Projectar com luz, cor e matéria

Dissertação para obtenção do grau de Mestre em Arquitectura com Especialização em Arquitectura de Interiores, apresentada na Universidade de Lisboa - Faculdade de Arquitectura.

A case-only genome-wide association study of gender- and age-specific risk markers for childhood leukemia

Males and age group 1 to 5 years show a much higher risk for childhood acute lymphoblastic leukemia (ALL). We performed a case-only genome-wide association study (GWAS), using the Illumina Infinium HumanCoreExome Chip, to unmask gender- and age-specific risk variants in 240 non-Hispanic white children with ALL recruited at Texas Children’s Cancer Center, Houston, Texas. Besides statistically most significant results, we also considered results that yielded the highest effect sizes. Existing experimental data and bioinformatic predictions were used to complement results, and to examine the biological significance of statistical results. ^ Our study identified novel risk variants for childhood ALL. The SNP, rs4813720 (RASSF2), showed the statistically most significant gender-specific associations (P < 2 x 10-6). Likewise, rs10505918 (SOX5) yielded the lowest P value (P < 1 x 10-5 ) for age-specific associations, and also showed the statistically most significant association with age-at-onset (P < 1 x 10-4). Two SNPs, rs12722042 and 12722039, from the HLA-DQA1 region yielded the highest effect sizes (odds ratio (OR) = 15.7; P = 0.002) for gender-specific results, and the SNP, rs17109582 (OR = 12.5; P = 0.006), showed the highest effect size for age-specific results. Sex chromosome variants did not appear to be involved in gender-specific associations. ^ The HLA-DQA1 SNPs belong to DQA1*01:07and confirmed previously reported male-specific association with DQA1*01:07. Twenty one of the SNPs identified as risk markers for gender- or age-specific associations were located in the transcription factor binding sites and 56 SNPs were non-synonymous variants, likely to alter protein function. Although bioinformatic analysis did not implicate a particular mechanism for gender- and age-specific associations, RASSF2 has an estrogen receptor-alpha binding site in its promoter. The unknown mechanisms may be due to lack of interest in gender- and age-specificity in associations. These results provide a foundation for further studies to examine the gender- and age-differential in childhood ALL risk. Following replication and mechanistic studies, risk factors for one gender or age group may have a potential to be used as biomarkers for targeted intervention for prevention and maybe also for treatment.^

Prenatal alcohol exposure and childhood balance ability:findings from a UK birth cohort study

OBJECTIVE: To investigate the association of prenatal alcohol exposure with balance in10-year-old children. DESIGN: Population-based prospective longitudinal study. SETTING: Former Avon region of UK (Southwest England). PARTICIPANTS: 6915 children from the Avon Longitudinal Study of Parents and Children who had a balance assessment at age 10 and had data on maternal alcohol consumption. OUTCOME MEASURES: 3 composite balance scores: dynamic balance (beam-walking), static balance eyes open, static balance eyes closed (heel-to-toe balance on a beam and standing on one leg, eyes open or closed). RESULTS: Most mothers (95.5%) consumed no-to-moderate amounts (3-7 glasses/week) of alcohol during pregnancy. Higher total-alcohol consumption was associated with maternal-social advantage, whereas binge drinking (≥4 units/day) and abstinence were associated with maternal social disadvantage. No evidence was found of an adverse effect of maternal-alcohol consumption on childhood balance. Higher maternal-alcohol use during pregnancy was generally associated with better offspring outcomes, with some specific effects appearing strong (static balance eyes open and moderate total alcohol exposure at 18 weeks, adjusted OR 1.23 (95% CI 1.01 to 1.49); static balance eyes closed and moderate total alcohol exposure at 18 weeks, adjusted OR 1.25 (95% CI 1.06 to 1.48). Similar results were found for both paternal and postnatal maternal alcohol exposure. A Mendelian-randomization approach was used to estimate the association between maternal genotype and offspring balance using the non-synonymous variant rs1229984*A (ADH1B) to proxy for lower maternal alcohol consumption; no strong associations were found between this genotype/proxy and offspring balance. CONCLUSIONS: No evidence was found to indicate that moderate maternal alcohol consumption in this population sample had an adverse effect on offspring balance at age 10. An apparent beneficial effect of higher total maternal alcohol consumption on offspring balance appeared likely to reflect residual confounding.

