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Small pelagic fish in the new millennium : a bottom-up view of global research effort
No full textSmall pelagic fish (SPF) play extremely important ecological roles in marine ecosystems, form some of the most economically valuable fisheries resources, and play a vital role in global food security. Due to their short generation times and tight coupling to lower trophic levels, populations of SPF display large boom-and-bust dynamics that are closely linked to climate variability. To reveal emerging global research trends on SPF as opposed to more recently published, ecosystem-specific reviews of SPF, we reviewed the literature published in two, 6-year periods in the new millennium (2001-2006, and 2011-2016) straddling the publication of a large, global review of the dynamics of SPF in 2009. We explored intrinsic and extrinsic (bottom-up) factors influencing the dynamics of SPF such as anchovies, sardines, herrings and sprats within the sub-order Clupeidae. Published research efforts within 16 different biogeographic ocean regions were compiled (more than 900 studies) and compared to identify i) new milestones and advances in our understanding, ii) emerging research trends and iii) remaining gaps in knowledge. Studies were separated into 5 categories (field, laboratory, mesocosms, long-term statistical analyses and spatially-explicit modelling) and discussed in relation to 10 bottom-up categories including 5 abiotic factors (temperature, salinity, pH, dissolved oxygen, density), 3 physical processes (advection, turbulence, turbidity) and 2 biotic factors (prey quantity and quality). The peer-reviewed literature reflects changes in the number of studies between the two time periods including increases (Mediterranean Sea, Humboldt Current) and decreases (Australia, Benguela Current). Our review highlights i) gaps in ecological knowledge on young juveniles and, in general, on the impacts of hypoxia and heatwaves on SPF, ii) the utility of paleo studies in exploring population drivers, iii) the continued need to develop spatially-explicit, full life-cycle models, iv) the importance of exploring how density-dependent processes impact vital rates (growth, survival, reproduction), and v) the benefits of international collaboration for knowledge transfer and building unifying hypotheses on the role of bottom-up factors and processes that regulate SPF populations
Chemometric discrimination of the geographical origin of three greek cultivars of olive oils by stable isotope ratio analysis
No full textAlpha stable isotope ratio mass spectrometer was used for stable isotope ratio (i.e., delta C-13, delta O-18, and delta H-2) measurements, achieving geographical discrimination using orthogonal projections to latent structures discriminant analysis. A total of 100 Greek monovarietal olive oil samples from three different olive cultivars (cv. Koroneiki, cv. Lianolia Kerkyras, and cv. Maurolia), derived from Central Greece and Peloponnese, were collected during the 2019-2020 harvest year aiming to investigate the effect of botanical and geographical origin on their discrimination through isotopic data. The selection of these samples was made from traditionally olive-growing areas in which no significant research has been done so far. Samples were discriminated mainly by olive cultivar and, partially, by geographical origin, which is congruent with other authors. Based on this model, correct recognition of 93.75% in the training samples and correct prediction of 100% in the test set were achieved. The overall correct classification of the model was 91%. The predictability based on the externally validated method of discrimination was good (Q(2) (cum) = 0.681) and illustrated that delta O-18 and delta H-2 were the most important isotope markers for the discrimination of olive oil samples. The authenticity of olive oil based on the examined olive varieties can be determined using this technique
InpactorDB : a classified lineage-level plant LTR retrotransposon reference library for free-alignment methods based on machine learning
No full textLong terminal repeat (LTR) retrotransposons are mobile elements that constitute the major fraction of most plant genomes. The identification and annotation of these elements via bioinformatics approaches represent a major challenge in the era of massive plant genome sequencing. In addition to their involvement in genome size variation, LTR retrotransposons are also associated with the function and structure of different chromosomal regions and can alter the function of coding regions, among others. Several sequence databases of plant LTR retrotransposons are available for public access, such as PGSB and RepetDB, or restricted access such as Repbase. Although these databases are useful to identify LTR-RTs in new genomes by similarity, the elements of these databases are not fully classified to the lineage (also called family) level. Here, we present InpactorDB, a semi-curated dataset composed of 130,439 elements from 195 plant genomes (belonging to 108 plant species) classified to the lineage level. This dataset has been used to train two deep neural networks (i.e., one fully connected and one convolutional) for the rapid classification of these elements. In lineage-level classification approaches, we obtain up to 98% performance, indicated by the F1-score, precision and recall scores
