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1.	López-Isac, Elena, et al. (author) Brief Report : IRF4 Newly Identified as a Common Susceptibility Locus for Systemic Sclerosis and Rheumatoid Arthritis in a Cross-Disease Meta-Analysis of Genome-Wide Association Studies 2016 In: Arthritis & Rheumatology. - : Wiley. - 2326-5191 .- 2326-5205. ; 68:9, s. 2338-2344 Journal article (peer-reviewed)abstract Objective: Systemic sclerosis (SSc) and rheumatoid arthritis (RA) are autoimmune diseases that have similar clinical and immunologic characteristics. To date, several shared SSc–RA genetic loci have been identified independently. The aim of the current study was to systematically search for new common SSc–RA loci through an interdisease meta–genome-wide association (meta-GWAS) strategy. Methods: The study was designed as a meta-analysis combining GWAS data sets of patients with SSc and patients with RA, using a strategy that allowed identification of loci with both same-direction and opposite-direction allelic effects. The top single-nucleotide polymorphisms were followed up in independent SSc and RA case–control cohorts. This allowed an increase in the sample size to a total of 8,830 patients with SSc, 16,870 patients with RA, and 43,393 healthy controls. Results: This cross-disease meta-analysis of the GWAS data sets identified several loci with nominal association signals (P < 5 × 10−6) that also showed evidence of association in the disease-specific GWAS scans. These loci included several genomic regions not previously reported as shared loci, as well as several risk factors that were previously found to be associated with both diseases. Follow-up analyses of the putatively new SSc–RA loci identified IRF4 as a shared risk factor for these 2 diseases (Pcombined = 3.29 × 10−12). Analysis of the biologic relevance of the known SSc–RA shared loci identified the type I interferon and interleukin-12 signaling pathways as the main common etiologic factors. Conclusion: This study identified a novel shared locus, IRF4, for the risk of SSc and RA, and highlighted the usefulness of a cross-disease GWAS meta-analysis strategy in the identification of common risk loci.
2.	Abolfathi, Bela, et al. (author) The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment 2018 In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2 Journal article (peer-reviewed)abstract The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
3.	Axfors, Cathrine, et al. (author) Association between convalescent plasma treatment and mortality in COVID-19 : a collaborative systematic review and meta-analysis of randomized clinical trials 2021 In: BMC Infectious Diseases. - : BioMed Central (BMC). - 1471-2334. ; 21:1 Research review (peer-reviewed)abstract Background: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, ). Methods: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. Results: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I-2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. Conclusions: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care.
4.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
5.	Blanton, Michael R., et al. (author) Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe 2017 In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1 Journal article (peer-reviewed)abstract We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
6.	Carraminana, Albert, et al. (author) Rationale and Study Design for an Individualized Perioperative Open Lung Ventilatory Strategy in Patients on One-Lung Ventilation (iPROVE-OLV) 2019 In: Journal of Cardiothoracic and Vascular Anesthesia. - : W B SAUNDERS CO-ELSEVIER INC. - 1053-0770 .- 1532-8422. ; 33:9, s. 2492-2502 Journal article (peer-reviewed)abstract Objective: The aim of this clinical trial is to examine whether it is possible to reduce postoperative complications using an individualized perioperative ventilatory strategy versus using a standard lung-protective ventilation strategy in patients scheduled for thoracic surgery requiring one-lung ventilation. Design: International, multicenter, prospective, randomized controlled clinical trial. Setting: A network of university hospitals. Participants: The study comprises 1,380 patients scheduled for thoracic surgery. Interventions: The individualized group will receive intraoperative recruitment maneuvers followed by individualized positive end-expiratory pressure (open lung approach) during the intraoperative period plus postoperative ventilatory support with high-flow nasal cannula, whereas the control group will be managed with conventional lung-protective ventilation. Measurements and Main Results: Individual and total number of postoperative complications, including atelectasis, pneumothorax, pleural effusion, pneumonia, acute lung injury; unplanned readmission and reintubation; length of stay and death in the critical care unit and in the hospital will be analyzed for both groups. The authors hypothesize that the intraoperative application of an open lung approach followed by an individual indication of high-flow nasal cannula in the postoperative period will reduce pulmonary complications and length of hospital stay in high-risk surgical patients. (C) 2019 Published by Elsevier Inc.
7.	Fernandez-Verdejo, Rodrigo, et al. (author) Deciphering the constrained total energy expenditure model in humans by associating accelerometer-measured physical activity from wrist and hip 2021 In: Scientific Reports. - : Nature Research. - 2045-2322. ; 11:1 Journal article (peer-reviewed)abstract The constrained total energy expenditure (TEE) model posits that progressive increases in physical activity (PA) lead to increases in TEE; but after certain PA threshold, TEE plateaus. Then, a compensatory reduction in the expenditure of non-essential activities constrains the TEE. We hypothesized that high PA levels as locomotion associate with a compensatory attenuation in arm movements. We included 209 adults (64% females, mean [SD] age 32.1 [15.0] years) and 105 children (40% females, age 10.0 [1.1] years). Subjects wore, simultaneously, one accelerometer in the non-dominant wrist and another in the hip for >= 4 days. We analyzed the association between wrist-measured (arm movements plus locomotion) and hip-measured PA (locomotion). We also analyzed how the capacity to dissociate arm movements from locomotion influences total PA. In adults, the association between wrist-measured and hip-measured PA was better described by a quadratic than a linear model (Quadratic-R-2=0.54 vs. Linear-R-2=0.52; P=0.003). Above the 80th percentile of hip-measured PA, wrist-measured PA plateaued. In children, there was no evidence that a quadratic model fitted the association between wrist-measured and hip-measured PA better than a linear model (R-2=0.58 in both models, P=0.25). In adults and children, those with the highest capacity to dissociate arm movements from locomotion-i.e. higher arm movements for a given locomotion-reached the highest total PA. We conclude that, in adults, elevated locomotion associates with a compensatory reduction in arm movements (probably non-essential fidgeting) that partially explains the constrained TEE model. Subjects with the lowest arm compensation reach the highest total PA.
8.	Acevedo-Prado, Antonio, et al. (author) Association of rhinitis with asthma prevalence and severity 2022 In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1 Journal article (peer-reviewed)abstract Asthma and rhinitis often co-exist in the same patient. Although some authors observed a higher prevalence and/or greater severity of asthma in patients with rhinitis, this view is not homogeneous and the debate continues. The aim of our study is to describe the prevalence of rhinitis in children and adolescents and to analyse their relationship with the prevalence of asthma. A multicentre study was conducted using the methodology of the International Study of Asthma and Allergies in Childhood (ISAAC). The target population of the study was all those school children aged 6–7 and 13–14 years from 6 of the main health catchment areas of Galicia (1.9 million inhabitants). The schools required were randomly selected, and all children in the targeted age ranges were included. Multiple logistic regression was used to obtain adjusted prevalence odds ratios (OR) between asthma symptoms of the schoolchildren and rhinitis prevalence. The results were adjusted for parental smoking habits, maternal education level, cat and dog exposure, and obesity. A total of 21,420 valid questionnaires were finally obtained. Rhinitis was associated with a significant increase in the prevalence of asthma in both age groups. The highest OR were 11.375 for exercise induced asthma (EIA) for children with recent rhinoconjunctivitis and 9.807 for children with recent rhinitis in 6–7 years old group. The prevalence OR’s are higher in EIA and severe asthmatics. Rhinitis in children and adolescents is associated with a higher prevalence and severity of asthma.
