cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5441/001/1.tj948m64/4
title: Glaucous gull Elliott Coats-twilights

description: Baak JE, Patterson A, Gilchrist HG, Elliott KH. 2021. First evidence of diverging migration and overwintering strategies in glaucous gulls (Larus hyperboreus) from the Canadian Arctic. Anim Migr. 8:98-109. doi:10.1515/ami-2020-0107
description: Many seabird populations differ in their migration strategies, where individuals travel in different directions to separate wintering areas. These migratory strategies may expose individuals to different threats, thus understanding migratory connectivity is crucial to assess risks to populations. Glaucous gulls (Larus hyperboreus) are generalist predators with flexible migratory behaviour that may alter these behaviours in response to climate change and anthropogenic activities, such as access to landfills, yet little is known about their migration. We deployed GPS and GLS tracking devices on glaucous gulls from Coats Island, Nunavut, Canada to obtain the first insights into their migration and habitat use outside of the breeding season. Gulls used two migration strategies during the non-breeding season, where one migrated as far as the Sea of Okhotsk in the Pacific and the remainder (n = 7) wintered in the North Atlantic. Gulls primarily overwintered in pelagic (56%) and coastal (38%) habitats. While in coastal habitats, one gull visited one landfill once, but visits increased with a 1 km and 3 km buffer, suggesting that urban glaucous gulls primarily used non-landfill habitats. This research can be used as a baseline to explore changes in migratory behaviour and inform future conservation of Arctic-breeding gulls.
DOI: 10.5441/001/1.tj948m64/5
title: Glaucous gull Elliott Coats-reference-data

description: Baak JE, Patterson A, Gilchrist HG, Elliott KH. 2021. First evidence of diverging migration and overwintering strategies in glaucous gulls (Larus hyperboreus) from the Canadian Arctic. Anim Migr. 8:98-109. doi:10.1515/ami-2020-0107
description: Many seabird populations differ in their migration strategies, where individuals travel in different directions to separate wintering areas. These migratory strategies may expose individuals to different threats, thus understanding migratory connectivity is crucial to assess risks to populations. Glaucous gulls (Larus hyperboreus) are generalist predators with flexible migratory behaviour that may alter these behaviours in response to climate change and anthropogenic activities, such as access to landfills, yet little is known about their migration. We deployed GPS and GLS tracking devices on glaucous gulls from Coats Island, Nunavut, Canada to obtain the first insights into their migration and habitat use outside of the breeding season. Gulls used two migration strategies during the non-breeding season, where one migrated as far as the Sea of Okhotsk in the Pacific and the remainder (n = 7) wintered in the North Atlantic. Gulls primarily overwintered in pelagic (56%) and coastal (38%) habitats. While in coastal habitats, one gull visited one landfill once, but visits increased with a 1 km and 3 km buffer, suggesting that urban glaucous gulls primarily used non-landfill habitats. This research can be used as a baseline to explore changes in migratory behaviour and inform future conservation of Arctic-breeding gulls.
DOI: 10.5281/zenodo.5809202
title: A revision of Geonoma (Arecaceae)

description: A taxonomic revision and phylogeny of the neotropical palm genus Geonoma based on morphological data and morphometric methods was carried out. 4990 herbarium specimens were scored for 44 qualitative variables and 27 quantitative variables. Qualitative variables were divided into 30 characters and 14 traits. Using the phylogenetic species concept, characters were used to recognize 68 species. These are widely distributed from southern Mexico to Bolivia and Paraguay, and reach the Lesser Antilles and Hispaniola. Analysis of each species for traits, geographic distribution, and quantitative variables led to recognition of 90 subspecies in 18 species, giving a total of 140 taxa. Twelve new species (G. bernalii, G. concinnoidea, G. deneversii, G. dindoensis, G. fosteri, G. galeanoae, G. gentryi, G. operculata, G. peruviana, G. sanmartinensis, G. schizocarpa, G. venosa) and 33 new subspecies (G. brongniartii subsp. pascoensis, G. concinna subsp. simplex, G. concinnoidea subsp. coclensis, G. concinnoidea subsp. jefensis, G. congesta subsp. osensis, G. cuneata subsp. guanacastensis, G. cuneata subsp. indivisa, G. cuneata subsp. minor, G. cuneata subsp. rubra, G. deversa subsp. belizenesis, G. deversa subsp. peninsularis, G. deversa subsp. quadriflora, G. ferruginea subsp. nicaraguensis, G. lehmannii subsp. corrugata, G. longivaginata subsp. copensis, G. longivaginata subsp. sanblasensis, G. longivaginata subsp. vallensis, G. maxima subsp. dispersa, G. maxima subsp. multiramosa, G. maxima subsp. sigmoidea, G. pohliana subsp. linharenseis, G. pohliana subsp. rodriguesii, G. pohliana subsp. unaensis, G. stricta subsp. antioquiensis, G. stricta subsp. bracteata, G. stricta subsp. divaricata, G. stricta subsp. pendula, G. stricta subsp. pliniana, G. stricta subsp. quibdoensis, G. stricta subsp. submontana, G. undata subsp. tacarcunensis, G. undata subsp. tumucensis, G. undata subsp. venezuelana) are described. Forty-one new combinations are made. Several of the most variable species are considered to be species complexes and are divided into morphotypes—groups of similar specimens with no formal taxonomic status. Nomenclature, descriptions and distribution maps are provided for each species and subspecies. Images of the type specimens of all new taxa are also provided. A phylogenetic analysis, using the same 30 characters used for the taxonomic revision was carried out using parsimony analysis. A sample tree and consensus tree are shown and a discussion is given of the various clades.<br>
DOI: 10.5281/zenodo.5809201
title: A revision of Geonoma (Arecaceae)