Single-nucleotide polymorphism in two representative multidrug-resistant Mycobacterium bovis isolates collected from patients in a Spanish hospital harboring a human infection outbreak

Mycobacterium bovis is the etiological agent of tuberculosis in domestic and wild animals. Its involvement as a human pathogen has been highlighted again with the recent descriptions of transmission through dairy products (18), reactivation or primary infection in human immunodeficiency virus-infected patients (5), and association with meat industry workers, animal keepers, or hunters (3). Strains resistant to antituberculous drugs (M. bovis is naturally resistant to pyrazinamide) pose an additional risk (2). Several studies have demonstrated that mutations in target genes are associated with resistance to antituberculous drugs (4, 7, 10, 11, 16). However, most of them have been developed in Mycobacterium tuberculosis strains and limited data are available regarding M. bovis isolates. The aim of this study was to characterize by sequencing the main genes involved in antibiotic resistance in two multidrug-resistant (MDR) M. bovis isolates in a human outbreak detected in a hospital in Madrid that subsequently spread to several countries (5, 6, 15). The isolates were resistant to 11 drugs, but only their rpoB and katG genes have been analyzed so far (1, 14). We studied the first (93/R1) and last (95/R4) M. bovis isolates of this nosocomial outbreak, characterized by spoligotyping as SB0426 (hexacode 63-5F-5E-7F-FF-60 in the database at www.mbovis.org) (1, 13). Several genes involved in resistance to isoniazid (katG, ahpC, inhA, and the oxyR-ahpC intergenic region), rifampin (rpoB), streptomycin (rrs, rpsL), ethambutol (embB), and quinolones (gyrA) were studied. These genes, or fragments of genes, were amplified and sequenced as previously described (12). The sequence analysis revealed polymorphisms in five (ahpC, rpoB, rpsL, embB, and gyrA) out of nine analyzed genes (Table 1). Nucleotide substitutions in four genes cause a change in the encoded amino acid. Two additional synonymous mutations in ahpC and rpsL differentiated the first and last isolates from the outbreak.

Eficacia de la infiltración de Plasma Rico en Plaquetas (PRP) en pacientes diagnosticados del Síndrome de la Fascia Plantar (SFP) desde el punto de vista clínico y funcional

On the basis of the knowledge that the entheses between the plantar fascia and the calcaneus may exhibit a varied pathology, we considered the need to value the pathological factors by illustrating the anatomical changes in the Plantar Fascia Syndrome (PFS) with easy-to-obtain images which allowed us to substantiate our claims. Accordingly, we analized the anatomical (Orts Llorca, 1977; Llusá, 2007; Sobotta, 2007; Domenech Mateu, 2012; Rodriguez Baeza 2012) and biomechanical (Arandes, 1956; Viladot 1979; Caturla, 2001; Safe, 2001) literature in order to better know the location of the pathology and also to assess the functional reasons that could favor this disease. A study of the affected area by Nuclear Magnetic Resonance (NMR) revealed the presence of bone affections such as bone edema, subchondral lesions and several other bone pathologies together with fascia intrinsic injuries such as myxoid degeneration, intrasubstance fissures and perifascial edematous lesions (Larroca, 2013; Conejero, 2014). Injuries not properly treated during the acute phase can evolve into chronic processes which, month after month, become ever more difficult to resolve. In addition, as seen throughout this study, there are changes in the anatomical normality of the foot usually associated with pathological conditions of the plantar fascia. Once the pathological aspects of PFS are identified and their location is established, clinical manifestations should be registered in order to define this syndrome. Pain is the main symptom in patients with PFS and is associated, in many occasions, with tightness or stiffness of the plantar area, limited mobility of the arch of the ankle and, inevitably, a progressive functional deterioration. Thus, that sharp and stabbing pain felt when one puts the foot on the floor after a period of rest located in the front lower face of the heel and irradiating and/or projecting to the middle of the sole of the foot would be synonymous with Plantar Fascia Syndrome (PFS)...

Saúde psicológica: Definição teórica do constructo e representação em profissionais de saúde.

