Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets

Transcriptional regulation in papillomaviruses depends on sequence-specific binding of the regulatory protein E2 to several sites in the viral genome. Crystal structures of bovine papillomavirus E2 DNA targets reveal a conformational variant of B-DNA characterized by a roll-induced writhe and helical repeat of 10.5 bp per turn. A comparison between the free and the protein-bound DNA demonstrates that the intrinsic structure of the DNA regions contacted directly by the protein and the deformability of the DNA region that is not contacted by the protein are critical for sequence-specific protein/DNA recognition and hence for gene-regulatory signals in the viral system. We show that the selection of dinucleotide or longer segments with appropriate conformational characteristics, when positioned at correct intervals along the DNA helix, can constitute a structural code for DNA recognition by regulatory proteins. This structural code facilitates the formation of a complementary protein–DNA interface that can be further specified by hydrogen bonds and nonpolar interactions between the protein amino acids and the DNA bases.

Dynamic investigation of an ancient masonry bell tower with operational modal analysis: a non-destructive experimental technique to obtain the dynamic characteristics of a structure

This paper shows the results of an experimental analysis on the bell tower of “Chiesa della Maddalena” (Mola di Bari, Italy), to better understand the structural behavior of slender masonry structures. The research aims to calibrate a numerical model by means of the Operational Modal Analysis (OMA) method. In this way realistic conclusions about the dynamic behavior of the structure are obtained. The choice of using an OMA derives from the necessity to know the modal parameters of a structure with a non-destructive testing, especially in case of cultural-historical value structures. Therefore by means of an easy and accurate process, it is possible to acquire in-situ environmental vibrations. The data collected are very important to estimate the mode shapes, the natural frequencies and the damping ratios of the structure. To analyze the data obtained from the monitoring, the Peak Picking method has been applied to the Fast Fourier Transforms (FFT) of the signals in order to identify the values of the effective natural frequencies and damping factors of the structure. The main frequencies and the damping ratios have been determined from measurements at some relevant locations. The responses have been then extrapolated and extended to the entire tower through a 3-D Finite Element Model. In this way, knowing the modes of vibration, it has been possible to understand the overall dynamic behavior of the structure.

Structural Analysis with ANSYS on Stone Constructions in the Historical Spanish Heritage

According to the importance of rehabilitation and recovery of Architectural Heritage in the live of people, this paper is aimed to strengthen the traditional methods of stone vaults calculation taking advantage of the technological characteristics of the powerful program ANSYS Workbench. As an example of this, it could find out the possible pathologies that could arise during the construction history of the building. To limit this research, the upper vault of the main chapel of the Santiago parish church in Orihuela -Alicante- is selected as a reference which is a Jeronimo Quijano´s important building work in the XVI century in the Renaissance. Moreover, it is an innovative stone masonry vault that consists of 8 double intercrossed arches with each other and braced by severies. During the seventeenth century there was a lantern in the central cap and it is unknown why it was removed. Its construction could justify the original constructive solution with intercrossed arches that freed the center to create a more enlightened and comfortable presbytery. By similarity with other Quijano’s works, it is considered a small lantern drilling the central spherical cap. It is proposed to carry out a comparative study of it with different architectural solutions from the same period and based on several common parameters such as: a vault of square plant with spherical surround, intercrossed arches, a possible lantern, the dimension of the permitted space, similar states of loads and compact limestone masonry. The three solutions are mainly differentiated by their size and the type of lantern and its comparison lets us know which one is the most resistant and stable. The other two building works maintain some connection with the Quijano's professional scope. It has selected the particular case of the Communion chapel of the Basilica in Elche (a large prismatic lantern with a large cylindrical drum that starts from the own arches and an upper hemispherical dome), for its conservation, its proximity to Orihuela and its implementation during the century XVIII. Finally, a significant Dome Spanish Renaissance complete the selection: a cross vault of the Benavides Chapel of the Saint Francisco Convent in Baeza - Jaén-, designed by Andres of Vandelvira in the sixteenth century (a large hemispherical dome that starts from the own arcs). To simplify the calculation and standardize the work that have to be contrasted, all of them were considered with some similar characteristics: 30 cm constant thickness, the intercrossed arches were specifically analyzed and had identical loads, Young's modulus and Poisson's ratio. Regarding the calculation solutions, in general terms, the compressive stresses predominate, influencing on it the joint collaboration of the filling material on the vault, the vault itself, the thick side walls, the buttresses and the top cover weight . In addition, the three solutions are suitable, being the Orihuela one the safest and the Baeza one the riskiest for its large dimensions. Thus, the idea of intercrossed arches with suitable thickness would allow carry out the heaviest lantern and this would confirm it as a Renaissance architectural typology built in stone.

