cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.20350/digitalcsic/13865
title: Clearance and ingestion rates of different stages of the copepod Paracartia grani feeding on Rhodomonas salina [Dataset]

description: The feeding activity of copepods is crucial for the structure and functioning of marine ecosystems. Quantification of feeding rates of different copepod life stages across a range of prey densities (functional response) is essential knowledge for improvement of plankton dynamic models. In this study, we conducted experiments to compare the feeding functional responses of nauplii, copepodites, and adults of the marine copepod Paracartia grani (formerly Acartia grani) when grazing on the flagellate Rhodomonas salina. We found that all copepod stages followed a sigmoid curve in their functional responses (Holling Type III model), indicating a metabolic threshold constraining foraging effort at low prey densities. Maximum clearance rates of nauplii and copepodites increased with body mass with a power scaling factor of 1, but maximum clearance rates of adults did not follow the pattern observed for juvenile stages, likely because of the relatively small prey size used in the experiments. Copepod maximum ingestion rates, however, showed allometric scaling along ontogeny that was closer to the typical 0.75 power law and seemed to not be so dependent on prey size. The insights obtained from our study highlight stage-specific differences in copepod feeding activity, and can help improve our capability to estimate the energy flow through copepods in marine food webs
description: Number of experiment, date of experiment, temperature, bottle volume, prey species, prey species AphiaID, copepod species, copepod species AphiaID, copepod stage, prey concentration, prey size, number of copepods per bottle, copepod size, incubation time, clearance rate, ingestion rate
DOI: 10.20350/digitalcsic/13856
title: Geles poliméricos para baterías secundarias de aluminio, preparados con el disolvente eutéctico profundo uralumina (urea:AlCl3) y poli(óxido de etileno) de distintos pesos moleculares y en distintas concentraciones

description: En los vídeos aparecen ilustradas su tenacidad, su elasticidad y su carácter pegajoso en geles preparados con: Poli(óxido de etileno) de peso molecular 8000000 g mol-1, añadido a la uralumina al 1 % en peso (PEO80-1U150), Poli(óxido de etileno) de peso molecular 5000000 g mol-1 añadido también al 1% en peso (PEO50-1-U150) y Poli(óxido de etileno) de peso molecular 900000 g mol-1 añadido al 5% en peso (P9-5-U150).
description: Geles poliméricos para baterías secundarias de aluminio, preparados con el disolvente eutéctico profundo uralumina (urea:AlCl3) y poli(óxido de etileno) de distintos pesos moleculares y en distintas concentraciones. Los geles son elásticos, tenaces, termorreversibles y se pegan muy bien a los electrodos, por lo que son excelentes electrolitos en gel.
DOI: 10.20350/digitalcsic/12724
title: GFFs generated for the work titled: Impact of transposable elements on the genome of the urban malaria vector Anopheles coluzzii

description: Description: ZIP file containing 14 GFFs. All 14 files are GFFs (general feature format) which is used to represent the position of genes and other features in a reference. Seven are the GFFs comprising the de novo TE annotation obtained using REPET (Flutre et al., 2011) using a library specific for An. coluzzii in the seven genomes used in the aforementioned work. The remaining seven GFFs contain the gene transfer from the AgamP4 genome to the seven genomes used in the aforementioned work using Liftoff (Shumate et al., 2020). For more details please see http://hdl.handle.net/10261/224389
DOI: 10.20350/digitalcsic/10544
title: Lack of evidence of a Pleistocene migratory switch in current bird long-distance migrants between Eurasia and Africa

description: Climatic maps used in the study, modified from Worldclim
description: Aim: During the Plio-Pleistocene, glacial cycles shaped Northern Hemisphere species' distributions causing range contractions followed by interglacial expansions. In bird migratory species, climatic changes could result in a rapid re-shape of their distribution ranges and/or migratory behaviour, given their movement capacity. In this context, it has been suggested that long-distance North American migratory species could have lost their migratory condition during cold periods regaining it later in warmer periods. Here, we explored this hypothesis in Eurasian-African extant migratory bird species. Location: Europe and Africa Taxon: migratory birds Methods: We used Species Distribution Models to infer the present and Last Glacial Maximum (LGM) distribution of 81 trans-Saharan bird migratory species and we revised the available fossil record for the Plio-Pleistocene covering Europe and Africa. Results: Our results show a southwards reduction of the breeding distributions during the LGM compared to the present. However, the current wintering areas were somehow similar in the Pleistocene, with the Saharan belt gap always present through time, not overlapping with their breeding ranges. Main conclusions: The paleo-distributions and absence of medullary bone in Pleistocene fossils from wintering African migratory species confirm that they were migratory, providing independent support for our models that suggest the same. The hypothesis of the loss of migratory condition in these species during the Pleistocene can be rejected.
DOI: 10.20350/digitalcsic/8970
title: Lack of evidence of a Pleistocene migratory switch in current bird long-distance migrants between Eurasia and Africa
DOI: 10.20350/digitalcsic/13894
title: BED files containing Transposable Element (TE) annotations for 33 Drosophila melanogaster genomes

