The effects of sequence context on DNA curvature.

Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.

Material and efficient cause interpretations of the formative model:resolving misunderstandings and clarifying conceptual language

This paper presents a causal explanation of formative variables that unpacks and clarifies the generally accepted idea that formative indicators are ‘causes’ of the focal formative variable. In doing this, we explore the recent paper by Diamantopoulos and Temme (AMS Review, 3(3), 160-171, 2013) and show that the latter misunderstand the stance of Lee, Cadogan, and Chamberlain (AMS Review, 3(1), 3-17, 2013; see also Cadogan, Lee, and Chamberlain, AMS Review, 3(1), 38-49, 2013). By drawing on the multiple ways that one can interpret the idea of causality within the MIMIC model, we then demonstrate how the continued defense of the MIMIC model as a tool to validate formative indicators and to identify formative variables in structural models is misguided. We also present unambiguous recommendations on how formative variables can be modelled in lieu of the formative MIMIC model.

A Public-Private Partnership strukturális modelljeinek összevetése = Comparison of Public-Private Partnership models

A tanulmány a PPP különböző strukturális modelljeinek csoportosítását mutatja be, az egyes típusok rövid rendszerező áttekintésével. A tipológiák vizsgálata hasznos ahhoz, hogy a PPP projektek struktúrájának kialakításakor a különböző lehetőségeket mérlegelni tudjuk. Többféle megközelítésben lehet a modelleket tipizálni. Az együttműködés célja alapján a hatékonyság-, a minőség- és a finanszírozás-orientált modellek a legelterjedtebbek, a kockázatmegosztás módja alapján BOT, DBFO és koncessziós változatok, a haszonmegosztás szabályozása alapján árplafon-szabályozású, közvetlen haszonszabályozású, fixdíjas és árnyékáras megoldások a leginkább bevettek. A tanulmány ezek elemző bemutatása alapján arra a következtetésre jut, hogy a gyakorlati megoldások a legtöbb esetben az elméleti típusok valamilyen kombinációját tartalmazzák, a konkrét eset feltételeinek megfelelően. Így a gyakorlatban a fix tipológiák helyett alkalmasabb úgy megközelítenünk a PPP-t, mint egy folyamatosan változó, a helyi igényekhez idomuló jelenséget. A haszonszabályozó tipológia kapcsán a tanulmány melléklete rövid áttekintést nyújt a PPP esetében kritikus méltányos haszon becslésének lehetséges megoldásairól is. = This study shows a categorization of the different structural models of Public-Private Partnership (PPP) projects. The typologies are useful to assess the available options when decisions on PPP project structures are made. There are different categorizing aspects. Based ont he key purpose of the partnership there are efficiency, quality and financing focused models. From a risk sharing point of view, BOT, DBFO and concession models are most typical. Regarding the regulation of returns price-cap models, ’open book’ models, fixed price and shadow pricing models are most common. Based on the analytical assessment of these, they study concludes that actual projects are mostly a combination of theoretical types, as required by the given case. Therefore in practice, it is more appropriate to approach PPP projects as a constantly shaping concept, adjustable to particular conditions. Supporting the approaches to the regulation of returns, an appendix of the study summarizes the different methods to estimate fair returns, a critical issue in PPP projects.

Centrifuge modeling of oblique pipe-soil interaction in dense and loose sand

Due to relative ground movement, buried pipelines experience geotechnical loads. The imposed geotechnical loads may initiate pipeline deformations that affect system serviceability and integrity. Engineering guidelines (e.g., ALA, 2005; Honegger and Nyman, 2001) provide the technical framework to develop idealized structural models to analyze pipe‒soil interaction events and assess pipe mechanical response. The soil behavior is modeled using discrete springs that represent the geotechnical loads per unit pipe length developed during the interaction event. Soil forces are defined along three orthogonal directions (i.e., axial, lateral and vertical) to analyze the response of pipelines. Nonlinear load-displacement relationships of soil defined by a spring, is independent of neighboring spring elements. However, recent experimental and numerical studies demonstrate significant coupling effects during oblique (i.e., not along one of the orthogonal axes) pipe‒soil interaction events. In the present study, physical modeling using a geotechnical centrifuge was conducted to improve the current understanding of soil load coupling effects of buried pipes in loose and dense sand. A section of pipeline, at shallow burial depth, was translated through the soil at different oblique angles in the axial-lateral plane. The force exerted by the soil on pipe is critically examined to assess the significance of load coupling effects and establish a yield envelope. The displacements required to soil yield force are also examined to assess potential coupling in mobilization distance. A set of laboratory tests were conducted on the sand used for centrifuge modeling to find the stress-strain behavior of sand, which was used to examine the possible mechanisms of centrifuge model test. The yield envelope, deformation patterns, and interpreted failure mechanisms obtained from centrifuge modeling are compared with other physical modeling and numerical simulations available in the literature.