description: A taxonomic revision and phylogeny of the neotropical palm genus Geonoma based on morphological data and morphometric methods was carried out. 4990 herbarium specimens were scored for 44 qualitative variables and 27 quantitative variables. Qualitative variables were divided into 30 characters and 14 traits. Using the phylogenetic species concept, characters were used to recognize 68 species. These are widely distributed from southern Mexico to Bolivia and Paraguay, and reach the Lesser Antilles and Hispaniola. Analysis of each species for traits, geographic distribution, and quantitative variables led to recognition of 90 subspecies in 18 species, giving a total of 140 taxa. Twelve new species (G. bernalii, G. concinnoidea, G. deneversii, G. dindoensis, G. fosteri, G. galeanoae, G. gentryi, G. operculata, G. peruviana, G. sanmartinensis, G. schizocarpa, G. venosa) and 33 new subspecies (G. brongniartii subsp. pascoensis, G. concinna subsp. simplex, G. concinnoidea subsp. coclensis, G. concinnoidea subsp. jefensis, G. congesta subsp. osensis, G. cuneata subsp. guanacastensis, G. cuneata subsp. indivisa, G. cuneata subsp. minor, G. cuneata subsp. rubra, G. deversa subsp. belizenesis, G. deversa subsp. peninsularis, G. deversa subsp. quadriflora, G. ferruginea subsp. nicaraguensis, G. lehmannii subsp. corrugata, G. longivaginata subsp. copensis, G. longivaginata subsp. sanblasensis, G. longivaginata subsp. vallensis, G. maxima subsp. dispersa, G. maxima subsp. multiramosa, G. maxima subsp. sigmoidea, G. pohliana subsp. linharenseis, G. pohliana subsp. rodriguesii, G. pohliana subsp. unaensis, G. stricta subsp. antioquiensis, G. stricta subsp. bracteata, G. stricta subsp. divaricata, G. stricta subsp. pendula, G. stricta subsp. pliniana, G. stricta subsp. quibdoensis, G. stricta subsp. submontana, G. undata subsp. tacarcunensis, G. undata subsp. tumucensis, G. undata subsp. venezuelana) are described. Forty-one new combinations are made. Several of the most variable species are considered to be species complexes and are divided into morphotypes—groups of similar specimens with no formal taxonomic status. Nomenclature, descriptions and distribution maps are provided for each species and subspecies. Images of the type specimens of all new taxa are also provided. A phylogenetic analysis, using the same 30 characters used for the taxonomic revision was carried out using parsimony analysis. A sample tree and consensus tree are shown and a discussion is given of the various clades.<br>
DOI: 10.6084/m9.figshare.3761562.v2088
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.5281/zenodo.5809629
title: HepG2 and K562 cCRE syntenic ages