9.	Ademuyiwa, Adesoji O., et al. (author) Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries 2016 In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4 Journal article (peer-reviewed)abstract Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
10.	Ahuja-Jensen, Poonam, et al. (author) Low glutathione peroxidase in rdl mouse retina increases oxidative stress and proteases 2007 In: NeuroReport. - 1473-558X. ; 18:8, s. 797-801 Journal article (peer-reviewed)abstract Malondialdehyde, reduced glutathione, glutathione peroxidase, glutathione reductase and cysteine protease cathepsins at postnatal (PN) days 2, 7, 14, 21 and 28 in controls (wt) and the retinal degeneration 1 (rd1) mouse model for retinitis pigmentosa retinas were measured to determine oxidative stress. In PN28 wt and PN2 rd1 retinas, elevated malondialdehyde and low glutathione peroxidase activity indicate higher oxidative load, despite higher reduced glutathione in PN2 rd1 retinas. This is due to physiological exposure to light and retinal vascular/neural restructuring, respectively. Compared with wt retinas, relatively high malondialdehyde at PN2 and cathepsin levels at PN14, 21 and 28 in rd1 retinas indicate that cells of the residual inner retina also contribute to the oxidative stress and retinal degeneration.
11.	Almanza-Aguilera, Enrique, et al. (author) Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women 2018 In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3907 .- 1535-3893. ; 17:8, s. 2600-2610 Journal article (peer-reviewed)abstract Little is known regarding metabolic benefits of weight loss (WL) on the metabolically healthy obese (MHO) patients. We aimed to examine the impact of a lifestyle weight loss (LWL) treatment on the plasma metabolomic profile in MHO individuals. Plasma samples from 57 MHO women allocated to an intensive LWL treatment group (TG, hypocaloric Mediterranean diet and regular physical activity, n = 30) or to a control group (CG, general recommendations of a healthy diet and physical activity, n = 27) were analyzed using an untargeted1H NMR metabolomics approach at baseline, after 3 months (intervention), and 12 months (follow-up). The impact of the LWL intervention on plasma metabolome was statistically significant at 3 months but not at follow-up and included higher levels of formate and phosphocreatine and lower levels of LDL/VLDL (signals) and trimethylamine in the TG. These metabolites were also correlated with WL. Higher myo-inositol, methylguanidine, and 3-hydroxybutyrate, and lower proline, were also found in the TG; higher levels of hippurate and asparagine, and lower levels of 2-hydroxybutyrate and creatine, were associated with WL. The current findings suggest that an intensive LWL treatment, and the consequent WL, leads to an improved plasma metabolic profile in MHO women through its impact on energy, amino acid, lipoprotein, and microbial metabolism.
12.	Amara-Gahete, Francisco J, et al. (author) Energy expenditure differences across lying,sitting, and standing positions in younghealthy adults 2019 In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14:7 Journal article (peer-reviewed)abstract The time spent in sedentary behaviour represents an important public health burden. Toreduce sedentary time in the general population, the simplest, most effective, and mostaccessible method is to decrease lying and sitting time. We aimed to compare differenceson energy expenditure (EE) across lying, sitting, and standing positions; and to analyse theassociations between the change on EE of changing from one position to another andanthropometric and body composition parameters in young healthy adults. A total of 55(69% women) young healthy adults aged 21.7 ± 2.2 participated in the study. We measuredEE by indirect calorimetry across lying, sitting, and standing positions following the standardprocedures. The EE was significantly higher in standing than in both lying and sitting positions(mean difference: 0.121±0.292 and 0.125±0.241 kcal/min, respectively; all P<0.001),and no differences were observed between lying and sitting positions (P = 1.000). Therewas a negative association between the EE differences in sitting vs. standing position andlean body mass (P = 0.048), yet no associations between EE differences with the rest of theanthropometric and body composition parameters were observed in each position pair studied(all P>0.321). Our findings support the fact that increasing the time spent standing couldbe a simple strategy to slightly increase EE. Therefore, our results have important clinicalimplications including a better monitoring, characterizing, and promoting countermeasuresto sedentariness through low-level physical activities.
13.	Antelius, Mikael, et al. (author) A photonic dye-based sensing system on a chip produced at wafer scale Journal article (other academic/artistic)
14.	Antelius, Mikael, et al. (author) A wafer-scale, dye-based, photonic sensing system Other publication (other academic/artistic)
15.	Aparicio, Francisco J., et al. (author) Dye-based photonic sensing systems 2016 In: Sensors and actuators. B, Chemical. - : Elsevier. - 0925-4005 .- 1873-3077. ; 228, s. 649-657 Journal article (peer-reviewed)abstract We report on dye-based photonic sensing systems which are fabricated and packaged at wafer scale. For the first time luminescent organic nanocomposite thin-films deposited by plasma technology are integrated in photonic sensing systems as active sensing elements. The realized dye-based photonic sensors include an environmental NO2 sensor and a sunlight ultraviolet light (UV) A+B sensor. The luminescent signal from the nanocomposite thin-films responds to changes in the environment and is selectively filtered by a photonic structure consisting of a Fabry-Perot cavity. The sensors are fabricated and packaged at wafer-scale, which makes the technology viable for volume manufacturing. Prototype photonic sensor systems have been tested in real-world scenarios. (C) 2016 Elsevier B.V. All rights reserved.
16.	Aparicio, Francisco J., et al. (author) Transparent Nanometric Organic Luminescent Films as UV-Active Components in Photonic Structures 2011 In: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 23:6, s. 761-765 Journal article (peer-reviewed)abstract A new kind of visible-blind organic thin-film material, consisting of a polymeric matrix with a high concentration of embedded 3-hydroxyflavone (3HF) dye molecules, that absorbs UV light and emits green light is presented. The thin films can be grown on sensitive substrates, including flexible polymers and paper. Their suitability as photonic active components in photonic devices is demonstrated.
17.	Arias, M. C., et al. (author) Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013 2013 In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 13:4, s. 760-762 Journal article (peer-reviewed)abstract This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.
18.	Arun, K. G., et al. (author) New horizons for fundamental physics with LISA 2022 In: Living Reviews in Relativity. - : Springer Science and Business Media LLC. - 1433-8351 .- 2367-3613. ; 25:1 Research review (peer-reviewed)abstract The Laser Interferometer Space Antenna (LISA) has the potential to reveal wonders about the fundamental theory of nature at play in the extreme gravity regime, where the gravitational interaction is both strong and dynamical. In this white paper, the Fundamental Physics Working Group of the LISA Consortium summarizes the current topics in fundamental physics where LISA observations of gravitational waves can be expected to provide key input. We provide the briefest of reviews to then delineate avenues for future research directions and to discuss connections between this working group, other working groups and the consortium work package teams. These connections must be developed for LISA to live up to its science potential in these areas.
