98 results on '"Ribeiro, Sofia"'
Search Results
2. Single‐cell DNA from West Greenland marine sediments suggests presence of Protoperidinium tricingulatum in the Arctic.
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Luostarinen, Tiia, Ribeiro, Sofia, Zimmermann, Heike H., Kvorning, Anna B., and Heikkilä, Maija
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BIOLOGICAL classification , *MARINE sediments , *DINOFLAGELLATE cysts , *DNA , *RECOMBINANT DNA , *MARINE toxins - Abstract
Spiny brown dinoflagellate cysts are commonly used as sea‐ice indicators in the Arctic, but their biological affinities are not well known. We present the first indication of hitherto temperate Protoperidinium tricingulatum in the Arctic based on single‐cell LSU rDNA sequencing from sediments of the Disko Bay‐Vaigat Sound, West Greenland. The morphological similarity of the sequenced cyst morphotype to the sea‐ice indicator Islandinium? cezare morphotype 1 is striking. The morphology of the isolated cysts, as well as those observed in the total cyst assemblage following standard palynological preparation, both resemble either I.? cezare morphotype 1 or P. tricingulatum, suggesting that the specimens may in fact be close morphological variants of the same species. In addition, nine LSU rDNA sequences were obtained from morphological variants assigned to Islandinium minutum s.l.: including both subspecies minutum and subspecies barbatum. The two subspecies could not be differentiated based on partial LSU rDNA sequencing. Overall, Arctic spiny brown dinoflagellate cyst species may be morphologically more diverse and taxonomically more complex than shown earlier and further genetic and morphological studies are needed. Importantly, the value of cysts as palaeoecological indicators depends on a sound understanding of their biological affinity and taxonomy. [ABSTRACT FROM AUTHOR]
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- 2024
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3. It Takes Two to Tango: Controlling Human Mesenchymal Stromal Cell Response via Substrate Stiffness and Surface Topography.
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Ribeiro, Sofia, Watigny, Alexandre, Bayon, Yves, Biggs, Manus, and Zeugolis, Dimitrios I.
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SURFACE topography , *STROMAL cells , *MECHANOTRANSDUCTION (Cytology) , *HUMAN beings - Abstract
Cells sense extracellular matrix‐induced biophysical signals, which are transduced into intracellular signaling cascades, and trigger a series of cell responses, including adhesion, migration, and lineage commitment. Traditionally, in in vitro context, monofactorial approaches are employed to control cell fate, despite the fact that in vivo cells are exposed simultaneously to a diverse range of signals. Herein, an overview of key mechanotransduction pathways is first provided. Conventional single‐factor and contemporary multifactorial methodologies, based on substrate rigidity and surface topography, are then reviewed to recapitulate in vitro the in vivo niche, in an attempt to elucidate the underlying mechanisms involved in human mesenchymal stromal cell‐material interactions. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Marine diatoms record Late Holocene regime shifts in the Pikialasorsuaq ecosystem.
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Limoges, Audrey, Ribeiro, Sofia, Van Nieuwenhove, Nicolas, Jackson, Rebecca, Juggins, Stephen, Crosta, Xavier, and Weckström, Kaarina
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ECOLOGICAL regime shifts , *DIATOMS , *HOLOCENE Epoch , *KEYSTONE species , *ECOSYSTEMS , *FOOD chains - Abstract
The Pikialasorsuaq (North Water polynya) is an area of local and global cultural and ecological significance. However, over the last decades, the region has been subject to rapid warming, and in some recent years, the seasonal ice arch that has historically defined the polynya's northern boundary has failed to form. Both factors are deemed to alter the polynya's ecosystem functioning. To understand how climate‐induced changes to the Pikialasorsuaq impact the basis of the marine food web, we explored diatom community‐level responses to changing conditions, from a sediment core spanning the last 3800 years. Four metrics were used: total diatom concentrations, taxonomic composition, mean size, and diversity. Generalized additive model statistics highlight significant changes at ca. 2400, 2050, 1550, 1200, and 130 cal years BP, all coeval with known transitions between colder and warmer intervals of the Late Holocene, and regime shifts in the Pikialasorsuaq. Notably, a weaker/contracted polynya during the Roman Warm Period and Medieval Climate Anomaly caused the diatom community to reorganize via shifts in species composition, with the presence of larger taxa but lower diversity, and significantly reduced export production. This study underlines the high sensitivity of primary producers to changes in the polynya dynamics and illustrates that the strong pulse of early spring cryopelagic diatoms that makes the Pikialasorsuaq exceptionally productive may be jeopardized by rapid warming and associated Nares Strait ice arch destabilization. Future alterations to the phenology of primary producers may disproportionately impact higher trophic levels and keystone species in this region, with implications for Indigenous Peoples and global diversity. [ABSTRACT FROM AUTHOR]
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- 2023
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5. Assessing the combined effect of surface topography and substrate rigidity in human bone marrow stem cell cultures.
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Ribeiro, Sofia, Pugliese, Eugenia, Korntner, Stefanie H., Fernandes, Emanuel M., Gomes, Manuela E., Reis, Rui L., O'Riordan, Alan, Bayon, Yves, and Zeugolis, Dimitrios I.
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STEM cell culture , *BONE marrow cells , *SURFACE topography , *CELL morphology , *OSTEOBLASTS , *ALKALINE phosphatase , *BIOLOGICALLY inspired computing - Abstract
The combined effect of surface topography and substrate rigidity in stem cell cultures is still under‐investigated, especially when biodegradable polymers are used. Herein, we assessed human bone marrow stem cell response on aliphatic polyester substrates as a function of anisotropic grooved topography and rigidity (7 and 12 kPa). Planar tissue culture plastic (TCP, 3 GPa) and aliphatic polyester substrates were used as controls. Cell morphology analysis revealed that grooved substrates caused nuclei orientation/alignment in the direction of the grooves. After 21 days in osteogenic and chondrogenic media, the 3 GPa TCP and the grooved 12 kPa substrate induced significantly higher calcium deposition and alkaline phosphatase (ALP) activity and glycosaminoglycan (GAG) deposition, respectively, than the other groups. After 14 days in tenogenic media, the 3 GPa TCP upregulated four and downregulated four genes; the planar 7 kPa substrate upregulated seven genes and downregulated one gene; and the grooved 12 kPa substrate upregulated seven genes and downregulated one gene. After 21 days in adipogenic media, the softest (7 kPa) substrates induced significantly higher oil droplet deposition than the other substrates and the grooved substrate induced significantly higher droplet deposition than the planar. Our data pave the way for more rational design of bioinspired constructs. [ABSTRACT FROM AUTHOR]
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- 2022
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6. From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr‐1‐carrying Enterobacteriaceae from chicken meat.
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Ribeiro, Sofia, Mourão, Joana, Novais, Ângela, Campos, Joana, Peixe, Luísa, and Antunes, Patrícia
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COLISTIN , *LOCAL foods , *ENTEROBACTERIACEAE , *FEED additives , *KLEBSIELLA pneumoniae , *FARMS - Abstract
Summary: Expansion of mcr‐carrying Enterobacteriaceae (MCR‐E) is a well‐recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food‐animal production, but their impact on poultry‐derived products is largely unknown, justifying comprehensive farm‐to‐fork studies. Occurrence of MCR‐E among 53 chicken‐meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT‐IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken‐meat batches (80%–100% – 4 months; 12% – the last month) with multiple MDR + mcr‐1‐carrying Escherichia coli (Ec‐including ST117 and ST648‐Cplx) and Klebsiella pneumoniae (Kp‐ST147‐O5:K35) clones, some of them persisting over time. The mcr‐1 was located in the chromosome (Ec‐ST297/16‐farms) or dispersed IncX4 (Ec‐ST602/ST6469/5‐farms), IncHI2‐ST2/ST4 (Ec‐ST533/ST6469/5 farms and Kp‐ST147/6‐farms) or IncI2 (Ec‐ST117/1‐farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry‐production chain as a source of mcr‐1 and the risk of foodborne transmission to poultry‐meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co‐selective pressures (e.g., metals‐Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective. [ABSTRACT FROM AUTHOR]
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- 2021
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7. Evaluation of Cocoa Bean Shell Antimicrobial Activity: A Tentative Assay Using a Metabolomic Approach for Active Compound Identification#.
