Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

The REFLEX project: Comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data

We describe a model-data fusion (MDF) inter-comparison project (REFLEX), which compared various algorithms for estimating carbon (C) model parameters consistent with both measured carbon fluxes and states and a simple C model. Participants were provided with the model and with both synthetic net ecosystem exchange (NEE) of CO2 and leaf area index (LAI) data, generated from the model with added noise, and observed NEE and LAI data from two eddy covariance sites. Participants endeavoured to estimate model parameters and states consistent with the model for all cases over the two years for which data were provided, and generate predictions for one additional year without observations. Nine participants contributed results using Metropolis algorithms, Kalman filters and a genetic algorithm. For the synthetic data case, parameter estimates compared well with the true values. The results of the analyses indicated that parameters linked directly to gross primary production (GPP) and ecosystem respiration, such as those related to foliage allocation and turnover, or temperature sensitivity of heterotrophic respiration, were best constrained and characterised. Poorly estimated parameters were those related to the allocation to and turnover of fine root/wood pools. Estimates of confidence intervals varied among algorithms, but several algorithms successfully located the true values of annual fluxes from synthetic experiments within relatively narrow 90% confidence intervals, achieving >80% success rate and mean NEE confidence intervals <110 gC m−2 year−1 for the synthetic case. Annual C flux estimates generated by participants generally agreed with gap-filling approaches using half-hourly data. The estimation of ecosystem respiration and GPP through MDF agreed well with outputs from partitioning studies using half-hourly data. Confidence limits on annual NEE increased by an average of 88% in the prediction year compared to the previous year, when data were available. Confidence intervals on annual NEE increased by 30% when observed data were used instead of synthetic data, reflecting and quantifying the addition of model error. Finally, our analyses indicated that incorporating additional constraints, using data on C pools (wood, soil and fine roots) would help to reduce uncertainties for model parameters poorly served by eddy covariance data.

The mechanical properties of amniotic membrane influence its effect as a biomaterial for ocular surface repair

The human amniotic membrane (AM) is a tissue of fetal origin and has proven to be clinically useful as a biomaterial in the management of various ocular surface disorders including corneal stem cell transplantation. However, its success rate displays a degree of clinical unpredictability. We suggest that the measured variability inAMstiffness offers an explanation for the poor clinical reproducibility when it is used as a substrate for stem cell expansion and transplantation. Corneal epithelial stem cells were expanded upon AM samples possessing different mechanical stiffness. To investigate further the importance of biological substrate stiffness on cell phenotype we replaced AM with type I collagen gels of known stiffness. Substrate stiffness was measured using shear rheometry and surface topography was characterized using scanning electron microscopy and atomic force microscopy. The differentiation status of epithelial cells was examined using RT-PCR, immunohistochemistry and Western blotting. The level of corneal stem cell differentiation was increased in cells expanded upon AM with a high dynamic elastic shear modulus and cell expansion on type I collagen gels confirmed that the level of corneal epithelial stem cell differentiation was related to the substrate’s mechanical properties. In this paper we provide evidence to show that the preparatory method of AM for clinical use can affect its mechanical properties and that these measured differences can influence the level of differentiation within expanded corneal epithelial stem cells.

Refereed journal papers: practice and process

Research must be published, otherwise it will be lost. The most important papers for a researcher to produce are those published in international refereed journals. Good practice in writing papers is something that can be learned. The editorial process involves sending submitted papers to independent experts in the field, usually anonymously, and their comments inform the editor, who decides whether and how to progress with a paper. Much of this is as obscure to experienced researchers as it is to new ones. With forethought and planning, the success rate of getting submitted papers accepted for publication can be increased. Editors and publishers are generally very keen to help people improve their success rate.

