RCAAP Repository

Response to chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (RC) is quite variable and it is urgent to find predictive biomarkers of response. We investigated miR-21 as tissue and plasma biomarker of response to CRT in a prospective cohort of RC patients; The expression of miR-21 was analyzed in pre- and post-CRT rectal tissue and plasma in 37 patients with RC. Two groups were defined: Pathological responders (TRG 0, 1 and 2) and non-responders (TRG 3). The association between miR-21, clinical and oncological outcomes was assessed; miR-21 was upregulated in tumor tissue and we found increased odds of overexpression in pre-CRT tumor tissue (OR: 1.63; 95% CI: 0.40–6.63, p = 0.498) and pre-CRT plasma (OR: 1.79; 95% CI: 0.45–7.19, p = 0.414) of non-responders. The overall recurrence risk increased with miR-21 overexpression in pre-CRT tumor tissue (HR: 2.175, p = 0.37); Significantly higher miR-21 expression is observed in tumor tissue comparing with non-neoplastic. Increased odds of non-response is reported in patients expressing higher miR-21, although without statistical significance. This is one of the first studies on circulating miR-21 as a potential biomarker of response to CRT in RC patients.

Background: The role played by Helicobacter pylori in the sinuses, and its association with the same organism’s gastric infection, are still unclear. Methods: In order to compare H.pylori colonization patterns in the nose and stomach we conducted a cohort analysis of 14 patients, eligible for sinus surgery due to chronic medically refractory rhinosinusitis, who were tested for simultaneous presence of H. pylori, by histology, culture and polymerase chain reaction, in pathologic sinus tissue collected during surgery and in gastric mucosa obtained through gastroduodenal endoscopy. Results: H. pylori DNA was found in the sinus mucosa of 15.4% of patients with chronic rhinosinusitis, and all of them showed concurrent H. pylori stomach infection. Sinus colonization was not found without simultaneous gastric colonization, although most patients with gastric infection did not have the bacterial DNA in their sinuses. H. pylori’s presence in the nose was not associated with local inflammatory status, and no cultures could be obtained from any of the sinus tissue samples, including those positive for H. pylori DNA. Conclusions: Only H. pylori DNA, and not the culturable active form of the microorganism, could be found in the sinus mucosa of some patients with H. pylori gastric infection. We could not find evidence, however, that the bacterium’s presence in the nose contributes to local mucosal inflammation.

Aim: Cationically modified solid lipid nanoparticles (SLN) were investigated as plasmid DNA (pDNA) carriers and transfection agents for the pulmonary route. Materials & methods:pDNA-loaded SLN were produced using glyceryl dibehenate or tristearate as matrix lipids and chitosan as surface charge modifier, and encapsulated by spray-drying in mannitol and trehalose microspheres. Results: Nanoparticles of 200 nm, and zeta potential around +15 mV were produced. Electrophorectic analysis confirmed plasmid stability and integrity. The pDNA-loaded SLN were able to transfect the Calu-3 and A549 pulmonary cell lines, while showing low cytotoxicity. Microencapsulation of SLN yielded dry powders suitable for inhalation that protected pDNA from degradation. Conclusion: Microencapsulated SLN are a promising safe and effective carrier system for pulmonary gene delivery following pulmonary administration.

A paralisia cerebral advém de uma lesão cerebral ou mau desenvolvimento do cérebro que para além de atingir funções motoras do ser humano (fala, postura e movimento) pode provocar uma grande variedade de disfunções perceptivas ou cognitivas (Valente, 1983). Dada a diversidade de funções que podem ser atingidas, os alunos com paralisia cerebral requerem estratégias de aprendizagem diferenciadas, com mecanismos de intervenção pedagógica adaptados a cada tipo de necessidade. Foi nesse sentido que nasceu este projeto. A robótica educativa em geral, e o Lego Mindstorms em particular, tem sido utilizada em diversos meios pedagógicos com diferentes anos de escolaridade no entanto tornava-se pertinente a existência de um estudo que analisa-se o seu potencial com utentes com paralisia cerebral ligeira. Para proceder a esta análise foram realizadas cinco sessões com dois utentes externos da Associação Portuguesa de Paralisia Cerebral. Os utentes têm hemiparesia sendo que um deles foi afetado na sua cognição. Durante as sessões recorreu-se à recolha de dados sobre os participantes (anamnese), à observação participante, à gravação audiovisual e à redação de um diário de bordo. Os dois utentes responderam a três questionários aplicados em momentos distintos e a fisioterapeuta dos utentes respondeu a uma entrevista estandardizada de final aberto. Os resultados obtidos indicaram que o Lego Mindstorms pode ser utilizado no contexto educativo destes utentes e como parte de uma terapia de reabilitação motora.