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Rojo-Poveda, Olga, Ribeiro, Sofia Oliveira, Anton-Sales, Cèlia, Keymeulen, Flore, Barbosa-Pereira, Letricia, Delporte, Cédric, Zeppa, Giuseppe, and Stévigny, Caroline
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POLYPHENOLS , *METABOLOMICS , *LIQUID chromatography , *CACAO , *ANTI-infective agents , *FUNGI , *STREPTOCOCCUS mutans , *MASS spectrometry , *PLANT extracts , *DATA analysis software , *METABOLITES , *PHARMACODYNAMICS - Abstract
Cocoa bean shell is one of the main by-products of chocolate manufacturing and possesses several compounds with biofunctionalities. It can function as an antibacterial agent, and its action is mostly reported against Streptococcus mutans. However, only a few studies have investigated the cocoa bean shell compounds responsible for this activity. This study aimed to evaluate several extracts of cocoa bean shells from different geographical origins and cocoa varieties and estimate their antimicrobial properties against different fungal and bacterial strains by determining their minimal inhibitory concentration. The results demonstrated antimicrobial activity of cocoa bean shell against one of the tested strains, S. mutans. Cocoa bean shell extracts were further analysed via LC-HRMS for untargeted metabolomic analysis. LC-HRMS data were analysed (preprocessing and statistical analyses) using the Workflow4Metabolomics platform. The latter enabled us to identify possible compounds responsible for the detected antimicrobial activity by comparing the more and less active extracts. Active extracts were not the most abundant in polyphenols but contained higher concentrations of two metabolites. After tentative annotation of these metabolites, one of them was identified and confirmed to be 7-methylxanthine. When tested alone, 7-methylxanthine did not display antibacterial activity. However, a possible cocktail effect due to the synergistic activity of this molecule along with other compounds in the cocoa bean shell extracts cannot be neglected. In conclusion, cocoa bean shell could be a functional ingredient with benefits for human health as it exhibited antibacterial activity against S. mutans. However, the antimicrobial mechanisms still need to be confirmed. [ABSTRACT FROM AUTHOR]
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- 2021
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8. Proposals for Antimicrobial Testing Guidelines Applied on Ajowan and Spanish Lavender Essential Oils#.
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Ribeiro, Sofia Oliveira, Fraselle, Stéphanie, Baudoux, Dominique, Zhiri, Abdesselam, Stévigny, Caroline, and Souard, Florence
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ESSENTIAL oils , *ANTI-infective agents , *MICROBIAL sensitivity tests - Abstract
To fight the rising resistance of microorganisms to antibiotics, a strategy followed by several researchers is to focus on natural compounds, such as essential oils, as a source of potent antibacterial compounds. These last decades, hundreds of original papers have been written about microbiological assays that prove the antibacterial activity of essential oils and their use in the medical field. But can we really compare all the data available in the literature when the raw material, the microbiological assays, and/or the strains are different from one article to another? This review will point out the differences and the inadequate practices found in published articles that tested 2 lesser-studied essential oils–Spanish lavender and the ajowan–by the broth dilution method against Staphylococcus aureus , a human pathogenic bacterium. Many pitfalls were found in the literature, for example, a variable chemical composition rarely underlined by the authors, unidentified strains or clinical strains used without a related antibiogram, a lack of quality controls, and the assertion of questionable positive results. At last, some general guidelines that should be followed by every scientific researcher will be discussed. [ABSTRACT FROM AUTHOR]
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- 2021
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9. Os reflexos profilático e pedagógico da educação alimentar nas escolas do Maciço de Baturité, Ceará.
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da Graça Varela Vaz, Eliane, Paiva Ribeiro, Sofia Regina, and do Socorro Moura Rufino, Maria
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This article is based on a study about the actions that involve an Extension Project: The role of healthy eating for health promotion "Program 5 a Day" held in municipal public schools of the Baturité massif, in Ceará. The target audience was students of the 9th grade of elementary school. The students originate from four educational institutions located in Acarape, Barreira, Baturité, and Redenção. The temporal clipping comprises the period from June 2018 to January 2019. The research aims to outline the profile of daily consumption of fruits and vegetables of the students, both in the family life and in the educational environment, and contribute to a healthier eating practice. Workshops, seminars, courses, and educational games were held. Among the thematic approached, one can highlight the relevance of a healthy and nutritious diet; Consumption of fruits and vegetables; Hygiene, and Food Preservation. The study contemplates theoretical and methodological criteria of exploratory bibliographic research, in loco findings and application of questionnaires, with semi-structured questions. It is noteworthy that after performing the activities, an evaluation was applied to measure the impact of the project with the community. From the data collected, it can be perceived that the students expanded their perceptions/learnings about the relevance of a balanced diet consisting of healthy, tasty, and nutritious foods and that the construction of good eating habits contributes significantly to the bio-psychosocial development of the individual. [ABSTRACT FROM AUTHOR]
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- 2020
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10. Reconstructing salinity changes and environmental influence on dinoflagellate cysts in the central Baltic Sea since the late 19th century.
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Sildever, Sirje, Ribeiro, Sofia, Mertens, Kenneth Neil, Andersen, Thorbjørn Joest, Moros, Matthias, and Kuijpers, Antoon
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DINOFLAGELLATE cysts , *ALGAE ecology , *CLASSIFICATION of algae , *TIME series analysis - Abstract
Abstract We present a record of dinoflagellate cyst assemblage composition, abundance, and morphology from the central Baltic Sea, spanning the late 19th to the early 21st centuries. Environmental time-series were analyzed in relation to changes in community structure and diversity as inferred from the sediment record, and average summer sea surface salinity (SSS) was reconstructed based on the average process length of Protoceratium reticulatum resting cysts. The reconstructed summer SSS was compared to instrumental data for a critical evaluation of this approach. The most abundant species in this record were P. reticulatum and Biecheleria baltica , and on average ten taxa were identified per sample. The cyst record of B. baltica indicated that although this species has been present in the Gotland Basin at least since the 1880s, its concentrations have increased significantly since the 1980s, possibly linked to eutrophication. Variations in assemblage composition and P. reticulatum cyst morphology reflected patterns of major, instrumentally recorded hydrographic and environmental changes in the Baltic Sea during the past century. The variability in microfossil relative abundances was best explained by the average spring SSS as well as by the average NO 3 concentrations during spring and by the combined effects of average summer SSS and NAO variability. Reconstructed summer SSS and instrumental SSS showed notable differences, depending on the year and function applied for reconstruction. Although roughly reflecting the same patterns, the reconstructed values are offset when compared to instrumental measurements. We put forward suggestions for improvement of the process-length method and recommend using the reconstructed values as an indication of relative changes in past summer sea surface salinity, preferably as part of a multiproxy approach. Highlights • New dinoflagellate cyst record from the Gotland Basin spanning the late 19th century to the early 21st century. • Statistical analysis on the long-term influence of environmental parameters on phytoplankton species. • Average summer sea surface salinity reconstructions based on cyst process-lenght of Protoperidinium reticulatum. • Critical evaluation of the process-lenght method for salinity reconstructions and recommendations for improvement. [ABSTRACT FROM AUTHOR]
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- 2019
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11. Unilateral Hypoglossal Nerve Palsy as a COVID-19 Sequel.
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Costa Martins, Daniela, Branco Ribeiro, Sofia, Jesus Pereira, Isabel, Mestre, Susana, and Rios, Jonathan
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DEGLUTITION , *HYPOGLOSSAL nerve , *MAGNETIC resonance imaging , *OCCUPATIONAL therapy , *PARALYSIS , *PHYSICAL therapy , *POLYMERASE chain reaction , *RARE diseases , *SPEECH therapy , *THERAPEUTICS , *TRACHEA intubation , *CRANIAL nerve diseases , *TREATMENT effectiveness , *REVERSE transcriptase polymerase chain reaction , *COVID-19 - Abstract
A newly case of unilateral HNP in a severe COVID-19 patient, which may be a new neurologic manifestation of SARS-CoV-2 infection. Supplemental digital content is available in the text. Coronavirus disease 2019, caused by severe acute respiratory syndrome coronavirus 2 is spreading around the world, and the outbreak continues to escalate. Recently, it has been noticed that besides the typical respiratory complications, some severely affected coronavirus disease 2019 patients also experience neurological manifestations. Here, we describe the case of a newly diagnosed unilateral hypoglossal nerve palsy in a severe coronavirus disease 2019 patient. The intubation procedure was uneventful, and magnetic resonance imaging excluded the most reported causes of isolated hypoglossal nerve injury. This case reports a rare condition. Although a reasonable doubt remains, it cannot be excluded that it may be a neurological manifestation of severe acute respiratory syndrome coronavirus 2, the authors believe it to be the cause of the palsy. The main importance of this article is to alert clinicians for neurological sequels that may require a targeted rehabilitation program. [ABSTRACT FROM AUTHOR]
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- 2020
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12. O café agroecológico produzido na região serrana de Baturité, Ceará.
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Paiva Ribeiro, Sofia Regina and do Socorro Moura Rufino, Maria
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The coffee produced in the mountainous region of Maciço de Baturité is appreciated because its agroforestry, arabic and free of pesticides, characteristics that result in a more nutritious aliment. In this geographic space, the coffee tree is consorted with other cultures, contributing to the environmental balance, the fertilization of the ground and the containment of plagues. For local producers, to utilize agrobiodiversity is a way to work the local productive arrangements respecting the varietys and variability of regional animals, plants and microorganisms. In this focus, the present work seeks to analyze the production of agroforestry coffee in the region, more precisely in the municipalities of Baturité, Mulungu and Guaramiranga, through a historical-social approach. The study covers the theoretical and methodological criteria of bibliographical research with findings in loco through participatory observations. The temporal cut-off covers the second half of 2016 and the first half of 2017, whereas different temporalities for the bibliographic study. It can be inferred that coffee production in an agroforestry system in the region is practiced seeing the knowledge acumulated about conservation and use of natural resources, made in an area with legal restrictions, favoring positive impacts on the environment by the bias sustainable extractivism, food securit y and income generation. [ABSTRACT FROM AUTHOR]
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- 2018
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13. Needs and Achievements of the Juvenile Justice System: Insights From Two Empirical Studies With Portuguese Young Adults.