19.	Attia, Zachi I., et al. (author) Rapid Exclusion of COVID Infection With the Artificial Intelligence Electrocardiogram 2021 In: Mayo Clinic proceedings. - : ELSEVIER SCIENCE INC. - 0025-6196 .- 1942-5546. ; 96:8, s. 2081-2094 Journal article (peer-reviewed)abstract Objective: To rapidly exclude severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using artificial intelligence applied to the electrocardiogram (ECG). Methods: A global, volunteer consortium from 4 continents identified patients with ECGs obtained around the time of polymerase chain reaction-confirmed COVID-19 diagnosis and age- and sex-matched controls from the same sites. Clinical characteristics, polymerase chain reaction results, and raw electrocardiographic data were collected. A convolutional neural network was trained using 26,153 ECGs (33.2% COVID positive), validated with 3826 ECGs (33.3% positive), and tested on 7870 ECGs not included in other sets (32.7% positive). Performance under different prevalence values was tested by adding control ECGs from a single high-volume site. Results: The area under the curve for detection of acute COVID-19 infection in the test group was 0.767 (95% CI, 0.756 to 0.778; sensitivity, 98%; specificity, 10%; positive predictive value, 37%; negative predictive value, 91%). To more accurately reflect a real-world population, 50,905 normal controls were added to adjust the COVID prevalence to approximately 5% (2657/58,555), resulting in an area under the curve of 0.780 (95% CI, 0.771 to 0.790) with a specificity of 12.1% and a negative predictive value of 99.2%. Conclusion: Infection with SARS-CoV-2 results in electrocardiographic changes that permit the artificial intelligence-enhanced ECG to be used as a rapid screening test with a high negative predictive value (99.2%). This may permit the development of electrocardiography-based tools to rapidly screen individuals for pandemic control. (C) 2021 Mayo Foundation Medical Education and Research
20.	Barber, Ramón, et al. (author) A Multirobot System in an Assisted Home Environment to Support the Elderly in Their Daily Lives 2022 In: Sensors. - : MDPI. - 1424-8220. ; 22:20 Journal article (peer-reviewed)abstract The increasing isolation of the elderly both in their own homes and in care homes has made the problem of caring for elderly people who live alone an urgent priority. This article presents a proposed design for a heterogeneous multirobot system consisting of (i) a small mobile robot to monitor the well-being of elderly people who live alone and suggest activities to keep them positive and active and (ii) a domestic mobile manipulating robot that helps to perform household tasks. The entire system is integrated in an automated home environment (AAL), which also includes a set of low-cost automation sensors, a medical monitoring bracelet and an Android application to propose emotional coaching activities to the person who lives alone. The heterogeneous system uses ROS, IoT technologies, such as Node-RED, and the Home Assistant Platform. Both platforms with the home automation system have been tested over a long period of time and integrated in a real test environment, with good results. The semantic segmentation of the navigation and planning environment in the mobile manipulator for navigation and movement in the manipulation area facilitated the tasks of the later planners. Results about the interactions of users with the applications are presented and the use of artificial intelligence to predict mood is discussed. The experiments support the conclusion that the assistance robot correctly proposes activities, such as calling a relative, exercising, etc., during the day, according to the user's detected emotional state, making this is an innovative proposal aimed at empowering the elderly so that they can be autonomous in their homes and have a good quality of life.
21.	Bautista, Rocío, et al. (author) Toward a Pinus pinaster bacterial artificial chromosome library 2007 In: Annals of Forest Science. - : Springer Science and Business Media LLC. - 1286-4560 .- 1297-966X. ; 64:8, s. 855-864 Journal article (peer-reviewed)abstract Conifers are of great economic and ecological importance, but little is known concerning their genomic organization. This study is an attempt to obtain high-quality high-molecular-weight DNA from Pinus pinaster cotyledons and the construction of a pine BAC library. The preparation incorporates modifications like low centrifugation speeds, increase of EDTA concentration for plug maintenance, use of DNase inhibitors to reduce DNA degradation, use of polyvinylpyrrolidone and ascorbate to avoid secondary metabolites, and a brief electrophoresis of the plugs prior to their use. A total of 72 192 clones with an average insert size of 107 kb, which represents an equivalent of 11X pine haploid genomes, were obtained. The proportions of clones lacking inserts or containing chloroplast DNA are both approximately 1.6%. The library was screened with cDNA probes for seven genes, and two clones containing Fd-GOGAT sequences were found, one of them seemingly functional. Ongoing projects aimed at constructing a pinebacterial artificial chromosome library may benefit from the methods described here.
22.	Bender, Anke, et al. (author) A Review of Methods and Models for Environmental Monitoring of Marine Renewable Energy 2017 In: Proceedings of the 12th European Wave and Tidal Energy Conference. - : EWTEC. Conference paper (peer-reviewed)abstract A continued expansion of the marine renewable energy sector will result in an increased demand in monitoring the natural marine environment. This may be due to a basic scientific interest but is foremost linked to the requirement of pre- and post-construction studies in relation to environmental impact assessments and consenting processes for marine renewable energy projects. With focus on wave and tidal power, but without attempting to provide a comprehensive list, we review methods, technologies and other scientific tools used for monitoring and predicting possible impacts from marine energy installations, on both population and behavioural levels. This includes traditional methods such as fishing gear, like nets and cages, modern technologies such as platforms with multi parameter equipment and the use of deterministic models. This paper is intended to serve as an overview for technology developers as well as authorities, regulators and decision makers with interests in general techniques, and naturally for scientists and consultants commonly being executors of studies and monitoring programs. By giving relevant and up to date references this paper may also be useful for finding more detailed information on study methods and variants. Finally, we give recommendations on where development of technologies is needed in order to face future requirements.
23.	Bender, Anke, et al. (author) Imaging-sonar observations of salmonid interactions with a vertical axis instream turbine 2023 In: Rivers Research and Applications. - : John Wiley & Sons. - 1535-1459 .- 1535-1467. Journal article (peer-reviewed)abstract Anthropogenic activities and their influences on aquatic systems is an important topic, especially considering the growing interest in using the earth's resources in a sustainable way. One of those anthropogenic activities is the introduction of renewable technologies into the aquatic environment such as instream turbines. Environmental studies around those technologies are often still ongoing due to their novelty. During the spring of 2018, juvenile individuals of two salmonid species, Atlantic salmon and brown trout were released upstream a vertical axis instream turbine in the river Dal (Dalälven) in eastern Sweden. The aim of this study was to investigate the swimming behavior of the salmonids around a small-scale prototype vertical axis instream turbine. The swimming pattern and the possible response of avoiding the vertical axis instream turbine were documented with a multi beam sonar. A control area, next to the turbine, was used as reference. No consistent results were shown for trout as they were passing the control area with a statistically high variation, and specimens were rarely observed in proximity of the turbine, neither if the turbine was operating nor at stand still. Salmon clearly avoided the operating turbine, but did not avoid the turbine when it was at stand still, and was often observed swimming straight through the turbine area. These findings indicate that operating this type of instream turbine in a river affects the swimming behavior of Atlantic salmon but is unlikely to affect its migration paths. For brown trout, the statistical results are inconclusive, although data indicate a response of avoiding the turbine. The species are in little risk to suffer physical harm as no fish entered the rotating turbine, despite very turbid water conditions.
