BUSCADOR RECOLECTA

Data file includes information about identity of each sampled individual, the species id, nest type, age, biometric measurements, the mean of the antagonistic halos shown against each 9 indicator bacteria, the antagonistic activity (average values of the width of antagonistic halos (mm) when tested against each of the nine indicator bacteria), the antagonistic range (Shannon index of the antagonistic activity) and the total density of bacteria on the gland., Ester Martínez Renau was financed by a predoctoral contract PRE2018-085378) while the whole research group received funds from the projects CGL2017-83103-P, PID2020-117429GB-C21 and PID2020-117429GB-C22, funded by the Ministerio de Ciencia e Innovación/Agencia Estatal de Investigación/10.13039/501100011033 and by “Fondo Europeo de Desarrollo Regional, a way of making Europe, Peer reviewed

[Description of methods used for collection/generation of data] In both stations a SAMI-pH (Sunburst Sensors LCC) was attached, at 1 m in the Bay of Palma and at 4 m depth in Cabrera. The pH sensors were measuring pH, in the total scale (pH𝑇T), hourly since December 2018 in the Bay of Palma and since November 2019 in Cabrera. The sensor precision and accuracy are < 0.001 pH and ± 0.003 pH units, respectively. Monthly maintenance of the sensors was performed including data download and surface cleaning. Temperature and salinity for the Cabrera mooring line was obtained starting November 2019 with a CT SBE37 (Sea-Bird Scientific©). Accuracy of the CT is ± 0.002 ∘C for temperature and ± 0.003 mS cm−1−1 for conductivity. Additionally, oxygen data from a SBE 63 (Sea-Bird Scientific ©) sensor attached to the CT in Cabrera were used. Accuracy of oxygen sensors is ± 2% for the SBE 63., [Methods for processing the data] Periodically water samplings for dissolved oxygen (DO), pH in total scale at 25 ∘C (pH𝑇25) and total alkalinity (TA) were obtained during the sensor maintenance campaigns. DO and (pH𝑇25) samples were collected in order to validate the data obtained by the sensors. DO concentrations were evaluated with the Winkler method modified by Benson and Krause by potentiometric titration with a Metrohm 808 Titrando with a accuracy of the method of ± 2.9 μmol kg−1μmol kg−1 and with an obtained standard deviation from the sensors data and the water samples collected of ± 5.9 μmol kg−1μmol kg−1. pH𝑇25T25 data was obtained by the spectrophotometric method with a Shimadzu UV-2501 spectrophotometer containing a 25 ∘C-thermostated cells with unpurified m-cresol purple as indicator following the methodology established by Clayton and Byrne by using Certified Reference Material (CRM Batch #176 supplied by Prof. Andrew Dickson, Scripps Institution of Oceanography, La Jolla, CA, USA). The accuracy obtained from the CRM Batch was of ± 0.0051 pH units and the precision of the method of ± 0.0034 pH units. The mean difference between the SAMI-pH and discrete samples was of 0.0017 pH units., Funding for this work was provided by the projects RTI2018-095441-B-C21 (SuMaEco) and, the BBVA Foundation project Posi-COIN and the Balearic Islands Government projects AAEE111/2017 and SEPPO (2018). SF was supported by a “Margalida Comas” postdoctoral scholarship, also from the Balearic Islands Government. FFP was supported by the BOCATS2 (PID2019-104279GB-C21) project funded by MCIN/AEI/10.13039/501100011033.This work is a contribution to CSIC’s Thematic Interdisciplinary Platform PTI WATER:iOS., Peer reviewed