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Basto-Pereira, Miguel, Ribeiro, Sofia, and Maia, Ângela
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JUVENILE justice administration , *INTERVENTION (Criminal procedure) , *CRIMINAL behavior , *PSYCHOLOGY of adults , *SOCIAL marginality , *PREVENTIVE detention - Abstract
Over the last decade, studies have evaluated the effectiveness of interventions for juvenile offenders; nonetheless, those studies were more focused on recidivism than on the mechanisms associated with criminal perpetration. The current study explores the role of juvenile justice involvement and detention measures in a set of psychological, social, and criminal behavior characteristics in early adulthood. Seventy-five young adults with official records of juvenile delinquency in 2010-2011 and 240 young adults from the community filled out our protocol in 2014-2015. Young adults with juvenile justice involvement showed worse psychological, social, and criminal outcomes than those from community. Detention appears to be related to the number of deviant friends, delinquency, and school achievement in early adulthood. Our findings are in line with the labeling and deviant peer contagion theories and establish the main areas of interventions that affect the identified needs. A set of policy implications is provided. [ABSTRACT FROM AUTHOR]
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- 2018
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14. Needs and Achievements of the Juvenile Justice System: Insights From Two Empirical Studies With Portuguese Young Adults.
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Basto-Pereira, Miguel, Ribeiro, Sofia, and Maia, Ângela
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CRIMINAL behavior , *JUVENILE justice administration , *RECIDIVISM , *YOUNG adult attitudes , *YOUNG adult psychology - Abstract
Over the last decade, studies have evaluated the effectiveness of interventions for juvenile offenders; nonetheless, those studies were more focused on recidivism than on the mechanisms associated with criminal perpetration. The current study explores the role of juvenile justice involvement and detention measures in a set of psychological, social, and criminal behavior characteristics in early adulthood. Seventy-five young adults with official records of juvenile delinquency in 2010-2011 and 240 young adults from the community filled out our protocol in 2014-2015. Young adults with juvenile justice involvement showed worse psychological, social, and criminal outcomes than those from community. Detention appears to be related to the number of deviant friends, delinquency, and school achievement in early adulthood. Our findings are in line with the labeling and deviant peer contagion theories and establish the main areas of interventions that affect the identified needs. A set of policy implications is provided. [ABSTRACT FROM AUTHOR]
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- 2018
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15. The long‐term persistence of phytoplankton resting stages in aquatic ‘seed banks’.
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Ellegaard, Marianne and Ribeiro, Sofia
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PHYTOPLANKTON , *PLANT gene banks , *VASCULAR plants , *CYANOBACTERIA , *MICROALGAE - Abstract
ABSTRACT: In the past decade, research on long‐term persistence of phytoplankton resting stages has intensified. Simultaneously, insight into life‐cycle variability in the diverse groups of phytoplankton has also increased. Aquatic ‘seed banks’ have tremendous significance and show many interesting parallels to terrestrial seed beds of vascular plants, but are much less studied. It is therefore timely to review the phenomenon of long‐term persistence of aquatic resting stages in sediment seed banks. Herein we compare function, morphology and physiology of phytoplankton resting stages to factors central for persistence of terrestrial seeds. We review the types of resting stages found in different groups of phytoplankton and focus on the groups for which long‐term (multi‐decadal) persistence has been shown: dinoflagellates, diatoms, green algae and cyanobacteria. We discuss the metabolism of long‐term dormancy in phytoplankton resting stages and the ecological, evolutionary and management implications of this important trait. Phytoplankton resting stages exhibiting long‐term viability are characterized by thick, often multi‐layered walls and accumulation vesicles containing starch, lipids or other materials such as pigments, cyanophycin or unidentified granular materials. They are reported to play central roles in evolutionary resilience and survival of catastrophic events. Promising areas for future research include the role of hormones in mediating dormancy, elucidating the mechanisms behind metabolic shut‐down and testing bet‐hedging hypotheses. [ABSTRACT FROM AUTHOR]
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- 2018
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16. Clinical Practice in Portuguese Sexology.
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Alarcão, Violeta, Ribeiro, Sofia, Almeida, Joana, and Giami, Alain
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SEXOLOGY , *HUMAN sexuality , *MENTAL health , *MENTAL depression , *META-analysis , *SOCIAL medicine - Abstract
Few studies explore the clinicians' knowledge, attitudes, and practices regarding sexuality, despite their role in the sexual-health socialization process. This study focuses on Portuguese sexologists engaged in clinical practice. It aims to characterize sexologists' sex education and training and their clinical practices, including diagnostic and therapeutic approaches. This research followed the methodology of an European survey on sexology as a profession (Euro-Sexo). From the 91 respondents who completed questionnaires, 51 (56%) were active in clinical practice. Results indicate that the Portuguese clinical sexologist is significantly older, predominantly male, has had training in sexology, performs more scientific research, and is more engaged in teaching activities when compared to nonclinical working sexologists. This article describes the main sexual problems presented by patients to Portuguese clinical sexologists and highlights differences in the professional groups and approaches toward treating these problems by medical doctors and nonmedical professionals. Results reinforce the idea that there are intra-European differences in the educational background of sexologists and reveal important variations in Portuguese sexologists' education, training, and clinical practice. The representations and practices of the sexologists in Portugal, as in other European countries, are embedded in cultural scenarios and sexual cultures, with implications for the clinical practice. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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17. TUNEL labeling with BrdUTP/anti-BrdUTP greatly underestimates the level of sperm DNA fragmentation in semen evaluation.
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Ribeiro, Sofia C., Muratori, Monica, De Geyter, Maria, and De Geyter, Christian
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NUCLEOTIDYLTRANSFERASES , *SPERMATOZOA , *SEMEN , *REPRODUCTIVE technology , *HUMAN fertility , *FLOW cytometry - Abstract
Many studies have now confirmed that sperm DNA fragmentation (SDF) is associated with a poorer outcome of some forms of assisted reproduction technology. For this reason, SDF is an important parameter to evaluate in male fertility assessment. TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) assay coupled to flow cytometry is one of the most promising methods for SDF quantification. Several kits for the detection of DNA fragmentation are currently available on the market and all are recommended as equally appropriate to quantify SDF. In this work we compared for the first time the efficacy of two different types of TUNEL kits for SDF quantification: one using an indirect antibody-based labeling system (BrdUTP/fluorescein-anti-BrdUTP) and another using a direct labeling system (fluorescein-dUTP). We demonstrated that TUNEL indirect labeling system largely underestimates SDF when compared with the direct labeling, the differences ranging from 19.2% to 85.3% (p<0.05, n = 22). We observed that these differences were most pronounced among dead spermatozoa where indirect labeling stained 40.1% [23.6%, 58.2%] and the direct system 65.7% [36.5%, 90.9%] (n = 10, p<0.05). Interestingly, we found that both systems stained the living spermatozoa with the same efficiency. We showed that the differences are due to the steric hindrance of the antibody during its binding to the BrdUTP. Indeed, after sperm DNA decondensation, the percentages of TUNEL positivity increased significantly from 46.3% [31.8%, 61.7%] to 97.5% [96.1%, 98.8%] (p<0.05, n = 5). Our results are important for future use of TUNEL in clinical practice. Laboratories relying on the use of an antibody-based system heavily underestimate SDF, most particularly in infertile patients with reduced sperm motility. As a consequence, the kit using BrdUTP/fluorescein-anti-BrdUTP should not be recommended as a method to assay DNA damage in semen. This study represents one further step in the standardization of TUNEL among laboratories. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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18. Exploring the impact of multidecadal environmental changes on the population genetic structure of a marine primary producer.
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Lundholm, Nina, Ribeiro, Sofia, Godhe, Anna, Rostgaard Nielsen, Lene, and Ellegaard, Marianne
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POPULATION genetics , *PROTISTA , *COASTAL sediments , *GERMINATION , *DINOFLAGELLATES - Abstract
Many marine protists form resting stages that can remain viable in coastal sediments for several decades. Their long-term survival offers the possibility to explore the impact of changes in environmental conditions on population dynamics over multidecadal time scales. Resting stages of the phototrophic dinoflagellate Pentapharsodinium dalei were isolated and germinated from five layers in dated sediment cores from Koljö fjord, Sweden, spanning ca. 1910-2006. This fjord has, during the last century, experienced environmental fluctuations linked to hydrographic variability mainly driven by the North Atlantic Oscillation. Population genetic analyses based on six microsatellite markers revealed high genetic diversity and suggested that samples belonged to two clusters of subpopulations that have persisted for nearly a century. We observed subpopulation shifts coinciding with changes in hydrographic conditions. The large degree of genetic diversity and the potential for both fluctuation and recovery over longer time scales documented here, may help to explain the long-term success of aquatic protists that form resting stages. [ABSTRACT FROM AUTHOR]
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- 2017
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19. Sea ice and primary production proxies in surface sediments from a High Arctic Greenland fjord: Spatial distribution and implications for palaeoenvironmental studies.