Accelerating elimination of sleeping sickness from the Guinean littoral through enhanced screening in the post-Ebola context : a retrospective analysis
No full textBackground Activities to control human African trypanosomiasis (HAT) in Guinea were severely hampered by the Ebola epidemic that hit this country between 2014 and 2016. Active screening was completely interrupted and passive screening could only be maintained in a few health facilities. At the end of the epidemic, medical interventions were progressively intensified to mitigate the risk of HAT resurgence and progress towards disease elimination. Methodology/Principal findings A retrospective analysis was performed to evaluate the medical activities that were implemented in the three most endemic prefectures of Guinea (Boffa, Dubreka and Forecariah) between January 2016 and December 2018. Passive screening using rapid diagnostic tests (RDTs) was progressively resumed in one hundred and one health facilities, and active screening was intensified by visiting individual households and performing RDTs, and by conducting mass screening in villages by mobile teams using the Card Agglutination Test for Trypanosomiasis. A total of 1885, 4897 and 8023 clinical suspects were tested in passive, while 5743, 14442 and 21093 people were actively screened in 2016, 2017 and 2018, respectively. The number of HAT cases that were diagnosed first went up from 107 in 2016 to 140 in 2017, then subsequently decreased to only 73 in 2018. A progressive decrease in disease prevalence was observed in the populations that were tested in active and in passive between 2016 and 2018. Conclusions/Significance Intensified medical interventions in the post-Ebola context first resulted in an increase in the number of HAT cases, confirming the fear that the disease could resurge as a result of impaired control activities during the Ebola epidemic. On the other hand, the decrease in disease prevalence that was observed between 2016 and 2018 is encouraging, as it suggests that the current strategy combining enhanced diagnosis, treatment and vector control is appropriate to progress towards elimination of HAT in Guinea. Author summary Guinea has been consistently reporting the largest number of sleeping sickness cases in Western Africa since 2002. The Ebola epidemic that severely hit this country between 2014 and 2016 resulted in an interruption of most medical activities to control sleeping sickness, which was associated with an increase in the number of cases reported in 2016. In order to contain the resurgence of sleeping sickness and to bring it back on the path towards elimination, activities to screen and diagnose patients were intensified by strengthening the capacity of health facilities, and by visiting villages and households to test at-risk populations, while vector control was extended to cover all active foci in the country. This article presents the results that were obtained by the National Sleeping Sickness Control Program of Guinea after the Ebola epidemic by enhancing medical activities in the coastal region, where most cases of sleeping sickness are found. These efforts first resulted in an increase in the number of cases being diagnosed in 2016 and in 2017, and was then followed by an encouraging decline in 2018, thus raising hopes that the disease could be eliminated in the near future in Guinea
Impact of systematic early tuberculosis detection using Xpert MTB/RIF Ultra in children with severe pneumonia in high tuberculosis burden countries (TB-Speed pneumonia) : a stepped wedge cluster randomized trial
No full textBackground: In high tuberculosis (TB) burden settings, there is growing evidence that TB is common in children with pneumonia, the leading cause of death in children under 5 years worldwide. The current WHO standard of care (SOC) for young children with pneumonia considers a diagnosis of TB only if the child has a history of prolonged symptoms or fails to respond to antibiotic treatments. As a result, many children with TB-associated severe pneumonia are currently missed or diagnosed too late. We therefore propose a diagnostic trial to assess the impact on mortality of adding the systematic early detection of TB using Xpert MTB/RIF Ultra (Ultra) performed on nasopharyngeal aspirates (NPA) and stool samples to the WHO SOC for children with severe pneumonia, followed by immediate initiation of anti-TB treatment in children testing positive on any of the samples. Methods: TB-Speed Pneumonia is a pragmatic stepped-wedge cluster randomized controlled trial conducted in six countries with high TB incidence rate (Cote d'Ivoire, Cameroon, Uganda, Mozambique, Zambia