Plant species, biomass and environmental characteristics of relevés along the North America Arctic bioclimate gradient

Question: How do interactions between the physical environment and biotic properties of vegetation influence the formation of small patterned-ground features along the Arctic bioclimate gradient? Location: At 68° to 78°N: six locations along the Dalton Highway in arctic Alaska and three in Canada (Banks Island, Prince Patrick Island and Ellef Ringnes Island). Methods: We analysed floristic and structural vegetation, biomass and abiotic data (soil chemical and physical parameters, the n-factor [a soil thermal index] and spectral information [NDVI, LAI]) on 147 microhabitat releves of zonalpatterned-ground features. Using mapping, table analysis (JUICE) and ordination techniques (NMDS). Results: Table analysis using JUICE and the phi-coefficient to identify diagnostic species revealed clear groups of diagnostic plant taxa in four of the five zonal vegetation complexes. Plant communities and zonal complexes were generally well separated in the NMDS ordination. The Alaska and Canada communities were spatially separated in the ordination because of different glacial histories and location in separate floristic provinces, but there was no single controlling environmental gradient. Vegetation structure, particularly that of bryophytes and total biomass, strongly affected thermal properties of the soils. Patterned-ground complexes with the largest thermal differential between the patterned-ground features and the surrounding vegetation exhibited the clearest patterned-ground morphologies.

The effect of vehicle structure characteristics on occupant restraint parameters. A parametric study. Technical report.

Mode of access: Internet.

Determination of Strouhal characteristics and power spectrum for elastically restrained H-shape sections /

Mode of access: Internet.

Functional recycling of C2 domains throughout evolution: A comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches

The C2 domain is one of the most frequent and widely distributed calcium-binding motifs. Its structure comprises an eight-stranded beta-sandwich with two structural types as if the result of a circular permutation. Combining sequence, structural and modelling information, we have explored, at different levels of granularity, the functional characteristics of several families of C2 domains. At the coarsest level,the similarity correlates with key structural determinants of the C2 domain fold and, at the finest level, with the domain architecture of the proteins containing them, highlighting the functional diversity between the various subfamilies. The functional diversity appears as different conserved surface patches throughout this common fold. In some cases, these patches are related to substrate-binding sites whereas in others they correspond to interfaces of presumably permanent interaction between other domains within the same polypeptide chain. For those related to substrate-binding sites, the predictions overlap with biochemical data in addition to providing some novel observations. For those acting as protein-protein interfaces' our modelling analysis suggests that slight variations between families are a result of not only complementary adaptations in the interfaces involved but also different domain architecture. In the light of the sequence and structural genomic projects, the work presented here shows that modelling approaches along with careful sub-typing of protein families will be a powerful combination for a broader coverage in proteomics. (C) 2003 Elsevier Ltd. All rights reserved.

Modelling the input-output behaviour of piezoelectric structural health monitoring systems for composite plates

This paper investigates the input-output characteristics of structural health monitoring systems for composite plates based on permanently attached piezoelectric transmitter and sensor elements. Using dynamic piezoelectricity theory and a multiple integral transform method to describe the propagating and scattered flexural waves an electro-mechanical model for simulating the voltage input-output transfer function for circular piezoelectric transmitters and sensors adhesively attached to an orthotropic composite plate is developed. The method enables the characterization of all three physical processes, i.e. wave generation, wave propagation and wave reception. The influence of transducer, plate and attached electrical circuit characteristics on the voltage output behaviour of the system is examined through numerical calculations, both in frequency and the time domain. The results show that the input-output behaviour of the system is not properly predicted by the transducers' properties alone. Coupling effects between the transducers and the tested structure have to be taken into account, and adding backing materials to the piezoelectric elements can significantly improve the sensitivity of the system. It is shown that in order to achieve maximum sensitivity, particular piezoelectric transmitters and sensors need to be designed according to the structure to be monitored and the specific frequency regime of interest.