Assessment of the CMD Mini-Explorer, a new low-frequency multi-coil electromagnetic device, for archaeological investigations

In this article we assess the abilities of a new electromagnetic (EM) system, the CMD Mini-Explorer, for prospecting of archaeological features in Ireland and the UK. The Mini-Explorer is an EM probe which is primarily aimed at the environmental/geological prospecting market for the detection of pipes and geology. It has long been evident from the use of other EM devices that such an instrument might be suitable for shallow soil studies and applicable for archaeological prospecting. Of particular interest for the archaeological surveyor is the fact that the Mini-Explorer simultaneously obtains both quadrature (‘conductivity’) and in-phase (relative to ‘magnetic susceptibility’) data from three depth levels. As the maximum depth range is probably about 1.5 m, a comprehensive analysis of the subsoil within that range is possible. As with all EM devices the measurements require no contact with the ground, thereby negating the problem of high contact resistance that often besets earth resistance data during dry spells. The use of the CMD Mini-Explorer at a number of sites has demonstrated that it has the potential to detect a range of archaeological features and produces high-quality data that are comparable in quality to those obtained from standard earth resistance and magnetometer techniques. In theory the ability to measure two phenomena at three depths suggests that this type of instrument could reduce the number of poor outcomes that are the result of single measurement surveys. The high success rate reported here in the identification of buried archaeology using a multi-depth device that responds to the two most commonly mapped geophysical phenomena has implications for evaluation style surveys. Copyright © 2013 John Wiley & Sons, Ltd.

Long-term storage of ectomycorrhizal basidiomycetes (Hebeloma spp.) at low temperature

A method for maintaining viable cultures of ectomycorrhizal Hebeloma strains in cold liquid culture medium is described. Isolates of Hebeloma spp., collected over a wide geographic range, were stored at 2 °C for a period of three years. All cultures survived this storage period, a greater time period and success rate than has previously been reported for the long term storage of ectomycorrhizal basidiomycetes. The method may prove useful for long-term storage of other basidiomycete genera.

Evaluation of Red Colour Segmentation Algorithms in Traffic Signs Detection

Colour segmentation is the most commonly used method in road signs detection. Road sign contains several basic colours such as red, yellow, blue and white which depends on countries.The objective of this thesis is to do an evaluation of the four colour segmentation algorithms. Dynamic Threshold Algorithm, A Modification of de la Escalera’s Algorithm, the Fuzzy Colour Segmentation Algorithm and Shadow and Highlight Invariant Algorithm. The processing time and segmentation success rate as criteria are used to compare the performance of the four algorithms. And red colour is selected as the target colour to complete the comparison. All the testing images are selected from the Traffic Signs Database of Dalarna University [1] randomly according to the category. These road sign images are taken from a digital camera mounted in a moving car in Sweden.Experiments show that the Fuzzy Colour Segmentation Algorithm and Shadow and Highlight Invariant Algorithm are more accurate and stable to detect red colour of road signs. And the method could also be used in other colours analysis research. The yellow colour which is chosen to evaluate the performance of the four algorithms can reference Master Thesis of Yumei Liu.

Identificação da estrutura de escritório de gerenciamento de projetos adequada a partir da avaliação do nível de maturidade em Gerenciamento de Projetos: Um Estudo sobre a Área de Tecnologia da Informação da Petrobras

Changing has been addressed by projects and it had happened in a fast and disarrenged way. In consequence of the increasing on demand for projects, to get better success rate is essential manage projects adequately. The creation of an organitional structure intended to concentrate the development of process and methodologies is a great initiative to spread the projects management concepts. The purpose of this work is to apply a model to analyse the maturity level on project management of the Petrobras IT Department and indicate an Project Management Office adequated to the level found, that could be improved with the increase of the maturity level.