Evaluation of creative problem solving abilities in undergraduate structural engineers through interdisciplinary problem based learning

For a structural engineer, effective communication and interaction with architects cannot be underestimated as a key skill to success throughout their professional career. Structural engineers and architects have to share a common language and understanding of each other in order to achieve the most desirable architectural and structural designs. This interaction and engagement develops during their professional career but needs to be nurtured during their undergraduate studies. The objective of this paper is to present the strategies employed to engage higher order thinking in structural engineering students in order to help them solve complex problem-based learning (PBL) design scenarios presented by architecture students. The strategies employed were applied in the experimental setting of an undergraduate module in structural engineering at Queen’s University Belfast in the UK. The strategies employed were active learning to engage with content knowledge, the use of physical conceptual structural models to reinforce key concepts and finally, reinforcing the need for hand sketching of ideas to promote higher order problem-solving. The strategies employed were evaluated through student survey, student feedback and module facilitator (this author) reflection. The strategies were qualitatively perceived by the tutor and quantitatively evaluated by students in a cross-sectional study to help interaction with the architecture students, aid interdisciplinary learning and help students creatively solve problems (through higher order thinking). The students clearly enjoyed this module and in particular interacting with structural engineering tutors and students from another discipline

The Role of Attachment in a Social Cognitive Model of Social Domain Satisfaction in College Students

The study examined a modified social cognitive model of domain satisfaction (Lent, 2004). In addition to social cognitive variables and trait positive affect, the model included two aspects of adult attachment, attachment anxiety and avoidance. The study extended recent research on well-being and satisfaction in academic, work, and social domains. The adjusted model was tested in a sample of 454 college students, in order to determine the role of adult attachment variables in explaining social satisfaction, above and beyond the direct and indirect effects of trait positive affect. Confirmatory factor analysis found support for 8 correlated factors in the modified model: social domain satisfaction, positive affect, attachment avoidance, attachment anxiety, social support, social self-efficacy, social outcome expectations, and social goal progress. Three alternative structural models were tested to account for the ways in which attachment anxiety and attachment avoidance might relate to social satisfaction. Results of model testing provided support for a model in which attachment avoidance produced only an indirect path to social satisfaction via self-efficacy and social support. Positive affect, avoidance, social support, social self-efficacy, and goal progress each produced significant direct or indirect paths to social domain satisfaction, though attachment anxiety and social outcome expectations did not contribute to the predictive model. Implications of the findings regarding the modified social cognitive model of social domain satisfaction were discussed.

Attenuation of omega mesons in cold nuclear matter

The attenuation of. mesons in cold nuclear matter has been investigated via the time-dependent multiple-scattering Monte Carlo multicollisional (MCMC) intranuclear cascade model. The inelastic. width deduced from CBELSA/TAPS Collaboration data of meson transparency in complex nuclei (Gamma* similar or equal to 30 MeV/c(2)) is approximately 5 times lower than the value obtained with recent theoretical models and consistent with an in-medium total omega N cross section within 25-30 mb for an average meson momentum of 1.1 GeV/c. The momentum-dependent transparency ratios suggest an elastic/total cross-section ratio around 40%. For the case of CLAS Collaboration data a much higher width is deduced (Gamma* greater than or similar to 120 MeV/c(2)), with the MCMC model providing a consistent interpretation of the data, assuming a much higher meson absorption (sigma(omega N)* greater than or similar to 100 mb) for p(omega) similar to 1.7 GeV/c.

