summarises the calculation methods included in guidelines as well as alternative formulations for old masonry walls as historic wall properties are more complicated to obtain due to heterogeneity and data gaps (specially for mortars). The next step is designing reinforcement system; to date there are scarce regulations for walls reinforcement with FRP: ACI 440 7R-10 includes a protocol without considering the potential benefits provided by anchorage devices and with conservative values for reinforcement efficiency. As noted above, the main problem of FRP masonry walls reinforcement is failure mode. Recently, some authors have performed studies with different anchorage systems, finding that these systems are able to delay or prevent debonding . Studies include the following anchorage systems: Overlap, embedded bars, shear keys, shear restraint and fiber anchors. Chapter 4 briefly describes several experimental works between years 2000 and 2013, concerning different anchorage systems. The main parameters that measure the anchorage efficiency are: failure mode, failure load increase, displacements (in order to evaluate the ductility of the system); all these data points strongly depend on: reinforcement system, FRP fibers, anchorage system, and also on the specific anchorage parameters. Specific anchorage parameters are a function of the anchorage system used. The embedded bar system have design variables which can be identified as: bar diameter and material, surface finish, groove dimensions, and adhesive. In FRP anchorages (spikes) a complete design characterisation should include: type of fiber, manufacturing process, diameter, fan orientation, anchor splay width, anchor longitudinal spacing and number or rows, number or FRP sheet plies, bonded length beyond anchorage devices,...the parameters considered differ from some authors to others, so the comparison of results is quite complicated. Chapter 5 includes the most common tests used in experimental investigations on bond-behaviour and anchorage characterisation: direct shear tests (with variations single-shear and double-shear), pullout tests and bending tests. Each of them may be used according to the data needed. The purpose of this text is to promote further investigation of anchor spikes, accepting that both FRP anchors and embedded bars are the most versatile anchorage systems of FRP reinforcement and considering that to date its efficiency cannot be evaluated as there are too many design uncertainties.

Simplified serviceability design of jointless structures. Experimental verification and application to typical bridge and building structures

In this article an experimental campaign aimed at validating a previously published simplified serviceability design method of the columns of long jointless structures is presented. The proposed method is also extended to include tension stiffening effects which proved to be significant in structures with small amount of reinforcement subjected to small axial loading. This extension allows significant improvement of predictions for this type of element. The campaign involved columns with different reinforcement and squashing load ratios, given that these parameters had been identified as crucial when designing columns subjected to imposed displacements. Experimental results are presented and discussed, with particular regard to cracking behaviour and structural stiffness. Considerations on tension stiffening effects are also made. Finally, the application of the method to typical bridge and building cases is presented, showing the feasibility of jointless construction, and the limits which should be respected.