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1.
  • 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.
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2.
  • 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.
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3.
  • Hudson, Lawrence N, et al. (author)
  • The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
  • 2017
  • In: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
  • Journal article (peer-reviewed)abstract
    • The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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4.
  • Aguado, D. S., et al. (author)
  • The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library
  • 2019
  • In: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2
  • Journal article (peer-reviewed)abstract
    • Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
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5.
  • 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.
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6.
  • Llorens, Carlos, et al. (author)
  • The Gypsy Database (GyDB) of mobile genetic elements : release 2.0.
  • 2011
  • In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 39:Database issue
  • Journal article (peer-reviewed)abstract
    • This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.
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7.
  • Matabuena, Marcos, et al. (author)
  • Identification of Asthma Phenotypes in the Spanish MEGA Cohort Study Using Cluster Analysis
  • 2023
  • In: Archivos de Bronconeumologia. - : Elsevier BV. - 0300-2896. ; 59:4, s. 223-231
  • Journal article (peer-reviewed)abstract
    • Introduction: The definition of asthma phenotypes has not been fully established, neither there are cluster studies showing homogeneous results to solidly establish clear phenotypes. The purpose of this study was to develop a classification algorithm based on unsupervised cluster analysis, identifying clusters that represent clinically relevant asthma phenotypes that may share asthma-related outcomes. Methods: We performed a multicentre prospective cohort study, including adult patients with asthma (N = 512) from the MEGA study (Mechanisms underlying the Genesis and evolution of Asthma). A standardised clinical history was completed for each patient. Cluster analysis was performed using the kernel k-groups algorithm. Results: Four clusters were identified. Cluster 1 (31.5% of subjects) includes adult-onset atopic patients with better lung function, lower BMI, good asthma control, low ICS dose, and few exacerbations. Cluster 2 (23.6%) is made of adolescent-onset atopic asthma patients with normal lung function, but low adherence to treatment (59% well-controlled) and smokers (48%). Cluster 3 (17.1%) includes adult-onset patients, mostly severe non-atopic, with overweight, the worse lung function and asthma control, and receiving combination of treatments. Cluster 4 (26.7%) consists of the elderly-onset patients, mostly female, atopic (64%), with high BMI and normal lung function, prevalence of smokers and comorbidities. Conclusion: We defined four phenotypes of asthma using unsupervised cluster analysis. These clusters are clinically relevant and differ from each other as regards FEV1, age of onset, age, BMI, atopy, asthma severity, exacerbations, control, social class, smoking and nasal polyps.
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8.
  • The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
  • 2022
  • In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
  • Journal article (peer-reviewed)abstract
    • This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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9.
  • Waeijen-Smit, Kiki, et al. (author)
  • Global mortality and readmission rates following COPD exacerbation-related hospitalisation : a meta-analysis of 65 945 individual patients
  • 2024
  • In: ERJ Open Research. - : European Respiratory Society. - 2312-0541. ; 10:1
  • Journal article (peer-reviewed)abstract
    • Background Exacerbations of COPD (ECOPD) have a major impact on patients and healthcare systems across the world. Precise estimates of the global burden of ECOPD on mortality and hospital readmission are needed to inform policy makers and aid preventive strategies to mitigate this burden. The aims of the present study were to explore global in-hospital mortality, post-discharge mortality and hospital readmission rates after ECOPD-related hospitalisation using an individual patient data meta-analysis (IPDMA) design. Methods A systematic review was performed identifying studies that reported in-hospital mortality, postdischarge mortality and hospital readmission rates following ECOPD-related hospitalisation. Data analyses were conducted using a one-stage random-effects meta-analysis model. This study was conducted and reported in accordance with the PRISMA-IPD statement. Results Data of 65 945 individual patients with COPD were analysed. The pooled in-hospital mortality rate was 6.2%, pooled 30-, 90- and 365-day post-discharge mortality rates were 1.8%, 5.5% and 10.9%, respectively, and pooled 30-, 90- and 365-day hospital readmission rates were 7.1%, 12.6% and 32.1%, respectively, with noticeable variability between studies and countries. Strongest predictors of mortality and hospital readmission included noninvasive mechanical ventilation and a history of two or more ECOPD-related hospitalisations < 12 months prior to the index event. Conclusions This IPDMA stresses the poor outcomes and high heterogeneity of ECOPD-related hospitalisation across the world. Whilst global standardisation of the management and follow-up of ECOPD-related hospitalisation should be at the heart of future implementation research, policy makers should focus on reimbursing evidence-based therapies that decrease (recurrent) ECOPD.
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10.
  • Abelev, Betty, et al. (author)
  • Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
  • 2012
  • In: Journal of High Energy Physics. - 1029-8479. ; :11
  • Journal article (peer-reviewed)abstract
    • The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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11.
  • Abelev, Betty, et al. (author)
  • Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
  • 2012
  • In: Journal of High Energy Physics. - 1029-8479. ; :7
  • Journal article (peer-reviewed)abstract
    • We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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12.
  • Ahearn, Thomas U., et al. (author)
  • Common variants in breast cancer risk loci predispose to distinct tumor subtypes
  • 2022
  • In: Breast Cancer Research. - : Springer Nature. - 1465-5411 .- 1465-542X. ; 24:1
  • Journal article (peer-reviewed)abstract
    • BackgroundGenome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear.MethodsAmong 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes.ResultsEighty-five of 173 variants were associated with at least one tumor feature (false discovery rate < 5%), most commonly ER and grade, followed by PR and HER2. Models for intrinsic-like subtypes found nearly all of these variants (83 of 85) associated at p < 0.05 with risk for at least one luminal-like subtype, and approximately half (41 of 85) of the variants were associated with risk of at least one non-luminal subtype, including 32 variants associated with triple-negative (TN) disease. Ten variants were associated with risk of all subtypes in different magnitude. Five variants were associated with risk of luminal A-like and TN subtypes in opposite directions.ConclusionThis report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.
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13.
  • Archambault, Alexi N., et al. (author)
  • Cumulative Burden of Colorectal Cancer Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
  • 2020
  • In: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 158:5, s. 1274-1286.e12
  • Journal article (peer-reviewed)abstract
    • BACKGROUND & AIMS: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC.METHODS: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants.RESULTS: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 x 10(-5)). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings.CONCLUSIONS: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.
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14.