description: We annotated TE copies only in the euchromatic regions of the genome since heterochromatic regions are gene-poor (Smith et al. 2007) and its assembly and annotation usually require specific methods and extensive curation (Chakraborty et al. 2019; Khost et al. 2017). In this work, we considered as euchromatic those genomic regions determined by the recombination rate calculator (RRC) (Fiston-Lavier et al. 2010) available at http://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl. Such coordinates were originally calculated based on release 5 of D. melanogaster genome so we converted them to release 6 coordinates using the coord_converter.pl script from FlyBase (Gramates et al. 2017), resulting in the following regions: 2L:530,000..18,870,000; 2R:5,982,495..24,972,477; 3L:750,000..19,026,900; 3R:6,754,278..31,614,278; X:1,325,967..21,338,973. In order to determine the coordinates of the euchromatic regions in each scaffolded genome, we mapped scaffolds to the euchromatic region of the ISO1 genome using MUMmer (v3.0) (Kurtz et al. 2004). We then determined the coordinates in the scaffolded genomes by parsing MUMmer´s output and extracting the coordinates mapping at the boundaries of the euchromatic region of the ISO1 genome. After running the TEannot pipeline over the euchromatic regions of each genome, we performed a post-annotation filtering step consisting in the removal of TE copies &lt;100bp. NOTE: Coordinates in the bed files refers to the strain’s genome, not the reference. Columns in the BED files: Columns 1-3: Chr, Start, End: Coordinates for the TE annotation. NOTE: Coordinates in the bed files refers to the strain’s genome, not the reference. Column 4: TE Name Column 5: TE Size Column 6: Strand Column 7: TE Family Column 8: TE Sueper Family Column 9: TE Order Column 10: TE Class Column 11: Source of the TE family classification. Column 12: TE Length Ratio: Length ratio: TE copy / TE consensus.
description: BED files containing Transposable Element (TE) annotations for 33 Drosophila melanogaster genomes. 32 of these genomes belong to strains from natural pulations and the remaining annotation (ISO1) belongs to the reference genome (dmel6). TE were annotated using the REPET package (v.2.5) (Flutre et al. 2011; Hoede et al. 2014; Quesneville et al. 2005) witn a Manually Curated Transposable Elements (MCTE) library from Drosophila melanogaster. NOTE: Coordinates in the bed files refers to the strain’s genome, not the reference.
DOI: 10.20350/digitalcsic/13878
title: Experimental Data of the Doctoral Thesis of Gaurang Patel (ESR4. ITN TREATMENT)

description: DATA EXPLANATION: [Folder 1]. Analysis of Drug concentration in plasma and mitochondria (1h and 24 h). The xls file shows the statistics analysis of the detected concentration in plasma and mitochondrial samples after 1 and 24 hours after adding the treatment by aripripazole (Ari), dehydroaripripazole (Dehydroari) or olanzapine (Ola). The .pzfx file can be opened with GraphPad Prism 8 XML Project and shows the decreased in the concentrations across the time in plasma samples. [Folder 2]. Seahorse Data Healthy volunteer study. The two xls files show (1) the raw data obtained from the measurement of oxygen flux, oxygen consumption rate [OCR] and proton flux, extracellular acidification rate [ECAR], in the medium immediately surrounding the cells in a microplate in a Seahorse analyzer and (2) the linear regression between these data. And, the .pzfx files can be opened with GraphPad Prism 8 XML Project and show the relationships between some of the parameters showed in xls files.
DOI: 10.20350/digitalcsic/13879
title: Hydrochemical data from saline lakes in Saskatchewan in 2011