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Ribeiro, Sofia, Sejr, Mikael, Limoges, Audrey, Heikkilä, Maija, Andersen, Thorbjørn, Tallberg, Petra, Weckström, Kaarina, Husum, Katrine, Forwick, Matthias, Dalsgaard, Tage, Massé, Guillaume, Seidenkrantz, Marit-Solveig, and Rysgaard, Søren
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SEA ice , *PRIMARY productivity (Biology) , *FJORDS , *GLOBAL warming , *CLIMATE change - Abstract
In order to establish a baseline for proxy-based reconstructions for the Young Sound-Tyrolerfjord system (Northeast Greenland), we analysed the spatial distribution of primary production and sea ice proxies in surface sediments from the fjord, against monitoring data from the Greenland Ecosystem Monitoring Programme. Clear spatial gradients in organic carbon and biogenic silica contents reflected marine influence, nutrient availability and river-induced turbidity, in good agreement with in situ measurements. The sea ice proxy IP was detected at all sites but at low concentrations, indicating that IP records from fjords need to be carefully considered and not directly compared to marine settings. The sea ice-associated biomarker HBI III revealed an open-water signature, with highest concentrations near the mid-July ice edge. This proxy evaluation is an important step towards reliable palaeoenvironmental reconstructions that will, ultimately, contribute to better predictions for this High Arctic ecosystem in a warming climate. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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20. Size differences of Arctic marine protists between two climate periods-using the paleoecological record to assess the importance of within-species trait variation.
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Mousing, Erik A., Ribeiro, Sofia, Chisholm, Chelsea, Kuijpers, Antoon, Moros, Matthias, and Ellegaard, Marianne
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PROTISTA , *CELL size , *DINOFLAGELLATE cysts , *COMPETITION (Biology) , *PALEOECOLOGY , *PHYSIOLOGICAL effects of temperature - Abstract
Mean body size decreases with increasing temperature in a variety of organisms. This size-temperature relationship has generally been tested through space but rarely through time. We analyzed the sedimentary archive of dinoflagellate cysts in a sediment record taken from the West Greenland shelf and show that mean cell size decreased at both intra- and interspecific scales in a period of relatively warm temperatures, compared with a period of relatively cold temperatures. We further show that intraspecific changes accounted for more than 70% of the change in community mean size, whereas shifts in species composition only accounted for about 30% of the observed change. Literature values on size ranges and midpoints for individual taxa were in several cases not representative for the measured sizes, although changes in community mean size, calculated from literature values, did capture the direction of change. While the results show that intraspecific variation is necessary to accurately estimate the magnitude of change in protist community mean size, it may be possible to investigate general patterns, that is relative size differences, using interspecific-level estimates. [ABSTRACT FROM AUTHOR]
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- 2017
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21. Efeitos da suplementação de zinco na fadiga e na qualidade de vida de pacientes com câncer colorretal.
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de Figueiredo Ribeiro, Sofia Miranda, Braga, Camila Bitu Moreno, Peria, Fernanda Maris, Martinez, Edson Zangiacomi, da Rocha, José Joaquim Ribeiro, and Cunha, Selma Freire Carvalho
- Abstract
Objective: To investigate the effects of oral zinc supplementation on fatigue intensity and quality of life of patients during chemotherapy for colorectal cancer. Methods: A prospective, randomized, doubleblinded, placebo-controlled study was conducted with 24 patients on chemotherapy for colorectal adenocarcinoma in a tertiary care public hospital. The study patients received zinc capsules 35mg (Zinc Group, n=10) or placebo (Placebo Group, n=14) orally, twice daily (70mg/day), for 16 weeks, from the immediate postoperative period to the fourth chemotherapy cycle. Approximately 45 days after surgical resection of the tumor, all patients received a chemotherapeutic regimen. Before each of the four cycles of chemotherapy, the Functional Assessment of Chronic Illness Therapy-Fatigue scale was completed. We used a linear mixed model for longitudinal data for statistical analysis. Results: The scores of quality of life and fatigue questionnaires were similar between the groups during the chemotherapy cycles. The Placebo Group presented worsening of quality of life and increased fatigue between the first and fourth cycles of chemotherapy, but there were no changes in the scores of quality of life or fatigue in the Zinc Group. Conclusion: Zinc supplementation prevented fatigue and maintained quality of life of patients with colorectal cancer on chemotherapy. [ABSTRACT FROM AUTHOR]
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- 2017
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22. Environmental change in the Western Iberia Upwelling Ecosystem since the preindustrial period revealed by dinoflagellate cyst records.
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Ribeiro, Sofia, Amorim, Ana, Abrantes, Fátima, and Ellegaard, Marianne
- Subjects
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CLIMATE change , *ECOSYSTEMS , *DINOFLAGELLATE cysts , *ARCHAEOLOGICAL assemblages , *INDUSTRIALIZATION - Abstract
We present the first multi-site study of dinoflagellate cyst records spanning ca. AD 1860-2000 from the west Iberian coast. Our aim was to reconstruct environmental changes in the Western Iberia Upwelling Ecosystem, one of the most biologically productive areas in the world, and an active fishery region. A major shift in cyst assemblages was recorded off the northwestern shelf sector between 1920 and 1950 towards autotrophic dominance, and consisted of a multi-fold increase in total cyst concentrations and cysts of Lingulodinium polyedrum, accompanied by an increase in Protoceratium reticulatum cysts. The observed changes pre-date the industrialization of agriculture in Portugal, and are concomitant with a shift in the North Atlantic Oscillation (NAO) towards negative indices (higher river input) and increasing sea-surface temperatures. The southernmost record, with reduced river- and human influence, showed only minor changes during the 20th century. Here, an increase in Protoperidinioid cysts after the 1980s is related to upwelling intensification. Our study indicates that the main changes recorded in the Western Iberian Upwelling system during the 20th century were driven by regional climate variability (warming, increased water stability and nutrient availability), possibly enhanced by anthropogenic nutrient input from the second half of the century. Our results highlight the complexity of the environmental drivers that may act upon dinoflagellate communities within the same region. The 20th-century environmental change in the Western Iberian Ecosystem has resulted in a shift towards marked autotrophic dominance of dinoflagellate cyst communities, and the northward expansion of species associated with Harmful Algal Blooms. [ABSTRACT FROM AUTHOR]
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- 2016
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23. Investigations of past climate and sea-ice variability in the fjord area by Station Nord, eastern North Greenland.
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Nørgaard-Pedersen, Niels, Ribeiro, Sofia, Mikkelsen, Naja, Limoges, Audrey, and Seidenkrantz, Marit-Solveig
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SEDIMENTS , *BATHYMETRY , *FJORDS , *SEA ice , *CESIUM , *LEAD - Abstract
The article presents preliminary results of the sediment coring work and information on the bathymetry in the fjord area in Greenland. Topics covered include the decrease in sea ice experienced in the northern hemisphere, the use of synthetic aperture radar (SAR) and visible band images to characterise the ice dynamics of the fjord system and the assessment of the lead and cesium content of the sediment cores.
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- 2016
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24. Uncommon aetiologies of chylothorax: superior vena cava syndrome and thoracic aortic aneurysm.
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Gomes, Ana O., Ribeiro, Sofia, Neves, João, and Mendonça, Teresa
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CHYLOTHORAX , *SUPERIOR vena cava syndrome , *THORACIC aneurysms , *THORACIC duct , *TRIGLYCERIDES , *CHYLOMICRONS , *PLEURAL effusions , *WOUNDS & injuries - Abstract
Background Chylothorax, an uncommon cause of pleural effusion, results from the accumulation of lymph in the pleural space due to damage or obstruction of the thoracic duct. The high content of triglycerides and the presence of chylomicrons in the pleural fluid sets the diagnosis. Objective To present a case report of a chylothorax due to superior vena cava compression or a thoracic aortic aneurysm, discuss the particularities, the investigation of chylothorax as well as its treatment options. Methods A review of the literature on chylothorax was performed using PubMed to assess the different aetiologies, investigation and treatments usually performed. Conclusion Chylothorax is usually secondary to malignancy, trauma, congenital diseases and infections. However, less common causes are also described, as the ones described in our case report. The gold standard for diagnosis is the identification of chylomicrons in the pleural fluid. Conservative management is recommended in most cases of chylothorax. [ABSTRACT FROM AUTHOR]
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- 2015
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25. General Practitioners' Procedures for Sexual History Taking and Treating Sexual Dysfunction in Primary Care.
