Improving the predictive accuracy of production frontier models for efficiency measurement using machine learning:The LSB-MAFS method

Making accurate predictions of the true production frontier is critical for reliable efficiency analysis. However, canonical deterministic methods like Data Envelopment Analysis (DEA) provide approximations of the production frontier that cannot accommodate noise satisfactorily and suffer from overfitting. This study combines machine learning techniques known as Least Squares Boosting (LSB) and Multivariate Adaptive Regression Splines (MARS), to introduce a new methodology that improves the accuracy of production frontiers predictions and overcomes previous limitations. The new method fits pairwise regression splines to the data while ensuring that the predicted production frontiers satisfy certain the required regularity conditions: envelopmentness, monotonicity, and concavity. The method, termed LSB-MAFS, is implemented through computational algorithms, and we illustrate its applicability by performing simulations with several data generating processes. We also compare its performance against the most popular alternatives, considering both deterministic and stochastic scenarios: DEA, bootstrapped DEA, Corrected Concave Non-Parametric Least Squares (C2NLS) and Stochastic Frontier Analysis (SFA). The new method outperforms these alternatives in the most complex scenarios, including stochastic settings where parametric methods like SFA should perform better in principle. We conclude that our approach to production frontier prediction is a valid and competitive alternative for dependable efficiency analysis.</p

Impact of region-of-interest delineation methods, reconstruction algorithms, and intra- and inter-operator variability on internal dosimetry estimates using PET

Purpose Human dosimetry studies play a central role in radioligand development for positron emission tomography (PET). Drawing regions of interest (ROIs) on the PET images is used to measure the dose in each organ. In the study aspects related to ROI delineation methods were evaluated for two radioligands of different biodistribution (intestinal vs urinary). Procedures PET images were simulated from a human voxel-based phantom. Several ROI delineation methods were tested: antero-posterior projections (AP), 3D sub-samples of the organs (S), and a 3D volume covering the whole-organ (W). Inter- and intra-operator variability ROI drawing was evaluated by using human data. Results The effective dose estimates using S and W methods were comparable to the true values. AP methods overestimated (49 %) the dose for the radioligand with intestinal biodistribution. Moreover, the AP method showed the highest inter-operator variability: 11 ± 1 %. Conclusions The sub-sampled organ method showed the best balance between quantitative accuracy and inter- and intra-operator variability.Postprint (author's final draft

Correlation of Plasma Protein Carbonyls and C-Reactive Protein with GOLD Stage Progression in COPD Patients

Oxidative stress plays an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). To investigate the correlation between the progression of COPD and plasma biomarkers of chronic inflammation and oxidative injury, blood samples were obtained from healthy volunteers (HV, n = 14) and stabilized COPD patients. The patients were divided into three groups according to their GOLD stage (II, n = 34; III, n = 18; IV, n = 20). C-reactive protein (CRP), protein carbonyls (PC), malondialdehyde (MDA), susceptible lipoperoxidation of plasma substrates (SLPS), and myeloperoxidase activity (MPO) were measured. The plasma concentration of SLPS was measured as the amount of MDA generated by a metal ion-catalyzed reaction in vitro. PC, SLPS, and CPR were increased significantly (p < 0.001) in COPD patients when compared to HV. MDA concentrations and MPO activities were not significantly different from those of the HV group. In conclusion, increased oxidation of lipids and proteins resulting in a progressive increase in the amount of total plasma carbonyls and oxidative stress the presence of oxidative stress during COPD progression, concomitant with an increased oxidation of lipids and proteins resulting in a progressive and significant increase in the amount of total carbonyls formed from lipid-derived aldehydes and direct amino acid side chain oxidation in plasma, may serve as a biomarker and independent monitor of COPD progression and oxidative stress injury

Assessment of the economic performance of the seabream and seabass aquaculture industry in the European Union

Production of gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax) is the second most important aquaculture industry in the European Union in value terms. During the last 10 years, the industry has experienced a process of industry concentration with the aim to overcome efficiency and profitability issues. However, the economic performance of the companies is still in general rather poor. The present work analyzes the economic performance of EU seabream and seabass companies in the period 2008?2016. The work is the first study to analyze companies? profitability in the EU as a whole, by country and company size, using economic and financial data extracted from companies? annual accounts. Based on the results, the study discusses the improvement of production and business profitability in recent years and the different factors that may have caused it, as well as the challenges and threats that seabream and seabass companies will have to face in order to achieve economic sustainability.This research was undertaken under the MedAID project, which has received funding from the European Union's Horizon 2020 Research and Innovation Programme under grant agreement no 727315 (http://www.medaid-h2020.eu/)

