4CitySemantics: GIS-semantic tool for urban intervention areas

Peer Reviewe

The Data Mining applied for the prediction of highway roughness due to overloaded trucks

Currently, the quality of the Indonesian national road network is inadequate due to several constraints, including overcapacity and overloaded trucks. The high deterioration rate of the road infrastructure in developing countries along with major budgetary restrictions and high growth in traffic have led to an emerging need for improving the performance of the highway maintenance system. However, the high number of intervening factors and their complex effects require advanced tools to successfully solve this problem. The high learning capabilities of Data Mining (DM) are a powerful solution to this problem. In the past, these tools have been successfully applied to solve complex and multi-dimensional problems in various scientific fields. Therefore, it is expected that DM can be used to analyze the large amount of data regarding the pavement and traffic, identify the relationship between variables, and provide information regarding the prediction of the data. In this paper, we present a new approach to predict the International Roughness Index (IRI) of pavement based on DM techniques. DM was used to analyze the initial IRI data, including age, Equivalent Single Axle Load (ESAL), crack, potholes, rutting, and long cracks. This model was developed and verified using data from an Integrated Indonesia Road Management System (IIRMS) that was measured with the National Association of Australian State Road Authorities (NAASRA) roughness meter. The results of the proposed approach are compared with the IIRMS analytical model adapted to the IRI, and the advantages of the new approach are highlighted. We show that the novel data-driven model is able to learn (with high accuracy) the complex relationships between the IRI and the contributing factors of overloaded trucksFundação para a Ciência e Tecnologia (FCT)We acknowledge the Directorate of Planning, DGH-Indonesia for providing the data for this research, and the Centre for Territory, Environment, and Construction and the Centre Algorithmic, University of Minho, Guimarães, Portugal for assistance in the research study

Bioinformatic Analysis of Chlamydia trachomatis Polymorphic Membrane Proteins PmpE, PmpF, PmpG and PmpH as Potential Vaccine Antigens

Chlamydia trachomatis is the most important infectious cause of infertility in women with important implications in public health and for which a vaccine is urgently needed. Recent immunoproteomic vaccine studies found that four polymorphic membrane proteins (PmpE, PmpF, PmpG and PmpH) are immunodominant, recognized by various MHC class II haplotypes and protective in mouse models. In the present study, we aimed to evaluate genetic and protein features of Pmps (focusing on the N-terminal 600 amino acids where MHC class II epitopes were mapped) in order to understand antigen variation that may emerge following vaccine induced immune selection. We used several bioinformatics platforms to study: i) Pmps' phylogeny and genetic polymorphism; ii) the location and distribution of protein features (GGA(I, L)/FxxN motifs and cysteine residues) that may impact pathogen-host interactions and protein conformation; and iii) the existence of phase variation mechanisms that may impact Pmps' expression. We used a well-characterized collection of 53 fully-sequenced strains that represent the C. trachomatis serovars associated with the three disease groups: ocular (N=8), epithelial-genital (N=25) and lymphogranuloma venereum (LGV) (N=20). We observed that PmpF and PmpE are highly polymorphic between LGV and epithelial-genital strains, and also within populations of the latter. We also found heterogeneous representation among strains for GGA(I, L)/FxxN motifs and cysteine residues, suggesting possible alterations in adhesion properties, tissue specificity and immunogenicity. PmpG and, to a lesser extent, PmpH revealed low polymorphism and high conservation of protein features among the genital strains (including the LGV group). Uniquely among the four Pmps, pmpG has regulatory sequences suggestive of phase variation. In aggregate, the results suggest that PmpG may be the lead vaccine candidate because of sequence conservation but may need to be paired with another protective antigen (like PmpH) in order to prevent immune selection of phase variants.AN is a recipient of a post-doctoral fellowship (SFRH/BPD/75295/2010) from Fundação para a Ciência e a Tecnologia (FCT)

