From habitat to management: a simulation framework for improving statistical methods in fisheries science

Monte Carlo simulation consists of computer experiments that involve creating data by pseudo-random sampling and has shown to be a powerful tool for studying the performance of statistical methods. In this thesis Monte Carlo simulation was used to improve statistical methodology related to three different fields of fisheries science: 1) Species distribution models (SDM) field, where focusing on regression-based models, we proposed using shape-constrained generalised additive models (SC-GAMs) to build SDMs in agreement with the ecological niche theory imposing concavity constraints in the linear predictor scale and testing their performance trough Monte Carlo simulation, 2) stock assessment models field, where uncertainty estimation methods for statistical catch-at-age models with non-parametric effects on fishing mortality were compared through simulation in addition to the comparison of two available stock assessment models to an ad-hoc Bayesian approach, and 3) management advice field, where a full-feedback management strategy evaluation (MSE) was developed for the sardine in the Bay of Biscay, incorporating the official Stoch Synthesis assessment model within the Monte Carlo simulation, and introducing gradually different sources of uncertainty such as process, parameter and observation error in order to study their effect in management advice. Monte Carlo simulation was an adequate tool to accomplish the objectives of this thesis that definitely could not have been achieved using only available real data or analytical solutions

Modelling species presence–absence in the ecological niche theory framework using shape-constrained generalized additive models

According to ecological niche theory, species response curves are unimodal with respect to environmental gradients. A variety of statistical methods have been developed for species distribution modelling. A general problem with most of these habitat modelling approaches is that the estimated response curves can display biologically implausible shapes which do not respect ecological niche theory. This work proposes using shapeconstrained generalized additive models (SC-GAMs) to build species distribution models under the ecological niche theory framework, imposing concavity constraints in the linear predictor scale. Based on a simulation study and a real data application, we compared performance with respect to other regression models without shape-constraints (such as standard GLMs and GAMs with varying degrees of freedom) and also to models based on so-called “Plateau” climate-envelopes. The imposition of concavity for response curves resulted in a good balance between the goodness of fit (GOF) and agreement with ecological niche theory. The approach has been applied to fit distribution models for three fish species given several environmental variables

Sequence, structure, and binding site analysis of kirkiin in comparison with ricin and other type 2 rips

Kirkiin is a new type 2 ribosome-inactivating protein (RIP) purified from the caudex of Adenia kirkii with a cytotoxicity compared to that of stenodactylin. The high toxicity of RIPs from Adenia genus plants makes them interesting tools for biotechnology and therapeutic applications, particularly in cancer therapy. The complete amino acid sequence and 3D structure prediction of kirkiin are here reported. Gene sequence analysis revealed that kirkiin is encoded by a 1572 bp open reading frame, corresponding to 524 amino acid residues, without introns. The amino acid sequence analysis showed a high degree of identity with other Adenia RIPs. The 3D structure of kirkiin preserves the overall folding of type 2 RIPs. The key amino acids of the active site, described for ricin and other RIPs, are also conserved in the kirkiin A chain. Sugar affinity studies and docking experiments revealed that both the 1α and 2γ sites of the kirkiin B chain exhibit binding activity toward lactose and D-galactose, being lower than ricin. The replacement of His246 in the kirkiin 2γ site instead of Tyr248 in ricin causes a different structure arrangement that could explain the lower sugar affinity of kirkiin with respect to ricin

Serum biomarkers and risk of hepatocellular carcinoma recurrence after liver transplantation

Liver transplantation (LT) is the only potentially curative treatment for selected patients with cirrhosis and hepatocellular carcinoma (HCC) who are not candidates for resection. When the Milan criteria are strictly applied, 75% to 85%of 3- to 4-year actuarial survival rates are achieved, but up to 20% of the patients experience HCC recurrence after transplantation. The Milan criteria are based on the preoperative tumor macromorphology, tumor size and number on computed tomography or magnetic resonance imaging that neither correlate well with posttransplant histological study of the liver explant nor accurately predict HCC recurrence after LT, since they do not include objective measures of tumor biology. Preoperative biological markers, including alpha-fetoprotein, desgamma- carboxiprothrombin or neutrophil-to-lymphocyte ratio and platelet-tolymphocyte ratio, can predict the risk for HCC recurrence after transplantation. These biomarkers have been proposed as surrogate markers of tumor differentiation and vascular invasion, with varied risk magnitudes depending on the defined cutoffs. Different studies have shown that the combination of one or several biomarkers integrated into prognostic models predict the risk of HCC recurrence after LT more accurately than Milan criteria alone. In this review, we focus on the potential utility of these serum biological markers to improve the performance of Milan criteria to identify patients at high risk of tumora