24.	Bennasar-Figueras, Antoni, et al. (author) Complete Genome Sequence of Pseudomonas balearica DSM 6083T. 2016 In: Genome Announcements. - 2169-8287. ; 4:2 Journal article (peer-reviewed)abstract The whole-genome sequence of ITALIC! Pseudomonas balearicaSP1402 (DSM 6083(T)) has been completed and annotated. It was isolated as a naphthalene degrader from water of a lagooning wastewater treatment plant. ITALIC! P.balearicastrains tolerate up to 8.5% NaCl and are considered true marine denitrifiers.
25.	Bentham, James, et al. (author) A century of trends in adult human height 2016 In: eLIFE. - 2050-084X. ; 5 Journal article (peer-reviewed)abstract Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
26.	Bentham, James, et al. (author) A century of trends in adult human height 2016 In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5 Journal article (peer-reviewed)abstract Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
27.	Berry, Madeleine, et al. (author) Salmonid response to a vertical axis hydrokinetic turbine in a stream aquarium. 2019 In: 13th European Wave and Tidal Energy Conference (EWTEC), Napoli, Italy, September 1-6, 2019. Conference paper (peer-reviewed)
28.	Bossini-Castillo, Lara, et al. (author) Confirmation of association of the macrophage migration inhibitory factor gene with systemic sclerosis in a large European population. 2011 In: Rheumatology (Oxford, England). - : Oxford University Press (OUP). - 1462-0332 .- 1462-0324. ; 50, s. 1976-1981 Journal article (peer-reviewed)abstract Objectives. The aim of this study was to confirm the implication of macrophage migration inhibitory factor (MIF) gene in SSc susceptibility or clinical phenotypes in a large European population.Methods. A total of 3800 SSc patients and 4282 healthy controls of white Caucasian ancestry from eight different European countries were included in the study. The MIF -173 single nucleotide polymorphism (SNP) was selected as genetic marker and genotyped using Taqman 5' allelic discrimination assay.Results. The MIF -173 SNP showed association with SSc [P = 0.04, odds ratio (OR) = 1.10, 95% CI 1.00, 1.19]. Analysis of the MIF -173 polymorphism according to SSc clinical phenotype revealed that the frequency of the -173C allele was significantly higher in the dcSSc group compared with controls (P = 5.30E-03, OR = 1.21, 95% CI 1.07, 1.38). Conversely, the frequency of the MIF -173C allele was significantly underrepresented in the lcSSc group compared with dcSSc patients, supporting previous findings [(P = 0.04, OR = 0.86, 95% CI 0.75, 0.99); meta-analysis including previous results (P = 0.005, OR = 0.83, 95% CI 0.73, 0.94)].Conclusion. Our results confirm the role of MIF -173 promoter polymorphism in SSc, and provide evidence of a strong association with the dcSSc subgroup of patients. Hence, the MIF -173 variant is confirmed as a promising clinical phenotype genetic marker.
29.	Broitman, Esteban, et al. (author) Microstructural, nanomechanical, and microtribological properties of Pb thin films prepared by pulsed laser deposition and thermal evaporation techniques 2016 In: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 34:2, s. 021505- Journal article (peer-reviewed)abstract In this work, the authors compare the morphological, structural, nanomechanical, and microtribological properties of Pb films deposited by thermal evaporation (TE) and pulsed laser deposition (PLD) techniques onto Si (111) substrates. Films were investigated by scanning electron microscopy, surface probe microscopy, and x-ray diffraction in theta-2 theta geometry to determine their morphology, root-mean-square (RMS) roughness, and microstructure, respectively. TE films showed a percolated morphology with densely packed fibrous grains while PLD films had a granular morphology with a columnar and tightly packed structure in accordance with the zone growth model of Thornton. Moreover, PLD films presented a more polycrystalline structure with respect to TE films, with RMS roughness of 14 and 10 nm, respectively. Hardness and elastic modulus vary from 2.1 to 0.8 GPa and from 14 to 10 GPa for PLD and TE films, respectively. A reciprocal friction test has shown that PLD films have lower friction coefficient and wear rate than TE films. Our study has demonstrated for first time that, at the microscale, Pb films do not show the same simple lubricious properties measured at the macroscale. (C) 2015 American Vacuum Society.
30.	Calatrava-Nicolás, Francisco M., et al. (author) Robotic-Based Well-Being Monitoring and Coaching System for the Elderly in Their Daily Activities 2021 In: Sensors. - : MDPI. - 1424-8220. ; 21:20 Journal article (peer-reviewed)abstract The increasingly ageing population and the tendency to live alone have led science and engineering researchers to search for health care solutions. In the COVID 19 pandemic, the elderly have been seriously affected in addition to suffering from isolation and its associated and psychological consequences. This paper provides an overview of the RobWell (Robotic-based Well-Being Monitoring and Coaching System for the Elderly in their Daily Activities) system. It is a system focused on the field of artificial intelligence for mood prediction and coaching. This paper presents a general overview of the initially proposed system as well as the preliminary results related to the home automation subsystem, autonomous robot navigation and mood estimation through machine learning prior to the final system integration, which will be discussed in future works. The main goal is to improve their mental well-being during their daily household activities. The system is composed of ambient intelligence with intelligent sensors, actuators and a robotic platform that interacts with the user. A test smart home system was set up in which the sensors, actuators and robotic platform were integrated and tested. For artificial intelligence applied to mood prediction, we used machine learning to classify several physiological signals into different moods. In robotics, it was concluded that the ROS autonomous navigation stack and its autodocking algorithm were not reliable enough for this task, while the robot's autonomy was sufficient. Semantic navigation, artificial intelligence and computer vision alternatives are being sought.
31.	Camacho, Juan Pedro M., et al. (author) Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution 2022 In: BMC Biology. - : Springer Nature. - 1741-7007. ; 20:1 Journal article (peer-reviewed)abstract BackgroundThe full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago.ResultsWe found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species.ConclusionsOur analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.
32.	Canales, Javier, et al. (author) Gene expression profiling in the stem of young maritime pine trees : detection of ammonium stress-responsive genes in the apex 2011 In: Trees. - : Springer Science and Business Media LLC. - 0931-1890 .- 1432-2285. ; 26:2, s. 609-619 Journal article (peer-reviewed)abstract The shoots of young conifer trees represent an interesting model to study the development and growth of conifers from meristematic cells in the shoot apex to differentiated tissues at the shoot base. In this work, microarray analysis was used to monitor contrasting patterns of gene expression between the apex and the base ofmaritime pine shoots. A group of differentially expressed genes were selected and validated by examining their relative expression levels in different sections along thestem, from the top to the bottom. After validation of the microarray data, additional geneexpression analyses were also performed in the shoots of young maritime pine treesexposed to different levels of ammonium nutrition. Our results show that the apex ofmaritime pine trees is extremely sensitive to conditions of ammonium excess or deficiency, as revealed by the observed changes in the expression of stress-responsivegenes. This new knowledge may be used to precocious detection of early symptoms of nitrogen nutritional stresses, thereby increasing survival and growth rates of young treesin managed forests.