PICH deficiency limits the progression of MYC-induced B-cell lymphoma

Plk1-interacting checkpoint helicase (PICH) is a DNA translocase involved in resolving ultrafine anaphase DNA bridges and, therefore, is important to safeguard chromosome segregation and stability. PICH is overexpressed in various human cancers, particularly in lymphomas such as Burkitt lymphoma, which is caused by MYC translocations. To investigate the relevance of PICH in cancer development and progression, we have combined novel PICH-deficient mouse models with the Eμ-Myc transgenic mouse model, which recapitulates B-cell lymphoma development. We have observed that PICH deficiency delays the onset of MYC-induced lymphomas in Pich heterozygous females. Moreover, using a Pich conditional knockout mouse model, we have found that Pich deletion in adult mice improves the survival of Eμ-Myc transgenic mice. Notably, we show that Pich deletion in healthy adult mice is well tolerated, supporting PICH as a suitable target for anticancer therapies. Finally, we have corroborated these findings in two human Burkitt lymphoma cell lines and we have found that the death of cancer cells was accompanied by chromosomal instability. Based on these findings, we propose PICH as a potential therapeutic target for Burkitt lymphoma and for other cancers where PICH is overexpressed.This work was supported by grants from Danish National Research Foundation (DNRF115), European Research Council (ERC-2015-STG-679068), the Spanish Ministry of Science and Innovation-Agencia Estatal de Investigacion (PID2020-119329RB-I00), the Novo Nordisk Foundation (NNF19OC0055203), and the Junta de Andalucía (P20_00755, PAIDI2020). M.C.-G. was supported with a postdoctoral fellowship from the Junta de Andalucía and the European Social Fund (202099908313734) and with a postdoctoral “Juan de la Cierva” fellowship from the MICINN (FJC2020-045915-I). D.P.-M. was supported with a PhD scholarship from the Lundbeck Foundation (R218-2016-415). L.S.-C. was supported with a Postdoctoral Research Contract from the AECC Scientific Foundation (Grant Number POSTD211274SIMÓ). P.A. was supported with a postdoctoral fellowship from the Junta de Andalucía and the European Social Fund (202099908313486). A.G. is funded with a PhD fellowship from the Junta de Andalucía. E.P. is supported by the HORIZON-MSCA ITN RepliFate (101072903). We thank Prof. Fernandez-Capetillo for kindly providing human lymphoma cell lines. We thank Patricia González from the CNIO Histopathology Core Unit, Irene Delgado, and Alexandra Avram for technical support.Peer reviewe

Novel genes and sex differences in COVID-19 severity

[EN] Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10−8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10−22 and P = 8.1 × 10−12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10−8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10−8) and ARHGAP33 (P = 1.3 × 10−8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10−8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.S

Characterization of Profilin Polymorphism in Pollen with a Focus on Multifunctionality

Profilin, a multigene family involved in actin dynamics, is a multiple partners-interacting protein, as regard of the presence of at least of three binding domains encompassing actin, phosphoinositide lipids, and poly-L-proline interacting patches. In addition, pollen profilins are important allergens in several species like Olea europaea L. (Ole e 2), Betula pendula (Bet v 2), Phleum pratense (Phl p 12), Zea mays (Zea m 12) and Corylus avellana (Cor a 2). In spite of the biological and clinical importance of these molecules, variability in pollen profilin sequences has been poorly pointed out up until now. In this work, a relatively high number of pollen profilin sequences have been cloned, with the aim of carrying out an extensive characterization of their polymorphism among 24 olive cultivars and the above mentioned plant species. Our results indicate a high level of variability in the sequences analyzed. Quantitative intra-specific/varietal polymorphism was higher in comparison to inter-specific/cultivars comparisons. Multi-optional posttranslational modifications, e.g. phosphorylation sites, physicochemical properties, and partners-interacting functional residues have been shown to be affected by profilin polymorphism. As a result of this variability, profilins yielded a clear taxonomic separation between the five plant species. Profilin family multifunctionality might be inferred by natural variation through profilin isovariants generated among olive germplasm, as a result of polymorphism. The high variability might result in both differential profilin properties and differences in the regulation of the interaction with natural partners, affecting the mechanisms underlying the transmission of signals throughout signaling pathways in response to different stress environments. Moreover, elucidating the effect of profilin polymorphism in adaptive responses like actin dynamics, and cellular behavior, represents an exciting research goal for the future

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications

Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425 and PI19/00321), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), European Regional Development Fund (FEDER), the Organización Nacional de Ciegos Españoles (ONCE), Fundación Ramón Areces, Fundación Conchita Rábago and the University Chair UAM-IIS-FJD of Genomic Medicine. Irene Perea-Romero is supported by a PhD fellowship from the predoctoral Program from ISCIII (FI17/00192). Ionut F. Iancu is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017-AI/BMD7256). Marta del Pozo-Valero is supported by a PhD grant from the Fundación Conchita Rábago. Berta Almoguera is supported by a Juan Rodes program from ISCIII (JR17/00020). Pablo Minguez is supported by a Miguel Servet program from ISCIII (CP16/00116). Marta Corton is supported by a Miguel Servet program from ISCIII (CPII17/00006). The funders played no role in study design, data collection, data analysis, manuscript preparation and/or publication decisions