Isolation, Characterization and Biological Action of Type-1 Ribosome-Inactivating Proteins from Tissues of Salsola soda L

Ribosome-inactivating proteins (RIPs) are known as RNA N-glycosylases. They depurinate the major rRNA, damaging ribosomes and inhibiting protein synthesis. Here, new single-chain (type-1) RIPs named sodins were isolated from the seeds (five proteins), edible leaves (one protein) and roots (one protein) of Salsola soda L. Sodins are able to release Endo’s fragment when incubated with rabbit and yeast ribosomes and inhibit protein synthesis in cell-free systems (IC50 = 4.83–79.31 pM). In addition, sodin 5, the major form isolated from seeds, as well as sodin eL and sodin R, isolated from edible leaves and roots, respectively, display polynucleotide:adenosine glycosylase activity and are cytotoxic towards the Hela and COLO 320 cell lines (IC50 = 0.41–1200 nM), inducing apoptosis. The further characterization of sodin 5 reveals that this enzyme shows a secondary structure similar to other type-1 RIPs and a higher melting temperature (Tm = 76.03 ± 0.30 °C) and is non-glycosylated, as other sodins are. Finally, we proved that sodin 5 possesses antifungal activity against Penicillium digitatum

Demographic connectivity of sardine in the Bay of Biscay and Iberian coast region

Demographic connectivity in sardine populatio

Elderberry ( Sambucus Nigra ) Bark Contains two Structurally Different Neusac(Α2,6)Gal/Galnac-Binding Type 2 Ribosome-Inactivating Proteins

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65709/1/j.1432-1033.1997.00648.x.pd

Lifestyle Patterns and Weight Status in Spanish Adults: The ANIBES Study

Limited knowledge is available on lifestyle patterns in Spanish adults. We investigated dietary patterns and possible meaningful clustering of physical activity, sedentary behavior, sleep time, and smoking in Spanish adults aged 18–64 years and their association with obesity. Analysis was based on a subsample (n = 1617) of the cross-sectional ANIBES study in Spain. We performed exploratory factor analysis and subsequent cluster analysis of dietary patterns, physical activity, sedentary behaviors, sleep time, and smoking. Logistic regression analysis was used to explore the association between the cluster solutions and obesity. Factor analysis identified four dietary patterns, “Traditional DP”, “Mediterranean DP”, “Snack DP” and “Dairy-sweet DP”. Dietary patterns, physical activity behaviors, sedentary behaviors, sleep time, and smoking in Spanish adults aggregated into three different clusters of lifestyle patterns: “Mixed diet-physically active-low sedentary lifestyle pattern”, “Not poor diet-low physical activity-low sedentary lifestyle pattern” and “Poor diet-low physical activity-sedentary lifestyle pattern”. A higher proportion of people aged 18–30 years was classified into the “Poor diet-low physical activity-sedentary lifestyle pattern”. The prevalence odds ratio for obesity in men in the “Mixed diet-physically active-low sedentary lifestyle pattern” was significantly lower compared to those in the “Poor diet-low physical activity-sedentary lifestyle pattern”. Those behavior patterns are helpful to identify specific issues in population subgroups and inform intervention strategies. The findings in this study underline the importance of designing and implementing interventions that address multiple health risk practices, considering lifestyle patterns and associated determinants

Updating the Food-Based Dietary Guidelines for the Spanish Population: The Spanish Society of Community Nutrition (SENC) Proposal

Diet-related risk factors and physical inactivity are among the leading risk factors for disability and are responsible for a large proportion of the burden of chronic non-communicable diseases. Food-based dietary guidelines (FBDGs) are useful tools for nutrition policies and public health strategies to promote healthier eating and physical activity. In this paper, we discuss the process followed in developing the dietary guidelines for the Spanish population by the Spanish Society of Community Nutrition (SENC) and further explain the collaboration with primary healthcare practitioners as presented in the context of the NUTRIMAD 2018 international congress of SENC. From a health in all policies approach, SENC convened a group of experts in nutrition and public health to review the evidence on diet-health, nutrient intake and food consumption in the Spanish population, as well as food preparation, determinants and impact of diet on environmental sustainability. The collaborative group drafted the document and designed the graphic icon, which was then subject to a consultation process, discussion, and qualitative evaluation. Next, a collaborative group was established to plan a dissemination strategy, involving delegates from all the primary healthcare scientific societies in Spain. A product of this collaboration was the release of an attractive, easy-to-understand publication