[Description of methods used for collection/generation of data] Data was acquired in both stations using a SAMI-pH (Sunburst Sensors LCC) was attached, at 1 m in the Bay of Palma and at 4 m depth in Cabrera. The pH sensors were measuring pH, in the total scale (pH𝑇), hourly since December 2018 in the Bay of Palma and since November 2019 in Cabrera. The sensor precision and accuracy are < 0.001 pH and ± 0.003 pH units, respectively. Monthly maintenance of the sensors was performed including data download and surface cleaning. Temperature and salinity for the Cabrera mooring line was obtained starting November 2019 with a CT SBE37 (Sea-Bird Scientific©). Accuracy of the CT is ± 0.002 ∘C for temperature and ± 0.003 mS cm−1−1 for conductivity. Additionally, oxygen data from a SBE 63 (Sea-Bird Scientific ©) sensor attached to the CT in Cabrera were used. Accuracy of oxygen sensors is ± 2% for the SBE 63., [Methods for processing the data] Once data (available at https://doi.org/XXX/DigitalCSIC/XXX) was validated, several processing steps were performed to ensure an optimal training process for the neural network models. First, all the data of the time series were re-sampled by averaging the data points obtaining a daily frequency. Afterwards, a standard feature-scaling procedure (min-max normalization) was applied to every feature (temperature, salinity and oxygen) and to pHT. Finally, we built our training and validations sets as tensors with dimensions (batchsize, windowsize, 𝑁features), where batchsize is the number of examples to train per iteration, windowsize is the number of past and future points considered and 𝑁features is the number of features used to predict the target series. Temperature values below 𝑇=12.5T=12.5 °C were discarded as they are considered outliers in sensor data outside the normal range in the study area. A BiDireccional Long Short-Term Memory (BD-LSTM) neural network was selected as the best architecture to reconstruct the pHT time series, with no signs of overfitting and achieving less than 1% error in both training and validation sets. Data corresponding to the Bay of Palma were used in the selection of the best neural network architecture. The code and data used to determine the best neural network architecture can be found in a GitHub repository mentioned in the context information., Funding for this work was provided by the projects RTI2018-095441-B-C21, RTI2018-095441-B-C22 (SuMaEco) and Grant MDM-2017-0711 (María de Maeztu Excellence Unit) funded by MCIN/AEI/10.13039/501100011033 and by the “ERDF A way of making Europe", the BBVA Foundation project Posi-COIN and the Balearic Islands Government projects AAEE111/2017 and SEPPO (2018). SF was supported by a “Margalida Comas” postdoctoral scholarship, also from the Balearic Islands Government. FFP was supported by the BOCATS2 (PID2019-104279GB-C21) project funded by MCIN/AEI/10.13039/501100011033.This work is a contribution to CSIC’s Thematic Interdisciplinary Platform PTI WATER:iOS (https://pti-waterios.csic.es/)., Peer reviewed

[Methods] Peptides and proteins from cardiomyocytes were trypsin-digested using the whole proteome in-gel digestion protocol, followed by 18O labeling as previously described (Bonzon-Kulichenko, E. et al Mol. Cell. Proteomics 2011, 10, M110 003335, doi:10.1074/mcp.M110.003335). The peptide pools were separated in 24 fractions ranging from pH 3-10 by IEF on a 3100 OFFGel fractionator (Agilent, Santa Clara, CA, USA) using the standard methods for peptides recommended by the manufacturer. The recovered fractions were desalted using OMIX C18 tips (Varian, Inc, Agilent, USA), and dried down before reverse phase-high performance liquid chromatography (RP-HPLC)-LIT analysis using a Surveyor LC System coupled to a linear ion trap mass spectrometer LTQ (Thermo Fisher Scientific, Waltham, MA USA). The LTQ was operated in a data-dependent ZoomScan and MS/MS switching mode as previously described (Lopez-Ferrer, D. et al. Proteomics 2006, 6 Suppl 1, S4-11, doi:10.1002/pmic.200500375). Protein identification was done using SEQUEST algorithm (Bioworks 3.2 package, Thermo Fisher Scientific). MS/MS raw files were searched against a Rat/Mouse Swissprot database supplemented with the sequence of bovine and porcine trypsin. SEQUEST results were analyzed using the probability ratio method (Martinez-Bartolome, S et al. Mol. Cell. Proteomics 2008, 7, 1135–1145, doi:10.1074/mcp.M700239-MCP200) and discovery rates (FDR) of peptide identifications were calculated as previously described ((Navarro, P. et al. J Proteome Res 2009, 8, 1792–1796, doi:10.1021/pr800362h). Peptide identification and quantification were done as previously described (Bonzon-Kulichenko, E. et al Mol. Cell. Proteomics 2011, 10, M110 003335, doi:10.1074/mcp.M110.003335; Navarro, P.; et al. J Proteome Res 2014, 13, 1234–1247, doi:10.1021/pr4006958). Statistical significance of protein abundance changes was assayed by controling the FDR, being a FDR less than 0.05 considered to be significant. Threshold-free analysis of coordinated protein responses was performed using the SBT model, as described (García-Marqués, F. et al. Mol. Cell. Proteomics 2016, 15, 1740–1760, doi:10.1074/mcp.M115.055905)., The biochemical mechanisms of cell injury and myocardial cell death after myocardial infarction remain unresolved. Cyclooxygenase 2 (COX-2), a key enzyme in prostanoid synthesis, is expressed in human ischemic myocardium and dilated cardiomyopathy, but it is absent in healthy hearts. To assess the role of COX-2 in cardiovascular physiopathology, we developed transgenic mice, thatconstitutively express functional human COX-2 in cardiomyocytes under the control of the α-myosin heavy chain promoter. These animals had no an apparent phenotype, but were protected against ischemia-reperfusion injury in isolated hearts, with an enhanced functional recovery and diminished cellular necrosis. To further explore the phenotype of this animal model, we carried out a differential proteome analysis of wild-type vs. transgenic cardiomyocytes. Here we include the results of this proteomic study with the list of identified proteins and their quantification, Ministerio de Economia y Competitividad (SAF2013-43713-R) and Generalitat Valenciana (ACOMP/2011/120), No