and Cambodia). We will enrol 3780 children under 5 years presenting with WHO-defined severe pneumonia across 15 hospitals over 18 months. All hospitals will start managing children using the WHO SOC for severe pneumonia; one hospital will be randomly selected to switch to the intervention every 5 weeks. The intervention consists of the WHO SOC plus rapid TB detection on the day of admission using Ultra performed on 1 nasopharyngeal aspirate and 1 stool sample. All children will be followed for 3 months, with systematic trial visits at day 3, discharge, 2 weeks post-discharge, and week 12. The primary endpoint is all-cause mortality 12 weeks after inclusion. Qualitative and health economic evaluations are embedded in the trial. Discussion: In addition to testing the main hypothesis that molecular detection and early treatment will reduce TB mortality in children, the strength of such pragmatic research is that it provides some evidence regarding the feasibility of the intervention as part of routine care. Should this intervention be successful, safe and well tolerated, it could be systematically implemented at district hospital level where children with severe pneumonia are referred
Soil-transmitted helminth infection in pregnancy and long-term child neurocognitive and behavioral development : a prospective mother-child cohort in Benin
No full textBackground An estimated 30% of women in Sub-Saharan Africa suffer from soil-transmitted helminth infection during pregnancy (SHIP), which has been shown to increase risk of pre-term birth, low birth weight, and maternal anemia. A previous study in Benin found that SHIP was associated with impaired cognitive and gross motor development scores in 635 one-year-old children. The objective of the present study was to follow children prospectively to investigate whether the association between SHIP and child neurocognitive and behavioral development persisted at age six. Principal findings Our prospective child cohort included 487 live-born singletons of pregnant women enrolled in the Malaria in Pregnancy Preventive Alternative Drugs clinical trial in Allada, Benin. SHIP was assessed at three antenatal visits (ANVs) through collection and testing of stool samples. Neurocognitive and behavioral development was assessed in six-year-old children by trained investigators using the Kaufman Assessment Battery for Children 2(nd) edition and the parent-reported Strengths and Difficulties Questionnaire (SDQ). Multiple linear regression models generated coefficients and 95% confidence intervals and potential mediating factors were tested. Prevalence of SHIP was 13% at the 1(st) ANV, 9% at the 2(nd) ANV, and 1% at delivery. SHIP was not associated with low neurocognitive scores in children at six years. Higher SDQ internalizing scores, indicating increased emotional impairments in children, were associated with helminth infection at the 2(nd) ANV/delivery 1.07 (95% CI 0.15, 2.00) and at least once during pregnancy 0.79 (95% CI 0.12, 1.46) in adjusted models. Mediation analysis did not reveal significant indirect effects of several mediators on this association. Conclusions Our study shows that while SHIP is not associated with impaired long-term neurocognitive development, infections may have significant negative impacts on emotional development in six-year-old children. SHIP remains a critical public health issue, and adequate prevention and treatment protocols should be enforced in low- and middle-income countries. Author summary Soil-transmitted helminth infections impact 1.5 billion individuals, primarily in low- and middle- income countries, each year and contribute to malnutrition, anemia, and impaired neurocognitive development in children. However, these infections in pregnancy and their impact on offspring have been less studied. One previous study found associations between soil-transmitted helminth infection during pregnancy and impaired cognitive functioning in offspring one year after birth. The current study aimed to follow these children prospectively until six years in order to confirm whether these associations persisted or not. Infections during pregnancy were no longer associated with cognitive or motor functioning in children; however, infections were associated with impaired behavioral development. Animal-based models have hypothesized maternal inflammation and poor birth outcomes to be the mechanisms behind this relationship; however, our findings did not support these mechanisms. This is one of very few prospective cohort studies in Sub-Saharan Africa to investigate these associations, and more research is needed to corroborate results. Limitations include limited power and the possibility that results are due to chance from multiple statistical tests. Adequate and accessible prevention and treatment efforts in pregnancy and childhood should be provided to populations in low- and middle- income countries at high risk of infection
Sénégal : comment assurer la continuité des soins de santé mentale en temps de Covid-19 ?
