A century and half of hydrogeomorphological disasters in Mainland Portugal

The disaster database lists disastrous floods and landslides registered in mainland Portugal in the period 1865–2015, based on data collected from newspapers. The database includes 1950 hydrogeomorphological disaster cases that caused 1256 deaths, 14,884 evacuated people and 41,977 displaced people. Disastrous floods are clustered in the Lisbon region and the Tagus valley, in the Oporto region and the Douro valley, in the Coimbra region and the Mondego valley and along the Vouga valley. Disastrous landslides are clustered in the Lisbon region and the Douro valley. The period 1935–1969 registered the highest number of disastrous floods and landslides, whereas the last 45 years of the series (1970–2015) do not show any clear temporal trend. However, the 10-year moving average increased at the beginning of the twenty-first century, for floods and landslides, and it is apparent the increasing number of disaster events consisting of several cases, which may result from the increasing occurrence of rainfall extreme events related with climate change. The spatial and temporal trends observed on disastrous floods and landslides reflect the distribution of conditioning factors, the temporal incidence of triggering factors, but also the evolution of the exposure and the vulnerability of people, structures and infrastructures.info:eu-repo/semantics/acceptedVersio

Screening forCronobacterSpecies in Powdered and Reconstituted Infant Formulas and from Equipment Used in Formula Preparation in Maternity Hospitals

Background/Aims: Cronobacter spp. have been identified as being of considerable risk to neonates. The occurrence of organism in infant formulas is therefore of considerable interest. Methods: The occurrence of Cronobacter spp. in infant feeds (formulas and fortified cow’s milk) was determined using most probable number (MPN) analysis, and from formula preparation utensils. Ninety nine samples were analyzed, of which 42 were unopened cans of powdered infant formula (PIF), 25 reconstituted infant formulas in feeding bottles, 27 utensils used from the preparation of infant formula, and 5 samples of fortified cow’s milk. Presumptive Cronobacter spp. isolates were identified using the 7 allele multilocus sequence typing (MLST) scheme. Results: C. sakazakii, C. malonaticus and C. muytjensii were recovered from PIF. Although the incidence of Cronobacter in PIF was 29% (12/42), the level was low with an average of 0.54 MPN/100g. According to MLST profiling, C. sakazakii was the most frequently isolated Cronobacter species, and C. sakazakii ST4 (associated with neonatal meningitis) was recovered from 2/42 PIF samples at 0.51 and 0.92 MPN/100g. Conclusions: Cronobacter spp. can be isolated from PIF and therefore strict hygienic practices during PIF preparation are important to minimize neonate exposure and reduce the risk of severe infections

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis.This research was supported by a Worldwide Cancer Research grant to CF and JCM (Reference 16-1352). RMF, JPM and IPR have fellowships from Fundacao para a Ciencia e a Tecnologia (FCT; SFRH/BPD/84084/2012, PD/BD/114014/2015 and SFRH/BD/110803/2015, respectively) through Programa Operacional Capital Humano (POCH) and the European Union. JPM's fellowship is in the framework of FCT's PhD Programme BiotechHealth (Ref PD/0016/2012). i3S-Instituto de Investigacao e Inovacao em Saude is funded by Fundo Europeu de Desenvolvimento Regional (FEDER) funds through the COMPETE 2020-Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through Fundacao para a Ciencia e a Tecnologia (FCT)/Ministerio da Ciencia, Tecnologia e Inovacao (POCI-01-0145-FEDER-007274)

P-selectin glycoprotein ligand 1 promotes T cell lymphoma development and dissemination

