cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24272092.v1
title: Figure 4. Alignment and tree of nifHDKT and of dreped MAGs for reconcilation and ancestral reconstruction

description: Sequences of the <i>nifH</i>, <i>nifD</i>, <i>nifK </i>and <i>nifT</i> genes were chosen to infer the evolutionary history of nitrogen fixation because they form an operon with the minimum catalytic gene set for the reaction (Dos Santos et al. 2012). Sequences were extracted from the DRAM annotation of the dereplicated MAGs, including the genome of <i>Vibrio natrigensis,</i> which also served as the outgroup for the gene tree. MAGs that did not contain the full set of genes and were excluded from the analysis. Each renamed gene extraction (Rodriguez-R and Konstantinidis 2016) was aligned independently with FSA v1.15.9 (Bradley et al. 2009) using the <i>--fast</i> flag. A tree was inferred from each alignment to ensure that the genes have evolved together. Subsequently, the alignments were concatenated using SeqKit v2.3.0 (Shen et al. 2016) and a tree inferred from it. For the reconstruction of ancestral states and the phylogenetic reconciliation we inferred a de-replicated version of the global symbiont phylogenomic tree. For this, the diversity of MAGs was reduced by following the dRep v3.2.2 (Olm et al. 2017) dereplicate workflow with the S_ANI parameter set to 0.99. To maintain the topology of the original tree, MAGs classified as <i>Ca. </i>Thiodiazotropha endolucinida Caribbean had to be dereplicated independently with the S_ANI flag set to 0.995 (to increase the represented diversity of the clade). The genome of <i>Vibrio natrigensis </i>genome (GCF_001456255.1), which was used as an outgroup, was downloaded from the NCBI database.Both trees wereinferred with IQ-Tree v2.2.2.1 (Minh et al. 2020; Hoang et al. 2018; Kalyaanamoorthy et al. 2017) with auto substitution model detection, 1,000 ultrafast bootstrap (UFB) replicates and 1,000 samples for SH-aLRT branch testing. Nodes with values of UFB greater or equal to 95% and of SH-aLRT greater or equal to 80% were considered to be strongly supported. The nifHDKT best-fit model was TN+F+I+G4, and the one for the dreped tree was Q.insect+F+I+G4
DOI: 10.6084/m9.figshare.13318137
title: Floral traits and chemical cues associated with rock bee (<i>Apis dorsata</i> Fabricius) for the host selection in West Bengal, India

description: In the present work, bee foraging plants were determined by palynological analysis of colony stored samples (honey and pollen) of <i>Apis dorsata</i> collected from southern West Bengal, India. Then flowering phenology and pollen morphologies were described to evaluate the forage preference of the bee species. In addition, chemical cues were analysed using gas chromatography-mass spectrometry (GC-MS). Foraging strategy of the bee species was profitable in that almost all the bee-visited plants were utilised for both nectar and pollen sources. The bee species became generalist visitor of several plants having diverse life form, flower characters and pollen morphologies. However, most of the bee-visited plants were of trees with synchronous type of flowering. Most plants had small-sized, yellow, cream and white coloured flowers and pollen was openly presented. We did not find any patterns in the morphological traits of bee collected pollen, though the pollen types were predominantly of medium sized with trizonocolporate apertural pattern and reticulate surface ornamentation. Floral volatile organic compounds (VOCs) of bee visited plants were also diversified. Compounds frequently found in the floral VOC bouquets were amphetamine-3-methyl; butane, 2-cyclopropyl; 2,3-butanediol; cyclohexan, 1-methyl-5-(1-methylethyl); d-limonene; methyl (2E)-2-methoxy-2-butenoate; phenol, 4-[2-(methylamino)ethyl]; phthalic acid, di(2-propylpentyl)ester; propanamide, <i>N</i>-(aminocarbonyl) and pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl). In conclusion, floral traits and chemical cues of plants influence the host selection specificity (to collect floral rewards) of the rock bees.
DOI: 10.6084/m9.figshare.13318137.v1
title: Floral traits and chemical cues associated with rock bee (<i>Apis dorsata</i> Fabricius) for the host selection in West Bengal, India