description: ### DESCRIPTION ### HepG2 and K562 ENCODE 3 cCRE pELS, dELS, pELS + CTCF, dELS +CTCF. ### METHOD ### To assign sequence ages enhancer cCRE .bed coordinates were intersected with hg38 100-way multiZ alignment syntenic blocks from UCSC genome browser. ### Column names ### [#chr start_syn end_syn enh_id #chr_enh start_enh end_enh segment_number simple_0_complex_1 core_0_derived_1 mrca_age] ### explanation of column names ### [#chr start_syn end_syn]: syntenic block .bed coordinates in hg38 [ enh_id #chr_enh start_enh end_enh]: cCRE .bed coordinates in hg38 [segment_number]: We count the number of syntenic block segments overlapping a single enhancer. [simple_0_complex_1]: Some syntenic blocks overlap multiple syntenic blocks, which we term "complex". Others overlap a single syntenic block, which we term "simple". Complex elements are annotated with 1 and simple elements are annotated with 0. [core_0_derived_1]: In complex enhancer sequences (i.e. enhancer sequences with multiple sequence ages). We refer to the oldest sequence in an enhancer is the "core" (annotated as 1) and the younger sequence age(s) as "derived" (annotated as 0). [mrca_age]: For each syntenic segment, we annotate the most recent common ancestor (MRCA) age. This corresponds to the estimated branch length between humans and the related MRCA. Taxon and summarized taxon ("Taxon2") for each MRCA age is annotated in the hg38_syn_taxon.bed file.
DOI: 10.5281/zenodo.5809628
title: HepG2 and K562 cCRE syntenic ages

description: ### DESCRIPTION ### HepG2 and K562 ENCODE 3 cCRE pELS, dELS, pELS + CTCF, dELS +CTCF. ### METHOD ### To assign sequence ages enhancer cCRE .bed coordinates were intersected with hg38 100-way multiZ alignment syntenic blocks from UCSC genome browser. ### Column names ### [#chr start_syn end_syn enh_id #chr_enh start_enh end_enh segment_number simple_0_complex_1 core_0_derived_1 mrca_age] ### explanation of column names ### [#chr start_syn end_syn]: syntenic block .bed coordinates in hg38 [ enh_id #chr_enh start_enh end_enh]: cCRE .bed coordinates in hg38 [segment_number]: We count the number of syntenic block segments overlapping a single enhancer. [simple_0_complex_1]: Some syntenic blocks overlap multiple syntenic blocks, which we term "complex". Others overlap a single syntenic block, which we term "simple". Complex elements are annotated with 1 and simple elements are annotated with 0. [core_0_derived_1]: In complex enhancer sequences (i.e. enhancer sequences with multiple sequence ages). We refer to the oldest sequence in an enhancer is the "core" (annotated as 1) and the younger sequence age(s) as "derived" (annotated as 0). [mrca_age]: For each syntenic segment, we annotate the most recent common ancestor (MRCA) age. This corresponds to the estimated branch length between humans and the related MRCA. Taxon and summarized taxon ("Taxon2") for each MRCA age is annotated in the hg38_syn_taxon.bed file.
DOI: 10.5519/qd.z6j4d0ol
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (7 records)
DOI: 10.5441/001/1.1732qn7j/1
title: Geolocators reveal variation and sex-specific differences in the migratory strategies of a long-distance migrant

description: Bell F, Bearhop S, Briedis M, El Harouchi M, Bell SC, Castello J, Burgess M. 2022. Geolocators reveal variation and sex-specific differences in the migratory strategies of a long-distance migrant. Ibis. doi:10.1111/ibi.13017
description: Songbird populations are in decline all over the world, and our understanding of the causal mechanisms remains surprisingly limited. It is important to identify the extent of individual variations in migratory behaviour to better understand species' ability to respond to environmental change. We describe the annual migratory behaviour of British breeding European Pied Flycatchers Ficedula hypoleuca by using light-recording geolocators. During both autumn and spring migrations, individuals used previously unknown staging areas on the Iberian Peninsula and northern West Africa. Furthermore, partial sex-specific segregation in the location of non-breeding areas was observed within West Africa, with females located west of males. We also found sex-based phenological differences, with females staying longer in non-breeding areas and undertaking the spring Sahara Desert crossing later than males. Irrespective of sex, multiple use of the two predominant staging regions was identified during both migrations, with 63% of individuals stopping more than once in these regions. We also identified instances of migratory behaviours rarely documented in individually tracked songbirds. These include making daytime landfall during the Sahara crossing, and a case of a temporary retreat migration, with an individual aborting a spring Sahara crossing before making a second successful crossing 14 days later. Together, our results show variability in migratory behaviour both between sexes and between individuals. For Pied Flycatchers, such flexible migratory behaviour may increase their resilience to environmental change.
DOI: 10.5441/001/1.1732qn7j/2
title: Geolocators reveal variation and sex-specific differences in the migratory strategies of a long-distance migrant-reference-data