Evolutionary conservation of the membrane fusion machine

Recent structural studies of proteins mediating membrane fusion reveal intriguing similarities between diverse viral and mammalian systems. Particularly striking is the close similarity between the transmembrane envelope glycoproteins from the retrovirus HTLV-1 and the filovirus Ebola. These similarities suggest similar mechanisms of membrane fusion. The model that fits most currently available data suggests fusion activation in viral systems is driven by a symmetrical conformational change triggered by an activation event such as receptor binding or a pH change. The mammalian vesicle fusion mediated by the SNARE protein complex most likely occurs by a similar mechanism but without symmetry constraints.

Análise estrutural de uma torre tubular sob acção do vento

Com a realização deste trabalho, pretende-se essencialmente dar a conhecer a influência que a acção do vento possui no dimensionamento de determinadas estruturas, neste caso específico, em torres tubulares de telecomunicações. É por todos sabido, da importância de um capaz e evoluído sistema de comunicações, no desenvolvimento sustentado do mundo moderno. Nesse sentido, o avanço galopante, principalmente nas últimas duas décadas, das tecnologias de Telecomunicações, implicou uma rápida resposta em consonância na implantação e proliferação de infraestruturas de suporte aos equipamentos dessas tecnologias. Assim, a estrutura em forma de torre tubular, entre as demais variadas secções que as constituem, foi adquirindo preponderância neste campo, constituindo a mais vasta utilização de estruturas de suporte aos equipamentos de telecomunicações, nomeadamente em meios rurais, onde escasseiam edificações com alturas suficientes para fazer face às necessidades das operadoras licenciadas para os devidos efeitos. Será efectuada uma breve descrição sobre as diversas e mais comuns tipologias de torres utilizadas no âmbito do suporte de equipamentos de telecomunicações. Descreve-se, em forma de relatório e levantamento fotográfico, a ocorrência do colapso de uma torre tubular de telecomunicações. Por último, e na sequência do incidente referido no ponto anterior, será efectuada com detalhe, a análise estrutural da torre tubular que foi instalada na posição da anteriormente instalada.

Benchmark exact solutions for the static analysis of multi-layered piezoelectric composite using PVDF

The three-dimensional (3D) exact solutions developed in the early 1970s by Pagano for simply supported multilayered orthotropic composite plates and later in the 1990s extended to piezoelectric plates by Heyliger have been extremely useful in the assessment and development of advanced laminated plate theories and related finite element models. In fact, the well-known test cases provided by Pagano and by Heyliger in those earlier works are still used today as benchmark solutions. However, the limited number of test cases whose 3D exact solutions have been published has somewhat restricted the assessment of recent advanced models to the same few test cases. This work aims to provide additional test cases to serve as benchmark exact solutions for the static analysis of multilayered piezoelectric composite plates. The method introduced by Heyliger to derive the 3D exact solutions has been successfully implemented using symbolic computing and a number of new test cases are here presented thoroughly. Specifically, two multilayered plates using PVDF piezoelectric material are selected as test cases under two different loading conditions and considering three plate aspect ratios for thick, moderately thick and thin plate, in a total of 12 distinct test cases. (C) 2013 Elsevier Ltd. All rights reserved.

Short-Run Strategies For Attracting Foreign Direct Investment

This paper empirically investigates the effectiveness and feasibility of two FDI policies, fiscal incentives and deregulation, aimed at improving the attractiveness of a country in the short run. Using disaggregated data on sales by US MNEs’ foreign affiliates in 43 developed and developing countries over the 1982-1994 period, results show that the provision of fiscal incentives or the deregulation of the labour market would exert a positive impact on total FDI. Given the drawbacks frequently associated with the use of incentive packages, economy-wide policies which ease firing procedures and reduce severance payments would certainly be the best policy option. This paper also highlights the different aggregation and omitted variable biases that have affected results of previous studies and provides some support to recent theoretical models of FDI by showing that third country effects and spatial interdependence influence respectively the location of export-platform FDI and vertical FDI.