Reflection of structural waves at a solid/liquid interface

This paper investigates the reflection characteristics of structural or guided waves in rods at a solid/liquid interface. Structural waves, whose wavelengths are much larger than the diameter of the rod, are described in a first approximation by classical one-dimensional wave theory. The reflection characteristics of such waves at a solid/liquid (melting) interface has been reported by two different ultrasonic measurement techniques: first, measuring the fast regression rate of a melting interface during the burning of metal rod samples in an oxygen-enriched environment, and second, monitoring the propagation of the solid/liquid interface during the slow melting and solidification of a rod sample in a furnace. The second work clearly shows that the major reflection occurs from the solid/liquid interface and not the liquid/gas interface as predicted by plane longitudinal wave reflectivity theory. The present work confirms this observation by reporting on the results of some specially designed experiments to identify the main interface of reflection for structural waves in rods. Hence, it helps in explaining the fundamental discrepancy between the reflection characteristics at a solid/liquid interface between low frequency structural waves and high frequency bulk waves, and confirms that the detected echo within a burning metallic rod clearly represents a reflection from the solid/liquid interface. (C) 2003 Elsevier Science B.V. All rights reserved.

The structural characterization of carbon molecular sieve membrane (CMSM) via gas adsorption

The microstructure of a carbon molecular sieve membrane (CMSM) is characterized using adsorption equilibrium information. The pore size distributions of the CMSM derived from N-2 and CH4 adsorption isotherm are found to be consistent with each other and in agreement with the results of gas permeation experiments as well as the general characteristics of such molecular sieve materials. (C) 2003 Elsevier B.V. All rights reserved.

Functional-structural plant modelling using a combination of architectural analysis, L-systems and a canonical model of function

This paper presents a new method for producing a functional-structural plant model that simulates response to different growth conditions, yet does not require detailed knowledge of underlying physiology. The example used to present this method is the modelling of the mountain birch tree. This new functional-structural modelling approach is based on linking an L-system representation of the dynamic structure of the plant with a canonical mathematical model of plant function. Growth indicated by the canonical model is allocated to the structural model according to probabilistic growth rules, such as rules for the placement and length of new shoots, which were derived from an analysis of architectural data. The main advantage of the approach is that it is relatively simple compared to the prevalent process-based functional-structural plant models and does not require a detailed understanding of underlying physiological processes, yet it is able to capture important aspects of plant function and adaptability, unlike simple empirical models. This approach, combining canonical modelling, architectural analysis and L-systems, thus fills the important role of providing an intermediate level of abstraction between the two extremes of deeply mechanistic process-based modelling and purely empirical modelling. We also investigated the relative importance of various aspects of this integrated modelling approach by analysing the sensitivity of the standard birch model to a number of variations in its parameters, functions and algorithms. The results show that using light as the sole factor determining the structural location of new growth gives satisfactory results. Including the influence of additional regulating factors made little difference to global characteristics of the emergent architecture. Changing the form of the probability functions and using alternative methods for choosing the sites of new growth also had little effect. (c) 2004 Elsevier B.V. All rights reserved.

Characteristics of left ventricular diastolic dysfunction in the community: an echocardiographic survey

Objective: To determine the prevalence and predictors of left ventricular (LV) diastolic dysfunction in older adults. Design, setting and participants: A cross-sectional survey of 1275 randomly selected residents of Canberra, aged 60 to 86 years (mean age 69.4; 50% men), conducted between February 2002 and June 2003. Main outcome measures: Prevalence of LV diastolic dysfunction as characterised by comprehensive Doppler echocardiography. Results: The prevalence of any diastolic dysfunction was 34.7% (95% CI 32.1% to 37.4%) and that of moderate to severe diastolic dysfunction was 7.3% (95% CI 5.9% to 8.9%). Of subjects with moderate to severe diastolic dysfunction, 77.4% had an LV ejection fraction (EF) > 50% and 76.3% were in a preclinical stage of disease. Predictors of diastolic dysfunction were higher age (p < 0.0001), reduced EF (p < 0.0001), obesity (p < 0.0001) and a history of hypertension (p < 0.0001), diabetes (p = 0.02) and myocardial infarction (p = 0.003). Moderate to severe diastolic dysfunction with normal EF, although predominantly preclinical, was independently associated with increased LV mass (p < 0.0001), left atrial volume (p < 0.0001), and circulating amino-terminal pro-B-type natriuretic peptide concentrations (p < 0.0001), and with decreased quality of life (p < 0.005). Conclusion: Diastolic dysfunction is common in the community and often unaccompanied by overt congestive heart failure. Despite the lack of symptoms, advanced diastolic dysfunction with normal EF is associated with reduced quality of life and structural abnormalities that reflect increased cardiovascular risk.