Phosphorylated silk fibroin matrix for methotrexate release

Silk-based matrix was produced for delivery of a model anticancer drug, methotrexate (MTX). The calculation of net charge of silk fibroin and MTX was performed to better understand the electrostatic interactions during matrix formation upon casting. Silk fibroin films were cast at pH 7.2 and pH 3.5. Protein kinase A was used to prepare phosphorylated silk fibroin. The phosphorylation content of matrix was controlled by mixing at specific ratios the phosphorylated and unphosphorylated solutions. In vitro release profiling data suggest that the observed interactions are mainly structural and not electrostatical. The release of MTX is facilitated by use of proteolytic enzymes and higher pHs. The elevated -sheet content and crystallinity of the acidified-cast fibroin solution seem not to favor drug retention. All the acquired data underline the prevalence of structural interactions over electrostatical interactions between methotrexate and silk fibroin.The authors would like to acknowledge the support, granted by European NOVO Project, Contract No. FP7-HEALTH 2011-two-stage 278402. This work was partially supported by FEDER through POFC-COMPETE and by national funds from FCT through the projects PEst-C/BIA/UI4050/2011 (CBMA). V.V. also wants to thank Dr. Claudia Botelho for her helpful discussion and comments made during the critical reading of the manuscript

Chlamydia trachomatis diversity viewed as a tissue-specific coevolutionary arms race

Analysis of 15 serovars of Chlamydia trachomatis reveals an evolutionary arms race in pathogen-host interactions

A statistical classifier for assessing the level of stress from the analysis of interaction patterns in a touch screen

This paper describes an approach for assessing the level of stress of users of mobile devices with tactile screens by analysing their touch patterns. Two features are extracted from touches: duration and intensity. These features allow to analyse the intensity curve of each touch.We use decision trees (J48) and support vector machines (SMO) to train a stress detection classifier using additional data collected in previous experiments. This data includes the amount of movement, acceleration on the device, cognitive performance, among others. In previous work we have shown the co-relation between these parameters and stress. Both algorithms show around 80% of correctly classified instances. The decision tree can be used to classify, in real time, the touches of the users, serving as an input to the assessment of the stress level.This work is funded by National Funds through the FCT Fundacao para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within project PEst-OE/EEI/UI0752/2011. The work of Davide Carneiro is also supported by a doctoral grant by FCT (SFRH/BD/64890/2009)

Enzymatic phosphorylation of silk fibroins : a platform for the production of biocompatible, cell-static, materials

Silks are natural protein polymers produced by insects. Silk heavy chain of B.mori is primarily composed of hydrophobic, –(–Ala–Gly–)n– -sheet crystalline domains. Based on silk biocompatibility, biodegradability and strength, different materials were developed. Silk offers a stabilizing environment for incorporated proteins and molecules. Silk properties can be controlled via structure manipulation, by coupling molecules of biological significance; its Tyr and Ser residues can be modified. Once incorporated into a protein, the phosphate group establishes hydrogen bonds that affect intra- and inter-molecular interactions16. Phosphorylation is stable under physiological conditions, thus directing the formation and reorganization of protein networks. Curiously, using phosphorylation for protein functionalization is largely unexplored. Significant research is devoted to bio-inspired materials with various cell-differentiating and cell-supporting features. However, little attention is paid to develop cell-static bio-materials. Such materials do not promote cell growth. That can be achieved by lowering the probability of cell attachment to the material, via creation of negatively charged material surface. The goal of this study was to produce bio-compatible materials with the cell-static properties by phosphorylation. Silk solutions were made to cast films of variable pH and phosphorylated content. Obtained materials were tested and a dependency between amount of phosphorylation and bio-chemical properties confirmed

Fabrication of AZ4562 refractive microlenses array for light enhancement on optical microsystems

This paper presents the fabrication of an array of high aspect ratio photoresist based refractive microlenses (ML) using photolithography and thermal reflow. First, and in order to evaluate and predict the MLs optical properties and physical dimensions, finite element analysis was done. These simulations helped to design the super high resolution chrome on soda lime glass photomask as well as the parameters for the lithographic processes. Then, an array of high aspect ratio structures (length 4.9 mm, width 30 μm and 5 μm spacing between adjacent structures) with 5 μm thickness were fabricated. The thermal reflow technique (using a hotplate) was applied and an array of MLs measuring 5 and 32 μm at the vertex and radius, respectively, was achieved. When the photoresist (PR) is heated up above its glass transition temperature, it melts and the surface tension effect causes the fabricated microstructure to obtain the spherical lens profile. The hotplate thermal reflow is simple and easy to control, thus permitting the fabrication of smooth and homogeneous surfaces essential for good quality refractive microlenses.This work was supported by the Portuguese Foundation for Science and Technology under the projects FCT/PTDC/EEA-ELC/109936/2009 and FCT/MITPT/ EDAM-SI/0025/2008