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Ribeiro, Sofia, Alarcão, Violeta, Simões, Rui, Miranda, Filipe Leão, Carreira, Mário, and Galvão-Teles, Alberto
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SEXUAL dysfunction , *GENERAL practitioners , *PRIMARY care , *PATIENTS , *DIAGNOSIS , *THERAPEUTICS - Abstract
Introduction Good history-taking skills are the first step towards achieving a correct diagnosis of sexual dysfunction ( SD). However, studies show most general practitioners ( GPs) do not take the initiative to ask the patient about SD, and when diagnosing a condition, they tend to give preference to their own criteria over clinical guidelines. Aim The aim of this study is to characterize GPs' attitudes towards taking sexual history, identifying its frequency and focus, and to describe GPs' diagnostics and therapeutic approaches including the use of clinical guidelines, exploring patients' and doctor-related differences. Methods Cross-sectional study using confidential self-administrated questionnaires applied to GPs working in primary healthcare units in the Lisbon region. Main Outcome Measures Data concerning GPs' consultation of guidelines, active exploration of SD in male and in female patients, and focus on sexual history taking was collected. Results Of the 50 participants (73.5% response rate), 15.5% actively ask their patients about SD. The main reasons for asking patients about their sexuality are diabetes (84.0%), prescription of medication with adverse effects on sexuality (78.0%), and family planning (72.0%), the latter being a significantly more frequent reason for GPs with 20 or less years of practice. Routine sexual history taking (22.0%) appears as one of the least mentioned motives. The percentage of appointments with active exploration of SD was positively associated with guidelines' consultation, as well as considering the specialty as a good source of information and having longer appointments when SD is mentioned. However, 76.0% report not having consulted any guidelines in the previous year. Lack of time (31.6%) and low accessibility (25.0%) were referred to as the main reasons for not consulting guidelines. Conclusions Routine sexual history taking and consultation of guidelines about SD are not yet a generalized practice in primary care. Data should be interpreted with caution as they are self-reported. Further objective measurement such as direct observation or clinical files consultation should be implemented. Ribeiro S, Alarcão V, Simões R, Miranda FL, Carreira M, and Galvão-Teles A. General practitioners' procedures for sexual history taking and treating sexual dysfunction in primary care. J Sex Med 2014;11:386-393. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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26. Changing appetites: the adaptive advantages of fuel choice.
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Stanley, Illana A., Ribeiro, Sofia M., Giménez-Cassina, Alfredo, Norberg, Erik, and Danial, Nika N.
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APPETITE , *FUEL , *PHYSIOLOGICAL stress , *CELL proliferation , *CELL differentiation , *MITOCHONDRIA - Abstract
Highlights: [•] Cells can use different metabolic fuels as an adaptive advantage to stress. [•] Proliferation and differentiation are accompanied by metabolic rewiring. [•] Mitochondrial architecture and metabolic compartmentalization influence fuel choice. [Copyright &y& Elsevier]
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- 2014
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27. Primary nasal tuberculosis during anti-tumour necrosis factor alpha treatment of a patient with rheumatoid arthritis.
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Ribeiro, Sofia, Ferreira, Betânia, Duarte, Raquel, Almeida, Isabel, and Vasconcelos, Carlos
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NOSE diseases , *RHEUMATOID arthritis treatment , *ANTINEOPLASTIC agents , *TUMOR necrosis factors , *INFLAMMATION , *ADVERSE health care events , *THERAPEUTICS - Abstract
Anti-tumour necrosis factor alpha (anti-TNFα) therapy is increasingly used in several inflammatory disease processes, including rheumatoid arthritis. However it has a significant potential for adverse events, such as reactivation of latent tuberculosis, which is frequently found in disseminated or extrapulmonary forms. We present a rare case of primary nasal tuberculosis within the context of anti-TNFα therapy for rheumatoid arthritis. To our knowledge, this is the first reported case of primary nasal tuberculosis in a patient with rheumatoid arthritis receiving anti-TNFα therapy. [ABSTRACT FROM AUTHOR]
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- 2013
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28. Hundred Years of Environmental Change and Phytoplankton Ecophysiological Variability Archived in Coastal Sediments.
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Ribeiro, Sofia, Berge, Terje, Lundholm, Nina, and Ellegaard, Marianne
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GLOBAL environmental change , *PHYTOPLANKTON , *ECOPHYSIOLOGY , *COASTAL sediments , *MICROPALEONTOLOGY , *POPULATION biology , *MARINE biology - Abstract
Marine protist species have been used for several decades as environmental indicators under the assumption that their ecological requirements have remained more or less stable through time. However, a growing body of evidence suggests that marine protists, including several phytoplankton species, are in fact highly diverse and may quickly respond to changes in the environment. Predicting how future climate will impact phytoplankton populations is important, but this task has been challenged by a lack of time-series of ecophysiological parameters at time-scales relevant for climate studies (i.e. at least decadal). Here, we report on ecophysiological variability in a marine dinoflagellate over a 100-year period of well-documented environmental change, by using the sedimentary archive of living cysts from a Scandinavian fjord (Koljö Fjord, Sweden). During the past century, Koljö Fjord has experienced important changes in salinity linked to the North Atlantic Oscillation (NAO). We revived resting cysts of Pentapharsodinium dalei preserved in the fjord sediments and determined growth rates for 18 strains obtained from 3 sediment core layers at salinity 15 and 30, which represent extreme sea-surface conditions during periods of predominantly negative and positive NAO phases, respectively. Upper pH tolerance limits for growth were also tested. In general, P. dalei grew at a higher rate in salinity 30 than 15 for all layers, but there were significant differences among strains. When accounting for inter-strain variability, cyst age had no effect on growth performance or upper pH tolerance limits for this species, indicating a stable growth response over the 100-year period in spite of environmental fluctuations. Our findings give some support for the use of morphospecies in environmental studies, particularly at decadal to century scales. Furthermore, the high intra-specific variability found down to sediment layers dated as ca. 50 years-old indicates that cyst-beds of P. dalei are repositories of ecophysiological diversity. [ABSTRACT FROM AUTHOR]
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- 2013
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29. General Practitioners' Knowledge, Attitudes, Beliefs, and Practices in the Management of Sexual Dysfunction-Results of the Portuguese SEXOS Study.
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Alarcão, Violeta, Ribeiro, Sofia, Miranda, Filipe Leão, Carreira, Mário, Dias, Teresa, Garcia e Costa, Joaquim, and Galvão-Teles, Alberto
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SEXUAL dysfunction , *GENERAL practitioners , *BELIEF & doubt , *PRIMARY health care , *DISEASE management , *SEXUAL health - Abstract
ABSTRACT Introduction. Evidence shows that sexual dysfunctions (SDs) are very prevalent in both sexes and that they share risk factors with many other conditions. It is known that only a minority of people experiencing sexual problems seek treatment, but the role of the general practitioner (GP) in SD diagnosis and treatment is relatively unexplored. No study has been conducted in Portugal in order to identify GPs' knowledge, attitudes, beliefs, and practices regarding SD and only a small amount of similar studies from other countries have been published. Aim. To characterize GPs' knowledge, attitudes, and beliefs concerning SD; practices of SD management in daily practice; self-perceived competence in discussing and treating SD; and need for training. Methods. Cross-sectional study using confidential self-administered questionnaires applied to GPs working in Primary Health Care Units in the Lisbon region. Main Outcome Measures. The questionnaire collected information concerning GPs' knowledge and perceptions regarding SD, training and practice in sexual health, criteria for initiating discussion and treatment, and the adoption of guidelines. Results. A total of 50 questionnaires (30 females) were obtained (73.5% response rate). On average, the 50 participants were 52 ± 8.6 years old, had 21 ± 8.2 years of family practice, and followed 1,613 ± 364 patients. The degree in medicine was never considered as an extremely adequate source of information both for male and female SD. Lack of time to obtain relevant information for clinical practice and to deal with sexual health issues were perceived as important barriers in initiating a discussion with the patient, as well as lack of academic training and experience in this area. Conclusions. GPs expressed a high need for continuous training in this area and more than half considered that their degree was not an adequate source of training. These results indicate that there is a need for both pregraduate and postgraduate training in this area. Alarcão V, Ribeiro S, Miranda FL, Carreira M, Dias T, Garcia e Costa J, and Galvão-Teles A. General practitioners' knowledge, attitudes, beliefs, and practices in the management of sexual dysfunction-Results of the Portuguese SEXOS Study. J Sex Med **;**:**-**. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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30. Climate variability in West Greenland during the past 1500 years: evidence from a high-resolution marine palynological record from Disko Bay.
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RIBEIRO, SOFIA, MOROS, MATTHIAS, ELLEGAARD, MARIANNE, and KUIJPERS, ANTOON
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CLIMATE change , *PALYNOLOGY , *HOLOCENE Epoch , *DINOFLAGELLATE cysts , *ICE sheets - Abstract
Ribeiro, S., Moros, M., Ellegaard, M. & Kuijpers, A. 2012 (January): Climate variability in West Greenland during the past 1500 years: evidence from a high-resolution marine palynological record from Disko Bay. Boreas, Vol. 41, pp. 68-83. 10.1111/j.1502-3885.2011.00216.x. ISSN 0300-9483. Here we document late-Holocene climate variability in West Greenland as inferred from a marine sediment record from the outer Disko Bay. Organic-walled dinoflagellate cysts and other palynomorphs were used to reconstruct environmental changes in the area through the last c. 1500 years at 30-40 years resolution. Sea ice cover and primary productivity were identified as the two main factors driving dinoflagellate cyst community changes through time. Our data provide evidence for an opposite climate trend in West Greenland relative to the NE Atlantic region from c. AD 500 to 1050. For the same period, sea-surface temperatures in Disko Bay are out-of-phase with Greenland ice-core reconstructed temperatures and marine proxy data from South and East Greenland. This is probably governed by an NAO-type pattern, which results in warmer sea-surface conditions with less extensive sea ice in the area for the later part of the Dark Ages cold period ( c. AD 500 to 750) and cooler conditions with extensive sea ice inferred for the first part of the Medieval Climate Anomaly (MCA) ( c. AD 750 to 1050). After c. AD 1050, the marine climate in Disko Bay becomes in-phase with trends described for the NE Atlantic, reflected in the warmer interval for the remainder of the MCA ( c. AD 1050-1250), followed by cooling towards the onset of the Little Ice Age at c. AD 1400. The inferred scenario of climate deterioration and extensive sea ice is concomitant with the collapse of the Norse Western Settlement in Greenland at c. AD 1350. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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31. Buried alive — germination of up to a century-old marine protist resting stages.