P-selectin glycoprotein ligand-1 (PSGL-1) is a membrane-bound glycoprotein expressed in lymphoid and myeloid cells. It is a ligand of P-, E- and L-selectin and is involved in T cell trafficking and homing to lymphoid tissues, among other functions. PSGL-1 expression has been implicated in different lymphoid malignancies, so here we aimed to evaluate the involvement of PSGL-1 in T cell lymphomagenesis and dissemination. PSGL-1 was highly expressed at the surface of human and mouse T cell leukemia and lymphoma cell lines. To assess its impact on T cell malignancies, we stably expressed human PSGL-1 (hPSGL-1) in a mouse thymic lymphoma cell line, which expresses low levels of endogenous PSGL-1 at the cell surface. hPSGL-1-expressing lymphoma cells developed subcutaneous tumors in athymic nude mice recipients faster than control empty vector or parental cells. Moreover, the kidneys, lungs and liver of tumor-bearing mice were infiltrated by hPSGL-1-expressing malignant T cells. To evaluate the role of PSGL-1 in lymphoma cell dissemination, we injected intravenously control and hPSGL-1-expressing lymphoma cells in athymic mice. Strikingly, PSGL-1 expression facilitated disease infiltration of the kidneys, as determined by histological analysis and anti-CD3 immunohistochemistry. Together, these results indicate that PSGL-1 expression promotes T cell lymphoma development and dissemination to different organs.We thank Roger McEver, José M Almendral, Hind Medyouf, João T Barata and Neil D Perkins for providing reagents and cells, André Mozes (CBMR Flow Cytometry Unit) for technical assistance and Sara Miranda and Nuno Bastos for immunohistochemistry technical assistance. This work was supported by Fundação para a Ciência e a Tecnologia (Portugal), European Social Fund , European Regional Development Fund ( PTDC/SAU-OBD/103336/2008 , PTDC/MED-ONC/32592/2017 , UID/BIM/04773/2013 , NORTE-01-0145-FEDER-000029 and POCI-01-0145-FEDER-007274 grants, IF/00056/2012 contract to NRdS and SFRH/BD/147979/2019 fellowship to JLP), and Gilead Sciences Portugal (Programa Gilead GÉNESE PGG/038/2017 grant). The authors acknowledge the support of the i3S Scientific Platform Histology and Electron Microscopy , member of the national infrastructure PPBI - Portuguese Platform of Bioimaging ( PPBI-POCI-01-0145-FEDER-022122 ). We thank Roger McEver, Jos? M Almendral, Hind Medyouf, Jo?o T Barata and Neil D Perkins for providing reagents and cells, Andr? Mozes (CBMR Flow Cytometry Unit) for technical assistance and Sara Miranda and Nuno Bastos for immunohistochemistry technical assistance. This work was supported by Funda??o para a Ci?ncia e a Tecnologia (Portugal), European Social Fund, European Regional Development Fund (PTDC/SAU-OBD/103336/2008, PTDC/MED-ONC/32592/2017, UID/BIM/04773/2013, NORTE-01-0145-FEDER-000029 and POCI-01-0145-FEDER-007274 grants, IF/00056/2012 contract to NRdS and SFRH/BD/147979/2019 fellowship to JLP), and Gilead Sciences Portugal (Programa Gilead G?NESE PGG/038/2017 grant). The authors acknowledge the support of the i3S Scientific Platform Histology and Electron Microscopy, member of the national infrastructure PPBI - Portuguese Platform of Bioimaging (PPBI-POCI-01-0145-FEDER-022122)

Pre-training autoencoder for lung nodule malignancy assessment using CT images

Lung cancer late diagnosis has a large impact on the mortality rate numbers, leading to a very low five-year survival rate of 5%. This issue emphasises the importance of developing systems to support a diagnostic at earlier stages. Clinicians use Computed Tomography (CT) scans to assess the nodules and the likelihood of malignancy. Automatic solutions can help to make a faster and more accurate diagnosis, which is crucial for the early detection of lung cancer. Convolutional neural networks (CNN) based approaches have shown to provide a reliable feature extraction ability to detect the malignancy risk associated with pulmonary nodules. This type of approach requires a massive amount of data to model training, which usually represents a limitation in the biomedical field due to medical data privacy and security issues. Transfer learning (TL) methods have been widely explored in medical imaging applications, offering a solution to overcome problems related to the lack of training data publicly available. For the clinical annotations experts with a deep understanding of the complex physiological phenomena represented in the data are required, which represents a huge investment. In this direction, this work explored a TL method based on unsupervised learning achieved when training a Convolutional Autoencoder (CAE) using images in the same domain. For this, lung nodules from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) were extracted and used to train a CAE. Then, the encoder part was transferred, and the malignancy risk was assessed in a binary classification—benign and malignant lung nodules, achieving an Area Under the Curve (AUC) value of 0.936. To evaluate the reliability of this TL approach, the same architecture was trained from scratch and achieved an AUC value of 0.928. The results reported in this comparison suggested that the feature learning achieved when reconstructing the input with an encoder-decoder based architecture can be considered an useful knowledge that might allow overcoming labelling constraints.This work is financed by National Funds through the Portuguese funding agency, FCT—Fundação para a Ciência e a Tecnologia within project UIDB/50014/2020

A genetic interaction of NRXN2 with GABRE, SYT1 and CASK in migraine patients: a case-control study