  • Benitez, Jose J., et al. (author)
  • Mechanical Performances of Isolated Cuticles Along Tomato Fruit Growth and Ripening
  • 2021
  • In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
  • Journal article (peer-reviewed)abstract
    • The cuticle is the most external layer that protects fruits from the environment and constitutes the first shield against physical impacts. The preservation of its mechanical integrity is essential to avoid the access to epidermal cell walls and to prevent mass loss and damage that affect the commercial quality of fruits. The rheology of the cuticle is also very important to respond to the size modification along fruit growth and to regulate the diffusion of molecules from and toward the atmosphere. The mechanical performance of cuticles is regulated by the amount and assembly of its components (mainly cutin, polysaccharides, and waxes). In tomato fruit cuticles, phenolics, a minor cuticle component, have been found to have a strong influence on their mechanical behavior. To fully characterize the biomechanics of tomato fruit cuticle, transient creep, uniaxial tests, and multi strain dynamic mechanical analysis (DMA) measurements have been carried out. Two well-differentiated stages have been identified. At early stages of growth, characterized by a low phenolic content, the cuticle displays a soft elastic behavior. Upon increased phenolic accumulation during ripening, a progressive stiffening is observed. The increment of viscoelasticity in ripe fruit cuticles has also been associated with the presence of these compounds. The transition from the soft elastic to the more rigid viscoelastic regime can be explained by the cooperative association of phenolics with both the cutin and the polysaccharide fractions.
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15.
  • Bernardi, Simona, et al. (author)
  • A systematic approach for performance assessment using process mining : An industrial experience report
  • 2018
  • In: Empirical Software Engineering. - : Springer. - 1382-3256 .- 1573-7616. ; 23:6, s. 3394-3441
  • Journal article (peer-reviewed)abstract
    • Software performance engineering is a mature field that offers methods to assess system performance. Process mining is a promising research field applied to gain insight on system processes. The interplay of these two fields opens promising applications in the industry. In this work, we report our experience applying a methodology, based on process mining techniques, for the performance assessment of a commercial data-intensive software application. The methodology has successfully assessed the scalability of future versions of this system. Moreover, it has identified bottlenecks components and replication needs for fulfilling business rules. The system, an integrated port operations management system, has been developed by Prodevelop, a medium-sized software enterprise with high expertise in geospatial technologies. The performance assessment has been carried out by a team composed by practitioners and researchers. Finally, the paper offers a deep discussion on the lessons learned during the experience, that will be useful for practitioners to adopt the methodology and for researcher to find new routes.
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16.
  • Dixon-Suen, Suzanne C, et al. (author)
  • Physical activity, sedentary time and breast cancer risk : a Mendelian randomisation study
  • 2022
  • In: British Journal of Sports Medicine. - : BMJ Publishing Group Ltd. - 0306-3674 .- 1473-0480. ; 56:20, s. 1157-1170
  • Journal article (peer-reviewed)abstract
    • OBJECTIVES: Physical inactivity and sedentary behaviour are associated with higher breast cancer risk in observational studies, but ascribing causality is difficult. Mendelian randomisation (MR) assesses causality by simulating randomised trial groups using genotype. We assessed whether lifelong physical activity or sedentary time, assessed using genotype, may be causally associated with breast cancer risk overall, pre/post-menopause, and by case-groups defined by tumour characteristics.METHODS: We performed two-sample inverse-variance-weighted MR using individual-level Breast Cancer Association Consortium case-control data from 130 957 European-ancestry women (69 838 invasive cases), and published UK Biobank data (n=91 105-377 234). Genetic instruments were single nucleotide polymorphisms (SNPs) associated in UK Biobank with wrist-worn accelerometer-measured overall physical activity (nsnps=5) or sedentary time (nsnps=6), or accelerometer-measured (nsnps=1) or self-reported (nsnps=5) vigorous physical activity.RESULTS: Greater genetically-predicted overall activity was associated with lower breast cancer overall risk (OR=0.59; 95% confidence interval (CI) 0.42 to 0.83 per-standard deviation (SD;~8 milligravities acceleration)) and for most case-groups. Genetically-predicted vigorous activity was associated with lower risk of pre/perimenopausal breast cancer (OR=0.62; 95% CI 0.45 to 0.87,≥3 vs. 0 self-reported days/week), with consistent estimates for most case-groups. Greater genetically-predicted sedentary time was associated with higher hormone-receptor-negative tumour risk (OR=1.77; 95% CI 1.07 to 2.92 per-SD (~7% time spent sedentary)), with elevated estimates for most case-groups. Results were robust to sensitivity analyses examining pleiotropy (including weighted-median-MR, MR-Egger).CONCLUSION: Our study provides strong evidence that greater overall physical activity, greater vigorous activity, and lower sedentary time are likely to reduce breast cancer risk. More widespread adoption of active lifestyles may reduce the burden from the most common cancer in women.
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17.
  • Domínguez, José L, et al. (author)
  • Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1
  • 2010
  • In: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 49:34, s. 7255-7263
  • Journal article (peer-reviewed)abstract
    • BACE-1 is one of the aspartic proteases involved in the cleavage of beta amyloid peptide, an initial step in the formation of amyloid plaques whose toxicity induces neuron death in Alzheimer's disease patients. One of the central issues in the search of novel BACE-1 inhibitors is the optimum pH for the binding of inhibitors to the enzyme. It is known that the enzyme has optimal catalytic activity at acidic pH, while cell active inhibitors may bind optimally at higher pH. In this work we determine the effect of the pH on the affinities of a set of inhibitors, with a variety of chemical motifs, for the ectodomain region of BACE-1 by a surface plasmon resonance (SPR) biosensor based assay. In order to understand the molecular interactions that underlie the diverse optimum pH for the binding of the various inhibitors as observed experimentally, we have calculated the titration curves for a set of BACE-1 ligand complexes. The results indicate that the pK(a) values of the titratable residues of the protein depend on the nature of the ligand involved, in disagreement with previous work. The enzyme-inhibitor structures with the resulting protonation states at pH values 4.5 and 7.4 served as the starting point for the prediction of the pH-dependent binding ranking. Our calculations reproduced the entire affinity ranking observed upon pH increase and most of the binding trends among inhibitors, especially at low pH. Finally, our cell-based assays indicate a possible correlation between high inhibitor affinity at both acidic and neutral pH values, with optimal cell response, a result that may open new venues for the search of potent BACE-1 inhibitors that are active at the cellular level.
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18.
  • Mueller, Stefanie H., et al. (author)
  • Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
  • 2023
  • In: Genome Medicine. - : BioMed Central (BMC). - 1756-994X. ; 15
  • Journal article (peer-reviewed)abstract
    • Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes.Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry.Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 x 10(-6)) and AC058822.1 (P = 1.47 x 10(-4)), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C.Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 x 10(-5)), demonstrating the importance of diversifying study cohorts.
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19.