Structural and cellular characterization of Idiopathic Pulmonary Fibrosis

La Fibrosi Polmonare Idiopatica (IPF) è una malattia polmonare cronica, irreversibile la cui eziologia risulta essere ignota, caratterizzata da un processo fibrotico progressivo che inizia nel tratto respiratorio inferiore. Le persone affette da IPF presentano età media compresa tra 55 e 77 anni. L’incidenza annuale di IPF è stata recentemente stimata tra 14 e 42,7 casi per 100.000 persone e tale dato risulta essere in aumento. IPF fa parte delle malattie Polmonari Idiopatiche Interstiziali (IIP) che comprendono patologie con quadri istologici e clinici differenti. Le affezioni su cui si concentrerà questo studio sono: UIP (Usual Interstitial Pneumonia) caratterizzata da fibrosi interstiziale e dalla presenza di foci fibrotici connessi alla pleura e corrispondente al quadro anatomopatologico della maggior parte dei casi di IPF; NSIP (Non Specific Interstitial Pneumonia) simile alla UIP ma con maggiore uniformità temporale e spaziale delle manifestazioni; Sarcoidosi, malattia granulomatosa ad eziologia ignota. Attualmente la gravità della IPF, che implica una mortalità del 50% dei pazienti a 5 anni dall’esordio, e la scarsa efficacia farmacologica nel rallentarne la progressione vedono il trapianto polmonare come unica possibilità di sopravvivenza nelle forme più severe. Al momento non è chiaro il meccanismo patogenetico di insorgenza e progressione della IPF anche se sono stati individuati alcuni fattori scatenanti quali fumo di sigaretta, infezioni respiratorie e inquinanti atmosferici; tuttavia nessuno di tali elementi può da solo determinare un così esteso e progressivo rimodellamento del parenchima polmonare. Numerose sono le evidenze di come il substrato genetico, le alterazioni del rapporto morte/proliferazione cellulare e le citochine svolgano un ruolo nella genesi e nella progressione della malattia, ma non sono ancora chiari i fenomeni biologico-cellulari che la sostengono e, quindi, quali siano i punti di attacco per poter incidere terapeuticamente nel modificare l’evoluzione della IPF. Poiché il nostro laboratorio ha partecipato alla scoperta dell’esistenza di cellule staminali nel polmone umano normale, uno degli obiettivi finali di questo progetto si basa sull’ipotesi che un’alterazione del compartimento staminale svolga un ruolo cruciale nella eziopatogenesi di IPF. Per questo in precedenti esperienze abbiamo cercato di identificare nella IPF cellule che esprimessero antigeni associati a staminalità quali c-kit, CD34 e CD133. Questo lavoro di tesi si è proposto di condurre un’indagine morfometrica ed immunoistochimica su biopsie polmonari provenienti da 9 pazienti affetti da UIP, 3 da NSIP e 5 da Sarcoidosi al fine di valutare le alterazioni strutturali principali imputabili alle patologie. Preparati istologici di 8 polmoni di controllo sono stati usati come confronto. Come atteso, è stato osservato nelle tre patologie esaminate (UIP, NSIP e Sarcoidosi) un significativo incremento nella sostituzione del parenchima polmonare con tessuto fibrotico ed un ispessimento dei setti alveolari rispetto ai campioni di controllo. L’analisi dei diversi pattern di fibrosi presenti fa emergere come vi sia una netta differenza tra le patologie con una maggiore presenza di fibrosi di tipo riparativo e quindi altamente cellulata nei casi di UIP, e NSIP mentre nelle Sarcoidosi il pattern maggiormente rappresentato è risultato essere quello della fibrosi replacement o sostitutiva. La quantificazione delle strutture vascolari è stata effettuata tenendo separate le aree di polmone alveolare rispetto a quelle occupate da focolai sostitutivi di danno (componente fibrotica). Nei campioni patologici analizzati era presente un significativo riarrangiamento di capillari, arteriole e venule rispetto al polmone di controllo, fenomeno principalmente riscontrato nel parenchima fibrotico. Tali modifiche erano maggiormente presenti nei casi di NSIP da noi analizzati. Inoltre le arteriole subivano una diminuzione di calibro ed un aumento dello spessore in special modo nei polmoni ottenuti da pazienti affetti da Sarcoidosi. Rispetto ai controlli, nella UIP e nella Sarcoidosi i vasi linfatici risultavano inalterati nell’area alveolare mentre aumentavano nelle aree di estesa fibrosi; quadro differente si osservava nella NSIP dove le strutture linfatiche aumentavano in entrambe le componenti strutturali. Mediante indagini immunoistochimiche è stata documentata la presenza e distribuzione dei miofibroblasti, positivi per actina muscolare liscia e vimentina, che rappresentano un importante componente del danno tissutale nella IPF. La quantificazione di questo particolare fenotipo è attualmente in corso. Abbiamo inoltre analizzato tramite immunoistochimica la componente immunitaria presente nei campioni polmonari attraverso la documentazione dei linfociti T totali che esprimono CD3, andando poi a identificare la sottopopolazione di T citotossici esprimenti la glicoproteina CD8. La popolazione linfocitaria CD3pos risultava notevolmente aumentata nelle tre patologie analizzate soprattutto nei casi di UIP e Sarcoidosi sebbene l`analisi della loro distribuzione tra i vari distretti tissutali risultasse differente. Risultati simili si sono ottenuti per l`analisi dei linfociti CD8pos. La componente monocito-macrofagica è stata invece identificata tramite la glicoproteina CD68 che ha messo in evidenza una maggiore presenza di cellule positive nella Sarcoidosi e nella UIP rispetto ai casi di NSIP. I dati preliminari di questo studio indicano che il rimodellamento strutturale emo-linfatico e cellulare infiammatorio nella UIP si differenziano rispetto alle altre malattie interstiziali del polmone, avanzando l’ipotesi che il microambiente vascolare ed immunitario giochino un ruolo importante nella patogenesi della malattia