Análises histológicas comparativas entre diferentes tamanhos de fragmentos ovarianos bovinos criopreservados

Objetivo: Investigar a influência do tamanho dos fragmentos ovarianos na preservação dos folículos primordiais e primários pós-congelamento. Desenho: Experimento laboratorial controlado. Foram realizadas análises histológicas comparativas em grupos controle e pós-congelamento de fragmentos de ovários bovinos. No grupo dos fragmentos menores, a menor das medidas era de 2mm e no grupo dos fragmentos maiores, todos as medidas eram maiores de 2mm. Local de Realização: Universidade Federal do Rio Grande do Sul (UFRGS), Faculdade de Veterinária da UFRGS e Centro de Reprodução Humana Nilo Frantz, Porto Alegre, RS, Brasil. Animais: Foi utilizado um ovário de vaca raça Hereford. Resultados Principais: Nos fragmentos congelados com medida de 2mm, e com medidas maiores de 2mm, a percentagem de folículos normais foi de 56% e 34%, respectivamente. O risco relativo para a manutenção dos folículos normais póscongelamento nos fragmentos com de 2mm e maiores de 2mm foi de 0,63 e de 0,47, respectivamente. A comparação desse dois riscos relativos mostrou, de forma significativa (qui-quadrado de heterogeneidade p=0,022), que o impacto do congelamento na redução das taxas de sucesso foi maior nos fragmentos com espessuras maiores de 2mm. Conclusões principais: Este estudo mostrou que há um comprometimento maior na preservação folicular em fragmentos ovarianos criopreservados com espessuras maiores de 2mm.

Color measurement using a smartphone applied to Madeira wines

Computer vision is a field that uses techniques to acquire, process, analyze and understand images from the real world in order to produce numeric or symbolic information in the form of decisions [1]. This project aims to use computer vision to prepare an app to analyze a Madeira Wine and characterize it (identify its variety) by its color. Dry or sweet wines, young or old wines have a specific color. It uses techniques to compare histograms in order to analyze the images taken from a test sample inside a special container designed for this purpose. The color analysis from a wine sample using an image captured by a smartphone can be difficult. Many factors affect the captured image such as, light conditions, the background of the sample container due to the many positions the photo can be taken (different to capture facing a white wall or facing the floor for example). Using new technologies such as 3D printing it was possible to create a prototype that aims to control the effect of those external factors on the captured image. The results for this experiment are good indicators for future works. Although it’s necessary to do more tests, the first tests had a success rate of 80% to 90% of correct results. This report documents the development of this project and all the techniques and steps required to execute the tests.

SysPRE: systematized process for requirements engineering in knowledge discovery projects

The domain of Knowledge Discovery (KD) and Data Mining (DM) is of growing importance in a time where more and more data is produced and knowledge is one of the most precious assets. Having explored both the existing underlying theory, the results of the ongoing research in academia and the industry practices in the domain of KD and DM, we have found that this is a domain that still lacks some systematization. We also found that this systematization exists to a greater degree in the Software Engineering and Requirements Engineering domains, probably due to being more mature areas. We believe that it is possible to improve and facilitate the participation of enterprise stakeholders in the requirements engineering for KD projects by systematizing requirements engineering process for such projects. This will, in turn, result in more projects that end successfully, that is, with satisfied stakeholders, including in terms of time and budget constraints. With this in mind and based on all information found in the state-of-the art, we propose SysPRE - Systematized Process for Requirements Engineering in KD projects. We begin by proposing an encompassing generic description of the KD process, where the main focus is on the Requirements Engineering activities. This description is then used as a base for the application of the Design and Engineering Methodology for Organizations (DEMO) so that we can specify a formal ontology for this process. The resulting SysPRE ontology can serve as a base that can be used not only to make enterprises become aware of their own KD process and requirements engineering process in the KD projects, but also to improve such processes in reality, namely in terms of success rate.

Desempenho e background familiar: um estudo no acesso a uma instituição de ensino técnico federal no Brasil