  • Ortiz-Rodriguez, Jose Manuel, et al. (author)
  • The incorporation of cystine by the soluble carrier family 7 member 11 (SLC7A11) is a component of the redox regulatory mechanism in stallion spermatozoa
  • 2019
  • In: Biology of Reproduction. - : OXFORD UNIV PRESS INC. - 0006-3363 .- 1529-7268. ; 101:1, s. 208-222
  • Journal article (peer-reviewed)abstract
    • Oxidative stress is considered amajor mechanism causing sperm damage during cryopreservation and storage, and underlies male factor infertility. Currently, oxidative stress is no longer believed to be caused only by the overproduction of reactive oxygen species, but rather by the deregulation of redox signaling and control mechanisms. With this concept in mind, here, we describe for the first time the presence of the soluble carrier family 7 member 11 (SLC7A11) antiporter, which exchanges extracellular cystine (Cyss) for intracellular glutamate, in stallion spermatozoa, as well as its impact on sperm function using the specific inhibitor sulfasalazine. Spermatozoa incubated with Cyss exhibited an increased intracellular GSH content compared with controls (P amp;lt; 0.01): 50% in fresh extended stallion spermatozoa and 30% in frozen-thawed spermatozoa. This effect was prevented by the addition of sulfasalazine to the media. Cystine supplementation also reduced the oxidation-reduction potential of spermatozoa, with sulfasalazine only preventing this effect on fresh spermatozoa that were incubated for 3 h at 37 degrees C, but not in frozen-thawed spermatozoa. While sulfasalazine reduced the motility of frozen-thawed spermatozoa, it increased motility in fresh samples. The present findings provide new and relevant data on the mechanism regulating the redox status of spermatozoa and suggest that a different redox regulatory mechanism exists in cryopreserved spermatozoa, thus providing new clues to improve current cryopreservation technologies and treat male factor infertility. Summary Sentence The SLC7A11 antiporter that exchanges cystine by intracellular glutamate is present and functional in stallion spermatozoa, but cryopreserved spermatozoa may present altered functionality.
  •  
20.
  • Perez-Nadales, Elena, et al. (author)
  • Predictors of mortality in solid organ transplant recipients with bloodstream infections due to carbapenemase-producing Enterobacterales : The impact of cytomegalovirus disease and lymphopenia
  • 2020
  • In: American Journal of Transplantation. - : WILEY. - 1600-6135 .- 1600-6143. ; 20:6, s. 1629-1641
  • Journal article (peer-reviewed)abstract
    • Treatment of carbapenemase-producing Enterobacterales bloodstream infections in solid organ transplant recipients is challenging. The objective of this study was to develop a specific score to predict mortality in solid organ transplant recipients with carbapenemase-producing Enterobacterales bloodstream infections. A multinational, retrospective (2004-2016) cohort study (INCREMENT-SOT, ClinicalTrials.gov NCT02852902) was performed. The main outcome variable was 30-day all-cause mortality. The INCREMENT-SOT-CPE score was developed using logistic regression. The global cohort included 216 patients. The final logistic regression model included the following variables: INCREMENT-CPE mortality score >= 8 (8 points), no source control (3 points), inappropriate empirical therapy (2 points), cytomegalovirus disease (7 points), lymphopenia (4 points), and the interaction between INCREMENT-CPE score >= 8 and CMV disease (minus 7 points). This score showed an area under the receiver operating characteristic curve of 0.82 (95% confidence interval [CI] 0.76-0.88) and classified patients into 3 strata: 0-7 (low mortality), 8-11 (high mortality), and 12-17 (very-high mortality). We performed a stratified analysis of the effect of monotherapy vs combination therapy among 165 patients who received appropriate therapy. Monotherapy was associated with higher mortality only in the very-high (adjusted hazard ratio [HR] 2.82, 95% CI 1.13-7.06, P = .03) and high (HR 9.93, 95% CI 2.08-47.40, P = .004) mortality risk strata. A score-based algorithm is provided for therapy guidance.
  •  
21.
  • Phillips, Helen R. P., et al. (author)
  • Global distribution of earthworm diversity
  • 2019
  • In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 366:6464, s. 480-
  • Journal article (peer-reviewed)abstract
    • Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
  •  
22.
  • Rothman, Nathaniel, et al. (author)
  • A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci
  • 2010
  • In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 42:11, s. 978-984
  • Journal article (peer-reviewed)abstract
    • We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis.
  •  
23.
  • Schmit, Stephanie L, et al. (author)
  • Novel Common Genetic Susceptibility Loci for Colorectal Cancer.
  • 2019
  • In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 111:2, s. 146-157
  • Journal article (peer-reviewed)abstract
    • Background: Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.Methods: We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.Results: The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.Conclusions: This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.
  •  
24.
  • Stratoulias, Vassilis, et al. (author)
  • ARG1-expressing microglia show a distinct molecular signature and modulate postnatal development and function of the mouse brain
  • 2023
  • In: Nature Neuroscience. - : Nature Publishing Group. - 1097-6256 .- 1546-1726. ; 26:6, s. 1008-1020
  • Journal article (peer-reviewed)abstract
    • Molecular diversity of microglia, the resident immune cells in the CNS, is reported. Whether microglial subsets characterized by the expression of specific proteins constitute subtypes with distinct functions has not been fully elucidated. Here we describe a microglial subtype expressing the enzyme arginase-1 (ARG1; that is, ARG1+ microglia) that is found predominantly in the basal forebrain and ventral striatum during early postnatal mouse development. ARG1+ microglia are enriched in phagocytic inclusions and exhibit a distinct molecular signature, including upregulation of genes such as Apoe, Clec7a, Igf1, Lgals3 and Mgl2, compared to ARG1- microglia. Microglial-specific knockdown of Arg1 results in deficient cholinergic innervation and impaired dendritic spine maturation in the hippocampus where cholinergic neurons project, which in turn results in impaired long-term potentiation and cognitive behavioral deficiencies in female mice. Our results expand on microglia diversity and provide insights into microglia subtype-specific functions.
  •  
25.
  • Taiebi, Julien, et al. (author)
  • Studies on Fission with Aladin
  • 2018
  • In: FISSION AND PROPERTIES OF NEUTRON-RICH NUCLEI. - 9789813229426 ; , s. 339-340
  • Conference paper (peer-reviewed)
  •  
26.