33.	Cañas, Rafael A, et al. (author) Molecular and functional analyses support a role of Ornithine-{delta}-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination 2008 In: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 148:1, s. 77-88 Journal article (peer-reviewed)abstract We report the molecular characterization and functional analysis of a gene (PsdeltaOAT) from Scots pine (Pinus sylvestris) encoding Orn-delta-aminotransferase (delta-OAT; EC 2.6.1.13), an enzyme of arginine metabolism. The deduced amino acid sequence contains a putative N-terminal signal peptide for mitochondrial targeting. The polypeptide is similar to other delta-OATs from plants, yeast, and mammals and encoded by a single-copy gene in pine. PsdeltaOAT encodes a functional delta-OAT as determined by expression of the recombinant protein in Escherichia coli and analysis of the active enzyme. The expression of PsdeltaOAT was undetectable in the embryo, but highly induced at early stages of germination and seedling development in all different organs. Transcript levels decreased in later developmental stages, although an increase was observed in lignified stems of 90-d-old plants. An increase of delta-OAT activity was observed in germinating embryos and seedlings and appears to mirror the observed alterations in PsdeltaOAT transcript levels. Similar expression patterns were also observed for genes encoding arginase and isocitrate dehydrogenase. Transcripts of PsdeltaOAT and the arginase gene were found widely distributed in different cell types of pine organs. Consistent with these results a metabolic pathway is proposed for the nitrogen flow from the megagametophyte to the developing seedling, which is also supported by the relative abundance of free amino acids in embryos and seedlings. Taken together, our data support that delta-OAT plays an important role in this process providing glutamate for glutamine biosynthesis during early pine growth.
34.	Costa, Joao, et al. (author) The burden of atherosclerosis in Portugal 2021 In: European Heart Journal - Quality of Care and Clinical Outcomes. - : Oxford University Press. - 2058-5225 .- 2058-1742. ; 7:2, s. 154-162 Journal article (peer-reviewed)abstract Aims This article sought to estimate the burden of disease attributable to atherosclerosis in mainland Portugal in 2016.Methods and results The burden of atherosclerosis was measured in disability-adjusted life years following the latest 2010 Global Burden of Disease (GBD) methodology. Disability-adjusted life years were estimated as the sum of years of life lost (YLL) with years lived with disability (YLD). The following clinical manifestations of atherosclerosis were included: ischaemic heart disease (IHD) (including acute myocardial infarction, stable angina, and ischaemic heart failure), ischaemic cerebrovascular disease (ICVD), and peripheral arterial disease (PAD). Years of life lost were estimated based on all-cause mortality data for the Portuguese population and mortality due to IHD, ICVD, and PAD for the year 2016 sourced from national statistics. Standard life expectancy was sourced from the GBD study. Years lived with disability corresponded to the product of the number of prevalent cases by an average disability weight for all possible combinations of disease. Prevalence data for the different clinical manifestations of atherosclerosis were sourced from epidemiological studies. Disability weights were sourced from the published literature. In 2016, 15123 deaths were attributable to atherosclerosis, which corresponded to 14.3% of overall mortality in mainland Portugal. Disability-adjusted life years totalled 260943, 75% due to premature death (196438 YLL) and 25% due to disability (64505 YLD).Conclusion Atherosclerosis entails a high disease burden to society. A large part of this burden would be avoidable if evidence-based effective and cost-effective interventions targeting known risk factors, from prevention to treatment, were implemented.
35.	Crespo, Alejandro J., et al. (author) On the state-of-the-art of CFD simulations for wave energy converters within the open-source numerical framework of DualSPHysics 2023 In: Proceedings of the 15th European Wave and Tidal Energy Conference, Bilbao, 3-7 September 2023. - : European Wave and Tidal Energy Conference. Conference paper (peer-reviewed)abstract There are currently several types of devices capable of harnessing wave energy, exploiting a broad variety of physical transformation processes. These devices – known as Wave Energy Converters (WECs) – are developed to maximize their power output. However, there are still uncertainties about their response and survivability to loads induced by adverse environmental conditions, with a consequent increase of the Levelized Cost of Energy (LCOE), which prevents in fact their commercial diffusion. As evidenced by a large body of research, marine renewable energy devices need to have more robust design practices. To address this issue, we propose the CFD-based DualSPHysics toolbox as a support in the design stages. DualSPHysics is high-fidelity software inherently suited to numerically address most challenges posed by multiphysics simulations, which are required to reliably predict WEC response in situations well beyond operational conditions. It should be noted that WECs, generally, may be connected to the seabed and comprise mechanical systems named Power Take-Offs (PTO) used to convert the energy from waves into electricity or other usable energies. To reproduce these features, DualSPHysics benefits from coupling with the multiphysics library Project Chrono and the dynamic mooring model Moordyn+. In this work, the augmented DualSPHysics framework is utilised to simulate a range of very different types of WECs with a variety of elements, such as catenary connections, taut mooring lines, or linear and nonlinear PTO actuators. Version 5.2 of the open-source licensed code was recently released, making the numerical framework publicly available as one unit. This work aims to provide a numerical review of past applications, and to demonstrate how the same open-source code is able to simulate very different technologies.Specifically, this paper proposes routine modeling and validation procedures using the SPH-based solver DualSPHysics applied to five different WEC types: i) a moored point absorber (PA); ii) an oscillating wave surge converter (OWSC); iii) a floating OWSC (so called FOSWEC); iv) a wave energy hyperbaric converter (WEHC); and v) a multi-body attenuator (so called Multi-float M4). For each device listed above, we provide validation proof against physical model data for various components of the floater(s) and PTO related quantities, performed under specific sea conditions that aim to challenge their survivability. Within the scope of this research, we present the WEC response with respect to the degrees of freedom that really matter for each of the floatings due to hydrodynamic interactions (i.e., heave, surge, and pitch), along with quantities more intimately connected to the anchoring systems (e.g., line tension) or the mechanical apparatus (e.g., end-stopper force). The quality of the results, the discussion built upon them and the demonstrated solver exploitability to a wide range of WECs show that one software model can run all cases using the exact same methodology, which is of great value for the marine energy R&D community. Finally, we discuss future research objectives, which include the implementation of automation to apply open control systems and possible applications to subsets of WEC farm arrays and other floating energy harnessing devices.
36.	Cruz, Raquel, et al. (author) Novel genes and sex differences in COVID-19 severity 2022 In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 31:22, s. 3789-3806 Journal article (peer-reviewed)abstract 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.
37.	Cubillos, Francisco A, et al. (author) High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. 2013 In: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 195:3, s. 1141-55 Journal article (peer-reviewed)abstract A large fraction of human complex trait heritability is due to a high number of variants with small marginal effects and their interactions with genotype and environment. Such alleles are more easily studied in model organisms, where environment, genetic makeup, and allele frequencies can be controlled. Here, we examine the effect of natural genetic variation on heritable traits in a very large pool of baker's yeast from a multiparent 12th generation intercross. We selected four representative founder strains to produce the Saccharomyces Genome Resequencing Project (SGRP)-4X mapping population and sequenced 192 segregants to generate an accurate genetic map. Using these individuals, we mapped 25 loci linked to growth traits under heat stress, arsenite, and paraquat, the majority of which were best explained by a diverging phenotype caused by a single allele in one condition. By sequencing pooled DNA from millions of segregants grown under heat stress, we further identified 34 and 39 regions selected in haploid and diploid pools, respectively, with most of the selection against a single allele. While the most parsimonious model for the majority of loci mapped using either approach was the effect of an allele private to one founder, we could validate examples of pleiotropic effects and complex allelic series at a locus. SGRP-4X is a deeply characterized resource that provides a framework for powerful and high-resolution genetic analysis of yeast phenotypes and serves as a test bed for testing avenues to attack human complex traits.