Background: Migraine is a multifactorial disorder that is more frequent (two to four times) in women than in men. In recent years, our research group has focused on the role of neurotransmitter release and its regulation. Neurexin (NRXN2) is one of the components of the synaptic vesicle machinery, responsible for connecting intracellular fusion proteins and synaptic vesicles. Our aim was to continue exploring the role and interaction of proteins involved in the control and promotion of neurotransmission in migraine susceptibility. Methods: A case-control study was performed comprising 183 migraineurs (148 females and 35 males) and 265 migraine-free controls (202 females and 63 males). Tagging single nucleotide polymorphisms of NRXN2 were genotyped to assess the association between NRXN2 and migraine susceptibility. The χ 2 test was used to compare allele frequencies in cases and controls and odds ratios were estimated with 95% confidence intervals. Haplotype frequencies were compared between groups. Gene-gene interactions were analysed using the Multifactor Dimensionality Reduction v2.0. Results: We found a statistically significant interaction model (p = 0.009) in the female group between the genotypes CG of rs477138 (NRXN2) and CT of rs1158605 (GABRE). This interaction was validated by logistic regression, showing a significant risk effect [OR = 4.78 (95%CI: 1.76–12.97)] after a Bonferroni correction. Our data also supports a statistically significant interaction model (p = 0.011) in the female group between the GG of rs477138 in NRXN2 and, the rs2244325's GG genotype and rs2998250’s CC genotype of CASK. This interaction was also validated by logistic regression, with a protective effect [OR = 0.08 (95%CI: 0.01–0.75)]. A weak interaction model was found between NRXN2-SYT1. We have not found any statistically significant allelic or haplotypic associations between NRXN2 and migraine susceptibility.This work was funded by Sociedade Portuguesa de Cefaleias (SPC), Fundação para a Ciência e Tecnologia (FCT; PTDC/MEC-NEU/29468/2017), Tecnifar fellowships and by European Commission and European Regional Development Fund under the project 'Análisis y correlación entre la epigenética y la actividad cerebral para evaluar el riesgo de migraña crónica y episódica en mujeres' (Cooperation Programme Interreg V-A Spain-Portugal, POCTEP 2014–2020, by the Ministerio de Ciencia, Innovación y Universidades)

A note on the use of the generalized odds ratio in meta-analysis of association studies involving bi- and tri-allelic polymorphisms

<p>Abstract</p> <p>Background</p> <p>The generalized odds ratio (GOR) was recently suggested as a genetic model-free measure for association studies. However, its properties were not extensively investigated. We used Monte Carlo simulations to investigate type-I error rates, power and bias in both effect size and between-study variance estimates of meta-analyses using the GOR as a summary effect, and compared these results to those obtained by usual approaches of model specification. We further applied the GOR in a real meta-analysis of three genome-wide association studies in Alzheimer's disease.</p> <p>Findings</p> <p>For bi-allelic polymorphisms, the GOR performs virtually identical to a standard multiplicative model of analysis (e.g. per-allele odds ratio) for variants acting multiplicatively, but augments slightly the power to detect variants with a dominant mode of action, while reducing the probability to detect recessive variants. Although there were differences among the GOR and usual approaches in terms of bias and type-I error rates, both simulation- and real data-based results provided little indication that these differences will be substantial in practice for meta-analyses involving bi-allelic polymorphisms. However, the use of the GOR may be slightly more powerful for the synthesis of data from tri-allelic variants, particularly when susceptibility alleles are less common in the populations (≤10%). This gain in power may depend on knowledge of the direction of the effects.</p> <p>Conclusions</p> <p>For the synthesis of data from bi-allelic variants, the GOR may be regarded as a multiplicative-like model of analysis. The use of the GOR may be slightly more powerful in the tri-allelic case, particularly when susceptibility alleles are less common in the populations.</p

EVALUATION OF BIOMASS PRODUCTION, CAROTENOID LEVEL AND ANTIOXIDANT CAPACITY PRODUCED BY THERMUS FILIFORMIS USING FRACTIONAL FACTORIAL DESIGN

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)A fractional factorial design 2(5-1) was used to evaluate the effect of temperature, pH, and concentrations of yeast extract, tryptone and Nitsch's trace elements on the biomass, total carotenoids and protection against singlet oxygen by carotenoid extracts of the bacterium Thermus filiformis. In addition, the carotenoid composition was determined by high-performance liquid chromatography connected to a diode array and mass spectrometer detectors (HPLC-DAD-MS/MS). The production of biomass ranged from 0.113 to 0.658 g/L, the total carotenoid from 137.6 to 1,517.4 mu g/g and the protection against singlet oxygen from 4.3 to 85.1 %. Results of the fractional factorial design showed that temperature had a negative effect on biomass production and a positive effect on carotenoid content and protection against singlet oxygen, besides, high levels of pH value, concentrations of yeast extract and tryptone had a positive effect on biomass production only at lower temperatures. The main carotenoids of T. filiformis were thermozeaxanthins. In the tested conditions, changes in the levels of the variables influenced the biomass, carotenoid production, and protection against singlet oxygen, although they did not influence the carotenoid profile. The results of this study provide a better understanding on the interactions among certain nutritional and cultivation conditions of a thermophile bacterium, Thermus filiformis, on biomass and carotenoid amounts, as well as on the antioxidant capacity.431126134Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq