Browsing by Issue Date, starting with "2023-08"
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- Estimating fishing effort in small-scale fisheries using high-resolution spatio-temporal tracking data (an implementation framework illustrated with case studies from Portugal)Publication . Rufino, Marta M.; Mendo, Tania; Samarão, João; Gaspar, MiguelSmall-scale fisheries (SSF, boats < 12 m) represent 90% of this sector at a worldwide scale and 84% of the EU fleet. Mapping the areas and intensity where the fishing operations occur is essential for spatial planning, safety, fisheries sustainability and biodiversity conservation. The EU is currently regulating position tracking of SSF fishing vessels requiring precision resolved geo-positional data (sec to min resolution).Here we developed a series of procedures aimed at categorizing fishing boats behaviour using high resolution data. Our integrated approach involve novel routines aimed at (i) produce an expert validated data set, (ii) pre-processing of positional data, (iii) establishing minimal required temporal resolution, and (iv) final assessment of an optimized classification model. Objective (iv) was implemented by using statistical and machine learning (ML) routines, using novel combinations of fixed thresholds estimates using regression trees and classification methods based on anti-mode, Gaussian Mixture Models (GMM), Expectation Maximisation (EM) algorithms, Hidden Markov Models (HMM) and Random Forest (RF). Of relevance, the final evaluation framework in-corporates both error quantification and fishing effort indicators. We tested the method by running through four SSF fisheries from Portugal recorded every 30 sec, with 183 boat trips validated, and concluded that the more robust time interval for data acquisition in these metiers should be <2 min and that mode and random forest methods with pre-data treatment gave the best results. A special effort was concentrated in a visual support provided by the results produced by this new method, making its interpretation easier, thus facilitating trans-ference and translation into other fishery levels. After the current validation in the Portuguese SSF fleet, we posit that our novel procedure has the potential to serve as an integrated quantitative approach to the EU SSF management.
- Data-specific substitution models improve protein-based phylogeneticsPublication . Brazão, João; Foster, Peter G.; J. Cox, CymonCalculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses.
- Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheriesPublication . Najafpour, Babak; Pinto, Patricia IS; Sanz, Eric Climent; Martinez-Blanch, Juan F.; Canario, Adelino; Moutou, Katerina A.; Power, Deborah16S rRNA gene sequencing and bacteria-and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalter-omonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
- The water culture of the Order of Christ in the making of a self-sufficient and sustainable hydric systemPublication . Rodrigues, Ana Duarte; Batista, Desidério; Marques, Clara; García-Pereda, Ignacio; Puga, JoãoFocusing on the Convent of Christ in Portugal, this article presents an overview of the power and control exercised by the Order of Christ over the territory's water management, inside the monastic enclosure and over the Nabao River, from the late fifteenth century until the nineteenth century. Based on multi-interdisci-plinary methodologies, we argue that the monastic enclosure was multi-functional, sus-tainable, self-sufficient and the stage for the most sophisticated hydraulic system of early modern Portugal. Following a recent review, and based on archival research, a 3D re-construction and mapping tools, we demonstrate that the system did not work exclusively through gravity. In an early phase, pumps were in use at the Convent of Christ circa 1537 to remove water from cisterns in a technology transferred from ships into gardens. Moreover, this article also reveals the total control of the Order wielded over the Nabao as a source of energy through to the abolition of Religious Orders in 1834.
- A systematic literature review of climate change research on Europe's threatened commercial fish speciesPublication . Predragovic, Milica; Cvitanovic, Christopher; Karcher, Denis B.; Tietbohl, Matthew D.; Sumaila, U. Rashid; Horta E Costa, BarbaraClimate change poses a major challenge for global marine ecosystems and species, leading to a wide range of biological and social-ecological impacts. Fisheries are among the well-known sectors influenced by multiple effects of climate change, with associated impacts highly variable among species and regions. To successfully manage fisheries, scientific evidence about the potential direct and indirect impacts of climate change on the species targeted by fisheries is needed to inform decision-making processes. This is particularly pertinent for fisheries within European seas, as they include some of the fastest warming water bodies globally, and are thus experiencing some of the greatest impacts. Here, we systematically examine the existing scientific climate-related literature of 68 species that are both commercially important in European seas and considered threatened ac-cording to the IUCN Red List to understand the extent of information that is available to inform fisheries management and identify critical knowledge gaps that can help to direct future research effort. We also explore the climate and fishing vulnerability indices of species as potential drivers of current scientific attention. We found no literature for most of these species (n = 45), and for many others (n = 19) we found fewer than five papers studying them. Climate change related research was dominated by a few species (i.e., Atlantic salmon, European pilchard, and Atlantic bluefin tuna) and regions, such as the Northeast Atlantic, revealing a highly uneven distribution of research efforts across European seas. Most studies were biologically focused and included how abundance, distribution, and physiology may be affected by warming. Few studies incorporated some level of social-ecological information. Moreover, it appears that research on species with high climate and fishing vulnerabilities is not currently prioritized. These results highlight a gap in our understanding of how climate change can impact already threatened species and the people who depend on them for food and income. Our findings also suggest that future climate-specific adaptation measures will likely suffer from a lack of robust information. More research is needed to include all the species from our list, their relevant geographic regions, and subsequent biological and social-ecological implications.
- A continuous characterization of PSPACE using polynomial ordinary differential equationsPublication . Bournez, Olivier; Gozzi, Riccardo; Graça, Daniel; Pouly, AmauryIn this paper we provide a characterization of the complexity class PSPACE by using a purely continuous model defined with polynomial ordinary differential equations.
- R2CHA2DS2-VA predictsthe cardiovascular risk after carotid endarterectomyPublication . Quesado, João; Dias, Lara; Pereira-Macedo, Juliana; Duarte-Gamas, Luís; Khairy, Ahmed; Pinheiro, Marina; Reis, Pedro; Andrade, José P.; Rocha-Neves, João; Marreiros, AnaBackground: R2CHA2DS2-VA score has been used to predict short and long-term outcomes in many cardiovascular diseases. This study aims to validate the R2CHA2DS2-VA score as a long-term major adverse cardiovascular events (MACE) predictor after carotid endarterectomy (CEA). Secondary outcomes were also assessed regarding the incidence of all-cause mortality, acute myocardial infarction (AMI), major adverse limb events (MALE), and acute heart failure (AHF).Methods: From January 2012 to December 2021, patients (n 1/4 205) from a Portuguese tertiary care and referral center that underwent CEA with regional anesthesia (RA) for carotid stenosis (CS) were selected from a previously collected prospective database, and a posthoc analysis was performed. Demographics and comorbidities were registered. Clinical adverse events were assessed 30 days after the procedure and in the subsequent long-term surveillance period. Statistical analysis was performed by the Kaplan-Meier method and Cox proportional hazards regression.Results: Of the patients enrolled, 78.5% were males with a mean age of 70.44 & PLUSMN; 8.9 years. Higher scores of R2CHA2DS2-VA were associated with long-term MACE (adjusted hazard ratio (aHR) 1.390; 95% confidence interval (CI) 1.173-1.647); and mortality (aHR 1.295; 95% CI 1.08-1.545). Conclusions: This study demonstrated the potential of the R2CHA2DS2-VA score to predict long-term outcomes, such as AMI, AHF, MACE, and all-cause mortality, in a population of pa-tients submitted to carotid endarterectomy.
