High-level of viral genomic diversity in cervical cancers: a Brazilian study on human papillomavirus type 16

Invasive cervical cancer (ICC) is the third most frequent cancer among women worldwide and is associated with persistent infection by carcinogenic human papillomaviruses (HPVs). The combination of large populations of viral progeny and decades of sustained infection may allow for the generation of intra-patient diversity, in spite of the assumedly low mutation rates of PVs. While the natural history of chronic HPVs infections has been comprehensively described, within-host viral diversity remains largely unexplored. In this study we have applied next generation sequencing to the analysis of intra-host genetic diversity in ten ICC and one condyloma cases associated to single HPV16 infection. We retrieved from all cases near full-length genomic sequences. All samples analyzed contained polymorphic sites, ranging from 3 to 125 polymorphic positions per genome, and the median probability of a viral genome picked at random to be identical to the consensus sequence in the lesion was only 40%. We have also identified two independent putative duplication events in two samples, spanning the L2 and the L1 gene, respectively. Finally, we have identified with good support a chimera of human and viral DNA. We propose that viral diversity generated during HPVs chronic infection may be fueled by innate and adaptive immune pressures. Further research will be needed to understand the dynamics of viral DNA variability, differentially in benign and malignant lesions, as well as in tissues with differential intensity of immune surveillance. Finally, the impact of intralesion viral diversity on the long-term oncogenic potential may deserve closer attention.

Non emergency patients transport - a mixed integer linear programming

This work presents a model and a heuristic to solve the non-emergency patients transport (NEPT) service issues given the new rules recently established in Portugal. The model follows the same principle of the Team Orienteering Problem by selecting the patients to be included in the routes attending the maximum reduction in costs when compared with individual transportation. This model establishes the best sets of patients to be transported together. The model was implemented in AMPL and a compact formulation was solved using NEOS Server. A heuristic procedure based on iteratively solving problems with one vehicle was presented, and this heuristic provides good results in terms of accuracy and computation time.

The non-emergency patient transport modelled as a team orienteering problem

This work presents an improved model to solve the non-emergency patients transport (NEPT) service issues given the new rules recently established in Portugal. The model follows the same principle of the Team Orienteering Problem by selecting the patients to be included in the routes attending the maximum reduction in costs when compared with individual transportation. This model establishes the best sets of patients to be transported together. The model was implemented in AMPL and a compact formulation was solved using NEOS Server. A heuristic procedure based on iteratively solving Orienteering Problems is presented, and this heuristic provides good results in terms of accuracy and computation time. Euclidean instances as well as asymmetric real data gathered from Google maps were used, and the model has a promising performance mainly with asymmetric cost matrices.

Genetic algorithms for the non emergency patients transport service

The authors would like to thank the anonymous reviewers for their valuable comments and suggestions to improve the paper. The authors would like to thank Dr. Elaine DeBock for reviewing the manuscript.

Study of the muscular activation in obese and non-obese subjects during lifting loads

The obesity prevalence is increasing among the workforce of the developed countries. However, obesity seems to negatively affect the individuals’ work performance. In occupational contexts, manual lifting tasks are frequent and can produce significant muscle loading. With the aim of analysing the possible effect of obesity on workers’ muscular activation, surface electromyography data were collected from six muscles recruited during these tasks. In the current study, 6 different tasks of manual lifting (3 loads × 2 lifting styles) were performed by 14 participants with different obesity levels. Electromyography data normalization was based on the percentage of maximum contraction during each task. The muscles’ activation times before each task were also calculated. The current study suggests that obesity can increase the maximum contraction during each task and the delays on muscles’ activation time. This study suggests that obese individuals can present some changes on their muscle activation during lifting, when comparing with non-obese individuals, and reinforces the need to develop further studies focused on obesity as a risk factor for musculoskeletal disorders development.