description: 1. The American brine shrimp Artemia franciscana is important in aquaculture and has become invasive in other continents, aided by dispersal via waterbirds. However, little is known about processes underlying its genetic diversity and population structure in its natural habitat in North America. These processes, including dispersal and local adaptation, are pivotal drivers of species distribution and community structure, and therefore central to aquatic biodiversity. 2. We studied 15 populations in natural saline lakes of Saskatchewan, Canada to determine the influence of variation in geological history, water chemistry, lake size and location. We aimed to determine the relative importance of isolation by distance (IBD) and isolation by environment (IBE) using the cytochrome c oxidase subunit 1 gene (CO1) as a mitochondrial marker and five nuclear microsatellite markers. 3. Geographic patterns for CO1 and microsatellites differed, with lakes clustering in different groups based on genetic distances according to the marker used. CO1 better indicated historical colonization processes, suggesting potential routes of initial colonization when lakes were formed after deglaciation 11,000-15,000 years ago. 4. Differentiation between lakes based on nuclear markers was strongly related to variation in hydrochemistry, suggested by distance-based redundancy analysis (dbRDA), but there was no indication of IBD. The ratio between alkalinity and the sum of Ca and Mg concentrations was particularly important, although a lake with a high Cl concentration caused by Potash mining also had a unique Artemia population. 5. Geochemistry is important in the adaptive radiation of anostracan crustaceans. Our study suggests it also underlies intraspecific genetic variation between populations, promoting IBE, and making dispersal ineffective when cysts are moved by birds between lakes with different hydrochemistry. This dataset was used in the following publication: Frisch, D., Lejeusne, C., Hayashi, M., Bidwell, M.T., Sánchez-Fontenla, J., Green, A.J. 2021. Brine chemistry matters: isolation by environment and by distance explain population genetic structure of Artemia franciscana in saline lakes. Freshwater Biology DOI: 10.1111/fwb.13737
DOI: 10.20350/digitalcsic/13864
title: Seguimiento de Redes Sociales del proyecto #pubarchMED

description: [ES] Conjunto de informes del seguimiento en redes sociales del proyecto #pubarchMED - Arqueología Pública en el contexto mediterráneo.
description: [EN] Set of reports (in Spanish) with an Executive report in English of the monitoring of social media for the project #pubarchMED - Public Archaeology in the Mediterranean Context.
description: Informe Final (ES): pubarchMED_InformeFinal_RedesSociales_ES (pdf).-- Executive Report (EN): pubarchMED_ExReport_SocialMedia_EN (pdf).-- Informes Anuales (ES): pubarchMED_AnualAc_RedesSociales_ES (pdf).-- Informes Mensuales (ES): pubarchMED_MensualAc_RedesSociales_ES (pdf)
DOI: 10.20350/digitalcsic/13850
title: UAV imagery in Deception Island (Antarctica): PiMetAn Antarctic campaing 2020-2021

description: February-March 2021. XXXIV Spanish Antarctic Campaign. Deception Island (Shetland of South, Antarctica). Dataset: Orthomosaic flight images.
description: This campaign report collects the orthomosaics generated with the images obtained from Unmanned Aerial Vehicles (UAV) during the XXXIV Spanish Antarctic Campaign in Deception Island (South Shetlands Islands, Antarctica) as part of the PiMetAn polar project (Ref RTI2018-098048-B-100). PiMetAn Project (http://pimetan.csic.es/) aims to evaluate the role of penguins in the biogeochemical cycles of trace elements in Antarctica and their effects on the Antarctic ecosystem. To achieve this, the Project includes, among many other activities, the use of different sensors boarded on UAVs to characterize and monitoring the regions of study. Thus, a total 42 UAV flights were carried out in different areas of Deception Island: Antarctic Spanish Base (BAE) Gabriel de Castilla, Vapour Col penguin colony, Baily Head penguin colony, Fumarole Bay, Murature’s region, Crater and Irizar lakes. The equipment used to collect the images were: these flights consists of the following UAVs and sensors: (1) Hexacopter (Condor, Dronetools ©) with three-bladed propellers with DJI6010 brushless type electric motor (130 kv) The drone could be equipped with the Micasense RedEdge-MX dual 10-band multispectral sensor, the FLIR Vue Pro R thermal camera, the Zenmuse Z30 video camera and the Alpha Sony 6000 RGB camera; (2) Quadcopter (Mavic 2 Pro, DJI ©) with integrated RGB sensor (Hasselblad Camera); and (3) Quadcopter (Phantom 4 Multispectral:P4M, DJI ©) with an integrated 5-band multispectral camera. After images were collected, orthomosaics was generated using the Pix4D Mapper software (Pix4D SA, Lausanne Switzerland).
DOI: 10.20350/digitalcsic/13835
title: Relative proportions of the volatiles compounds found in the secretion of the uropygial gland of European blackbirds (Turdus merula) according with their age and sex