  • Zanti, Maria, et al. (author)
  • A Likelihood Ratio Approach for Utilizing Case-Control Data in the Clinical Classification of Rare Sequence Variants : Application to BRCA1 and BRCA2
  • 2023
  • In: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 2023
  • Journal article (peer-reviewed)abstract
    • A large number of variants identified through clinical genetic testing in disease susceptibility genes are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion) can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analysis of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC) and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity-findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared with classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and preformatted Excel calculators for implementation of the method for rare variants in BRCA1, BRCA2, and other high-risk genes with known penetrance.
  •  
27.
  • Adam, A, et al. (author)
  • Abstracts from Hydrocephalus 2016.
  • 2017
  • In: Fluids and Barriers of the CNS. - : Springer Science and Business Media LLC. - 2045-8118. ; 14:Suppl 1
  • Journal article (peer-reviewed)
  •  
28.
  • Ali, Alaa M. G., et al. (author)
  • Alcohol Consumption and Survival after a Breast Cancer Diagnosis: A Literature-Based Meta-analysis and Collaborative Analysis of Data for 29,239 Cases
  • 2014
  • In: Cancer Epidemiology Biomarkers & Prevention. - 1538-7755 .- 1055-9965. ; 23:6, s. 934-945
  • Journal article (peer-reviewed)abstract
    • Background: Evidence for an association of alcohol consumption with prognosis after a diagnosis of breast cancer has been inconsistent. We have reviewed and summarized the published evidence and evaluated the association using individual patient data from multiple case cohorts. Methods: A MEDLINE search to identify studies published up to January 2013 was performed. We combined published estimates of survival time for "moderate drinkers" versus nondrinkers. An analysis of individual participant data using Cox regression was carried out using data from 11 case cohorts. Results: We identified 11 published studies suitable for inclusion in the meta-analysis. Moderate postdiagnosis alcohol consumption was not associated with overall survival [HR, 0.95; 95% confidence interval (CI), 0.85-1.05], but there was some evidence of better survival associated with prediagnosis consumption (HR, 0.80; 95% CI, 0.73-0.88). Individual data on alcohol consumption for 29,239 cases with 4,839 deaths were available from the 11 case cohorts, all of which had data on estrogen receptor (ER) status. For women with ER-positive disease, there was little evidence that pre-or postdiagnosis alcohol consumption is associated with breast cancer-specific mortality, with some evidence of a negative association with all-cause mortality. On the basis of a single study, moderate postdiagnosis alcohol intake was associated with a small reduction in breast cancer-specific mortality for women with ER-negative disease. There was no association with prediagnosis intake for women with ER-negative disease. Conclusion: There was little evidence that pre- or post-diagnosis alcohol consumption is associated with breast cancer-specific mortality for women with ER-positive disease. There was weak evidence that moderate post-diagnosis alcohol intake is associated with a small reduction in breast cancer-specific mortality in ER-negative disease. Impact: Considering the totality of the evidence, moderate postdiagnosis alcohol consumption is unlikely to have a major adverse effect on the survival of women with breast cancer. (C) 2014 AACR.
  •  
29.
  • Andrews, Harry Arthur, et al. (author)
  • Novel tools and observables for jet physics in heavy-ion collisions
  • 2020
  • In: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 47:6
  • Journal article (peer-reviewed)abstract
    • Studies of fully-reconstructed jets in heavy-ion collisions aim at extracting thermodynamical and transport properties of hot and dense QCD matter. Recently, a plethora of new jet substructure observables have been theoretically and experimentally developed that provide novel precise insights on the modifications of the parton radiation pattern induced by a QCD medium. This report, summarizing the main lines of discussion at the 5th Heavy Ion Jet Workshop and CERN TH institute 'Novel tools and observables for jet physics in heavy-ion collisions' in 2017, presents a first attempt at outlining a strategy for isolating and identifying the relevant physical processes that are responsible for the observed medium-induced jet modifications. These studies combine theory insights, based on the Lund parton splitting map, with sophisticated jet reconstruction techniques, including grooming and background subtraction algorithms.
  •  
30.
  • Aoyama, T., et al. (author)
  • The anomalous magnetic moment of the muon in the Standard Model
  • 2020
  • In: Physics reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 887, s. 1-166
  • Research review (peer-reviewed)abstract
    • We review the present status of the Standard Model calculation of the anomalous magnetic moment of the muon. This is performed in a perturbative expansion in the fine-structure constant α and is broken down into pure QED, electroweak, and hadronic contributions. The pure QED contribution is by far the largest and has been evaluated up to and including O(α5) with negligible numerical uncertainty. The electroweak contribution is suppressed by (mμ/MW)2 and only shows up at the level of the seventh significant digit. It has been evaluated up to two loops and is known to better than one percent. Hadronic contributions are the most difficult to calculate and are responsible for almost all of the theoretical uncertainty. The leading hadronic contribution appears at O(α2) and is due to hadronic vacuum polarization, whereas at O(α3) the hadronic light-by-light scattering contribution appears. Given the low characteristic scale of this observable, these contributions have to be calculated with nonperturbative methods, in particular, dispersion relations and the lattice approach to QCD. The largest part of this review is dedicated to a detailed account of recent efforts to improve the calculation of these two contributions with either a data-driven, dispersive approach, or a first-principle, lattice-QCD approach. The final result reads aμSM = 116 591 810(43) x 10-11 and is smaller than the Brookhaven measurement by 3.7 σ. The experimental uncertainty will soon be reduced by up to a factor four by the new experiment currently running at Fermilab, and also by the future J-PARC experiment. This and the prospects to further reduce the theoretical uncertainty in the near future - which are also discussed here - make this quantity one of the most promising places to look for evidence of new physics.
  •  
31.