Observation and measurements of the production of prompt and non-prompt J/ψ mesons in association with a Z boson in pp collisions at s√ = 8 TeV with the ATLAS detector

The production of a Z boson in association with a J/ψ meson in proton--proton collisions probes the production mechanisms of quarkonium and heavy flavour in association with vector bosons, and allows studies of multiple parton scattering. Using 20.3fb−1 of data collected with the ATLAS experiment at the LHC, in pp collisions at s√=8 TeV, the first measurement of associated Z+J/ψ production is presented for both prompt and non-prompt J/ψ production, with both signatures having a significance in excess of 5σ. The inclusive production cross-sections for Z boson production (in μ+μ− or e+e− decay modes) in association with prompt and non-prompt J/ψ(→μ+μ−) are measured relative to the inclusive production rate of Z bosons in the same fiducial volume to be (88±16±6)×10−8 and (157±22±10)×10−8 respectively. Normalised differential production cross-sections are also determined as a function of the J/ψ transverse momentum. The fraction of signal events arising from single and double parton scattering is estimated, and a lower limit of 5.3 (3.7)mb at 68 (95) confidence level is placed on the effective cross-section regulating double parton interactions.

Combining non-dominance, objective-order and spread metric to extend firefly algorithm to multi-objective optimization

In this paper, we propose an extension of the firefly algorithm (FA) to multi-objective optimization. FA is a swarm intelligence optimization algorithm inspired by the flashing behavior of fireflies at night that is capable of computing global solutions to continuous optimization problems. Our proposal relies on a fitness assignment scheme that gives lower fitness values to the positions of fireflies that correspond to non-dominated points with smaller aggregation of objective function distances to the minimum values. Furthermore, FA randomness is based on the spread metric to reduce the gaps between consecutive non-dominated solutions. The obtained results from the preliminary computational experiments show that our proposal gives a dense and well distributed approximated Pareto front with a large number of points.

The economic crisis in Portugal and children’s rights to non-discrimination

The consequences that arose from the ‘global economy’ have been significant in Portuguese children’s lives and we believe it is fundamental to reflect on the ongoing structuring of childhood through this global culture/ideology and the concrete implications that they have. It is also important to understand how childhood is constructed and experienced, as well as to consider the impacts of political economic conditions on children’s lives and in childhood in general, taking into account the effects brought on by public policies. The aim of this paper is to reflect on the ways through which the economic crisis affecting the general Portuguese population has impacted children in particular and promoted discrimination and a lack of opportunities in childhood. We will focus on two dimensions: first, on general data about the ongoing policies that have been reducing social rights, increasing poverty rates and threatening basic rights such as educational and health rights, to show their impact on children´s lives. Second, we will discuss some data collected with children throughout different research projects in order to characterize the meanings and impacts of the crisis in their lives from their points of view

Local non-negative initial data scalar characterization of the Kerr solution

For any vacuum initial data set, we define a local, non-negative scalar quantity which vanishes at every point of the data hypersurface if and only if the data are Kerr initial data. Our scalar quantity only depends on the quantities used to construct the vacuum initial data set which are the Riemannian metric defined on the initial data hypersurface and a symmetric tensor which plays the role of the second fundamental form of the embedded initial data hypersurface. The dependency is algorithmic in the sense that given the initial data one can compute the scalar quantity by algebraic and differential manipulations, being thus suitable for an implementation in a numerical code. The scalar could also be useful in studies of the non-linear stability of the Kerr solution because it serves to measure the deviation of a vacuum initial data set from the Kerr initial data in a local and algorithmic way.