The microbiota of the upper respiratory tract (URT) plays an important role in protecting the host against respiratory pathogens. Most of the microbial communities in the URT are commensal bacteria. However, some of the colonizers are opportunistic pathogens such as Streptococcus pneumoniae. S. pneumoniae is a Gram-positive bacterium responsible for causing infections such as otitis media, sinusitis, meningitis, bacteremia and pneumonia. Such infections remain common among children, elders and immunocompromised patients despite the introduction of vaccines. Furthermore, the emergence of antibiotic resistance has narrowed the treatment options. Previously at the Molecular Microbiology of Human Pathogens Laboratory, seven strains were identified as commensal streptococci - Streptococcus oralis and Streptococcus mitis - which inhibited most strains of a diverse pneumococcal collection. The genomic analysis of these commensal strains identified multiple putative bacteriocin loci. In this work, the inhibitory potential of three bacteriocin loci (B2 from a S. oralis strain and B6 and C3 from a S. mitis strain) against the pneumococci was evaluated. Deletion mutants for each locus were constructed and cell-free supernatants were obtained and tested for inhibitory potential. A partial loss of inhibition was observed when the supernatants of the B2 and B6 loci deletion mutants were tested against pneumococci in well-diffusion assays and during planktonic growth. Bacterial cytological profiling was performed to obtain insights on the mechanism of action of the bacteriocins in the loci under study. Fluorescence microscopy imaging suggested an increased permeability in cells treated with the supernatant of the S. mitis wild-type strain which was not observed in cells treated with the supernatant of the corresponding B6 deletion mutant. In conclusion, in the conditions tested the bacteriocins from the B2 and B6 loci have a small effect on the inhibition of S. pneumoniae. The B6 locus possibly targets the pneumococcal cell membrane leading to its disruption.

Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability of horizontal gene transfer, bacteria are capable of “borrowing” and “lending” defensive and evasive maneuvers against antibiotics from other neighboring bacteria. As a consequence of antibiotic use, the frequency of antibiotic-resistant bacteria increases in the microbiome, eventually containing mobile genetic elements coding for antimicrobial resistance genes, thus favoring the dissemination of these genes which can lead to the ineffectiveness of the antibiotic. Furthermore, recent studies have shown that, as a side effect of antibiotic intake in medicine, people may be selecting more virulent strains. The quick rise of resistant bacteria threatens the effectiveness of antibiotics worldwide. For this reason, it is crucial to understand the relationship between antibiotic resistance (AR), virulence factors (VF) and mobile genetic elements (MGEs). With this project, we aim to study the metagenomes of domesticated and wild animals. To have an understanding of the impact of AR pollution and dissemination, we created a bioinformatic workflow to make a comparative study of the richness and diversity of the determinants of bacterial AR, VFs and MGEs in the microbiomes of domestic and wild animals. We retrieved metagenomic files of geese, mice, horses and yaks from NCBI, MG-RAST and NCBC, and utilized MetaSPADES and Prokka to assemble, annotate and translate them. In order to compare the richness and diversity of the animals’ microbiomes, we used two files for each metagenome: one with the complete DNA sequence (FNA) and another one in which the translated proteins were clustered at 90% identity. We used these files as input for BLAST and ran them against dedicated databases for AR (Resfinder), VFs (VFDB) and MGEs (ICEberg, ReTrIn, Prophage DB). Afterwards, each BLAST output file was prepared and normalized for statistical analysis using R. Kruskal-Wallis and Wilcoxon tests were applied to compare the orthologs in the microbiomes of the animals’ and linear regression and correlation coefficient were used to study the relationship between AR, VFs and MGEs. We were unable to create to validate scientific knowledge from our dataset due to its small sample size, but we were successful in defining and testing a bioinformatic workflow to compare the metagenomes of domestic and wild animals.