  • Babjuk, Marko, et al. (author)
  • European Association of Urology Guidelines on Non–muscle-invasive Bladder Cancer (Ta, T1, and Carcinoma in Situ)
  • 2022
  • In: European Urology. - : Elsevier BV. - 0302-2838. ; 81:1, s. 75-94
  • Research review (peer-reviewed)abstract
    • Context: The European Association of Urology (EAU) has released an updated version of the guidelines on non–muscle-invasive bladder cancer (NMIBC). Objective: To present the 2021 EAU guidelines on NMIBC. Evidence acquisition: A broad and comprehensive scoping exercise covering all areas of the NMIBC guidelines since the 2020 version was performed. Databases covered by the search included Medline, EMBASE, and the Cochrane Libraries. Previous guidelines were updated, and the level of evidence and grade of recommendation were assigned. Evidence synthesis: Tumours staged as Ta, T1 and carcinoma in situ (CIS) are grouped under the heading of NMIBC. Diagnosis depends on cystoscopy and histological evaluation of tissue obtained via transurethral resection of the bladder (TURB) for papillary tumours or via multiple bladder biopsies for CIS. For papillary lesions, a complete TURB is essential for the patient's prognosis and correct diagnosis. In cases for which the initial resection is incomplete, there is no muscle in the specimen, or a T1 tumour is detected, a second TURB should be performed within 2–6 wk. The risk of progression may be estimated for individual patients using the 2021 EAU scoring model. On the basis of their individual risk of progression, patients are stratified as having low, intermediate, high, or very high risk, which is pivotal to recommending adjuvant treatment. For patients with tumours presumed to be at low risk and for small papillary recurrences detected more than 1 yr after a previous TURB, one immediate chemotherapy instillation is recommended. Patients with an intermediate-risk tumour should receive 1 yr of full-dose intravesical bacillus Calmette-Guérin (BCG) immunotherapy or instillations of chemotherapy for a maximum of 1 yr. For patients with high-risk tumours, full-dose intravesical BCG for 1–3 yr is indicated. For patients at very high risk of tumour progression, immediate radical cystectomy should be considered. Cystectomy is also recommended for BCG-unresponsive tumours. The extended version of the guidelines is available on the EAU website at https://uroweb.org/guideline/non-muscle-invasive-bladder-cancer/. Conclusions: These abridged EAU guidelines present updated information on the diagnosis and treatment of NMIBC for incorporation into clinical practice. Patient summary: The European Association of Urology has released updated guidelines on the classification, risk factors, diagnosis, prognostic factors, and treatment of non–muscle-invasive bladder cancer. The recommendations are based on the literature up to 2020, with emphasis on the highest level of evidence. Classification of patients as having low, intermediate, or and high risk is essential in deciding on suitable treatment. Surgical removal of the bladder should be considered for tumours that do not respond to bacillus Calmette-Guérin (BCG) treatment and tumours with the highest risk of progression.
  •  
32.
  • Baudette, Maxime, 1989-, et al. (author)
  • Validating a real-time PMU-based application for monitoring of sub-synchronous wind farm oscillations
  • 2014
  • In: 2014 IEEE PES Innovative Smart Grid Technologies Conference. - 9781479936526 ; , s. 1-5
  • Conference paper (peer-reviewed)abstract
    • This paper presents validation experiments performed on a Phasor Measurement Unit (PMU) based fast oscillation detection application. The monitoring application focuses on the detection of sub-synchronous oscillations, utilizing real-time measurements from PMUs. The application was first tested through Hardware-In-the-Loop (HIL) simulation. Validation experiments were carried out with a different set-up by utilizing a micro grid laboratory. This second experimental set-up as well as the results of the validation experiments are presented in this paper.
  •  
33.
  • Brugulat-Serrat, Anna, et al. (author)
  • APOE -ε4 modulates the association between regional amyloid deposition and cognitive performance in cognitively unimpaired middle-aged individuals
  • 2023
  • In: EJNMMI Research. - : Springer Science and Business Media LLC. - 2191-219X. ; 13:1
  • Journal article (peer-reviewed)abstract
    • Purpose: To determine whether the APOE-ε4 allele modulates the relationship between regional β-amyloid (Aβ) accumulation and cognitive change in middle-aged cognitively unimpaired (CU) participants. Methods: The 352 CU participants (mean aged 61.1 [4.7] years) included completed two cognitive assessments (average interval 3.34 years), underwent [18F]flutemetamol Aβ positron emission tomography (PET), T1w magnetic resonance imaging (MRI), as well as APOE genotyping. Global and regional Aβ PET positivity was assessed across five regions-of-interest by visual reading (VR) and regional Centiloids. Linear regression models were developed to examine the interaction between regional and global Aβ PET positivity and APOE-ε4 status on longitudinal cognitive change assessed with the Preclinical Alzheimer’s Cognitive Composite (PACC), episodic memory, and executive function, after controlling for age, sex, education, cognitive baseline scores, and hippocampal volume. Results: In total, 57 participants (16.2%) were VR+ of whom 41 (71.9%) were APOE-ε4 carriers. No significant APOE-ε4*global Aβ PET interactions were associated with cognitive change for any cognitive test. However, APOE-ε4 carriers who were VR+ in temporal areas (n = 19 [9.81%], p = 0.04) and in the striatum (n = 8 [4.14%], p = 0.01) exhibited a higher decline in the PACC. The temporal areas findings were replicated when regional PET positivity was determined with Centiloid values. Regionally, VR+ in the striatum was associated with higher memory decline. As for executive function, interactions between APOE-ε4 and regional VR+ were found in temporal and parietal regions, and in the striatum. Conclusion: CU APOE-ε4 carriers with a positive Aβ PET VR in regions known to accumulate amyloid at later stages of the Alzheimer’s disease (AD) continuum exhibited a steeper cognitive decline. This work supports the contention that regional VR of Aβ PET might convey prognostic information about future cognitive decline in individuals at higher risk of developing AD. ClinicalTrials.gov Identifier: NCT02485730. Registered 20 June 2015 https://clinicaltrials.gov/ct2/show/NCT02485730 and ClinicalTrials.gov Identifier:NCT02685969. Registered 19 February 2016 https://clinicaltrials.gov/ct2/show/NCT02685969.
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34.
  • Brönnimann, Stefan, et al. (author)
  • Unlocking Pre-1850 Instrumental Meteorological Records : A Global Inventory
  • 2019
  • In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 100:12, s. ES389-ES413
  • Journal article (peer-reviewed)abstract
    • Instrumental meteorological measurements from periods prior to the start of national weather services are designated early instrumental data. They have played an important role in climate research as they allow daily to decadal variability and changes of temperature, pressure, and precipitation, including extremes, to be addressed. Early instrumental data can also help place twenty-first century climatic changes into a historical context such as defining preindustrial climate and its variability. Until recently, the focus was on long, high-quality series, while the large number of shorter series (which together also cover long periods) received little to no attention. The shift in climate and climate impact research from mean climate characteristics toward weather variability and extremes, as well as the success of historical reanalyses that make use of short series, generates a need for locating and exploring further early instrumental measurements. However, information on early instrumental series has never been electronically compiled on a global scale. Here we attempt a worldwide compilation of metadata on early instrumental meteorological records prior to 1850 (1890 for Africa and the Arctic). Our global inventory comprises information on several thousand records, about half of which have not yet been digitized (not even as monthly means), and only approximately 20% of which have made it to global repositories. The inventory will help to prioritize data rescue efforts and can be used to analyze the potential feasibility of historical weather data products. The inventory will be maintained as a living document and is a first, critical, step toward the systematic rescue and reevaluation of these highly valuable early records. Additions to the inventory are welcome.
  •  
35.