No full textExplorer l'impact environnemental des transformations agraires en Asie du Sud-Est grâce à l'évaluation participative des services écosystémiques
No full textDifférents mécanismes d'intervention sont proposés pour transformer les paysages agricoles de manière à ce qu'ils remplissent de multiples fonctions, compatibles avec les objectifs du développement durable. Dans le cas de l'atténuation et de l'adaptation au changement climatique, des politiques incitatives et des mécanismes de rémunération des acteurs locaux sont promues dans le cadre des initiatives REDD+. Sur le terrain, ces interventions visent à assurer simultanément la fourniture de services écosystémiques et le maintien, voire l'amélioration, des moyens d'existence locaux. Dans cet article, nous explorons le rôle que peut jouer l'évaluation participative dans la mise en oeuvre de paiements pour services environnementaux au sein de communautés rurales d'Indonésie, du Laos, du Vietnam et de Chine. Engagées dans un processus d'intégration rapide à l'économie de marché, ces communautés ont transformé leurs systèmes d'abattis brûlis traditionnels pour s'orienter vers différentes voies d'intensification agricole au cours des dernières années. L'évaluation positive ou négative de ces évolutions fait nécessairement l'objet de jugements de valeur dans les choix effectués entre différentes options possibles. La formulation de ces options en termes de services écosystémiques rendus permet de comparer les trajectoires paysagères et leur impact sur les conditions de vie locales. Sur ces bases, les communautés peuvent explorer des scénarios de transformation de leurs pratiques agricoles, négocier des compromis entre services écosystémiques et identifier les "gagnants" et les "perdants" potentiels. Ces simulations ont montré l'importance du calendrier de mise en place des programmes REDD+ par rapport aux transformations agraires en cours. Elles pointent le risque de s'éloigner des ambitions initiales d'un impact sur les émissions de carbone pour devenir un instrument supplémentaire de développement durabl
Understanding the impact of climate change on the oceanic circulation in the Chilean island ecoregions
No full textThe largest changes in the circulation of the South-eastern Pacific resulting from global warming are associated with the southward shift and intensification of the anticyclone and with coastal surface warming. Coastal upwelling is projected to be increase off central Chile, due to an increase in equatorward winds, although increased oceanic stratification and associated enhanced nearshore turbulence will yield an onshore deepening/flattening of the thermocline. The overall increase in south-easterly trade winds of the South-eastern Pacific in a warmer climate are likely to increase the connectivity pattern between Juan Fernandez and Desventuradas islands, and along the Sala y Gomez ridge, through increasing wind-driven mean ocean currents. Deoxygenation associated with the warmer temperatures and changes in ventilation are likely to modify marine habitat and the respiratory barriers of species in the seamounts located in the vicinity of the limits of the minimum oxygen zone. In the South-eastern Pacific, the prevailing 2D understanding of the responses of marine life to climate change needs to be expanded to 3D approaches, integrating the vertical habitat compression of marine organisms as a result of ocean warming and deoxygenation, as climate velocities for temperature and oxygen have contrasting vertical and horizontal patterns. There is a need for regional biogeochemical-coupled modelling studies dedicated to the Chilean islands in order to provide an integrated view of the impact of anthropogenic stressors (e.g. deoxygenation, increased stratification, and climate shift) at the scale required for addressing socio-ecological interactions. A refined understanding of the large-scale biogeography and spatial dynamics of marine populations through experimentation with high-resolution regional ocean models is a prerequisite for scaling-up regional management planning and optimizing the conservation of interconnected marine ecosystems across large scales
Women's empowerment and elective cesarean section for a single pregnancy : a population-based and multivariate study in Vietnam
No full textBackground Women's empowerment, and maternal and neonatal health are important targets of the Sustainable Development Goals. Our objective is to examine the relationship between women's empowerment and elective cesarean section (ECS), focusing on Vietnam, a country where the use of CS has increased rapidly in recent decades, which raises public health concerns. Methods We hypothesized that in the context of the developing biomedicalization of childbirth, women's empowerment increases the use of ECS due to a woman's enhanced ability to decide her mode of delivery. By using microdata from the 2013-2014 Multiple Indicator Clusters Survey, we conducted a multivariate analysis of the correlates of ECS. We studied a representative sample of 1343 institutional single birth deliveries. Due to higher ECS rates among multiparous (18.4%) than primiparous women (10.1%) and the potential interaction between parity and other correlates, we used separate models for primiparous and multiparous women. Results Among the indicators of women's external resources, which include a higher level of education, having worked during the previous 12 months, and having one's own mobile phone, only education differed between primiparous and multiparous women, with a higher level among primiparous women. Among primiparous women, no resource indicator was significantly linked to ECS. However, considering women's empowerment facilitated the identification of the negative impact of having had fewer than 3 antenatal care visits on the use of ECS. Among multiparous women, disapproval of intimate partner violence (IPV) was associated with a doubled likelihood of undergoing ECS (odds ratio = 2.415), and living in an urban area also doubled the likelihood of ECS. The positive association with living in the richest household quintile was no longer significant when attitude towards IPV was included in the model. In both groups, being aged 35 or older increased the likelihood of undergoing ECS, and this impact was stronger in primiparous women. Conclusions These results underline the multidimensionality of empowerment, its links to other correlates and its contribution to clarifying the influence of these correlates, particularly for distinguishing between medical and sociocultural determinants. The results advocate for the integration of women's empowerment into policies aimed at reducing ECS rates