description: Bell F, Bearhop S, Briedis M, El Harouchi M, Bell SC, Castello J, Burgess M. 2022. Geolocators reveal variation and sex-specific differences in the migratory strategies of a long-distance migrant. Ibis. doi:10.1111/ibi.13017
description: Songbird populations are in decline all over the world, and our understanding of the causal mechanisms remains surprisingly limited. It is important to identify the extent of individual variations in migratory behaviour to better understand species' ability to respond to environmental change. We describe the annual migratory behaviour of British breeding European Pied Flycatchers Ficedula hypoleuca by using light-recording geolocators. During both autumn and spring migrations, individuals used previously unknown staging areas on the Iberian Peninsula and northern West Africa. Furthermore, partial sex-specific segregation in the location of non-breeding areas was observed within West Africa, with females located west of males. We also found sex-based phenological differences, with females staying longer in non-breeding areas and undertaking the spring Sahara Desert crossing later than males. Irrespective of sex, multiple use of the two predominant staging regions was identified during both migrations, with 63% of individuals stopping more than once in these regions. We also identified instances of migratory behaviours rarely documented in individually tracked songbirds. These include making daytime landfall during the Sahara crossing, and a case of a temporary retreat migration, with an individual aborting a spring Sahara crossing before making a second successful crossing 14 days later. Together, our results show variability in migratory behaviour both between sexes and between individuals. For Pied Flycatchers, such flexible migratory behaviour may increase their resilience to environmental change.
DOI: 10.5281/zenodo.5809634
title: hg38 syntenic ages

description: ### METHOD ### Sequence ages were estimated from hg38 100-way multiZ vertebrate sequence alignments from the UCSC genome browser. Briefly, sequence ages were estimated as the branch length between humans (hg38) and the oldest most recent common ancestor (MRCA) from the 100-way neutral tree. MRCA to taxon mappings are available in the hg38_syn_taxon.bed file. # Hg38 100-way vertebrate tree syntenic block age files. Information for hg38 100-way vertebrate multiple sequence alignment can be found here - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/README.txt # Scripts generating these files (1) Creating syntenic block .bed files https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_spec_count_msa-hg19.py (2) Assigning most recent common ancestor (MRCA) and patristic distances to syntenic blocks https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_synteny_age_hg19.py
DOI: 10.5281/zenodo.5809633
title: hg38 syntenic ages

description: ### METHOD ### Sequence ages were estimated from hg38 100-way multiZ vertebrate sequence alignments from the UCSC genome browser. Briefly, sequence ages were estimated as the branch length between humans (hg38) and the oldest most recent common ancestor (MRCA) from the 100-way neutral tree. MRCA to taxon mappings are available in the hg38_syn_taxon.bed file. # Hg38 100-way vertebrate tree syntenic block age files. Information for hg38 100-way vertebrate multiple sequence alignment can be found here - http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/README.txt # Scripts generating these files (1) Creating syntenic block .bed files https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_spec_count_msa-hg19.py (2) Assigning most recent common ancestor (MRCA) and patristic distances to syntenic blocks https://github.com/slifong08/enh_ages/blob/54084ff12e521c20cc5288d6cb3590fac93c11ed/age_arch/manuscript_scripts/get_synteny_age_hg19.py
DOI: 10.5066/p92ydisc
title: Groundwater Quality Data of the Chicot aquifer system

description: This dataset contains digitized groundwater quality data from 435 wells that are screened in the Chicot aquifer system. Reported values of interest included specific conductance, total dissolved solids, and chloride (Cl) concentration; other parameters and major/trace element concentrations were included if reported. Values listed as "NA" or "-9999" represent data that was not reported in the physical dataset. A concentration of 0 ppm or ppb represents a reported concentration of 0 and not a null value. Data were collected from scanned versions of well registration records obtained from the Louisiana Department of Natural Resources. Most well registration records may be accessed through Strategic Online Natural Resources Information System (SONRIS database found at https://www.sonris.com), however some records may only be available in hard copy format.
DOI: 10.5281/zenodo.5809609
title: Pentamera pediparva decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5809608
title: Pentamera pediparva decontaminated FSCR