  • Cantillo-Luna, Sergio, et al. (author)
  • Locational Marginal Price Forecasting Using SVR-Based Multi-Output Regression in Electricity Markets
  • 2022
  • In: Energies. - : MDPI AG. - 1996-1073. ; 15:1
  • Journal article (peer-reviewed)abstract
    • Electricity markets provide valuable data for regulators, operators, and investors. The use of machine learning methods for electricity market data could provide new insights about the market, and this information could be used for decision-making. This paper proposes a tool based on multi-output regression method using support vector machines (SVR) for LMP forecasting. The input corresponds to the active power load of each bus, in this case obtained through Monte Carlo simulations, in order to forecast LMPs. The LMPs provide market signals for investors and regulators. The results showed the high performance of the proposed model, since the average prediction error for fitting and testing datasets of the proposed method on the dataset was less than 1%. This provides insights into the application of machine learning method for electricity markets given the context of uncertainty and volatility for either real-time and ahead markets.
  •  
36.
  • Castillejo-Lopez, Casimiro, et al. (author)
  • Genetic and physical interaction of the B-cell systemic lupus erythematosus-associated genes BANK1 and BLK
  • 2012
  • In: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 71:1, s. 136-142
  • Journal article (peer-reviewed)abstract
    • ObjectivesAltered signalling in B cells is a predominant feature of systemic lupus erythematosus (SLE). The genes BANK1 and BLK were recently described as associated with SLE. BANK1 codes for a B-cell-specific cytoplasmic protein involved in B-cell receptor signalling and BLK codes for an Src tyrosine kinase with important roles in B-cell development. To characterise the role of BANK1 and BLK in SLE, a genetic interaction analysis was performed hypothesising that genetic interactions could reveal functional pathways relevant to disease pathogenesis.MethodsThe GPAT16 method was used to analyse the gene-gene interactions of BANK1 and BLK. Confocal microscopy was used to investigate co-localisation, and immunoprecipitation was used to verify the physical interaction of BANK1 and BLK.ResultsEpistatic interactions between BANK1 and BLK polymorphisms associated with SLE were observed in a discovery set of 279 patients and 515 controls from northern Europe. A meta-analysis with 4399 European individuals confirmed the genetic interactions between BANK1 and BLK. As BANK1 was identified as a binding partner of the Src tyrosine kinase LYN, the possibility that BANK1 and BLK could also show a protein-protein interaction was tested. The co-immunoprecipitation and co-localisation of BLK and BANK1 were demonstrated. In a Daudi cell line and primary naive B cells endogenous binding was enhanced upon B-cell receptor stimulation using anti-IgM antibodies.ConclusionsThis study shows a genetic interaction between BANK1 and BLK, and demonstrates that these molecules interact physically. The results have important consequences for the understanding of SLE and other autoimmune diseases and identify a potential new signalling pathway.
  •  
37.
  • Castineira-Alvarino, M., et al. (author)
  • The role of high fat diet in the development of complications of chronic pancreatitis
  • 2013
  • In: Clinical Nutrition. - : Elsevier BV. - 0261-5614. ; 32:5, s. 830-836
  • Journal article (peer-reviewed)abstract
    • Background: Little is known about risk factors for complications in chronic pancreatitis (CP). High fat diet (HFD) has been demonstrated to aggravate pancreatic injury in animal models. The aim of this study was to investigate the role of HFD in age at diagnosis of CP and probability of CP related complications. Methods: A cross-sectional case-case study was performed within a prospectively collected cohort of patients with CP. Diagnosis and morphological severity of CP was established by endoscopic ultrasound. Pancreatic exocrine insufficiency (PEI) was diagnosed by C-13 mixed triglyceride breath test. Fat intake was assessed by a specific nutritional questionnaire. Odds ratios (OR) for CP related complications were estimated by multivariate logistic regression analysis. Results: 168 patients were included (128 (76.2%) men, mean age 44 years (SD 13.5)). Etiology of CP was alcohol abuse in 89 patients (53.0%), other causes in 30 (17.9%) and idiopathic in the remaining 49 subjects (29.2%). 24 patients (14.3%) had a HFD. 68 patients (40.5%) had continuous abdominal pain, 39 (23.2%) PEI and 43 (25.7%) morphologically severe CP. HFD was associated with an increased probability for continuous abdominal pain (OR = 2.84 (95%Cl, 1.06-7.61)), and a younger age at diagnosis (37.0 +/- 13.9 versus 45.8 +/- 13.0 years, p = 0.03) but not with CF related complications after adjusting for sex, years of follow-up, alcohol and tobacco consumption, etiology and body mass index. Conclusions: Compared with a normal fat diet, HFD is associated with a younger age at diagnosis of CP and continuous abdominal pain, but not with severity and complications of the disease. (C) 2013 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.
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38.
  • Conti, David, V, et al. (author)
  • Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction
  • 2021
  • In: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 53:1, s. 65-75
  • Journal article (peer-reviewed)abstract
    • Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction. A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.
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39.
  • 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.
  •  
40.
  • De Angelis, A., et al. (author)
  • Science with e-ASTROGAM A space mission for MeV-GeV gamma-ray astrophysics
  • 2018
  • In: Journal of High Energy Astrophysics. - : Elsevier. - 2214-4048 .- 2214-4056. ; 19, s. 1-106
  • Journal article (peer-reviewed)abstract
    • e-ASTROGAM ('enhanced ASTROGAM') is a breakthrough Observatory space mission, with a detector composed by a Silicon tracker, a calorimeter, and an anticoincidence system, dedicated to the study of the non-thermal Universe in the photon energy range from 0.3 MeV to 3 GeV - the lower energy limit can be pushed to energies as low as 150 keV for the tracker, and to 30 keV for calorimetric detection. The mission is based on an advanced space-proven detector technology, with unprecedented sensitivity, angular and energy resolution, combined with polarimetric capability. Thanks to its performance in the MeV-GeV domain, substantially improving its predecessors, e-ASTROGAM will open a new window on the non-thermal Universe, making pioneering observations of the most powerful Galactic and extragalactic sources, elucidating the nature of their relativistic outflows and their effects on the surroundings. With a line sensitivity in the MeV energy range one to two orders of magnitude better than previous generation instruments, e-ASTROGAM will determine the origin of key isotopes fundamental for the understanding of supernova explosion and the chemical evolution of our Galaxy. The mission will provide unique data of significant interest to a broad astronomical community, complementary to powerful observatories such as LIGO-Virgo-GEO600-KAGRA, SKA, ALMA, E-ELT, TMT, LSST, JWST, Athena, CTA, IceCube, KM3NeT, and LISA.
