| 1. |
- Bouakaze, Caroline, et al.
(författare)
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Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex) : Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters
- 2020
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Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
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Tidskriftsartikel (refereegranskat)abstract
- We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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| 2. |
- Duffy, J. Emmett, et al.
(författare)
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Toward a Coordinated Global Observing System for Seagrasses and Marine Macroalgae
- 2019
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 6
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Forskningsöversikt (refereegranskat)abstract
- In coastal waters around the world, the dominant primary producers are benthic macrophytes, including seagrasses and macroalgae, that provide habitat structure and food for diverse and abundant biological communities and drive ecosystem processes. Seagrass meadows and macroalgal forests play key roles for coastal societies, contributing to fishery yields, storm protection, biogeochemical cycling and storage, and important cultural values. These socio-economically valuable services are threatened worldwide by human activities, with substantial areas of seagrass and macroalgal forests lost over the last half-century. Tracking the status and trends in marine macrophyte cover and quality is an emerging priority for ocean and coastal management, but doing so has been challenged by limited coordination across the numerous efforts to monitor macrophytes, which vary widely in goals, methodologies, scales, capacity, governance approaches, and data availability. Here, we present a consensus assessment and recommendations on the current state of and opportunities for advancing global marine macrophyte observations, integrating contributions from a community of researchers with broad geographic and disciplinary expertise. With the increasing scale of human impacts, the time is ripe to harmonize marine macrophyte observations by building on existing networks and identifying a core set of common metrics and approaches in sampling design, field measurements, governance, capacity building, and data management. We recommend a tiered observation system, with improvement of remote sensing and remote underwater imaging to expand capacity to capture broad-scale extent at intervals of several years, coordinated with strati fied in situ sampling annually to characterize the key variables of cover and taxonomic or functional group composition, and to provide ground-truth. A robust networked system of macrophyte observations will be facilitated by establishing best practices, including standard protocols, documentation, and sharing of resources at all stages of work flow, and secure archiving of open-access data. Because such a network is necessarily distributed, sustaining it depends on close engagement of local stakeholders and focusing on building and long-term maintenance of local capacity, particularly in the developing world. Realizing these recommendations will producemore effective, efficient, and responsive observing, a more accurate global picture of change in vegetated coastal systems, and stronger international capacity for sustaining observations.
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| 3. |
- Fortes Brollo, Maria Eugenia, et al.
(författare)
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Magnetic properties of nanoparticles as a function of their spatial distribution on liposomes and cells
- 2018
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 20:26, s. 17829-17838
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Tidskriftsartikel (refereegranskat)abstract
- The aggregation processes of magnetic nanoparticles in biosystems are analysed by comparing the magnetic properties of three systems with different spatial distributions of the nanoparticles. The first one is iron oxide nanoparticles (NPs) of 14 nm synthesized by coprecipitation with two coatings, (3-aminopropyl)trimethoxysilane (APS) and dimercaptosuccinic acid (DMSA). The second one is liposomes with encapsulated nanoparticles, which have different configurations depending on the NP coating (NPs attached to the liposome surface or encapsulated in its aqueous volume). The last system consists of two cell lines (Pan02 and Jurkat) incubated with the NPs. Dynamic magnetic behaviour (AC) was analysed in liquid samples, maintaining their colloidal properties, while quasi-static (DC) magnetic measurements were performed on lyophilised samples. AC measurements provide a direct method for determining the effect of the environment on the magnetization relaxation of nanoparticles. Thus, the imaginary (χ'') component shifts to lower frequencies as the aggregation state increases from free nanoparticles to those attached or embedded into liposomes in cell culture media and more pronounced when internalized by the cells. DC magnetization curves show no degradation of the NPs after interaction with biosystems in the analysed timescale. However, the blocking temperature is shifted to higher temperatures for the nanoparticles in contact with the cells, regardless of the location, the incubation time, the cell line and the nanoparticle coating, supporting AC susceptibility data. These results indicate that the simple fact of being in contact with the cells makes the nanoparticles aggregate in a non-controlled way, which is not the same kind of aggregation caused by the contact with the cell medium nor inside liposomes.
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| 4. |
- Glynn, James, et al.
(författare)
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Economic Impacts of Future Changes in the Energy System : National Perspectives
- 2015
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Ingår i: Informing Energy and Climate Policies Using Energy Systems Models. - Cham : Encyclopedia of Global Archaeology/Springer Verlag. - 9783319165394 - 9783319165400 ; , s. 359-387
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Bokkapitel (refereegranskat)abstract
- In a climate constrained future, hybrid energy-economy model coupling gives additional insight into interregional competition, trade, industrial delocalisation and overall macroeconomic consequences of decarbonising the energy system. Decarbonising the energy system is critical in mitigating climate change. This chapter summarises modelling methodologies developed in the ETSAP community to assess economic impacts of decarbonising energy systems at a national level. The preceding chapter focuses on a global perspective. The modelling studies outlined here show that burden sharing rules and national revenue recycling schemes for carbon tax are critical for the long-term viability of economic growth and equitable engagement on combating climate change. Traditional computable general equilibrium models and energy systems models solved in isolation can misrepresent the long run carbon cost and underestimate the demand response caused by technological paradigm shifts in a decarbonised energy system. The approaches outlined within have guided the first evidence based decarbonisation legislation and continue to provide additional insights as increased sectoral disaggregation in hybrid modelling approaches is achieved
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| 5. |
- Glynn, James, et al.
(författare)
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Economic Impacts of Future Changes in the Energy System : Global Perspectives
- 2015
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Ingår i: Informing Energy and Climate Policies Using Energy Systems Models. - Cham : Encyclopedia of Global Archaeology/Springer Verlag. - 9783319165394 - 9783319165400 ; , s. 333-358
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Bokkapitel (refereegranskat)abstract
- In a climate constrained future, hybrid energy-economy model coupling gives additional insight into interregional competition, trade, industrial delocalisation and overall macroeconomic consequences of decarbonising the energy system. Decarbonising the energy system is critical in mitigating climate change. This chapter summarises modelling methodologies developed in the ETSAP community to assess economic impacts of decarbonising energy systems at a global level. The next chapter of this book focuses on a national perspective. The range of economic impacts is regionally dependent upon the stage of economic development, the level of industrialisation, energy intensity of exports, and competition effects due to rates of relative decarbonisation. Developed nation’s decarbonisation targets are estimated to result in a manageable GDP loss in the region of 2 % by 2050. Energy intensive export driven developing countries such as China and India, and fossil fuel exporting nations can expect significantly higher GDP loss of up to 5 % GDP per year by mid-century.
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