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Lundholm, Nina, Ribeiro, Sofia, Andersen, Thorbjørn J., Koch, Trine, Godhe, Anna, Ekelund, Flemming, and Ellegaard, Marianne
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GERMINATION , *PROTISTA , *DINOFLAGELLATE cysts , *MARINE sediments , *BIOTURBATION - Abstract
We report on the survival and germination of up to a century-old marine protist resting stages naturally preserved in sediments from Koljö Fjord on the west coast of Sweden. This work has focused on germination of dinoflagellate cysts, but diatom resting stages were also observed. We record the longest known survival of dormant dinoflagellate cells. We individually isolated more than 1200 cysts of the three most abundant dinoflagellate taxa: Pentapharsodinium dalei, Lingulodinium polyedrum and Scrippsiella spp. Germination success decreased with core depth, and all successful germinations took place within the first 2 wk of incubation. Pentapharsodinium dalei had the highest germination success rate, with a maximum of up to 80% in 28-yr-old sediment, and could successfully germinate from core sediments dated to 1920 ± 12. Scrippsiella spp. cysts with cell contents occurred down to c. 90-yr-old sediment and could germinate from down to ca. 40-yr-old sediments, with a maximum germination rate of 50-60% in recent sediments. Cysts of L. polyedrum germinated frequently down to 20 yr and rarely to c. 80 yr, with a maximum of 20-50% germination success in recent sediments. Cyst isolation under cooled conditions rather than at room temperature resulted in a significantly higher germination success in P. dalei, while no effect was observed for L. polyedrum. The time elapsed since slicing of the core affected survival of L. polyedrum cysts negatively, most likely due to the effect of oxygen. The long-term survival potential of benthic resting stages that we report here has important implications, as viable resting stages accumulated in bottom sediments can be transported back to the water column by, for example, bioturbation and human-mediated sediment dredging. Hence, the sediment may to a higher degree than previously considered play a role as seed bank. This is important in a changing climate and might have particularly severe impacts in the case of harmful species. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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32. Gene delivery to human bone marrow mesenchymal stem cells by microporation
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Madeira, Catarina, Ribeiro, Sofia C., Pinheiro, Irina S.M., Martins, Sofia A.M., Andrade, Pedro Z., da Silva, Cláudia L., and Cabral, Joaquim M.S.
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ELECTROPORATION , *BONE marrow cells , *MESENCHYMAL stem cells , *GREEN fluorescent protein , *IMMUNOPHENOTYPING , *GENE transfection , *DNA , *SUCROSE , *CELL proliferation - Abstract
Abstract: Electroporation has been considered one of the most efficient non-viral based methods to deliver genes regardless of frequently observed high cell mortality. In this study we used a microporation technique to optimise the delivery of plasmid DNA encoding green fluorescence protein (GFP) to human bone marrow mesenchymal stem cells (BM-MSC). Using resuspension buffer (RB) and as low as 1.5×105 cells and 1μg of DNA, we achieved 40% of cells expressing the transgene, with cell recovery and cell viabilities of 85% and 90%, respectively. An increase in DNA amount did not significantly increase the number of transfected cells but clearly reduced cell recovery. A face-centered composite design was used to unveil the conditions giving rise to optimal plasmid delivery efficiencies when using a sucrose based microporation buffer (SBB). The BM-MSC proliferation kinetics were mainly affected by the presence of plasmid and not due to the microporation process itself although no effect was observed on their immunophenotypic characteristics and differentiative potential. Based on the data shown herein microporation demonstrated to be a reliable and efficient method to genetically modify hard-to-transfect cells giving rise to the highest levels of cell survival reported so far along with superior gene delivery efficiencies. [ABSTRACT FROM AUTHOR]
- Published
- 2011
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33. Evidence for the in vivo expression of a distant downstream gene under the control of ColE1 replication origin.
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Ribeiro, Sofia C., Prazeres, Duarte M. F., and Monteiro, Gabriel A.
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PLASMIDS , *GENETIC vectors , *GENES , *AMINOGLYCOSIDES , *PHOSPHOTRANSFERASES , *DNA replication , *RNA , *GENE expression , *ESCHERICHIA coli - Abstract
ColE1-like plasmids are widely used as expression vectors and as gene delivery vehicles. We have recently described a naturally occurring plasmid deletion phenomenon in the ColE1-type plasmid, pCI-neo, which leads to the detectable expression of an apparently promotorless kanamycin resistance gene. In the current work, we found that the expression of that aminoglycoside phosphotransferase ( aph) gene is regulated by an RNAII preprimer promoter located within the plasmid ColE1 replication origin, as a consequence of the extension of the RNA II species for at least 1.5 kb, up to the aph gene. This mechanism is dependent on the nonformation and/or dissociation of the hybrid between plasmid DNA and RNA II preprimer transcript. This is the first in vivo description of RNA II transcription beyond ori in wild-type Escherichia coli strains and nonmutated RNAII plasmid sequences resulting in productive transcription of distant downstream genes. Our results raise questions about unwanted expression of genes from expression or cloning vectors of ColE1 type and highlight the importance of a more careful design of ColE1-derived plasmid vectors. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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34. Protoperidinium minutum (Dinophyceae) from Portugal: cyst-theca relationship and phylogenetic position on the basis of single-cell SSU and LSU rDNA sequencing.
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Ribeiro, Sofia, Lundholm, Nina, Amorim, Ana, and Ellegaard, Marianne
- Subjects
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DINOFLAGELLATES , *RECOMBINANT DNA , *PHYLOGENY , *GENETIC engineering - Abstract
Round brown spiny cysts are common elements of Recent and Quaternary dinoflagellate cyst records and are often used to infer past climate conditions. Echinidinium and Islandinium, two cyst-based genera composed of round brown spiny cysts, are believed to have affinities within the Protoperidiniaceae. However, their biological counterparts are still virtually unknown. In this study, we examined the cyst-theca relationship of an Echinidinium-like cyst isolated from recent sediments of the Portuguese coast. The cysts (25-34 μm) had an intercalary theropylic archeopyle and numerous processes (4-9 μm) with tapered stems and minutely expanded tips. Germinated cells were identified as Protoperidinium minutum on the basis of theca morphology and tabulation. This taxon has a complicated taxonomic history and most likely represents a complex of species with very similar thecae but different cyst morphologies. To provide a first step in elucidating the phylogeny of P. minutum and its evolutionary relationship among the Protoperidiniaceae, we undertook the first molecular study of this taxon on the basis of small-subunit (SSU) and large-subunit (LSU) ribosomal (r)DNA genetic sequences obtained through single-cell polymerase chain reaction. On the basis of SSU rDNA analysis, P. minutum formed a clade together with the Diplopsaloideae, not grouping together with the other Protoperidinium species. LSU rDNA-based phylogenies indicate P. minutum as early divergent within the Protoperidiniaceae. The evolutionary significance of round brown spiny cysts produced by P. minutum-like species and diplopsalids is discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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35. Expression, purification and in vitro functional reconstitution of the chemokine receptor CCR1
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Allen, Samantha J., Ribeiro, Sofia, Horuk, Richard, and Handel, Tracy M.