38.	Danaei, Goodarz, et al. (author) Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331288 participants 2015 In: The Lancet Diabetes & Endocrinology. - 2213-8595 .- 2213-8587. ; 3:8, s. 624-637 Journal article (peer-reviewed)abstract Background Diabetes has been defined on the basis of different biomarkers, including fasting plasma glucose (FPG), 2-h plasma glucose in an oral glucose tolerance test (2hOGTT), and HbA(1c). We assessed the effect of different diagnostic definitions on both the population prevalence of diabetes and the classification of previously undiagnosed individuals as having diabetes versus not having diabetes in a pooled analysis of data from population-based health examination surveys in different regions. Methods We used data from 96 population-based health examination surveys that had measured at least two of the biomarkers used for defining diabetes. Diabetes was defined using HbA(1c) (HbA(1c) >= 6 . 5% or history of diabetes diagnosis or using insulin or oral hypoglycaemic drugs) compared with either FPG only or FPG-or-2hOGTT definitions (FPG >= 7 . 0 mmol/L or 2hOGTT >= 11 . 1 mmol/L or history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated diabetes prevalence, taking into account complex survey design and survey sample weights. We compared the prevalences of diabetes using different definitions graphically and by regression analyses. We calculated sensitivity and specificity of diabetes diagnosis based on HbA1c compared with diagnosis based on glucose among previously undiagnosed individuals (ie, excluding those with history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated sensitivity and specificity in each survey, and then pooled results using a random-effects model. We assessed the sources of heterogeneity of sensitivity by meta-regressions for study characteristics selected a priori. Findings Population prevalence of diabetes based on FPG- or-2hOGTT was correlated with prevalence based on FPG alone (r= 0 . 98), but was higher by 2-6 percentage points at different prevalence levels. Prevalence based on HbA(1c) was lower than prevalence based on FPG in 42 . 8% of age-sex-survey groups and higher in another 41 . 6%; in the other 15 . 6%, the two definitions provided similar prevalence estimates. The variation across studies in the relation between glucose-based and HbA(1c)-based prevalences was partly related to participants' age, followed by natural logarithm of per person gross domestic product, the year of survey, mean BMI, and whether the survey population was national, subnational, or from specific communities. Diabetes defined as HbA(1c) 6 . 5% or more had a pooled sensitivity of 52 . 8% (95% CI 51 . 3-54 . 3%) and a pooled specificity of 99 . 74% (99 . 71-99 . 78%) compared with FPG 7 . 0 mmol/L or more for diagnosing previously undiagnosed participants; sensitivity compared with diabetes defined based on FPG-or-2hOGTT was 30 . 5% (28 . 7-32 . 3%). None of the preselected study-level characteristics explained the heterogeneity in the sensitivity of HbA(1c) versus FPG. Interpretation Different biomarkers and definitions for diabetes can provide different estimates of population prevalence of diabetes, and differentially identify people without previous diagnosis as having diabetes. Using an HbA(1c)-based definition alone in health surveys will not identify a substantial proportion of previously undiagnosed people who would be considered as having diabetes using a glucose-based test.
39.	de Jong, Yde, et al. (author) PESI - a taxonomic backbone for Europe 2015 In: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 3, s. 1-51 Journal article (peer-reviewed)abstract Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
40.	Di Cesare, Mariachiara, et al. (author) Trends in adult body-mass index in 200 countries from 1975 to 2014: A pooled analysis of 1698 population-based measurement studies with 19.2 million participants 2016 In: The Lancet. - : Lancet Publishing Group. - 0140-6736 .- 1474-547X. ; 387:10026, s. 1377-1396 Journal article (peer-reviewed)
41.	Fernández-Pozo, Noé, et al. (author) EuroPineDB : a high-coverage web database for maritime pine transcriptome 2011 In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 12, s. 366- Journal article (peer-reviewed)abstract BACKGROUND: Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. DESCRIPTION: EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine), since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili) and embryonic (germinated embryos, buds, callus) maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes). As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5%) of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information) and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. CONCLUSIONS: The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including microarray hybridisation), and provides deeper knowledge on the maritime pine transcriptome.
42.	Fernandez-Prieto, Armando, et al. (author) Glide Symmetry Applied to the Design of Common-Mode Rejection Filters Based on Complementary Split-Ring Resonators 2023 In: IEEE Transactions on Circuits and Systems - II - Express Briefs. - : Institute of Electrical and Electronics Engineers (IEEE). - 1549-7747 .- 1558-3791. ; 70:6, s. 1911-1915 Journal article (peer-reviewed)abstract In this brief, glide symmetry is applied to design common-mode rejection filters based on defected ground structures with bandstop response. To this aim, complementary split-ring resonators are chosen as the basic components for common-mode rejection. To illustrate the advantages of using glide symmetry, three implementations are studied and compared. The results reveal that glide symmetry offers the best performance in terms of common-mode rejection level and fractional bandwidth. Furthermore, glide symmetry barely affects the integrity of the differential mode. A prototype of each of the considered symmetries has been designed, simulated, and tested for practical validation. Good agreement is observed between the simulated and measured results, experimentally demonstrating the advantages of glide symmetry.
43.	Ferrando, Carlos, et al. (author) Effects of oxygen on post-surgical infections during an individualised perioperative open-lung ventilatory strategy : a randomised controlled trial 2020 In: British Journal of Anaesthesia. - : ELSEVIER SCI LTD. - 0007-0912 .- 1471-6771. ; 124:1, s. 110-120 Journal article (peer-reviewed)abstract Background: We aimed to examine whether using a high fraction of inspired oxygen (FIO2) in the context of an individualised intra- and postoperative open-lung ventilation approach could decrease surgical site infection (SSI) in patients scheduled for abdominal surgery. Methods: We performed a multicentre, randomised controlled clinical trial in a network of 21 university hospitals from June 6, 2017 to July 19, 2018. Patients undergoing abdominal surgery were randomly assigned to receive a high (0.80) or conventional (0.3) FIO2 during the intraoperative period and during the first 3 postoperative hours. All patients were mechanically ventilated with an open-lung strategy, which included recruitment manoeuvres and individualised positive end-expiratory pressure for the best respiratory-system compliance, and individualised continuous postoperative airway pressure for adequate peripheral oxyhaemoglobin saturation. The primary outcome was the prevalence of SSI within the first 7 postoperative days. The secondary outcomes were composites of systemic complications, length of intensive care and hospital stay, and 6-month mortality. Results: We enrolled 740 subjects: 371 in the high FIO2 group and 369 in the low FIO2 group. Data from 717 subjects were available for final analysis. The rate of SSI during the first postoperative week did not differ between high (8.9%) and low (9.4%) FIO2 groups (relative risk [RR]: 0.94; 95% confidence interval [CI]: 0.59-1.50; P=0.90]). Secondary outcomes, such as atelectasis (7.7% vs 9.8%; RR: 0.77; 95% CI: 0.48-1.25; P=0.38) and myocardial ischaemia (0.6% [n=2] vs 0% [n=0]; P=0.47) did not differ between groups. Conclusions: An oxygenation strategy using high FIO2 compared with conventional FIO2 did not reduce postoperative SSIs in abdominal surgery. No differences in secondary outcomes or adverse events were found.