En este manual se describe el procedimiento utilizado en el muestreo de suelos de las parcelas de la Red Española de NIVELII del programa ICP-Forests. Estas parcelas forman parte de la Red de Seguimiento Intensivo (Nivel II) del Programa de Cooperación internacional para la evaluación y seguimiento de los efectos de la contaminación atmosférica en los bosques (ICP Forests). En ella se establecieron a principio de los años 90 más de 860 parcelas de observación de los ecosistemas forestales más importantes de Europa. España contribuyó con 53 parcelas de seguimiento permanente repartidas por toda su geografía. La Red iniciada en España en 1993 está conformada por 53 parcelas localizadas en ecosistemas forestales representativos de nuestro país. El objetivo del muestreo inicial (1993-96) fue la caracterización físico-química y edáfica del suelo sobre el que se desarrolla la masa forestal, como punto de partida para la monitorización de los cambios temporales en sus propiedades., Convenio ICONA-INIA para prestar apoyo científico, experimental y metodológico a la creación y seguimiento de una Red de estaciones permanentes para evaluar el estado de vigor y conservación de nuestras masas forestales, mediante la vigilancia intensiva y continua de los daños ocasionados entre otros por la contaminación atmosférica (1993-97)., Peer reviewed

Una buena fotografía representa un trozo de la Naturaleza tal como estaba en el momento de ser tomada, en este caso constituye un documento científico, que conserva indefinidamente su valor, y cuya contemplación y análisis serán siempre convenientes cualquiera que sean las interpretaciones que puedan hacerse, cuando se observe ese trozo de una realidad pasada., Fototeca Forestal Española. Ministerio de Medio Ambiente., Peer reviewed

This data set contains information on the rumen microbiome of 340 dairy cows, sequenced within the METALGEN project (RTA2015-00022-C03).-- Sequenced with a MinION from Oxford Nanopore Technology., The purpose of this data set is to serve as a training exercise to predict a complex phenotype using metagenomic data within the workshop SUPREMET 2019 "Supercomputación para la predicción de enfermedades y caracteres complejos usando información del metagenoma"., METALGEN, Ministerio de Ciencia, Innovación y Universidades, RTA2015-00022-C03., Peer reviewed

Cereales de invierno 2020., Peer reviewed

[Methodological information] Velocity probability density functions (vpdfs) and breakthrough curves (BTC) for different saturation degrees (65, 70, 80, and 100) and molecular diffusion coefficents (D) were calculated from direct numerical simulation using COMSOL multiphysics as described in the paper "Solute Trapping and the Mechanisms of Non-Fickian Transport in Partially Saturated Porous Media", With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2018-000794-S)., I.B.N, M.D. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. HORIZON-MSCA-2021-PF-01 (USFT). I.B.N. , J.J.H. and M.D. acknowledge the support of the Spanish Research Agency (10.13039/501100011033), Spanish Ministry of Science and Innovation through grants CEX2018-000794-S and HydroPore PID2019-106887GB-C31. J.J.H. acknowledges the support of the Spanish Research Agency (10.13039/501100011033), the Spanish Ministry of Science and Innovation and the European Social Fund ``Investing in your future'' through the ``Ram\'on y Cajal'' fellowship (RYC-2017-22300). J.J.M. gratefully acknowledges the financial support from the Swiss National Science Foundation (SNF, grant nr. 200021 178986)., Peer reviewed

The temperature-size rule hypothesized that there is a negative relationship between the size (volume) of an organism and the temperature. This applies to both unicellular and pluricellular organisms. Here, we question this hypothesis for the particular case of protozoans, because in these organisms the volume is directly related to the consumption of prey, and on most of the occasions the true volume of the cell is unknown. To prove our arguments, we designed a series of experiments with the heterotrophic dinoflagellate O. marina, including functional and numerical responses, time-dependent acclimation responses, and estimation of the protozoan volume during long periods of starvation. Our data showed that, in fact, the observed temperature-size rule in unicellular grazers results from anabolic and catabolic imbalances, and that the relationship between size and temperature weakens after proper thermal adaptation. We also showed that once prey are fully digested, the protozoan’ size is the same irrespectively of the temperature. Finally, we set the basis for proper acclimation during short-term temperature experiments, which specifies that at least 3 days should be allowed for proper temperature acclimation. We also suggest that, for trustable experiments, the grazer should be incubated at the target prey concentration for at least 24h before conducting the experiments. The ecological implications of a lack of correlation between microzooplankton size and temperature are also discussed, This research was funded by Grant PID2020-118645RB-I00 by Ministerio de Ciencia e innovación (MCIN)/AEI/ 10.13039/501100011033 and by “ERDF A way of making Europe”. It is a contribution of the Marine Zooplankton Ecology Group (2017 SGR 87). With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), Para Oxyrrhis marina: Tasas de ingestion a diferentes concentraciones de alimento (presa/ind/d), Tasa crecimiento (µ 1/d), Volumen (µm3); para la presa (Rhodomonas salina): volume (µm3), Peer reviewed