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GENE expression , *MEMBRANE proteins , *CHEMOKINES , *CELL migration , *IMMUNOREGULATION , *LIGAND binding (Biochemistry) , *FLUORESCENCE - Abstract
Abstract: Chemokine receptors are a specific class of G-protein-coupled receptors (GPCRs) that control cell migration associated with routine immune surveillance, inflammation and development. In addition to their roles in normal physiology, these receptors and their ligands are involved in a large number of inflammatory diseases, cancer and AIDS, making them prime therapeutic targets in the pharmaceutical industry. Like other GPCRs, a significant obstacle in determining structures and characterizing mechanisms of activation has been the difficulty in obtaining high levels of pure, functional receptor. Here we describe a systematic effort to express the chemokine receptor CCR1 in mammalian cells, and to purify and reconstitute it in functional form. The highest expression levels were obtained using an inducible HEK293 system. The receptor was purified using a combination of N- (StrepII or Hemagglutinin) and C-terminal (His8) affinity tags. Function was assessed by ligand binding using a novel fluorescence polarization assay with fluorescein-labeled chemokine. A strict dependence of function on the detergent composition was observed, as solubilization of CCR1 in n-dodecyl-β-d-maltopyranoside/cholesteryl hemisuccinate yielded functional receptor with a K d of 21nM for the chemokine CCL14, whereas it was non-functional in phosphocholine detergents. Differences in function were observed despite the fact that both these detergent types maintained the receptor in a state characterized by monomers and small oligomers, but not large aggregates. While optimization is still warranted, yields of ∼0.1–0.2mg of pure functional receptor per 109 cells will permit biophysical studies of this medically important receptor. [Copyright &y& Elsevier]
- Published
- 2009
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36. Process length variation in cysts of a dinoflagellate, Lingulodinium machaerophorum, in surface sediments: Investigating its potential as salinity proxy
- Author
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Mertens, Kenneth N., Ribeiro, Sofia, Bouimetarhan, Ilham, Caner, Hulya, Combourieu Nebout, Nathalie, Dale, Barrie, De Vernal, Anne, Ellegaard, Marianne, Filipova, Mariana, Godhe, Anna, Goubert, Evelyne, Grøsfjeld, Kari, Holzwarth, Ulrike, Kotthoff, Ulrich, Leroy, Suzanne A.G., Londeix, Laurent, Marret, Fabienne, Matsuoka, Kazumi, Mudie, Peta J., and Naudts, Lieven
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DINOFLAGELLATES , *BIOMETRY , *PLANKTON , *MARINE biology - Abstract
Abstract: A biometrical analysis of the dinoflagellate cyst Lingulodinium machaerophorum [Deflandre, G., Cookson, I.C., 1955. Fossil microplankton from Australia late Mesozoic and Tertiary sediments. Australian journal of Marine and Freshwater Research 6: 242–313.] Wall, 1967 in 144 globally distributed surface sediment samples revealed that the average process length is related to summer salinity and temperature at a water depth of 30 m by the equation (salinity/temperature) = (0.078⁎average process length+0.534) with R 2 =0.69. This relationship can be used to reconstruct palaeosalinities, albeit with caution. The particular ecological window can be associated with known distributions of the corresponding motile stage Lingulodinium polyedrum (Stein) Dodge, 1989. Confocal laser microscopy showed that the average process length is positively related to the average distance between process bases (R 2 =0.78), and negatively related to the number of processes (R 2 =0.65). These results document the existence of two end members in cyst formation: one with many short, densely distributed processes and one with a few, long, widely spaced processes, which can be respectively related to low and high salinity/temperature ratios. Obstruction during formation of the cysts causes anomalous distributions of the processes. From a biological perspective, processes function to facilitate sinking of the cysts through clustering. [Copyright &y& Elsevier]
- Published
- 2009
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37. Environmental drivers of temporal succession in recent dinoflagellate cyst assemblages from a coastal site in the North-East Atlantic (Lisbon Bay, Portugal)
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Ribeiro, Sofia and Amorim, Ana
- Subjects
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DINOFLAGELLATE cysts , *MARINE sediments , *BAYS - Abstract
Abstract: Temporal changes in the community structure of recent dinoflagellate cyst assemblages of Lisbon Bay (Iberian upwelling system) were investigated between 2000 and 2005. The assemblages were diverse and characterized by high inter-annual variability, rather than a clear seasonal pattern. In order to identify the main environmental drivers of community changes, several regional (river runoff, rainfall, upwelling, radiation, daylength) and in situ (sea surface temperature, salinity, bottom and surface chlorophyll a concentration) environmental parameters were tested. Multivariate statistical analysis allowed the identification of water stability as the main environmental gradient influencing the community composition, with river runoff in the preceding rain season and upwelling being the two drivers of stratification and turbulence, respectively. Both these processes can be described as nutrient enrichment processes, but the cyst signal indicates that the two mechanisms select for different functional groups. The main upwelling cyst signal is characterised by the dominance of heterotrophic species (Protoperidinioid species) and presence of the autotrophic chain-forming Gymnodinium catenatum, while the river runoff cyst signal is characterised by dominance of autotrophs forming calcareous cysts, mainly Scrippsiella spp. Lingulodinium polyedrum is suggested to be indicative of upwelling conditions in the region but reflecting an ecological niche different from the more classical heterotrophic assemblage and G. catenatum. Our results reinforce the applicability of dinoflagellate cysts as environmental tracers in the warm-temperate region of the NE Atlantic, and contribute to the development of palaeoenvironmental cyst-based signals. [Copyright &y& Elsevier]
- Published
- 2008
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38. The clinical potential of chemokine receptor antagonists
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Ribeiro, Sofia and Horuk, Richard
- Subjects
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CHEMOKINES , *IMMUNOREGULATION , *G proteins , *AUTOANTIBODIES - Abstract
Abstract: Chemokines belong to a family of chemotactic cytokines that direct the migration of immune cells towards sites of inflammation. They mediate their biological effects by binding to cell surface receptors, which belong to the G protein-coupled receptor superfamily. Since chemokines and their receptors have been implicated in the pathophysiology of a number of autoinflammatory diseases, chemokine receptor antagonists could prove to be useful therapeutics to target these diseases. Here, we review the role of chemokines in autoimmunity, concentrating mainly on the chemokine receptors CCR1 and CCR5, and discuss the potential utility of antagonists that target these 2 receptors as they progress through the clinic. [Copyright &y& Elsevier]
- Published
- 2005
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39. Controlled ripple texturing of suspended graphene membranes due to coupling with ultracold atoms.
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Ribeiro, Sofia and Scheel, Stefan
- Subjects
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ULTRA-cold atom collisions , *GRAPHENE , *ARTIFICIAL membranes , *FORCE & energy , *CASIMIR effect - Abstract
We explore the possibility to create hybrid quantum systems that combine ultracold atoms with graphene membranes. We investigate a setup in which a cold atom cloud is placed close to a free-standing sheet of graphene at distances of a few hundred nanometers. The atoms then couple strongly to the graphene membrane via Casimir-Polder forces. Temporal changes in the atomic state of the atomic cloud changes the Casimir-Polder interaction, thereby leading to the creation of a back-action force in the graphene sheet. This setup provides a controllable way to engineer ripples in a graphene sheet with cold atoms. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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40. Shielding vacuum fluctuations with graphene.
- Author
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Ribeiro, Sofia and Scheel, Stefan
- Subjects
- *
FLUCTUATIONS (Physics) , *GRAPHENE , *GROUND state (Quantum mechanics) , *VACUUM , *EXCITED states , *TEMPERATURE effect , *POTENTIAL theory (Physics) - Abstract
The Casimir-Polder interaction of ground-state and excited atoms with graphene is investigated with the aim to establish whether graphene systems can be used as a shield for vacuum fluctuations of an underlying substrate. We calculate the zero-temperature Casimir-Polder potential from the reflection coefficients of graphene within the framework of the Dirac model. For both doped and undoped graphene we show limits at which graphene could be used effectively as a shield. Additional results are given for AB-stacked bilayer graphene. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
41. Second-order coupling between excited atoms and surface polaritons.
- Author
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Ribeiro, Sofia, Buhmann, Stefan Y., and Scheel, Stefan
- Subjects
- *
EXCITON theory , *ATOMS , *POLARITONS , *SURFACES (Physics) , *CASIMIR effect , *TEMPERATURE effect , *INTERFACES (Physical sciences) - Abstract
Casimir-Polder interactions between an atom and a macroscopic body are typically regarded as being due to the exchange of virtual photons. This is strictly true only at zero temperature. At finite temperatures, real-photon exchange can provide a significant contribution to the overall dispersion interaction. Here, we describe a resonant two-photon process between an atom and a planar interface. We derive a second-order effective Hamiltonian to explain how atoms can couple resonantly to the surface polariton modes of the dielectric medium. This leads to second-order energy exchanges which we compare with the standard nonresonant Casimir-Polder energy. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
42. Geoprivacy in Neighbourhoods and Health Research: A Mini-Review of the Challenges and Best Practices in Epidemiological Studies.
- Author
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Isabel Ribeiro, Ana, Dias, Vasco, Ribeiro, Sofia, Pedro Silva, José, and Barros, Henrique
- Subjects
- *
GENERAL Data Protection Regulation, 2016 , *LOCATION data , *NEIGHBORHOODS , *PUBLIC health research , *BEST practices - Abstract
Neighbourhood and health research often relies on personal location data (e.g., home address, daily itineraries), despite the risks of geoprivacy breaches. Thus, geoprivacy is an important emerging topic, contemplated in international regulations such as the General Data Protection Regulation. In this mini-review, we briefly assess the potential risks associated with the usage of personal location data and provide geoprivacy-preserving recommendations to be considered in epidemiological research. Risks include inference of personal information that the individual does not wish to disclose, reverse-identification and security breaches. Various measures should be implemented at different stages of a project (pre-data collection, data processing, data analysis/publication and data sharing) such as informed consent, pseudo-anonymization and geographical methods. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
43. An annual cycle of diatom succession in two contrasting Greenlandic fjords: from simple sea-ice indicators to varied seasonal strategists.