44.	Ferrando, Carlos, et al. (author) Individualised perioperative open-lung approach versus standard protective ventilation in abdominal surgery (iPROVE) : a randomised controlled trial 2018 In: The Lancet Respiratory Medicine. - : ELSEVIER SCI LTD. - 2213-2600 .- 2213-2619. ; 6:3, s. 193-203 Journal article (peer-reviewed)abstract Background The effects of individualised perioperative lung-protective ventilation (based on the open-lung approach [OLA]) on postoperative complications is unknown. We aimed to investigate the effects of intraoperative and postoperative ventilatory management in patients scheduled for abdominal surgery, compared with standard protective ventilation. Methods We did this prospective, multicentre, randomised controlled trial in 21 teaching hospitals in Spain. We enrolled patients who were aged 18 years or older, were scheduled to have abdominal surgery with an expected time of longer than 2 h, had intermediate-to-high-risk of developing postoperative pulmonary complications, and who had a body-mass index less than 35 kg/m(2). Patients were randomly assigned (1: 1: 1: 1) online to receive one of four lung-protective ventilation strategies using low tidal volume plus positive end-expiratory pressure (PEEP): open-lung approach (OLA)-iCPAP (individualised intraoperative ventilation [individualised PEEP after a lung recruitment manoeuvre] plus individualised postoperative continuous positive airway pressure [CPAP]), OLA-CPAP (intraoperative individualised ventilation plus postoperative CPAP), STD-CPAP (standard intraoperative ventilation plus postoperative CPAP), or STD-O-2 (standard intraoperative ventilation plus standard postoperative oxygen therapy). Patients were masked to treatment allocation. Investigators were not masked in the operating and postoperative rooms; after 24 h, data were given to a second investigator who was masked to allocations. The primary outcome was a composite of pulmonary and systemic complications during the first 7 postoperative days. We did the primary analysis using the modified intention-to-treat population. This trial is registered with ClinicalTrials.gov, number NCT02158923. Findings Between Jan 2, 2015, and May 18, 2016, we enrolled 1012 eligible patients. Data were available for 967 patients, whom we included in the final analysis. Risk of pulmonary and systemic complications did not differ for patients in OLA-iCPAP (110 [46%] of 241, relative risk 0.89 [95% CI 0.74-1.07; p=0.25]), OLA-CPAP (111 [47%] of 238, 0.91 [0.76-1.09; p=0.35]), or STD-CPAP groups (118 [48%] of 244, 0.95 [0.80-1.14; p=0.65]) when compared with patients in the STD-O-2 group (125 [51%] of 244). Intraoperatively, PEEP was increased in 69 (14%) of patients in the standard perioperative ventilation groups because of hypoxaemia, and no patients from either of the OLA groups required rescue manoeuvres. Interpretation In patients who have major abdominal surgery, the different perioperative open lung approaches tested in this study did not reduce the risk of postoperative complications when compared with standard lung-protective mechanical ventilation.
45.	Ferrando, Carlos, et al. (author) Rationale and study design for an individualised perioperative open-lung ventilatory strategy with a high versus conventional inspiratory oxygen fraction (iPROVE-O2) and its effects on surgical site infection : study protocol for a randomised controlled trial 2017 In: BMJ Open. - : BMJ. - 2044-6055. ; 7:7 Journal article (peer-reviewed)abstract Introduction Surgical site infection (SSI) is a serious postoperative complication that increases morbidity and healthcare costs. SSIs tend to increase as the partial pressure of tissue oxygen decreases: previous trials have focused on trying to reduce them by comparing high versus conventional inspiratory oxygen fractions (FIO 2) in the perioperative period but did not use a protocolised ventilatory strategy. The open-lung ventilatory approach restores functional lung volume and improves gas exchange, and therefore it may increase the partial pressure of tissue oxygen for a given FIO 2. The trial presented here aims to compare the efficacy of high versus conventional FIO 2 in reducing the overall incidence of SSIs in patients by implementing a protocolised and individualised global approach to perioperative open-lung ventilation. Methods and analysis This is a comparative, prospective, multicentre, randomised and controlled two-arm trial that will include 756 patients scheduled for abdominal surgery. The patients will be randomised into two groups: (1) a high FIO 2 group (80% oxygen; FIO 2 of 0.80) and (2) a conventional FIO 2 group (30% oxygen; FIO 2 of 0.30). Each group will be assessed intra-and postoperatively. The primary outcome is the appearance of postoperative SSI complications. Secondary outcomes are the appearance of systemic and pulmonary complications. Ethics and dissemination The iPROVE-O2 trial has been approved by the Ethics Review Board at the reference centre (the Hospital Clinico Universitario in Valencia). Informed consent will be obtained from all patients before their participation. If the approach using high FIO 2 during individualised open-lung ventilation decreases SSIs, use of this method will become standard practice for patients scheduled for future abdominal surgery. Publication of the results is anticipated in early 2019.
46.	Ferrando, Carlos, et al. (author) Rationale and study design for an individualized perioperative open lung ventilatory strategy (iPROVE) : study protocol for a randomized controlled trial 2015 In: Trials. - : Springer Science and Business Media LLC. - 1745-6215. ; 16 Journal article (peer-reviewed)abstract Background: Postoperative pulmonary and non-pulmonary complications are common problems that increase morbidity and mortality in surgical patients, even though the incidence has decreased with the increased use of protective lung ventilation strategies. Previous trials have focused on standard strategies in the intraoperative or postoperative period, but without personalizing these strategies to suit the needs of each individual patient and without considering both these periods as a global perioperative lung-protective approach. The trial presented here aims at comparing postoperative complications when using an individualized ventilatory management strategy in the intraoperative and immediate postoperative periods with those when using a standard protective ventilation strategy in patients scheduled for major abdominal surgery. Methods: This is a comparative, prospective, multicenter, randomized, and controlled, four-arm trial that will include 1012 patients with an intermediate or high risk for postoperative pulmonary complications. The patients will be divided into four groups: (1) individualized perioperative group: intra-and postoperative individualized strategy; (2) intraoperative individualized strategy + postoperative continuous positive airway pressure (CPAP); (3) intraoperative standard ventilation + postoperative CPAP; (4) intra-and postoperative standard strategy (conventional strategy). The primary outcome is a composite analysis of postoperative complications. Discussion: The Individualized Perioperative Open-lung Ventilatory Strategy (iPROVE) is the first multicenter, randomized, and controlled trial to investigate whether an individualized perioperative approach prevents postoperative pulmonary complications.