Extreme heat is a current and future issue on urban areas, with negative impacts on health and quality of life (increasing morbidity and mortality rates). This paper analyses day (12:00–15:00 h) and nighttime (00:00–03:00 h) thermophysiological comfort (TC) conditions by Local Climate Zones (LCZ) in Lisbon during a particular Local Weather Type (LWT), very hot summer days. For this, 13 different microscale sample areas were chosen covering urban and non-urban land cover classes (LCZs 1–3, 4–6, 8, 9, A and B). Universal Thermal Climate Index (UTCI) and Mean Radiant Temperature (MRT) were modeled on SkyHelios software for 163 days between 2008 and 2014. Results show that during the day all urban LCZ samples depict the same average TC conditions (average UTCI of 34°C—strong heat stress) and densely wooded areas are 2°C cooler (average UTCI of 32°C—moderate heat stress). However, compact areas (LCZs 1–3) with low sky view factor and some vegetation (street trees) display lower percentages of area with higher thermo-physiological discomfort (TD) levels (83% with strong heat stress against 98% in LCZs 8 and 9 and 100% in LCZs 4–6). When considering the hottest days (air temperatures equal or above 35°C—75th percentile), the moderate heat stress class disappears in all samples and the very strong heat stress class appears only on urban areas, occupying between 12% and 16% on LCZs 1–3, 10%–22% on LCZs 4–6, 16%–22% on LCZs 8 and 9 on LCZ 9. During the nighttime period all samples show no thermal stress, favoring nocturnal physiological recovery. TC conditions in Lisbon are strongly influenced by solar radiation and wind, which explains the need to increase the shading area, preferably by trees, and to promote and preserve ventilation paths.

The upstream exploration in the Campos Basin began in the late 1950s in shallow waters and moved to the ultra-deep waters in the 21st century with different levels of success. The purpose of this study is to carry out an integrated regional petroleum system model in the southern region of the Campos basin, attempting to explain the different oils densities and distribution across the region. To perform the petroleum systems modeling in the Southern part of the basin, it was necessary to generate a set of key grids that allowed to capture the main geological events of the basin. Therefore, the basement, top rift, base salt, top salt, eocene and sea bottom regional horizons were interpreted in 2D and 3D seismic, from which grids for each horizon were generated to provide a regional framework of the geological model. A temperature database with the available measurements data from relevant wells was created for thermal calibration and the regional crustal structure was considered on the developed thermal model. Several 1D models were created and integrated on a regional petroleum systems model. Based on the distribution of source rock facies in the basin, two source rock intervals were modelled, one at the base of the sag and other at the intra-rift. The lacustrine facies available in the modelling software were considered a good approach to the facies reported on the basin. The findings support the correlation where higher oil maturity and formation temperature corresponds to a higher API value and therefore lighter oils. In some regions of the study area there were no favorable temperature conditions for the maturation of the kerogens and the consequent transformation into hydrocarbons. The estimated qualitative volumes of oil and gas expelled presented expulsion results aligned with the regional distribution of hydrocarbon fields and highlighted areas where oil expulsion was predicted. The heavy oils in the West are a result of lower maturities from the inboard kitchen and the biodegradation in the post salt reservoirs. The processes of migration and accumulation of hydrocarbons are linked to the dynamics of the evaporitic sequence which, due to its very low permeability, acted as a conditioning to the flow of hydrocarbons generated in the rift section. The migration model expelled hydrocarbons towards areas where the lack of seal allowed migration into the post salt section and charge the turbiditic reservoirs of the Cenozoic. The accumulation occurred in traps at different stratigraphic intervals. The current study presented a qualitative regional approach integrating data analysis, geological, thermal and petroleum system models, setting a regional geohistory framework of the southern part of the Campos basin to provide a petroleum system interpretation of the hydrocarbons generation, migration and distribution to achieve an outcome complementary to regional studies in the southern part of the Campos basin.

The relationship between disaster resilience and sustainability in the context of urban risk has gained significant attention in recent years as the research and technical community work towards a safer, more sustainable way of living. Urban risk is a complex matrix that involves multiple elements at risk, hazards, temporal scales, and vulnerabilities, and this is why traditional risk assessment approaches that focus on addressing the impacts of a single hazard are inadequate for effectively assessing and managing urban risk, particularly in the current climate change context. With this in mind, the present chapter provides an introduction to the concept of multi-hazard risk and its relevance to resilient and sustainable cities by listing and briefly discussing the types of natural hazards that impact cities the most and examining the importance of risk assessment and management in reducing the risks posed by these hazards. The chapter also explores strategies for building resilience in cities, including the strengthening of physical infrastructure and the enhancement of social and economic resilience, and concludes by discussing future directions for research and practice in multi-hazard risk management for resilient and sustainable cities.