  •  
41.
  • Domínguez-Carretero, Diego, et al. (author)
  • Ultramafic-hosted volcanogenic massive sulfide deposits from Cuban ophiolites
  • 2022
  • In: Journal of South American Earth Sciences. - : Elsevier. - 0895-9811 .- 1873-0647. ; 119
  • Journal article (peer-reviewed)abstract
    • Ultramafic-hosted volcanogenic massive sulfide deposits (UM-VMS) located in the Havana-Matanzas ophiolite (Cuba) are the only known example of this type of mineralization in the Caribbean realm. UM-VMS from Havana-Matanzas are enriched in Cu, Ni, Co, Au, and Ag. The mineralization consists of massive sulfide bodies mostly composed of pyrrhotite and hosted by serpentinized upper mantle peridotites. Chemical composition of unaltered cores in Cr-spinel grains found within the massive sulfide mineralization and in the peridotite host indicates formation in the fore-arc region of the Greater Antilles volcanic arc. A first stage of serpentinization probably took place prior to the sulfide mineralization event. The UM-VMS mineralization formed by the near-complete replacement of the silicate assemblage of partially serpentinized peridotites underneath the seafloor. The sequence of sulfide mineralization has been divided into two stages. The first stage is characterized by a very reduced hydrothermal mineral assemblage consisting of pyrrhotite, Co–Ni–Fe diarsenides, chalcopyrite, Co-rich pentlandite, and electrum. In the second stage, pyrite and Co–Ni–Fe sulfarsenides partially replaced pyrrhotite and diarsenides, respectively, under a more oxidizing regime during the advanced stages of ongoing serpentinization. The proposed conceptual genetic model presented here can be useful for future exploration targeting this type of deposit in the Caribbean region and elsewhere.
  •  
42.
  • Dominguez-Garcia, José Luís, et al. (author)
  • Validation Experiment Design of a PMU-€“Based Application for Detection of Sub-Synchronous Oscillations
  • 2015
  • In: 15th IEEE International Conference on Environment and Electrical Engineering. - : IEEE Computer Society Digital Library. ; , s. 1898-1903
  • Conference paper (peer-reviewed)abstract
    • This paper presents an approach to design laboratory experiments able to test the functional performance of a PMU-based application. The function of this application is to detect sub-synchronous oscillatory dynamics product of wind farm-to-grid interactions. The designed experiments are carried out in operation conditions similar to those that the PMU-based application would experience in field implementations, while the approach adopted for experiment design takes into account technical limitations of laboratory equipment. The experiments are performed in a laboratory which has been equipped with synchrophasor technology for the purposes of this work. Real PMU devices physically connected on a small replica of a three-phase low voltage micro-grid where oscillations can be systematically injected.
  •  
43.
  • Dominguez, Jose L., et al. (author)
  • Experimental and 'in silico' analysis of the effect of pH on HIV-1 protease inhibitor affinity : Implications for the charge state of the protein ionogenic groups
  • 2012
  • In: Bioorganic & Medicinal Chemistry. - : Elsevier BV. - 0968-0896 .- 1464-3391. ; 20:15, s. 4838-4847
  • Journal article (peer-reviewed)abstract
    • The pH dependence of the HIV-1 protease inhibitor affinity was studied by determining the interaction kinetics of a series of inhibitors at three pH values by surface plasmon resonance (SPR) biosensor analysis. The results were rationalized by molecular mechanics based protocols that have as a starting point the structures of the HIV-1 protease inhibitor complexes differing in the protonation states as predicted by our calculations. The SPR experiments indicate a variety of binding affinity pH dependencies which are rather well reproduced by our simulations. Moreover, our calculations are able to pinpoint the possible changes in the charged state of the protein binding site and of the inhibitor that underlie the observed effects of the pH on binding affinity. The combination of SPR and molecular mechanics calculations has afforded novel insights into the pH dependence of inhibitor interactions with their target. This work raises the possibility of designing inhibitors with different pH binding affinity profiles to the ones described here.
  •  
44.
  • Domínguez-Rodrigo, Manuel, et al. (author)
  • Early Pleistocene faunivorous hominins were not kleptoparasitic, and this impacted the evolution of human anatomy and socio-ecology
  • 2021
  • In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Humans are unique in their diet, physiology and socio-reproductive behavior compared to other primates. They are also unique in the ubiquitous adaptation to all biomes and habitats. From an evolutionary perspective, these trends seem to have started about two million years ago, coinciding with the emergence of encephalization, the reduction of the dental apparatus, the adoption of a fully terrestrial lifestyle, resulting in the emergence of the modern anatomical bauplan, the focalization of certain activities in the landscape, the use of stone tools, and the exit from Africa. It is in this period that clear taphonomic evidence of a switch in diet with respect to Pliocene hominins occurred, with the adoption of carnivory. Until now, the degree of carnivorism in early humans remained controversial. A persistent hypothesis is that hominins acquired meat irregularly (potentially as fallback food) and opportunistically through klepto-foraging. Here, we test this hypothesis and show, in contrast, that the butchery practices of early Pleistocene hominins (unveiled through systematic study of the patterning and intensity of cut marks on their prey) could not have resulted from having frequent secondary access to carcasses. We provide evidence of hominin primary access to animal resources and emphasize the role that meat played in their diets, their ecology and their anatomical evolution, ultimately resulting in the ecologically unrestricted terrestrial adaptation of our species. This has major implications to the evolution of human physiology and potentially for the evolution of the human brain.
  •  
45.
  • Escala-Garcia, Maria, et al. (author)
  • A network analysis to identify mediators of germline-driven differences in breast cancer prognosis
  • 2020
  • In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies similar to 7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.
  •  
46.
  • Figueroa, Jonine D., et al. (author)
  • Identification of a novel susceptibility locus at 13q34 and refinement of the 20p12.2 region as a multi-signal locus associated with bladder cancer risk in individuals of European ancestry
  • 2016
  • In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 25:6, s. 1203-1214
  • Journal article (peer-reviewed)abstract
    • Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P < 1 × 10−6), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 × 10−11) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 × 10−10). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast, we detected two signals in the 20p12.2 region—the first signal is marked by rs6104690, and the second signal is marked by two moderately correlated SNPs (r2 = 0.53), rs6108803 and the previously reported rs62185668. The second 20p12.2 signal is more strongly associated with the risk of muscle-invasive (T2-T4 stage) compared with non-muscle-invasive (Ta, T1 stage) bladder cancer (case–case P ≤ 0.02 for both rs62185668 and rs6108803). Functional analyses are needed to explore the biological mechanisms underlying these novel genetic associations with risk for bladder cancer.