Short-Run Strategies For Attracting Foreign Direct Investment

This paper empirically investigates the effectiveness and feasibility of two FDI policies, fiscal incentives and deregulation, aimed at improving the attractiveness of a country in the short run. Using disaggregated data on sales by US MNEs’ foreign affiliates in 43 developed and developing countries over the 1982-1994 period, results show that the provision of fiscal incentives or the deregulation of the labour market would exert a positive impact on total FDI. Given the drawbacks frequently associated with the use of incentive packages, economy-wide policies which ease firing procedures and reduce severance payments would certainly be the best policy option. This paper also highlights the different aggregation and omitted variable biases that have affected results of previous studies and provides some support to recent theoretical models of FDI by showing that third country effects and spatial interdependence influence respectively the location of export-platform FDI and vertical FDI.

Assessing excess profits from different entry regulations

Entry regulations affecting professional services such as pharmacies are common practice in many European countries. We assess the impact of entry regulations on profits estimating a structural model of entry using the information provided by a policy experiment. We use the case of different regional policies governing the opening of new pharmacies in Spain to show that structural models of entry ought to be estimated with data from policy experiments to pin down how entry regulations change payoffs functions of the incumbents. Contrary to the public interest rationales, regulations are not boosting only small town pharmacies payoffs nor increasing all pharmacies payoffs alike. The gains from regulations are very unevenly distributed,suggesting that private interests are shaping the current mix of entry and markup regulations.

Expression, purification and biochemical characterization of recombinant Ca-dependent protein kinase 2 of the malaria parasite Plasmodium falciparum.

Calcium-dependent protein kinases (CDPKs) are serine/threonine kinases that react in response to calcium which functions as a trigger for several mechanisms in plants and invertebrates, but not in mammals. Recent structural studies have defined the role of calcium in the activation of CDPKs and have elucidated the important structural changes caused by calcium in order to allow the kinase domain of CDPK to bind and phosphorylate the substrate. However, the role of autophosphorylation in CDPKs is still not fully understood. In Plasmodium falciparum, seven CDPKs have been identified by sequence comparison, and four of them have been characterized and assigned to play a role in parasite motility, gametogenesis and egress from red blood cells. Although PfCDPK2 was already discovered in 1997, little is known about this enzyme and its metabolic role. In this work, we have expressed and purified PfCDPK2 at high purity in its unphosphorylated form and characterized its biochemical properties. Moreover, propositions about putative substrates in P. falciparum are made based on the analysis of the phosphorylation sites on the artificial substrate myelin basic protein (MBP).

Virologic and immunologic responses in treatment-naive patients to ritonavir-boosted atazanavir or efavirenz with a common backbone.

Background: Atazanavir boosted with ritonavir (ATV/r) and efavirenz (EFV) are both recommended as first-line therapies for HIV-infected patients. We compared the 2 therapies for virologic efficacy and immune recovery. Methods: We included all treatment-naïve patients in the Swiss HIV Cohort Study starting therapy after May 2003 with either ATV/r or EFV and a backbone of tenofovir and either emtricitabine or lamivudine. We used Cox models to assess time to virologic failure and repeated measures models to assess the change in CD4 cell counts over time. All models were fit as marginal structural models using both point of treatment and censoring weights. Intent-to-treat and various as-treated analyses were carried out: In the latter, patients were censored at their last recorded measurement if they changed therapy or if they were no longer adherent to therapy. Results: Patients starting EFV (n = 1,097) and ATV/r (n = 384) were followed for a median of 35 and 37 months, respectively. During follow-up, 51% patients on EFV and 33% patients on ATV/r remained adherent and made no change to their first-line therapy. Although intent-to-treat analyses suggest virologic failure was more likely with ATV/r, there was no evidence for this disadvantage in patients who adhered to first-line therapy. Patients starting ATV/r had a greater increase in CD4 cell count during the first year of therapy, but this advantage disappeared after one year. Conclusions: In this observational study, there was no good evidence of any intrinsic advantage for one therapy over the other, consistent with earlier clinical trials. Differences between therapies may arise in a clinical setting because of differences in adherence to therapy.