This paper comprises an investigation on the influence of the variable family backgrounds (father school level, mother school level and family income) over the pupil s performance in admissions examination (entrance test or PROITEC) at Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Norte (IFRN). From that point of view, the main goal of this research is to analyze the influence of the family background as a determiner of the pupil´s performance in the access to Technical and Professional education at IFRN. Secondary data were used from two databases (entrance test and PROITEC) adding up to 19.226 observations to the vacancies offered in the year of 2013. Aiming at achieving the proposed goal, a conceptual model composed of three hypothesis was developed. The results were presented in four stages: stage I presentation of the descriptive statistical results of the two databases; stage II separation of the campi in clusters; stage III analysis of multiple regressions; stage IV analysis of the logistics regressions. Two statistical tests were used to validate the hypothesis: T-test and Wald test. Hypothesis 1 and 2 were confirmed and H3 was refused. The results presented favorable causal connections to the family income and the father school level variables (with bigger effect for fathers with a higher education degree). The mother school level variable did not provide statistical significance for this research. Based on this result, after this work, this institution is to develop a strategic plan to assist in the success rate of students preparing diagnoses in order to diminish the effects of the variables that impacted negatively

Análise de desempenho baseada em simulação de redes WirelessHART

This dissertation describes the implementation of a WirelessHART networks simulation module for the Network Simulator 3, aiming for the acceptance of both on the present context of networks research and industry. For validating the module were imeplemented tests for attenuation, packet error rate, information transfer success rate and battery duration per station

Detecção de predadores por dicromatas e tricromatas humanos e a sua implicação na evolução da visão de cores em primatas

Among placental mammals, primates are the only ones to present trichromatic color vision. However, the distribution of trichromacy among primates is not homogeneous: Old World primates shows an uniform trichromacy (with all individuals being trichromats) and New World primates exhibit a color vision polymorphism (with dichromatic males and dichromatic or trichromatic females). Visual ecology studies have investigated which selective pressures may have been responsible for the evolution of trichromacy in primates, diverging from the dichromat standard found in other mammals. Cues associated with foraging and the socio-reproductive status were analyzed, indicating a trichromatic advantage for the rapid detection of visually conspicuous objects against a green background. However, dichromats are characterized by an efficient capture of cryptic and camouflaged stimuli. These advantages regarding phenotype may be responsible for the maintenance of the visual polymorphism in New World primates and for the high incidence of color blindness in humans (standing around 8% in Caucasian men). An important factor that has not yet been experimentally taken into account is the predation risk and its effect on the evolution of trichromacy in primates. To answer this question, we prepared and edited pictures of animals with different coats: oncillas (Leopardus spp.), puma (Puma concolor) and ferret (Galictis cuja). The specimens were taxidermized and the photographs were taken in three different vegetation scenarios (dense forest, cerrado and grassland). The images of the predators were manipulated so that they fit into two categories of stimulus size (small or large). After color calibration and photo editing, these were presented to 40 humans (20 dichromats and 20 trichromats) by a computer program, which presented a set of four photos at a time (one picture containing the taxidermized animal amid the background vegetation and three depicting only the background vegetation) and recorded the response latency and success rate of the subjects. The results show a trichromatic advantage in detecting potential predators. The predator detection was influenced by the background, the predator species, the dimension of the stimulus and the observer s visual phenotype. As humans have a high rate of dyschromatopsias, when compared to wild Catarrhini or human tribal populations, it is possible that the increased rate of dichromats is a result of reduced pressure for rapid predator detection. Since our species came to live in more cohesive groups and resistant to attack by predators, with the advent of agriculture and the formation of villages, it is possible that the lower risk of predation has reduced the selection in favor of trichromats

Análise das dificuldades de aprendizagem numa disciplina de química orgânica do curso de química na modalidade à distância da UFRN

In today`s society the use of so-called information technology and communication (ICT), is promoting a revolution in the forms of teaching and learning through the methods of distance learning courses, especially in higher education. Studies show that students in this way have great difficulties in the learning process, especially when dealing with experimental subjects that require high power of abstraction as chemistry. The goal of this work is to promote improvement in the teaching and learning in the discipline Chemistry of Life offered for the Bachelor`s Degree in Chemistry in distance UFRN. For this we analyzed evidence of the semester 2011.2, in order to identify what are the main difficulties of the students on the assessments. That`s why video lessons related to matters that create the majority of difficulties for students were developed, the final product this work. Being obtained the improvements by video classes in the learning process of the students, from a questionnaire answered by the students in the virtual learning environment, and from their success rate at the end of the course