- Author
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Luostarinen, Tiia, Ribeiro, Sofia, Weckström, Kaarina, Sejr, Mikael, Meire, Lorenz, Tallberg, Petra, and Heikkilä, Maija
- Subjects
- *
SEA ice , *DIATOMS , *FJORDS , *WATER depth , *THALASSIOSIRA , *TUNDRAS - Abstract
We recorded diatom species succession over one full year (May 2017–May 2018) using automated sediment traps installed in two contrasting Greenlandic fjords: the seasonally ice-covered Young Sound in high-arctic Northeast Greenland and the nearly sea-ice free Godthåbsfjord in subarctic Southwest Greenland. The traps were positioned at differing water depths (37 m in Young Sound vs. 300 m in Godthåbsfjord). Distinct differences between the study sites were observed in both sediment and diatom fluxes. In Young Sound, total diatom flux was extremely seasonal and as high as 880 × 106 valves m−2 d−1 in the spring. In Godthåbsfjord, total diatom flux was more stable throughout the year, with a maximum of 320 × 106 valves m−2 d−1 in the summer. The diatom assemblage in Young Sound was dominated by the sea-ice species Fragilariopsis oceanica , Fragilariopsis reginae-jahniae and Fossula arctica , which exhibited pulse-like deposition in the trap during and after the ice melt. In Godthåbsfjord, the fluxes were dominated by Chaetoceros (resting spores), while the remaining assemblage was characterised by the cold-water indicator species Detonula confervacea (resting spores) and Thalassiosira antarctica var. borealis (resting spores) together with Fragilariopsis cylindrus. Our data show that, F. oceanica , F. reginae-jahniae and F. arctica exhibit similar seasonal behaviour and a clear link to sea ice. Fragilariopsis cylindrus seems to have a more flexible niche, and based on our study, cannot be considered an unequivocal ice indicator. Taking into account these ecological and seasonal preferences of individual diatom species is crucial when reconstructing past sea-ice conditions both qualitatively and quantitatively. • Distinct differences observed in the seasonal diatom succession between Young Sound and Godthåbsfjord • Species-specific response to sea ice differs between diatom species • Fragilariopsis oceanica, Fragilariopsis reginae-jahniae and F. arctica exhibit similar seasonal behaviour and clear affiliation to sea ice • Ecological understanding of individual diatom species is crucial in past sea-ice reconstruction [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
44. Learning from the past: Impact of the Arctic Oscillation on sea ice and marine productivity off northwest Greenland over the last 9,000 years.
- Author
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Limoges, Audrey, Weckström, Kaarina, Ribeiro, Sofia, Georgiadis, Eleanor, Hansen, Katrine E., Martinez, Philippe, Seidenkrantz, Marit‐Solveig, Giraudeau, Jacques, Crosta, Xavier, and Massé, Guillaume
- Subjects
- *
ARCTIC oscillation , *MARINE productivity , *SEA ice , *MARINE biodiversity , *PHASE oscillations , *MARINE ecology , *HOLOCENE Epoch - Abstract
Climate warming is rapidly reshaping the Arctic cryosphere and ocean conditions, with consequences for sea ice and pelagic productivity patterns affecting the entire marine food web. To predict how ongoing changes will impact Arctic marine ecosystems, concerted effort from various disciplines is required. Here, we contribute multi‐decadal reconstructions of changes in diatom production and sea‐ice conditions in relation to Holocene climate and ocean conditions off northwest Greenland. Our multiproxy study includes diatoms, sea‐ice biomarkers (IP25 and HBI III) and geochemical tracers (TOC [total organic carbon], TOC:TN [total nitrogen], δ13C, δ15N) from a sediment core record spanning the last c. 9,000 years. Our results suggest that the balance between the outflow of polar water from the Arctic, and input of Atlantic water from the Irminger Current into the West Greenland Current is a key factor in controlling sea‐ice conditions, and both diatom phenology and production in northeastern Baffin Bay. Our proxy record notably shows that changes in sea‐surface conditions initially forced by Neoglacial cooling were dynamically amplified by the shift in the dominant phase of the Arctic Oscillation (AO) mode that occurred at c. 3,000 yr BP, and caused drastic changes in community composition and a decline in diatom production at the study site. In the future, with projected dominant‐positive AO conditions favored by Arctic warming, increased water column stratification may counteract the positive effect of a longer open‐water growth season and negatively impact diatom production. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
45. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant Salmonella successful clones is associated with diverse ars operons and genetic contexts.
- Author
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Mourão, Joana, Rebelo, Andreia, Ribeiro, Sofia, Peixe, Luísa, Novais, Carla, and Antunes, Patrícia
- Subjects
- *
POLLUTANTS , *OPERONS , *ARSENIC , *SALMONELLA , *ARSENIC compounds , *INSECTICIDES , *FOOD contamination - Abstract
Summary: Emergence and expansion of frequent multidrug‐resistant (MDR) major Salmonella clones/serotypes has been a significant threat in the last years. Metal compounds, such as copper, commonly used in animal‐production settings, have been pointed out as possible contributors for the selection of such strains/clones. However, the scarcity of studies limits our understanding of the impact of other metal environmental contaminants as arsenic (used in insecticides/herbicides/coccidiostats). We analysed arsenic tolerance (AsT) dispersion by phenotypic and genotypic (PCR/sequencing/I‐CeuI/S1/XbaI‐PFGE/hybridization) assays among Salmonella with diverse epidemiological and genetic backgrounds. Then, to better understand ars operon genetic contexts, the whole genome of five representative strains was sequenced. We found a high dispersion of ars operons conferring AsT, especially among copper‐tolerant and relevant serotypes/clones related to pig‐production setting. The acr3‐type was found dispersed in the chromosome of diverse serotypes, including the emergent S. Rissen. Conversely, arsBII was almost confined to the MDR ST34 European clone of S. Typhimurium/S. 4,[5],12:i:‐, always along with copper/silver tolerance sil + pco clusters in an integrative conjugative element. These data suggest that AsT is an essential adaptive feature for the ecological success of these epidemic clones/serotypes and alerts for global strategies to reduce arsenic‐based compounds' impact thus preventing environmental/food contamination with frequent MDR foodborne pathogens. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
46. Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.
- Author
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Westbury, Michael V., Brown, Stuart C., Lorenzen, Julie, O'Neill, Stuart, Scott, Michael B., McCuaig, Julia, Cheung, Christina, Armstrong, Edward, Valdes, Paul J., Samaniego Castruita, José Alfredo, Cabrera, Andrea A., Blom, Stine Keibel, Dietz, Rune, Sonne, Christian, Louis, Marie, Galatius, Anders, Fordham, Damien A., Ribeiro, Sofia, Szpak, Paul, and Lorenzen, Eline D.
- Subjects
- *
TUNDRAS , *TOP predators , *SEA ice , *POLAR bear , *OCEAN temperature , *HOLOCENE Epoch , *ECOLOGICAL models - Abstract
The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
47. Quantum thermal machines driven by vacuum forces.
- Author
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Terças, Hugo, Ribeiro, Sofia, Pezzutto, Marco, and Omar, Yasser
- Subjects
- *
QUANTUM thermodynamics , *VACUUM , *RESONATORS - Abstract
We propose a quantum thermal machine composed of two nanomechanical resonators (two membranes suspended over a trench in a substrate) placed a few μm from each other. The quantum thermodynamical cycle is powered by the Casimir interaction between the resonators and the working fluid is the polariton resulting from the mixture of the flexural (out-of-plane) vibrations. With the help of piezoelectric cells, we select and sweep the polariton frequency cyclically. We calculate the performance of the proposed quantum thermal machines and show that high efficiencies are achieved thanks to (i) the strong coupling between the resonators and (ii) the large difference between the membrane stiffnesses. Our findings can be of particular importance for applications in nanomechanical technologies where a sensitive control of temperature is needed. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
48. Training European public health professionals—the role of young professional networks.
- Author
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Boyle, Louise E. and Ribeiro, Sofia
- Subjects
- *
BUSINESS networks , *CLINICAL competence , *INTERDISCIPLINARY education , *MEDICAL personnel , *PROFESSIONAL employee training , *PUBLIC health , *ROLE playing , *ADULT education workshops - Abstract
The authors discuss the role of young professional networks in training European public health professionals. They talk about the efforts to introduce competency-based education in public health training to facilitate the transition from the educational level to the professional world. Also tackled is example of a young professional health network, which is the Young Forum Gastein initiative developed by the non-profit association International Forum Gastein.
- Published
- 2014
- Full Text
- View/download PDF
49. Sea-level rise in Denmark: bridging local reconstructions and global projections.
- Author
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Colgan, William, Box, Jason E., Ribeiro, Sofia, and Kjeldsen, Kristian K.
- Subjects
- *
ABSOLUTE sea level change , *SEA ice , *GLACIAL isostasy - Published
- 2019
- Full Text
- View/download PDF
50. Sea-level rise in Denmark: bridging local reconstructions and global projections.
- Author
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Colgan, William, Box, Jason E., Ribeiro, Sofia, and Kjeldsen, Kristian K.
- Subjects
- *
ABSOLUTE sea level change , *SEA ice , *GLACIAL isostasy - Published
- 2018
- Full Text
- View/download PDF
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