description: In the present work, bee foraging plants were determined by palynological analysis of colony stored samples (honey and pollen) of <i>Apis dorsata</i> collected from southern West Bengal, India. Then flowering phenology and pollen morphologies were described to evaluate the forage preference of the bee species. In addition, chemical cues were analysed using gas chromatography-mass spectrometry (GC-MS). Foraging strategy of the bee species was profitable in that almost all the bee-visited plants were utilised for both nectar and pollen sources. The bee species became generalist visitor of several plants having diverse life form, flower characters and pollen morphologies. However, most of the bee-visited plants were of trees with synchronous type of flowering. Most plants had small-sized, yellow, cream and white coloured flowers and pollen was openly presented. We did not find any patterns in the morphological traits of bee collected pollen, though the pollen types were predominantly of medium sized with trizonocolporate apertural pattern and reticulate surface ornamentation. Floral volatile organic compounds (VOCs) of bee visited plants were also diversified. Compounds frequently found in the floral VOC bouquets were amphetamine-3-methyl; butane, 2-cyclopropyl; 2,3-butanediol; cyclohexan, 1-methyl-5-(1-methylethyl); d-limonene; methyl (2E)-2-methoxy-2-butenoate; phenol, 4-[2-(methylamino)ethyl]; phthalic acid, di(2-propylpentyl)ester; propanamide, <i>N</i>-(aminocarbonyl) and pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl). In conclusion, floral traits and chemical cues of plants influence the host selection specificity (to collect floral rewards) of the rock bees.
DOI: 10.5281/zenodo.10025338
title: SIC, SIT, SST and SSS from HYCOM-CICE with LAON assimilation of SIC

description: This data is generated using the Norwegian High-resolution (3-5km) pan-Arctic ocean and sea ice Prediction System (NorHAPS), which is based on a coupled HYCOM-CICE model with the Local Analytical Optimal Nudging (LAON) for assimilation. The twin experiment simulations cover the pan-Arctic domain from 1 January 2021 to 30 April 2022, with and without assimilation of sea ice concentration. The data includes sea ice concentration and thickness, sea surface temperature and salinity.
description: The updated version includes OSTIA skin SST data for the same period, which was obtained from CMEMS.
DOI: 10.5281/zenodo.7533371
title: SIC, SIT, SST and SSS from HYCOM-CICE with LAON assimilation of SIC

description: This data is generated using the Norwegian High-resolution (3-5km) pan-Arctic ocean and sea ice Prediction System (NorHAPS), which is based on a coupled HYCOM-CICE model with the Local Analytical Optimal Nudging (LAON) for assimilation. The twin experiment simulations cover the pan-Arctic domain from 1 January 2021 to 30 April 2022, with and without assimilation of sea ice concentration. The data includes sea ice concentration and thickness, sea surface temperature and salinity.
description: The updated version includes OSTIA skin SST data for the same period, which was obtained from CMEMS.
DOI: 10.5281/zenodo.7533372
title: SIC, SIT, SST and SSS from HYCOM-CICE with LAON assimilation of SIC

description: This data is generated using the Norwegian High-resolution (3-5km) pan-Arctic ocean and sea ice Prediction System (NorHAPS), which is based on a coupled HYCOM-CICE model with the Local Analytical Optimal Nudging (LAON) for assimilation. The twin experiment simulations cover the pan-Arctic domain from 1 January 2021 to 30 April 2022, with and without assimilation of sea ice concentration. The data includes sea ice concentration and thickness, sea surface temperature and salinity.
DOI: 10.6084/m9.figshare.23716995.v3
title: <strong>Use of milk</strong> <strong>mid-infrared spectra</strong> <strong>to predict serum non-esterified fatty acids concentrations in Chinese Holstein cows</strong>

description: Tail venous blood samples were collected from four dairy farms in Shandong province, China. Milk MIR spectra data was detected at Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences.
DOI: 10.6073/pasta/854b92439ccceec557a810d09dfaf174
title: Eight Mile Lake Research Watershed, Thaw Gradient: Seasonal thaw depth 2004-2021