Enhanced resistive switching and multilevel behavior in bilayered HfAlO/HfAlOx structures for non-volatile memory applications

In this work, hafnium aluminum oxide (HfAlO) thin films were deposited by ion beam sputtering deposition technique on Si substrate. The presence of oxygen vacancies in the HfAlOx layer deposited in oxygen deficient environment is evidenced from the photoluminescence spectra. Furthermore, HfAlO(oxygen rich)/HfAlOx(oxygen poor) bilayer structures exhibit multilevel resistive switching (RS), and the switching ratio becomes more prominent with increasing the HfAlO layer thickness. The bilayer structure with HfAlO/HfAlOx thickness of 30/40 nm displays the enhanced multilevel resistive switching characteristics, where the high resistance state/ intermediate resistance state (IRS) and IRS/low resistance state resistance ratios are 102 and 5 105 , respectively. The switching mechanisms in the bilayer structures were investigated by the temperature dependence of the three resistance states. This study revealed that the multilevel RS is attributed to the coupling of ionic conduction and the metallic conduction, being the first associated to the formation and rupture of conductive filaments related to oxygen vacancies and the second with the formation of a metallic filament. Moreover, the bilayer structures exhibit good endurance and stability in time.

Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of non-B and -G Subtypes

Existing data supports Portugal as the Western Europe country with highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1 infected individuals followed in the reference Hospital of the province of Minho, Portugal, in which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%), C (14.5%), F1 (7.3%) and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with A1 and F1 subtype increased over the years when compared with B, G, C or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of subtypes B and G were found. However, transmission clusters of non-B and -G viruses among native individuals were also found with the dates of the most recent common ancestor estimated to the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and were mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route.

Clinical characteristics of women diagnosed with carcinoma who tested positive for cervical and anal high-risk human papillomavirus DNA and E6 RNA

High-risk human papillomavirus (hrHPV) is an essential cause of cervical carcinoma and is also strongly related to anal cancer development. The hrHPV E6 oncoprotein plays a major role in carcinogenesis. We aimed to evaluate the frequency of hrHPV DNA and E6 oncoprotein in the anuses of women with cervical carcinoma. We analyzed 117 women with cervical cancer and 103 controls for hrHPV and the E6 oncogene. Positive test results for a cervical carcinoma included 66.7 % with hrHPV-16 and 7.7 % with hrHPV-18. One case tested positive for both HPV variants (0.9 %). The samples from the anal canal were positive for HPV-16 in 59.8 % of the cases. Simultaneous presence of HPV in the cervix and anal canal was found in 53.8 % of the cases. Regarding expression of E6 RNA, positivity for HPV-16 in the anal canal was found in 21.2 % of the cases, positivity for HPV-16 in the cervix was found in 75.0 %, and positivity for HPV-18 in the cervix was found in 1.9 %. E6 expression in both the cervix and anal canal was found in 19.2 % of the cases. In the controls, 1 % tested positive for HPV-16 and 0 % for HPV-18. Anal samples from the controls showed a hrHPV frequency of 4.9 % (only HPV16). The presence of hrHPV in the anal canal of women with cervical cancer was detected at a high frequency. We also detected E6 RNA expression in the anal canal of women with cervical cancer, suggesting that these women are at risk for anal hrHPV infection.

Assessment of innovative solutions for non-load bearing masonry enclosures

This paper presents some of the results of the research project “Masonry Enclosures” developed in the framework of the transnational access (TA) to LNEC’s triaxial shake table within the FP7 project SERIES.

The powerful in vitro bioactivity of Euterpe oleracea Mart. seeds and related phenolic compounds

The Euterpe oleracea Mart. (açaí) is a plant from the Amazon region, classified as "super fruit" because of its various functional properties. However, limited investigation has been performed on açaí by-products, such as seeds. Therefore, the aim of this work was to characterized the phenolic compounds of the aqueous extract of açaí seeds and further evaluate its bioactivity (antioxidant and cytotoxic activities. Only proanthocyanidins were detected, being a B-type (epi)catechin tetramer the most abundant; however, procyanidin trimmers were the most predominant form. Açaí seeds extract revealed a high antioxidant (EC50 ranging from 3.6 to 19.4 μg/mL) and cytotoxic activity, being more effective in the cervical carcinoma cell line (HeLa; GI50 = 18 μg/mL); it did not show toxicity for non-tumor cells. Açaí seeds are considered a waste and could have an added economic benefit, through the extraction of natural antioxidants, particularly proanthocyanidins, that could find applications in food and pharmaceutical industries.