Dissertação de Mestrado apresentada no ISPA - Instituto Universitário

A new redescription of Galeus atlanticus (Vaillant, 1888) (Chondrichthyes: Scyliorhinidae) based on field marks

The Atlantic sawtail catshark, Galeus atlanticus, has long been synonymous with the blackmouth catshark, Galeus melastomus, until the validity of G. atlanticus was resurrected by Muñoz-Chapuli and Ortega (1985). Despite this resurrection, the two species are still often confused because of their close resemblance. Consequently, field characters are proposed to distinguish the two sibling species. In particular, the internal colour of the labial furrows is easily observable on fresh specimens and also on preserved ones in museum collections, since it is blackish in G. atlanticus as opposed to white in G. melastomus. The two Atlanto-Mediterranean species are also compared to the West-African species G. polli.

A real time Taqman RT-PCR for the detection of rabbit hemorrhagic disease virus 2 (RHDV2)

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2- RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains, meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

Tracking the Origin of a Rabbit Haemorrhagic Virus 2 Outbreak in a Wild Rabbit Breeding Centre in Portugal; Epidemiological and Genetic Investigation

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2-RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains,meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

Memoires de Soie en Inde: La Ville de Kanchipuram et son art de Tissage

A cidade de Kanchipuram, no Estado de Tamilnadu, sul da Índia, é sinónimo de templos hindus, mas também do sari em seda. A migração de comunidades de tecelão para esta cidade começou durante o reinado da Dinastia Chola nos Séculos 8-13 d. C. Anteriormente, o pano de seda foi considerado como tecido dos Deuses e os tecelões satisfizeram as necessidades religiosas do templo da cidade. Paulatinamente, um tecido de seda torna-se, tanto um tecido dos "mortais", como dos Deuses, e houve um aumento da procura dos têxteis em seda, especialmente, do sari em seda. A particularidade dos tecelões de Kanchipuram reside na sua técnica complicada de tecelagem e nos ricos motivos que são uma expressão da paixão do tecelão. Nosso trabalho de investigação centra-se nas técnicas de tecelagem e no seu produto final - o sari - para destacar a sua singularidade. Neste contexto, quero propor um projecto de documentação dos motivos do sari, para ilustrar um dos principais meios de valorização desta tradição de tecelagem que remonta a vários séculos. RÉSUMÉ: La ville de Kanchipuram, située dans l'état du Tamilnadu, dans le sud de l'Inde, fait souvent écho aux temples hindous mais également au sari en soie. Les tisserands ont migré à l'époque Chola (850- 1279 ap.J.C.) pour répondre aux besoins religieux de la ville car au départ, la soie était un tissu destiné à I 'usage des dieux. Au fur et à mesure, la soie est devenue aussi bien un tissu destiné aux 'mortels' qu'aux dieux. Ces tisserands ont connu par la suite, une forte demande, plus particulierement, pour les saris en soie. La particularité des tisserands de la ville de Kanchipuram réside dans sa technique laborieuse de tissage et dans les motifs élaborés parle billet desquels s'exprime la passion du tisserand dans sa tâche. Le présent mémoire s'attache à la technique de tissage et à son produit final - le sari - pour mettre en valeur son unicité. Dans ce cadre, je propose un projet de documentation des motifs des saris pour illustrer un des vecteurs clés de valorisation de cette tradition de tissage qui remonte à plusieurs siecles. ABSTRACT: The city of Kanchipuram, located in the State of Tamilnadu in southern India, is synonymous with Hindu temples and silk saris. The migration of weaver communities to the city started during the Chola reign (81 131 centuries A.D). Early on, silk was considered the cloth of the gods and these weavers met the needs of the temple city by producing silk textiles for religious use. Gradually, silk became a cloth as much for the 'mortais' as for the gods and demand increased for silk textiles, especially saris. The importance of Kanchipuram weaving lies in its complex techniques and rich motifs as expressions of the. weaver’s passion. This text examines the weaving techniques popularly known as the korvai technique, as well as the saris produced using this technique. ln addition, it attempts to catalogue certain motifs woven into the saris as a first step in promoting and valorizing the cultural richness of an art dating back several centuries.