description: In this larger study, we are asking the question: Is old carbon that comprises the bulk of the soil organic matter pool released in response to thawing of permafrost? We are answering this question by using a combination of field and laboratory experiments to measure radiocarbon isotope ratios in soil organic matter, soil respiration, and dissolved organic carbon, in tundra ecosystems. The objective of these proposed measurements is to develop a mechanistic understanding of the SOM sources contributing to C losses following permafrost thawing. We are making these measurements at an established tundra field site near Healy, Alaska in the foothills of the Alaska Range. Field measurements center on a natural experiment where permafrost has been observed to warm and thaw over the past several decades. This area represents a gradient of sites each with a different degree of change due to permafrost thawing. As such, this area is unique for addressing questions at the time and spatial scales relevant for change in arctic ecosystems.
DOI: 10.6084/m9.figshare.24272092.v2
title: Figure 4. Alignment and tree of nifHDKT and of dreped MAGs for reconcilation and ancestral reconstruction

description: Sequences of the <i>nifH</i>, <i>nifD</i>, <i>nifK </i>and <i>nifT</i> genes were chosen to infer the evolutionary history of nitrogen fixation because they form an operon with the minimum catalytic gene set for the reaction (Dos Santos et al. 2012). Sequences were extracted from the DRAM annotation of the dereplicated MAGs, including the genome of <i>Vibrio natrigensis,</i> which also served as the outgroup for the gene tree. MAGs that did not contain the full set of genes and were excluded from the analysis. Each renamed gene extraction (Rodriguez-R and Konstantinidis 2016) was aligned independently with FSA v1.15.9 (Bradley et al. 2009) using the <i>--fast</i> flag. A tree was inferred from each alignment to ensure that the genes have evolved together. Subsequently, the alignments were concatenated using SeqKit v2.3.0 (Shen et al. 2016) and a tree inferred from it. For the reconstruction of ancestral states and the phylogenetic reconciliation we inferred a de-replicated version of the global symbiont phylogenomic tree. For this, the diversity of MAGs was reduced by following the dRep v3.2.2 (Olm et al. 2017) dereplicate workflow with the S_ANI parameter set to 0.99. To maintain the topology of the original tree, MAGs classified as <i>Ca. </i>Thiodiazotropha endolucinida Caribbean had to be dereplicated independently with the S_ANI flag set to 0.995 (to increase the represented diversity of the clade). The genome of <i>Vibrio natrigensis </i>genome (GCF_001456255.1), which was used as an outgroup, was downloaded from the NCBI database.Both trees wereinferred with IQ-Tree v2.2.2.1 (Minh et al. 2020; Hoang et al. 2018; Kalyaanamoorthy et al. 2017) with auto substitution model detection, 1,000 ultrafast bootstrap (UFB) replicates and 1,000 samples for SH-aLRT branch testing. Nodes with values of UFB greater or equal to 95% and of SH-aLRT greater or equal to 80% were considered to be strongly supported. The nifHDKT best-fit model was TN+F+I+G4, and the one for the dreped tree was Q.insect+F+I+G4
DOI: 10.5281/zenodo.10025335
title: Data for "Nishimori's cat: stable long-range entanglement from finite-depth unitaries and weak measurements"
DOI: 10.5281/zenodo.10025334
title: Data for "Nishimori's cat: stable long-range entanglement from finite-depth unitaries and weak measurements"
DOI: 10.18167/dvn1/wgnko1
title: Arthropods inventory from PELEBINA (BENIN)

description: The file contains taxonomic data of Arthropods collected during the rainy season (2013) and dry season (first semester 2014) in the rice lowland of Pelebina in Benin (Africa).
DOI: 10.5517/ccdc.csd.cc2791sd
title: CCDC 2064283: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791tf
title: CCDC 2064284: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791vg
title: CCDC 2064285: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791rc
title: CCDC 2064282: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791wh
title: CCDC 2064286: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791xj
title: CCDC 2064287: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791yk
title: CCDC 2064288: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2791zl
title: CCDC 2064289: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27w4w5
title: CCDC 2081677: Experimental Crystal Structure Determination

description: Related Article: Thibaut Martinez, Avassaya Vanitcha, Claire Troufflard, Nicolas Vanthuyne, Jérémy Forté, Geoffrey Gontard, Gilles Lemière, Virginie Mouriès-Mansuy, Louis Fensterbank|2021|Angew.Chem.,Int.Ed.|60|19879|doi:10.1002/anie.202106142
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.18167/dvn1/pgqgql
title: Valorcarn-TETIS: Terms extracted with Biotex