47.	Francisco, Francisco, 1985- (author) Adapting sonar systems for monitoring ocean energy technologies 2018 Doctoral thesis (other academic/artistic)abstract The global energy sector is under profound reforms aiming towards renewable energy sources, clean technologies and expansion of smart grids, all with the additional aim of providing affordable and dependable electricity for everyone. A reduction of carbon dioxide emissions is a priority on the global agenda, and to achieve that, cleaner energy technologies has to be more integrated into the energy mix. This thesis focus on a sustainable implementation of wave, tidal and offshore wind power, wherefore there is a need to investigate more about the prerequisites and consequences ocean energy can have on the marine environment. For that, reliable, cost effective and continuous environmental monitoring framework is necessary in order to support and safeguard ocean energy operations.The main objectives of the research presented in this thesis are to develop a multifunctional environmental monitoring platform based on sonar systems for ocean energy applications, by adapting high resolution multibeam, dual beam and split beam sonar systems and also underwater cameras; Propose data acquisition and processing protocols capable of decipher sonar data in order to provide continuous environmental monitoring and reporting; Conduct qualitative and quantitative observations of fish and marine mammals using the built monitoring platform; And investigate the feasibility of utilizing the Uppsala University wave energy converter technology to generate electricity worldwide. As a result, a multifunctional platform was designed, built and tested. This included the hardware, the data acquisition system, and a data analysis framework comprising new algorithms necessary to process the new acoustic data. The multibeam, dual beam, and split beam sonar systems and underwater cameras produced both qualitative and quantitative data of biomass, occurrence and behavior of fish and marine mammals in the vicinity of ocean energy devices. With this platform, it was also possible to conduct seabed and structural inspections within ocean energy devices, observe cavitating flows, etc. One of the most important results of this research was the possibility of extracting visual signatures of fish and marine mammals through acoustic images. This can be valuable for training algorithms for manual or automatic identification and classification of underwater targets through imaging sonar systems, a technique that can be widely used in the offshore activities. Regarding feasibility studies and wave power resource assessment, this study concluded that mild wave climates can provide enough energy to run reverse osmosis desalination systems as well as produce sufficient electricity to integrate into a national grid.In summary, this thesis concludes that the implementation of ocean energy can be facilitated by creating environmental monitoring, risk and resource assessment frameworks such as the presented research work that contribute to lowering the risks associated with subsea work and thereby costs of ocean energy projects.
48.	Francisco, Francisco, 1985-, et al. (author) An alternative technique for ultra-high resolution bathymetry and seabed inspection for marine renewables Other publication (other academic/artistic)abstract Marine renewable energy technologies have a great potential in supplying clean electricity to millions of people across the globe, if technical and economic conditions are in right. So far, ocean energy projects are commonly started by SMEs or educational institutions with limited budgets. Therefore, any effort to reduce expenses is of great value. One of the areas involving substantial expenses are the inevitable seabed inspection prior to deployment of marine renewable energy device. Detailed seabed inspections can also reduce the risk of associated with deployment of structures on uneven seabed, especially marine renewable energy devices with gravity foundations. By reducing the costs and risks of such surveys prior and during the installation phases, the feasibility of marine renewable energy projects can be more favoured and competitive. In this perspective, this study proposes a cost and time effective technique for seabed surveys. The proposed technique involves the use of high precision and inexpensive sonar systems and underwater optical cameras integrated into a versatile and compact subsea monitoring platform. It also involves simple and practical data acquisition and processing protocols that do not requires hi expertise for operation. The results obtained showed that high resolution bathymetric maps and detailed seabed inspections imagery can be acquired. This study concludes that a simple and inexpensive subsea monitoring platform comprising a multibeam, dual beam and video cameras can be effective for high resolution seabed inspection and bathymetric measurements for marine energy applications.
49.	Francisco, Francisco, 1985-, et al. (author) Detection of Visual Signatures of Marine Mammals and Fish within Marine Renewable Energy Farms Using Multibeam Imaging Sonar 2019 In: Nutrients. - : MDPI. - 2072-6643. ; 7:2 Journal article (peer-reviewed)abstract Techniques for marine monitoring have evolved greatly over the past decades, making the acquisition of environment data safer, reliable and more efficient. On the other hand, the exploration of marine renewable energy introduced dissimilar ways of exploring the oceans and with that arises the need for new techniques for environmental data acquisition, processing and analysis. Marine energy is mostly harvested in murky and high energetic places where conventional data acquisition techniques are impractical. Modern sonar systems, operating at high frequencies, can acquire detailed images of the underwater environment. Variables such as occurrence, size, class and behaviour of a variety of aquatic species of fish, birds, mammals, coexisting within marine energy sites can be gathered using imaging sonar systems. Although sonar images can provide high level of details, still in most of the cases they are difficult to decipher. Therefore, to facilitate the classification of targets through sonar images, this study introduces a framework of extracting visual features of marine targets that would serve as unique signatures. The acoustic measure of visibility (AVM) is here introduced as an indirect technique of identification and classification of targets by comparing the observed size with a standard value. This information can be used to instruct manual and automatic algorithms for identification and classification of underwater targets using imaging sonar systems. Using image processing algorithms embedded in Proviwer4 and FIJI software, this study found that acoustic images can be effectively used to classify cod, harbour and grey seals, and orcas through their size, shape and swimming behaviour. Data showed that cod occurred as bright, 0.9 m long, ellipsoidal targets shoaling in groups of up to 50 individuals. Harbour seals occurred as bright torpedo-like fast moving target, whereas grey seals occurred as bulky-ellipsoidal targets with serpentine movement. Orca or larger marine mammals occurred with relatively low visibility on the acoustic images compared to their body size which measured between 4 m and 7 m. This framework provide a new window of performing qualitative and quantitative observations of underwater targets, and with further improvements, this method can be useful for environmental studies within marine renewable energy farms and for other purposes.
50.	Francisco, Francisco, 1985-, et al. (author) Evaluation of Underwater Acoustic and Optical Imaging for Structural Inspections for Marine Renewables In: IEEE Journal of Oceanic Engineering. Journal article (other academic/artistic)abstract Environmental monitoring and visual inspections are indispensable tasks in the marine renewable energy sector. Today, acoustic and electromagnetic instrumentation are used to observe the underwater environment. However, depending on the application, both electromagnetic and acoustic instruments have limitations mostly due to signal attenuation. For visual inspections, electromagnetic instruments e.g. optical cameras provide the best method of observation enabling an easy identification and classification of targets. However, electromagnetic radiation is more attenuated in water than sound, limiting the use of optical cameras to nearfield observations. In murky and turbid waters, acoustic imaging sonar systems can be used to observe underwater objects at much longer ranges up to 100 m away. Presumably, underwater optical images are mostly appropriate in clear waters or at nearfield, and acoustic images are suitable for murky and turbid waters. This study aimed to find the optimal ranges in which optical and acoustic images can be acquired in In Situ conditions. A multibeam imaging sonar and several different optical cameras were used to acquire underwater images of the surroundings of marine renewable energy devices. The results from observation showed that optical images were significantly affected by the decreasing of luminosity, increasing depth and water velocity. And acoustic images were mostly affected by water column stratification, bubbles and reverberation. In summary, optical cameras had superior performance for nearfield and high accuracy image acquisition, while imaging sonar provided superior performance at acquiring images at mid to long range.

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