description: Datos de las proporciones relativas de los compuestos volátiles presentes en la secreción de la glándula uropigial de Mirlo común (Turdus merula), que pertenecen a grandes grupos de compuestos, tales como alcoholes, aldehídos, alkanos, amidas, ácidos carboxílicos, ésteres de ácidos carboxílicos, furanonas, ketonas, pyrazinas, esteroides y ceras. Se indica en cada individuo la proporción relativa de los compuestos detectados, a partir del área que cada compuesto ocupaba en el cromatograma generado en el programa Xcalibur. Estas secreciones fueron recogidas en 2015 en Sevilla en dos áreas de muestreo diferentes: en el Corredor Verde del Guadiamar, y en el parque María Luisa. Para cada individuo se indica la edad (adulto/juvenil) y el sexo (macho/hembra).
description: The uropygial gland of birds produces an oily secretion with different functions, mainly related to plumage protection. In addition, the volatile compounds of this secretion may act as chemical signals that provide information to conspecifics, but it is also possible that those compounds may further attract hematophagous insect vectors such as those responsible for avian malaria transmission. Individual characteristics such as sex and age are usually associated with variation in the composition of the uropygial secretion. Different studies have shown that mosquitoes are more attracted towards individual birds infected by avian malaria parasites. However, whether the individual infection status by these parasites may lead to differences in the composition of this secretion remains poorly known. We used Gas Chromatography-Mass Spectrometry (GC-MS) to characterise the chemical composition of the volatile lipophilic fraction of the uropygial gland secretions of wild European blackbirds and compare its composition in an urban and a forest locality according to their age, sex and infection status by blood parasites. We found differences in the composition of the secretion between age classes and also between sexes within adult birds. However, no differences were found in the chemical composition of the uropygial gland secretion of birds according to their infection status by blood-parasites and habitat type. These results suggest that haemosporidian infection does not alter the composition of the volatile fraction of uropygial gland secretions in infected birds.
DOI: 10.20350/digitalcsic/13829
title: Chemical gardens under Mars conditions: Imaging chemical garden growth in situ in an environmental scanning electron microscope [Dataset]

description: This dataset is a comprised file, insitu_Al_chemgarden.zip, where several graphical files, analysis raw set of scanning electron microscope and the frames of a movie.
description: The dataset deposited in CSIC Digital repository corresponds to the raw data and supplementary data related with the manuscript submitted and almost accepted to Geophysical Research Letters (2021).
DOI: 10.20350/digitalcsic/13834
title: Atlas of Mediterranean and Canary/Iberian/Biscay Atlantic currents (V.1.0) [Dataset]

description: Data provided by Copernicus Marine Service MEDSEA_MULTIYEAR_:PHY_006_004 SEALEVEL_MED_PHY_L4_REP_OBSERVATIONS_008_051 MULTIOBS_GLO_PHY_015_004
description: The creation of a data base of historical trajectories of floating and drifting devices around the Iberian Peninsula and a climatology of surface ocean currents to assess search and rescue emergencies, pollution emergencies and speed up forensic investigations. Data source Mediterranean and Atlantic CMEMS products. Time coverage 12 months. Time resolution 1 month. Spatial coverage Latitude range: 25ºN-52ºN Longitude range: 25ºW-36.5ºE. Spatial resolution Atlantic: 1/4º Mediterranean:1/8º. Spatial projection Geographical latitude / longitude projection. Spatial datum WGS84 – World Geodetic System 1984 (EPGS: 4326)
description: Climatologic value of zonal and meridional velocity, associated statistical magnitudes (number of measures, standard deviation, kurtosis and skewness), and multimodal status flag
DOI: 10.20350/digitalcsic/13828
title: Ongoing anthropogenic eutrophication of the catchment area threatens the Doñana World Heritage Site (South west Spain)