- Socio-emotional skills profiles and their relations with career exploration and perceived parental support among 8th grade studentsPublication . Gamboa, Vítor; Rodrigues, Suzi; Bértolo, Filipa; Marcelo, Beatriz; Paixão, OlímpioSocio-emotional skills can play a crucial role in students career development. This study used a person-centered approach to explore socio-emotional skills (curiosity, optimism, empathy, sociability, and responsibility) profiles among 8 degrees grade students (N = 310). We also explored the relations of these profiles with career exploration (self and environmental), perceived parental support (emotional support, instrumental assistance, career-related modeling, and verbal encouragement) and school achievement. Using Latent Profile Analysis (LPA), four distinct profiles emerged that differed in terms of level and shape, namely: Other and Task oriented profile, Socio-emotional Adaptive profile, Socio-emotional non-Adaptive profile, Self- Oriented profile. Our results show that the "Socio-emotional Adaptive" profile can be clearly differentiated from the "Socio-emotional non-Adaptive" profile given the higher values it presents regarding all the variables in study. However, the differences between the "Other and Task Oriented" profile and "Self-Oriented" profile (intermediate profiles) were analyzed and discussed from qualitative point-of-view and adopting an exploratory approach. Overall, the findings of this study indicate that socio-emotional profiles have the potential to account for variations in career behaviors and academic performance. These results provide valuable insights for the development and implementation of career-oriented interventions targeted at 8th grade students and their immediate relational environments.
- From the molecular hallmarks to motor behavior: characterization of a new transgenic mouse model for spinocerebellar ataxia type 2Publication . Afonso, Inês T.; Koppenol, Rebekah; Conceição, André; Paulino, Rodrigo; Mirapalheta, Lourenzo; Matos, Carlos A; Nóbrega, ClévioSpinocerebellar ataxia type 2 (SCA2) is a rare disease with no cure, and therefore patients depend on symptomatic and supportive treatments. It is a highly debilitating disease affecting predominantly the brain with symptoms that include motor and coordination impairment. SCA2 is caused by an abnormal expansion of the CAG triplet in the coding region of the ATXN2 gene. When it has above 33 CAG repeats, it originates a protein with an abnormally expanded glutamine tract. The mutant protein impairs several cellular functions, leading to neuronal degeneration and death. Several rodent models were developed to study the neuropathology and potential therapies for SCA2. However, most of them fail to mimic a complete SCA2 phenotype, taking too long to develop diseaserelated symptoms or failing to display neuronal-associated deficits.
- Towards a global Fishing Vessel Ocean Observing Network (FVON): state of the art and future directionsPublication . Van Vranken, Cooper; Jakoboski, Julie; Carroll, John W.; Cusack, Christopher; Gorringe, Patrick; Hirose, Naoki; Manning, James; Martinelli, Michela; Penna, Pierluigi; Pickering, Mathew; Santos, A. Miguel P.; Roughan, Moninya; de Souza, João; Moustahfid, HassanOcean observations are the foundation of our understanding of ocean processes. Improving these observations has critical implications for our ability to sustainably derive food from the ocean, predict extreme weather events that take a toll on human life, and produce the goods and services that are needed to meet the needs of a vast and growing population. While there have been great leaps forward in sustained operational monitoring of our oceans there are still key data gaps which result in sub-optimal ocean management and policy decisions. The global fishing industry represents a vast opportunity to create a paradigm shift in how ocean data are collected: the spatio-temporal extent of ocean data gaps overlaps significantly with fishers' activities; fishing vessels are suitable platforms of opportunity to host communications and sensor equipment; and many fishing vessels effectively conduct a depth-profile through the water column in the course of normal fishing activities, representing a powerful subsurface data collection opportunity. Fishing vessel-collected ocean data can complement existing ocean observing networks by enabling the cost-effective collection of vast amounts of subsurface ocean information in data-sparse regions. There is an emerging global network of fishing vessels participating in collaborative efforts to collect oceanographic data accelerated by innovations in enabling technologies. While there are clear opportunities that arise from partnering with fishing vessels, there are also challenges ranging from geographic and cultural differences in fleets, fishing methods and practices, data processing and management for heterogeneous data, as well as long term engagement of the fishers. To advance fishing vessel-based ocean observation on a global scale, the Fishing Vessel Ocean Observing Network (FVON) aims to maximize data value, establish best practices around data collection and management, and facilitate observation uptake. FVON's ultimate goals are to foster collaborative fishing vessel-based observations, democratize ocean observation, improve ocean predictions and forecasts, promote sustainable fishing, and power a data-driven blue economy.