description: Text-Mining: Terms extracted with Biotex tool (http://tubo.lirmm.fr/biotex) from "Valorcarn Corpus" (http://dx.doi.org/10.18167/DVN1/7YTQGQ). -- Valorcarn Project (2015-2017) [project supported by GloFoodS program (INRA-Cirad)]. Topic: Mining of scientific documents for identification of process that enables to reduce losses and waste.
DOI: 10.18167/dvn1/ygyl3w
title: Valorcarn-TETIS: Terms extracted with Rake

description: Text-Mining: Terms extracted with Rake tool (https://github.com/aneesha/RAKE) from "Valorcarn Corpus" (http://dx.doi.org/10.18167/DVN1/7YTQGQ). Valorcarn Project (2015-2017) [project supported by GloFoodS program (INRA-Cirad)]. Mining of scientific documents for identification of process that enables to reduce losses and waste.
DOI: 10.6073/pasta/62f779fab3be6e90f008d163455f8559
title: Anthropogenic nitrogen Balance and Riverine Nitrogen Footprint of Agriculture in the Mississippi-Atchafalaya River Basin during 1970-2019

description: These data support the findings of a manuscript by Lu et al. under review in Environmental Research Letters. We used data synthesis and a well-calibrated hydro-ecological model to quantify the dynamics and controls of the riverine N footprint (RNF) within the Mississippi-Atchafalaya River Basin (MARB) from 1970 to 2019. These supportive data include (1) Annual synthetic N fertilizer and manure N input from 1970 to 2019 in sub-basins in the MARB; (2) Annual N inputs, outputs, and N balance from 1970 to 2017 in the MARB; (3) Changes in crop production, N load and riverine N footprint in response to key agricultural activities in MARB; (4) Changes in crop production, N load, and riverine N footprint under key agricultural activities at sub-basin level; (5) Annual acreage of major grain crops and total cropland areas in sub-basins of the MARB.
DOI: 10.4121/95a4bb4e-3ca4-4fcc-ba34-4be76a9ab578
title: Data underlying the publication: Modelling perceived risk and trust in driving automation reacting to merging and braking vehicles

description: This dataset is derived from a driving simulator study that explored the dynamics of perceived risk and trust in the context of driving automation. The study involved 25 participants who were tasked with monitoring SAE Level 2 driving automation features (Adaptive Cruise Control and Lane Centering) while encountering various driving scenarios on a motorway. These scenarios included merging and hard-braking events with different levels of criticality. This dataset contains kinetic data from the driving simulator, capturing variables such as vehicle position, velocity, and acceleration among others. Subjective ratings of perceived risk and trust, collected post-event for regression analysis are also included.
DOI: 10.4121/95a4bb4e-3ca4-4fcc-ba34-4be76a9ab578.v1
title: Data underlying the publication: Modelling perceived risk and trust in driving automation reacting to merging and braking vehicles

description: This dataset is derived from a driving simulator study that explored the dynamics of perceived risk and trust in the context of driving automation. The study involved 25 participants who were tasked with monitoring SAE Level 2 driving automation features (Adaptive Cruise Control and Lane Centering) while encountering various driving scenarios on a motorway. These scenarios included merging and hard-braking events with different levels of criticality. This dataset contains kinetic data from the driving simulator, capturing variables such as vehicle position, velocity, and acceleration among others. Subjective ratings of perceived risk and trust, collected post-event for regression analysis are also included.
DOI: 10.18167/dvn1/aptzoc
title: Medium density genotyping dataset of 39 cattle from five West African breeds, associated to the article "A Comparison of Phenotypic Traits Related to Trypanotolerance in Five West African Cattle Breeds Highlights the Value of Shorthorn Taurine Breeds" (Berthier et al 2015)

description: This dataset consists of genotypes of 39 animals belonging to five cattle breeds genotyped using the Illumina BovineSNP50 chip assay v2 [39] at the INRA Labogena platform (Jouy-en-Josas, France) using standard procedures. The animals were further infected by Trypanosoma congolense IL1180 to assess their phenotypes related to trypanotolerance (published in Berthier et al 2015 DOI: 10.1371/journal‧pone.0126498) and characterise the transcriptome of their blood cells before and after infection (see the Cirad dataverse: Whole blood transcriptome data of five West African cattle breeds before and during an infection by Trypanosoma congolense IL1180, inference on bovine trypanotolerance)