description: Eutrophication is a major cause of wetland degradation worldwide. In recent decades, reductions in nutrient inputs have led to improvements in water quality in many rivers and lakes in central and northern Europe, but long-term trends are less clear in southern Europe. We conducted the first comprehensive study of water quality in Doñana (SW Spain), one of the most important wetland complexes in Europe and the Mediterranean region. The core area of Doñana is a large shallow, seasonal marsh (UNESCO World Heritage Site—WHS) that floods during rainy, cool winter months, then dries out during the summer. The marsh is fed by three main streams whose catchments are within a Biosphere Reserve but are impacted by greenhouses (for cultivating fruit, irrigated with groundwater), poorly treated urban wastewaters and tourism. From 2013 to 2016, we monitored nutrient (Total P, Total N, PO4−3, NH4+, NO3−, NO2−) and phytoplankton chlorophyll-a (chla) concentrations in surface waters of the Doñana marsh and the three main streams. We quantified changes in greenhouse cover since 1995 using satellite images. Nutrient concentrations in streams were consistently higher than in the marsh, particularly in the Partido and Rocina streams that regularly reached concentrations equivalent to a “bad physico-chemical status” under the EU Water Framework Directive (WFD), and whose catchments suffered a fivefold expansion of greenhouses from 1995 to 2016. The Partido was the most polluted stream, and the most affected by wastewater effluents, and had particularly high concentrations of NH4+ (Geometric Mean = 0.3 mg L−1) and NO2− (GM = 0.52 mg L−1) across seasons. Patterns in chla concentrations were less consistent, but streams (GM = 6.78 µg L−1) generally had higher concentrations than the marsh (GM = 4.27 µg L−1). Nutrient concentrations in spot samples within the marsh largely depended on a combination of evaporation (as revealed by higher stable isotope δ2H values in the water column) and spatial processes (concentrations increase close to stream entry points, where conductivity is lower). Anthropogenic nutrient pollution in entry streams is a serious problem in Doñana, with extensive stretches too toxic for fish. Reinforcement of policies aimed at reducing nutrient inputs to Doñana are urgently required to meet the biodiversity conservation and environmental objectives for the WHS and WFD, respectively. Paradoxically, the marsh is currently relied upon to purify the water entering from streams.
DOI: 10.20350/digitalcsic/13823
title: Characterization of a Low-Cost FPGA-based Time-to-Digital Converter with Maximized Readout Speed

description: This dataset reports the specifications of a low-cost FPGA-based TDC whose readout speed is maximized. The evaluated TDC is composed of a toggling input stage to shape the hit signal and maximize the readout speed, a coarse counter to count the number of clocks between start and stop signals, a tuned tapped delay line to achieve high resolution, a dual-mode counter-based encoder to convert the output of the delay line to a binary number, a controller to determine the encoding mode, and a bin-width calibration to improve the TDC performance. To measure the exact bin widths and calculate the DNL and INL of the TDC, the code density test that is a statistical estimation approach, is hired.
description: This dataset includes: (i) code density test results obtained from 116272 collected samples; (ii) Differential and integral nonlinearities (DNL and INL) of uncalibrated and calibrated outputs calculated from estimated widths of delay elements; and (iii) Graphs of measured bin widths, bin width distribution, comparison of ideal, uncalibrated, and calibrated transfer functions, uncalibrated DNL and INL, and calibrated DNL and INL.
DOI: 10.20350/digitalcsic/13825
title: Plant population MONITO dataset. 2010-2019

description: Population sizes, threats, and abundance change through time, for monitored plants in the Aragon Region (Spain) between 2010 and 2019.
DOI: 10.20350/digitalcsic/13821
title: Chromatin regulation by Histone H4 acetylation at Lysine 16 during cell death and differentiation in the myeloid compartment

description: Supplementary data files corresponding to manuscript: Urdinguio, Lopez et al.
description: Histone H4 acetylation at Lysine 16 (H4K16ac) is a key epigenetic mark involved in gene regulation, DNA repair and chromatin remodeling, and though it is known to be essential for embryonic development, its role during adult life is still poorly understood. Here we show that this lysine is massively hyperacetylated in peripheral neutrophils. Genome-wide mapping of H4K16ac in terminally differentiated blood cells, along with functional experiments, supported a role for this histone post-translational modification in the regulation of cell differentiation and apoptosis in the hematopoietic system. Furthermore, in neutrophils, H4K16ac was enriched at specific DNA repeats. These DNA regions presented an accessible chromatin conformation and were associated with the cleavage sites that generate the 50 kb DNA fragments during the first stages of programmed cell death. Our results thus suggest that H4K16ac plays a dual role in myeloid cells as it not only regulates differentiation and apoptosis, but it also exhibits a non-canonical structural role in poising chromatin for cleavage at an early stage of neutrophil cell death.