Carbonatos autigénicos e estruturas de escape de fluidos no Golfo de Cádis

Doutoramento em GeociênciasEste trabalho foca-se no estudo das ocorrências de carbonatos autigénicos do Golfo de Cádis. A mineralogia, textura e valores de δ13Ccarbonatos indica que as diferentes litologias são formadas a partir de oxidação de metano que induz a cimentação dos sedimentos por precipitação de dolomite, calcite magnesiana, calcite e aragonite autigénicas. Os diferentes carbonatos autigénicos derivados de metano (CADM) ocorrem associados a vulcões e cones de lama, cristas diapiricas ou ao longo de falhas. Dois grupos distintos de CADM foram descritos. Um grupo cuja mineralogia é dominada por dolomite e que ocorrem como crostas, chaminés ou nódulos, e um outro grupo com a mineralogia dominada por aragonite e que ocorrem sub a forma de crostas, pavimentos ou montículos, no fundo do mar. Os diferentes grupos de CADM reflectem diferentes ambientes geoquímicos de formação. Os CADM aragoniticos formam-se próximo da interface sedimento/água, enquanto que os CADM dolomíticos formam-se por cimentação ao longo de condutas por onde o fluido circulou dentro da coluna sedimentar em ambientes confinados relativamente à água do mar. A ocorrência destes CADM é interpretada como indicadora de extenso escape de metano na área do Golfo de Cádis. Biomarcadores indicadores de Archaea capaz de realizar oxidação anaeróbica de metano (OAM) e biomarcadores indicadores de bactérias sulfato-redutoras foram identificados nas amostras de CADM. Estes resultados, apoiados também pelas observações de microscópio electrónico e micro-texturas características dos CADM, confirmam um activo envolvimento microbiano na formação destes CADM. A composição isotópica destes CADM indica que na sua formação estiveram envolvidos fluidos intersticiais com um claro contributo de água resultante da dissociação de hidratos de metano. As idades de amostras representativas de CADM, calculadas pela análise de U/Th indica que estes carbonatos se formaram no decorrer dos últimos 250 ka, em períodos correlacionados com rápidas variações paleoceanográficas, como as terminações dos períodos glaciares.This work focus on the occurrences of authigenic carbonates in the Gulf of Cadiz. Mineralogy, texture and δ13Ccarbonate values clearly indicate that the different carbonate lithologies are methane-derived (MDAC), formed by the lithification of sediments as result of the precipitation of authigenic dolomite, calcite, Mg-calcite and aragonite. The MDAC are found associated with mud volcanoes and mud cones, diapiric ridges or along faults. Two distinct groups of MDAC were described in the Gulf of Cadiz. A group dominated by dolomite mineralogy (dolomite crusts, nodules and chimneys) and a group of aragonite dominated carbonates (aragonite pavements, slabs, crusts and buildups). The different MDAC morphologic types reflect different geochemical formation environments. The aragonite pavements represent precipitation of authigenic carbonates at the sediment-seawater interface or close to it. The dolomite nodules, crusts and chimneys result from the cementation along fluid conduits inside the sediment column, in more confined geochemical environments. The widespread abundance of MDAC is interpreted as an evidence of several episodes of extensive methane seepage in the Gulf of Cadiz. Specific 13C-depleted lipid biomarkers indicating archaea involvement in the anaerobic oxidation of methane and bacterial lipid biomarkers also 13Cdepleted and related to sulphate reducing bacteria were both identified on the MDAC. These results, substantiated by SEM observations and by microbial related microfabrics, confirm that microbial activity has played an important role in carbonate authigenesis. Considering the minimum and maximum temperature limits admitted to be possible to occur in the Gulf of Cadiz, some of the MDAC samples indicate a formation from 18O-enriched pore fluids, interpreted as resulting from a contribution of dissociated gas hydrates to the pore waters from which the authigenic carbonates were formed. The estimated U/Th ages of selected dolomite chimneys indicate episodes of intense precipitation of the authigenic carbonates, at least during the last 250 ka, that correlate with periods of rapid paleoceanographic changes as the onsets of glacial/interglacial terminations

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Characterisation of microbial attack on archaeological bone

As part of an EU funded project to investigate the factors influencing bone preservation in the archaeological record, more than 250 bones from 41 archaeological sites in five countries spanning four climatic regions were studied for diagenetic alteration. Sites were selected to cover a range of environmental conditions and archaeological contexts. Microscopic and physical (mercury intrusion porosimetry) analyses of these bones revealed that the majority (68%) had suffered microbial attack. Furthermore, significant differences were found between animal and human bone in both the state of preservation and the type of microbial attack present. These differences in preservation might result from differences in early taphonomy of the bones. © 2003 Elsevier Science Ltd. All rights reserved

Global variation in postoperative mortality and complications after cancer surgery: a multicentre, prospective cohort study in 82 countries

© 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0 licenseBackground: 80% of individuals with cancer will require a surgical procedure, yet little comparative data exist on early outcomes in low-income and middle-income countries (LMICs). We compared postoperative outcomes in breast, colorectal, and gastric cancer surgery in hospitals worldwide, focusing on the effect of disease stage and complications on postoperative mortality. Methods: This was a multicentre, international prospective cohort study of consecutive adult patients undergoing surgery for primary breast, colorectal, or gastric cancer requiring a skin incision done under general or neuraxial anaesthesia. The primary outcome was death or major complication within 30 days of surgery. Multilevel logistic regression determined relationships within three-level nested models of patients within hospitals and countries. Hospital-level infrastructure effects were explored with three-way mediation analyses. This study was registered with ClinicalTrials.gov, NCT03471494. Findings: Between April 1, 2018, and Jan 31, 2019, we enrolled 15 958 patients from 428 hospitals in 82 countries (high income 9106 patients, 31 countries; upper-middle income 2721 patients, 23 countries; or lower-middle income 4131 patients, 28 countries). Patients in LMICs presented with more advanced disease compared with patients in high-income countries. 30-day mortality was higher for gastric cancer in low-income or lower-middle-income countries (adjusted odds ratio 3·72, 95% CI 1·70–8·16) and for colorectal cancer in low-income or lower-middle-income countries (4·59, 2·39–8·80) and upper-middle-income countries (2·06, 1·11–3·83). No difference in 30-day mortality was seen in breast cancer. The proportion of patients who died after a major complication was greatest in low-income or lower-middle-income countries (6·15, 3·26–11·59) and upper-middle-income countries (3·89, 2·08–7·29). Postoperative death after complications was partly explained by patient factors (60%) and partly by hospital or country (40%). The absence of consistently available postoperative care facilities was associated with seven to 10 more deaths per 100 major complications in LMICs. Cancer stage alone explained little of the early variation in mortality or postoperative complications. Interpretation: Higher levels of mortality after cancer surgery in LMICs was not fully explained by later presentation of disease. The capacity to rescue patients from surgical complications is a tangible opportunity for meaningful intervention. Early death after cancer surgery might be reduced by policies focusing on strengthening perioperative care systems to detect and intervene in common complications. Funding: National Institute for Health Research Global Health Research Unit

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

© 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licenseBackground: Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide. Methods: A multimethods analysis was performed as part of the GlobalSurg 3 study—a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital. Findings: Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3·85 [95% CI 2·58–5·75]; p<0·0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63·0% vs 82·7%; OR 0·35 [0·23–0·53]; p<0·0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer. Interpretation: Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised. Funding: National Institute for Health and Care Research