description: .
DOI: 10.6084/m9.figshare.17704289
title: data_lab assays.xlsx

description: The file contains data from the laboratory experiments performed during the study described in the manuscript "Study from microcosms and mesocosms reveals <i>Escherichia coli</i> removal in high rate algae ponds is primarily caused by dark decay"
DOI: 10.6084/m9.figshare.17704289.v1
title: data_lab assays.xlsx

description: The file contains data from the laboratory experiments performed during the study described in the manuscript "Study from microcosms and mesocosms reveals <i>Escherichia coli</i> removal in high rate algae ponds is primarily caused by dark decay"
DOI: 10.6084/m9.figshare.17704283
title: data_bench_assays.xlsx

description: The file contains data set obtained from the bench experiment performed during the study described in the manuscript "Study from microcosms and mesocosms reveals <i>Escherichia coli</i> removal in high rate algae ponds is primarily caused by dark decay"
DOI: 10.6084/m9.figshare.17704283.v1
title: data_bench_assays.xlsx

description: The file contains data set obtained from the bench experiment performed during the study described in the manuscript "Study from microcosms and mesocosms reveals <i>Escherichia coli</i> removal in high rate algae ponds is primarily caused by dark decay"
DOI: 10.5281/zenodo.2390874
title: Carrillo-Briceño et al. 2018 (raw isotopic data) - Neogene Caribbean elasmobranchs: diversity, paleoecology and paleoenvironmental significance of the Cocinetas Basin assemblage (Guajira Peninsula, Colombia)

description: The file contains the raw isotopic data for the article entitled '<strong>Neogene Caribbean elasmobranchs: diversity, paleoecology and paleoenvironmental significance of the Cocinetas Basin assemblage (Guajira Peninsula, Colombia)</strong>'. It includes the correction for the values first produced by our mass spectrometer and how the corrections were proceeded. Several runs were performed and these are detailed with comments and remarks. Any doubt or question about these corrections are welcomed by me, László Kocsis and Torsten Vennemann for discussion or further considerations.
DOI: 10.5281/zenodo.5809647
title: Observed Kapuas River water level in 2018

description: This is supplement data for our publication in Biogeosciences (https://doi.org/10.5194/bg-2021-273). To use this data, please give us credit by citing our article. <strong>How to cite</strong><strong>: </strong>Sampurno, J., Vallaeys, V., Ardianto, R., and Hanert, E.: Modeling interactions between tides, storm surges, and river discharges in the Kapuas River delta, Biogeosciences Discuss. [preprint], https://doi.org/10.5194/bg-2021-273, in review, 2021.
DOI: 10.5281/zenodo.5809646
title: Observed Kapuas River water level in 2018

description: This is supplement data for our publication in Biogeosciences (https://doi.org/10.5194/bg-2021-273). To use this data, please give us credit by citing our article. <strong>How to cite</strong><strong>: </strong>Sampurno, J., Vallaeys, V., Ardianto, R., and Hanert, E.: Modeling interactions between tides, storm surges, and river discharges in the Kapuas River delta, Biogeosciences Discuss. [preprint], https://doi.org/10.5194/bg-2021-273, in review, 2021.
DOI: 10.6084/m9.figshare.17704376
title: Burkholderia pseudomaelli

description: RNA seq data set for Burkholderia Pseudomallei.<br>Six independent samples were grown in a T75 flask either in Media only or Media + CaCl2 as a biofilm for 3 days. The supernatant was removed and biofilm gently washed with PBS. Zymogen NA extractant was used to extract RNA which was sequenced.
DOI: 10.5281/zenodo.5809649
title: Ecological interactions in breast cancer: Cell facilitation promotes growth and survival under drug pressure

description: Spheroids of different composition (100% sensitive, 50% sensitive – 50% resistant, 100% resistant) were initiated from Venus-labeled CAMA-1 and mCherry-labeled CAMA-1_ribociclib_resistant cells and were subjected to 1 uM ribociclib treatment. After 11 days, speroids were harvested, washed and cell suspensions were viably frozen for single cell RNA-seq analysis.
DOI: 10.5281/zenodo.5809648
title: Ecological interactions in breast cancer: Cell facilitation promotes growth and survival under drug pressure

description: Spheroids of different composition (100% sensitive, 50% sensitive – 50% resistant, 100% resistant) were initiated from Venus-labeled CAMA-1 and mCherry-labeled CAMA-1_ribociclib_resistant cells and were subjected to 1 uM ribociclib treatment. After 11 days, speroids were harvested, washed and cell suspensions were viably frozen for single cell RNA-seq analysis.