Neurodegenerative diseases are a group of diseases characterised by the loss of neurons and tend to be fatal. The most researched being Parkinson’s disease, some connections have been established between this disease and the use of text-entry towards its diagnosis and monitoring. With such scattered information regarding neurodegenerative diseases and text-entry, a systematic review was carried out to show which diseases have been researched in that direction, being mainly PD but also MCI and MS. The main metrics collected were flight time, hold time and pressure. As previous research did not include clinicians participation towards the design of diagnosing and monitoring tools, this dissertation went a step further and worked together with clinicians to understand their expectations on data and its visualisations. Clinicians believe that text-entry does have potential towards the diagnosis and monitoring of neurodegenerative diseases. Clinicians also provided concepts of interest against recently suggested metrics, such as apraxia, bradykinesia and dyskinesia. Finally, it was possible to understand how clinicians would deem to be the best way to view the data for the patients’ assessments.

The manifestation of a hazardous process in a given location is clear evidence of a threat to individuals and communities. Without hazard, there is no risk. Vulnerability, however, plays a less evident role in explaining the losses that are observed in databases, whether global or local. Social vulnerability, in particular, represents the underneath conditions that turn individuals and communities more or less able to endure the impacts of hazardous events. A detailed-level analysis of social vulnerability was performed in the Lisbon Metropolitan Area, considering the dimension of the individuals’ characteristics—that we define as criticality—and the characteristics of the surrounding territories in the ability to provide support during and timely recovery after the event—that we define as support capability. The study area is highly contrasting in terms of this later dimension, with urban areas concentrating most of the services and equipment that reduce vulnerability. Regarding criticality, the methodology allowed to identify very-localized hotspots laid out to high propensity to losses from two drivers: employment and education (first principal component of criticality) and age, gender, and old urban fabric (second principal component). Analysed separately or combined in a single social vulnerability index, this information is useful in the planning of short-term actions in the strict field of civil protection operations and in mid- to long-term actions considering a wider perspective of risk governance, bringing to the table public policies in the areas of social care, mobility, urban planning, education, and health services, that address the very deep roots of vulnerability.

Flood processes are one of the most challenging to risk assessment and management. In many situations, peak flows are generated kilometers away from the places where inundation is observed. Scale in flood risk assessments is a fundamental factor when estimating hazard, exposure, and vulnerability. Municipal, civil parish, and building-level information are used to construct flood risk indexes and profiles. It is observed that, depending on the scale at which it is represented, the same root information provides distinct insights into flood risk expression in the Lisbon Metropolitan Area. When compared with the Flood Directive critical areas, the results show they are mostly consistent with the results at the different scales, identifying the same hotspots of flood risk (in the Loures, V. F. Xira, and Setúbal municipalities) as those selected during the Directive’s implementation. Flood loss reduction implies the involvement of distinct risk practitioners and decision-makers, acting at distinct scales and sectors related to risk governance. Interconnections between flood risk components and between flood processes and other potential cascading processes are still insufficiently known and require the priority of society.

Urban fires are one the major threats to the security of the urban population. Given their spatial context, they have a direct impact on the economy, inhabitants, and destruction of property and heritage in the community. In the Lisbon metropolitan area (LMA), almost 75% of the urban fires occurred in residential buildings between 2006 and 2020 and were recorded with 150 deaths and 275 severely injured victims. Despite the damages caused by urban fires in LMA, there is a lack of studies on the predisposing factors of residential fire susceptibility and susceptibility zonation at the parish and building levels. This study constructed a residential fire susceptibility model using the information value method, a dataset of socio-economic and building predisposing factors, and an urban fires database for the period 2006–2020. The results suggest that the nearest suburban municipalities from Lisbon record the highest susceptibility to residential fires. Allied with geographic information techniques, these detailed studies are crucial for suited risk reduction strategies and proper urban planning in metropolitan areas.

The current TileCal hadronic calorimeter high voltage distribution system (HVDS) of the ATLAS experience was developed in the 1990s. A large part of its components is already obsolete and since it is expected to have performance degraded in the near future due to continuous exposure to very high levels of radiation, it is necessary to update the HVDS. The new remote HVDS will be placed outside of the detector, in a region that will not be affected by the radiation, that maximizes the reliability and robustness of the system. The remote high voltage distribution system is based on a pair of boards, the HV Remote board that individually regulates and monitors the high voltage for 48 outputs and the HV Supplies board that generates the primary high voltages and supplies the low voltages necessary for the HV Remote to work. Each output will supply a photomultiplier tube (PMT). It is a complicated task to test the 48 high voltage outputs manually, so the need arose to have a board that automatically monitors the outputs individually. Therefore, the present work consists of the development of a board that automatically monitors the high voltage and low voltage outputs, that is called HV Test. This was developed to monitor 96 high voltage outputs, which corresponds to two pairs of HV Remote cards, and 4 low voltages supplied by the crate. The crate is a bin that houses 16 pairs of cards that are connected to an intermediate card, which connects them to the FPGA digital control card. The HV Test board allows for internal monitoring using an ADC and/or external monitoring using a voltmeter. This was developed on the synchronous serial communication protocol, called Serial Peripheral Interface (SPI). The user interface for communication with the HV Test was developed, and the communication code between the interface and the card was developed both for the 1st and the 2nd prototypes, and the respective classes for operation and communication with the ADCs. To control the card, only a device based on the system on chip system is needed, which allows implementing the SPI communication protocol and communication with the ATLAS digital control system. In this work, the Raspberry Pi is used. Finally, a set of stability tests was carried out HV distribution system in the Test Beam Module at CERN.

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This study assesses the physical vulnerability of buildings (PVB) in the Lisbon Metropolitan Area (LMA) exposed to landslides triggered by both rainfall and earthquakes. Firstly, a statistical model (Information Value), validated with a ROC curve, was adopted to assess susceptibility to landslides caused by rainfall. Secondly, an Analytic Hierarchy Process was adopted to assess the susceptibility to landslides caused by earthquakes. In this case, the model was validated with an inventory of historical landslides in the LMA. The vulnerability assessment included all residential buildings surveyed in the 2011 Census, considering a set of vulnerability parameters, namely: the presence of reinforced structure, number of floors, conservation status, and need for repairs in the structure and finishes. These parameters, and their respective weights, were based on expert opinion and literature. Through this analysis, it was possible to identify meaningful regional interactions between the earthquake and rainfall-triggered landslides, leading to complex damage scenarios for residential buildings. It was also possible to identify risk hotspots and potential risk adaptation and mitigation measures.

The Lisbon Metropolitan Area is a risk hotspot in Portugal due to excessive exposure to natural and environmental hazards. In this work, a multi-hazard susceptibility assessment is performed for the 118 parishes that constitute the study area, considering the spatial incidence of seven hazardous processes: earthquakes, tsunami, beach erosion and coastal flooding, coastal erosion and cliff retreat, landslides, floods, and forest fires. The relative importance of hazardous processes was established through the Analytic Hierarchy Process (AHP), based on the frequency-magnitude relationship of each process and its damage capacity. All the parishes exhibiting very high multi-hazard susceptibility have high earthquake susceptibility and most are located in riverine or coastal zones, thus subjected to floods and/or coastal erosion (affecting beaches and/or cliffs).

Landslide inventories are essential for developing an accurate susceptibility assessment. However, the complete and systematic updating of these inventories is a time-consuming and challenging task. Therefore, we aimed to verify if the temporal updating of historical inventories improves the susceptibility models and if the size of the study area plays a relevant role in the decision to update or not landslide inventories. To answer these questions, the work was carried out in two study areas with different sizes but with a similar geomorphological context. The landslide susceptibility modelling, developed using the Information Value method, was performed for distinct types of landslides and using three landslide inventories: one with landslides that occurred before 2012; a second with landslides that occurred during the event of 2010; and a third with landslides that occurred up to 2019. The results indicate no improvement or only a residual enhancement in the susceptibility models’ predictive capacity, regardless of the type of landslide or the study area’s size.

For over ten years, I have been conducting research across (and about) several agro-industrial enclaves in Italy, with a special focus on Tavoliere (coinciding roughly with the flatlands in the province of Foggia, northern Apulia) and the plain of Gioia Tauro (in the province of Reggio Calabria, the southernmost tip of the Italian peninsula). These are among the top production districts for made-in- Italy agri-food — one of the country’s leading exports and a source of international renown. But their claim to fame derives not so much from the role these enclaves play in quality farming, as from less flattering, if related reasons. They are mostly known for what have been defined as “zones of social abandonment” (Biehl 2013; cf. Povinelli 2011): here as elsewhere, from Sicily to Piedmont, large slums, official labor camps, and a range of hybrid in-between spaces have developed since the late 1980s, inhabited today mainly by West African (and in some cases Roma) migrants. Many of them are employed as day laborers in the harvest of different crops — from citrus fruit, grapes, and olives to tomatoes and other horticultural produce.

No summary/description provided