A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector

Legionella pneumophila is an accidental human pathogen that causes the potentially fatal Legionnaires' disease, a severe type of pneumonia. The main virulence mechanism of L. pneumophila is a Type 4B Secretion System (T4SS) named Icm/Dot that transports effector proteins into the host cell cytosol. The concerted action of effectors on several host cell processes leads to the formation of an intracellular Legionella-containing vacuole that is replication competent and avoids phagolysosomal degradation. To date over 300 Icm/Dot substrates have been identified. In this study, we searched the genome of a L. pneumophila strain (Pt/VFX2014) responsible for the second largest L. pneumophila outbreak worldwide (in Vila Franca de Xira, Portugal, in 2014) for genes encoding potential novel Icm/Dot substrates. This strain Pt/VFX2014 belongs to serogroup 1 but phylogenetically segregates from all other serogroup 1 strains previously sequenced, displaying a unique mosaic genetic backbone. The ability of the selected putative effectors to be delivered into host cells by the T4SS was confirmed using the TEM-1 β-lactamase reporter assay. Two previously unknown Icm/Dot effectors were identified, VFX05045 and VFX10045, whose homologs Lpp1450 and Lpp3070 in clinical strain L. pneumophila Paris were also confirmed as T4SS substrates. After delivery into the host cell cytosol, homologs VFX05045/Lpp1450 remained diffused in the cell, similarly to Lpp3070. In contrast, VFX10045 localized to the host cell nucleus. To understand how VFX10045 and Lpp3070 (94% of identity at amino acid level) are directed to distinct sites, we carried out a comprehensive site-directed mutagenesis followed by analyses of the subcellular localization of the mutant proteins. This led to the delineation of region in the C-terminal part (residues 380 to 534) of the 583 amino acid-long VFX10045 as necessary and sufficient for nuclear targeting and highlighted the fundamental function of the VFX10045-specific R440 and I441 residues in this process. These studies revealed a strain-specific nucleotropism for new effector VFX10045/Lpp3070, which anticipates distinct functions between these homologs.This project has been funded by: Research Grant 2016 by the European Society of Clinical Microbiology and lnfectious Diseases (ESCMID) to IF; by National funds from FCT - Fundação para a Ciência e a Tecnologia, I.P., in the scope of the project UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences - UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB.info:eu-repo/semantics/publishedVersio

SEM analysis of bond epoxy based layer between hardened concrete and SFRC repairing

Thin bonded concrete overlay are commonly used nowadays in repairing concrete structures. Nevertheless, the performance of the structural system (repaired structure) depends on the sound bond behaviour between old and new concretes. Frequently, adhesives based on epoxy resins provide this liaison. In this work the behaviour of three different types of based epoxy adhesives was observed in the bonding of different strength concrete class. Samples for backscattered scanning electron microscopy (BSE) were prepared from extracted pieces - containing the bonding layer - of non reinforced concrete slabs overlaid with thin bonded steel fibre reinforced concrete (SFRC) layer. Different features of each bonding layer epoxy resin type which may explain differentiate mechanical pull-off results as well as failure modes were observed. Micrographs obtained with BSE give clearly bond layer arrangement and minimum and maximum thickness, typical air voids porosity, presence of hydrated cement paste embedded in epoxy layer, mineral admixtures contained in epoxy, and also relevant micro fissures existing in concrete substrate.Fundação para a Ciência e a Tecnologia (FCT) - PhD grant number SFRH/BD/11232/ 2002.Sika SA.Companhia Geral de Cal e Cimento SA (SECIL).Degussa Construction Chemicals Portugal SA.Pedreiras Bezerras.Bekaert NV