Tracking the Origin of a Rabbit Haemorrhagic Virus 2 Outbreak in a Wild Rabbit Breeding Centre in Portugal; Epidemiological and Genetic Investigation

As key prey, the wild rabbit downsize constitutes a major drawback on the endangered Iberian lynx (Lynx pardinus) re-introduction in the Iberia. Several captive breeding units mostly located in Alentejo, endeavour the wild rabbit repopulation of depleted areas assigned for the lynx re-introduction. Here we report an RHDV2 outbreak that occurred in early 2016 in a wild rabbit captive breeding unit located in Barrancos municipality. The estimated mortality rate between March and April 2016 was approximately 8.67%. Anatomopathologic examination was carried out for 13 victimized rabbits. Molecular characterization was based on the complete vp60 capsid gene. The 13 rabbit carcasses investigated showed typical macroscopic RHD lesions testing positive to RHDV2- RNA. Comparison of the vp60 nucleotide sequences obtained from two specimens with others publically available disclosed similarities below 98.22% with RHDV2 strains originated in the Iberia and Azores and revealed that the two identical strains from Barrancos-2016 contain six unique single synonymous nucleotide polymorphisms. In the phylogenetic analysis performed, the Barrancos-2016 strains clustered apart from other known strains, meaning they may represent new evolutionary RHDV2 lineages. No clear epidemiological link could be traced for this outbreak where the mortalities were lower compared with previous years. Yet, network analysis suggested a possible connection between the missing intermediates from which the strains from Barrancos 2013, 2014 and 2016 have derived. It is therefore possible that RHDV2 has circulated endemically in the region since 2012, with periodic epizootic occurrences. Still, six years after its emergence in wild rabbits, RHDV2 continues to pose difficulties to the establishment of natural wild rabbit populations that are crucial for the self-sustainability of the local ecosystems.

Mitochondrial Inheritance, Mito-nuclear Coevolution, and Sex-associated Genes in Bivalve Molluscs: Transcriptomics and Molecular Evolution

Bivalvia represents an ancient taxon including around 25,000 living species that have adapted to a wide range of environmental conditions, and show a great diversity in body size, shell shapes, and anatomic structure. Bivalves are characterized by highly variable genome sizes and extremely high levels of heterozygosity, which obstacle complete and accurate genome assemblies and hinder further genomic studies. Moreover, some bivalve species presented a stable evolutionary exception to the strictly maternal inheritance of mitochondria, namely doubly uniparental inheritance (DUI), making these species a precious model to study mitochondrial biology. During my PhD, I focused on a DUI species, the Manila clam Ruditapes philippinarum, and my work was two-folded. First, taking advantage of a newly assembled draft genome and a large RNA-seq dataset from different tissues of both sexes, I investigated 1) the role of gene expression and alternative splicing in tissue differentiation; 2) the relationship across tissue specificity, regulatory network connectivity, and sequence evolution; 3) sexual contrasting genetic markers potentially associated with sexual differentiation. The detailed information for this part is in Chapter 2. Second, using the same RNA-seq data, I investigated how nuclear oxidative phosphorylation (OXPHOS) genes coordinate with two divergent mitochondrial genomes in DUI species (mito-nuclear coordination and coevolution). To address this question, I compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of R. philippinarum in Chapter 3. To my knowledge, this thesis represents the first study exploring the role of alternative splicing in tissue differentiation, and the first study analyzing both transcriptional regulation and sequence evolution to investigate the coordination of OXPHOS genes in bivalves.

Applied deep learning and data science with a human-centric and data-centric approach

The term Artificial intelligence acquired a lot of baggage since its introduction and in its current incarnation is synonymous with Deep Learning. The sudden availability of data and computing resources has opened the gates to myriads of applications. Not all are created equal though, and problems might arise especially for fields not closely related to the tasks that pertain tech companies that spearheaded DL. The perspective of practitioners seems to be changing, however. Human-Centric AI emerged in the last few years as a new way of thinking DL and AI applications from the ground up, with a special attention at their relationship with humans. The goal is designing a system that can gracefully integrate in already established workflows, as in many real-world scenarios AI may not be good enough to completely replace its humans. Often this replacement may even be unneeded or undesirable. Another important perspective comes from, Andrew Ng, a DL pioneer, who recently started shifting the focus of development from “better models” towards better, and smaller, data. He defined his approach Data-Centric AI. Without downplaying the importance of pushing the state of the art in DL, we must recognize that if the goal is creating a tool for humans to use, more raw performance may not align with more utility for the final user. A Human-Centric approach is compatible with a Data-Centric one, and we find that the two overlap nicely when human expertise is used as the driving force behind data quality. This thesis documents a series of case-studies where these approaches were employed, to different extents, to guide the design and implementation of intelligent systems. We found human expertise proved crucial in improving datasets and models. The last chapter includes a slight deviation, with studies on the pandemic, still preserving the human and data centric perspective.