  •  
47.
  • Frawley, Timothy H., et al. (author)
  • Self-governance mediates small-scale fishing strategies, vulnerability and adaptive response
  • 2024
  • In: Global Environmental Change. - 0959-3780 .- 1872-9495. ; 84
  • Journal article (peer-reviewed)abstract
    • As global change accelerates, natural resource-dependent communities must respond and adapt. Small-scale fisheries, essential for coastal livelihoods and food security, are considered among the most vulnerable of these coupled social-ecological systems. While previous studies have examined vulnerability and adaptation in fisheries at the individual, household, and community level, these scales of organization are inconsistent with many of the legal and regulatory frameworks that function in practice to mediate behavior, decision-making, and adaptation. Here, we use cooperative- and privately-owned fishing enterprises in Northwest Mexico as a case study to examine how different forms of marine self-governance experience and respond to climate shocks. Leveraging social-ecological network methods to examine changes in fisheries participation and vulnerability during a recent period of pronounced regional oceanographic change, our analysis suggests that: 1) different forms of SSF self-governance (and the fishing strategies and harvest portfolios with which they are associated) help determine the impacts of and response to environmental change; and 2) that there may be important tradeoffs between short-term responses which function to prevent or mitigate lost fishing revenue and long-term changes in climate vulnerability. In particular large fishing cooperatives, predicted to be highly vulnerable on the basis of network theoretic metrics, exceeded expectations (maintaining or increasing resource revenues) while demonstrating a degree of path dependency that may function to increase sensitivity and undermine resilience as climate change progresses. In providing an empirical evaluation of how self-governance arrangements characterized by different group sizes, access regimes and levels of cooperation respond to system perturbation, we aim to advance common pool resource theory while offering targeted guidance for the development of more nuanced and equitable climate adaptation policies.
  •  
48.
  • García, Diego, et al. (author)
  • Conditioned Fully Convolutional Denoising Autoencoder for Energy Disaggregation
  • 2023
  • In: Artificial Intelligence Applications and Innovations. AIAI 2023 IFIP WG 12.5 International Workshops. - : Springer Nature. - 9783031341731 - 9783031341717 ; , s. 421-433
  • Conference paper (peer-reviewed)abstract
    • Energy management increasingly requires tools to support decisions for improving consumption. This is achieved not only obtaining feedback from current systems but also using prior knowledge about human behaviour. The advances of data-driven models provide techniques like Non-Intrusive Load Monitoring (NILM) which are capable of estimating energy demand of appliances from total consumption. In addition, deep learning models have improved accuracy in energy disaggregation using separated networks for each device. However, the complexity can increase in large facilities and feedback may be impaired for a proper interpretation. In this work, a deep neural network based on a Fully Convolutional denoising AutoEncoder is proposed for energy disaggregation that uses a conditioning input to modulate the estimation aimed to one specific appliance. The model performs a complete disaggregation using a network whose modulation to target the estimation can be steered by the user. Experiments are done using data from a hospital facility and evaluating reconstruction errors and computational efficiency. The results show acceptable errors compared to methods that require various networks and a reduction of the complexity and computational costs, which can allow the user to be integrated into the analysis loop.
  •  
49.
  • Goded, Sandra, et al. (author)
  • Effects of eucalyptus plantations on avian and herb species richness and composition in North-West Spain
  • 2019
  • In: Global Ecology & Conservation. - : Elsevier BV. - 2351-9894. ; 19:e00690
  • Journal article (peer-reviewed)abstract
    • Eucalyptus plantations have been established in many areas of the world due to their fast growth and profitability. In NW Spain, Eucalyptus plantations now cover a larger area than native forests. Although Eucalyptus plantations have been shown to affect biodiversity, relatively few studies have compared their effect on multiple taxonomic groups and different aspects of biodiversity. We compared herb and bird species richness and bird abundance between 14 paired patches of native deciduous forest and Eucalyptus plantations in a heterogeneous agro-forest region of NW Spain. We also investigated whether Eucalyptus plantations contribute to shifts in community composition by analysing species nestedness and turnover. We found that species richness of both herbs and birds was consistently lower in Eucalyptus plantations compared to native forests. Furthermore, the abundances of bird species characteristic of agricultural, forest, scrubland and other habitats, were all much lower in Eucalyptus plantations than in native forests. Herb and bird communities were also significantly dissimilar between the two habitats, but as a result of different ecological processes. Species turnover explained variation between habitats in herb composition, such that species present in native forests were typical for both farmland and forest habitats, whereas those present in Eucalyptus plantations were typical for scrub and farmland habitats. In contrast, bird assemblages showed a significant nested subset pattern, with fewer species in Eucalyptus plantations compared to native forests. In total, the relative abundance of cavity-nesting forest birds was at least 64% higher in native forests. Our results show that Eucalyptus plantations cannot replace native forests as they harbour different herb species and only a subset of the bird species found in native forests. Considering the current rate of increase of Eucalyptus plantations and the fragmentation of native forests in NW Spain, a lack of conservation of native forests could result in future loss of biodiversity in general and forest specialist species in particular.
  •  
50.
  • Goded, Sandra, et al. (author)
  • Effects of organic farming on bird diversity in North-West Spain
  • 2018
  • In: Agriculture, Ecosystems and Environment. - : Elsevier BV. - 0167-8809. ; 257, s. 60-67
  • Journal article (peer-reviewed)abstract
    • Many studies have investigated effects of organic farming on the abundance and diversity of farmland birds, but few have considered how these effects vary between seasons. We analysed the effects of organic farming during an entire year in a previously understudied region, Galicia (North-West Spain), a relatively heterogeneous landscape which is an important wintering and breeding ground for birds. We compared bird abundance and species richness on farmland in 0.5 × 0.5 km study squares on 16 paired organic and conventional farms. In addition, at each organic farm we compared bird abundance and species richness between one similar study square with a high and one with a low proportion of organic farming, respectively. During winter, species richness was higher in organic farms compared to conventional ones. Throughout the year bird abundance was higher in squares with a high proportion of organic farming compared to those with a low proportion of organic farming, but only when they were surrounded by land with a low proportion of agriculture. Bird abundance in organic squares increased with the proportion of land being native forest resulting in more mosaic landscapes. Seedeaters particularly benefited from organic farming, with high abundances on organic farms in landscapes with a low proportion of agricultural land. Our results suggest that organic farming can benefit farmland birds in heterogeneous landscapes, particularly during winter, probably due to increased food availability, but future studies are needed to clarify the mechanism behind the effects.
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