Structural behaviour and design of load-bearing falsework

Tne object of this research was to investigate the behaviour of birdcage scaffolding as used in falsework structures, assess the suitability of existing design methods and make recommendations for a set of design rules. Since excessive deflection is as undesirable in a structure as total collapse, the project was divided into two sections. These were to determine the ultimate vertical and horizontal load-carrying capacity and also the deflection characteristics of any falsework. So theoretical analyses were developed to ascertain the ability of both the individual standards to resist vertical load, and of the bracing to resist horizontal load.Furthermore a model was evolved which would predict the horizontal deflection of a scaffold under load using strain energy methods. These models were checked by three series of experiments. The first was on individual standards under vertical load only. The second series was carried out on full scale falsework structures loading vertically and horizontally to failure. Finally experiments were conducted on scaffold couplers to provide additional verification of the method of predicting deflections. This thesis gives the history of the project and an introduction into the field of scaffolding. It details both the experiments conducted and the theories developed and the correlation between theory and experiment. Finally it makes recommendations for a design method to be employed by scaffolding designers.

Structural design of contact lens-based drug delivery systems; in vitro and in vivo studies of ocular triggering mechanisms

This study identifies and investigates the potential use of in-eye trigger mechanisms to supplement the widely available information on release of ophthalmic drugs from contact lenses under passive release conditions. Ophthalmic dyes and surrogates have been successfully employed to investigate how these factors can be drawn together to make a successful system. The storage of a drug-containing lens in a pH lower than that of the ocular environment can be used to establish an equilibrium that favours retention of the drug in the lens prior to ocular insertion. Although release under passive conditions does not result in complete dye elution, the use of mechanical agitation techniques which mimic the eyelid blink action in conjunction with ocular tear chemistry promotes further release. In this way differentiation between passive and triggered in vitro release characteristics can be established. Investigation of the role of individual tear proteins revealed significant differences in their ability to alter the equilibrium between matrix-held and eluate-held dye or drug. These individual experiments were then investigated in vivo using ophthalmic dyes. Complete elution was found to be achievable in-eye; this demonstrated the importance of that fraction of the drug retained under passive conditions and the triggering effect of in-eye conditions on the release process. Understanding both the structure-property relationship between drug and material and in-eye trigger mechanisms, using ophthalmic dyes as a surrogate, provides the basis of knowledge necessary to design ocular drug delivery vehicles for in-eye release in a controllable manner.