cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9996203.v2
title: Performance enhancement and sample throughput increase of a multiresidue pesticides method in fruits and vegetables using Data-Dependent MS acquisition

description: Due to the growing number of analysed pesticide residues, analytical strategies have evolved for the data processing of 100s of pesticides in a single analysis. We present herein a LC-MS/MS method based on triple quadrupole technology capable of detecting concentrations at 5 ng/g and confirming 381 pesticides in a single injection. Confirmatory analysis is performed using data-dependent acquisition that compares full MS/MS spectra of candidates to a fast library interrogation within the same injection. A comparison on more than 200 samples of fruits and vegetables (representing principal types: normal, pigmented, and fatty) with pre-existing workflow based on single MRM analysis per compound was performed to validate this approach. A fast turnaround time was demonstrated due to more-unambiguous identification suppressing the need for reinjection to confirm candidates. The automated library searching and confirmation only of putative hits also allowed focusing on the manual verification and validation steps just for putative candidates which hence also increased overall throughput and results quality. Superior robustness of the method due partially to a reduced volume injected was also one of the key points achieved using this methodology. An interesting feature is also the capability to enrich the library and the number of pesticides screened with ease.
DOI: 10.6084/m9.figshare.9996077
title: Equity in Academia 2019

description: We hosted a one day event at St Catherine's College in Oxford in September 2019, supported by the Oxford University Nuffield Department of Medicine and Oxford Tropical Network Centres in Kenya, Vietnam and Thailand, to discuss and address challenges for equity and diversity in our working lives. <br>A short summary of the event is posted here, together with the day's programme of activities.<br>We plan to follow up with a written report of recommendations arising from the meeting.
DOI: 10.6084/m9.figshare.9996203.v1
title: Performance enhancement and sample throughput increase of a multiresidue pesticides method in fruits and vegetables using Data-Dependent MS acquisition

description: Due to the growing number of analysed pesticide residues, analytical strategies have evolved for the data processing of 100s of pesticides in a single analysis. We present herein a LC-MS/MS method based on triple quadrupole technology capable of detecting concentrations at 5 ng/g and confirming 381 pesticides in a single injection. Confirmatory analysis is performed using data-dependent acquisition that compares full MS/MS spectra of candidates to a fast library interrogation within the same injection. A comparison on more than 200 samples of fruits and vegetables (representing principal types: normal, pigmented, and fatty) with pre-existing workflow based on single MRM analysis per compound was performed to validate this approach. A fast turnaround time was demonstrated due to more-unambiguous identification suppressing the need for reinjection to confirm candidates. The automated library searching and confirmation only of putative hits also allowed focusing on the manual verification and validation steps just for putative candidates which hence also increased overall throughput and results quality. Superior robustness of the method due partially to a reduced volume injected was also one of the key points achieved using this methodology. An interesting feature is also the capability to enrich the library and the number of pesticides screened with ease.
DOI: 10.6084/m9.figshare.9995957
title: Metadata record for: A suite of global accessibility indicators

description: This dataset contains key characteristics about the data described in the Data Descriptor A suite of global accessibility indicators. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.15131/shef.data.9995945
title: Suspect loci BED files

description: Suspect loci identified in datasets 1, 2 and 3 in our Genome Research article
DOI: 10.15131/shef.data.9995945.v1
title: Suspect loci BED files

description: Suspect loci identified in datasets 1, 2 and 3 in our Genome Research article
DOI: 10.6084/m9.figshare.9995957.v2
title: Metadata record for: A suite of global accessibility indicators

description: This dataset contains key characteristics about the data described in the Data Descriptor A suite of global accessibility indicators. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9995873
title: Table 2. Coding Table

description: Content analysis.
DOI: 10.6084/m9.figshare.9995957.v1
title: Metadata record for: A suite of global accessibility indicators

description: This dataset contains key characteristics about the data described in the Data Descriptor A suite of global accessibility indicators. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.9995846
title: Mapping_2.zip

description: Mapped reads from Hendrikson et al. 2017, used as example input for TOBIAS software (https://github.com/loosolab/TOBIAS/) <br>
DOI: 10.6084/m9.figshare.9995810
title: Spatiotemporal effects of Hurricane Ivan on an endemic epiphytic orchid: 10 years of follow-up

description: <b>Background</b>: Hurricanes have a strong influence on the ecological dynamics and structure of tropical forests. Orchid populations are especially vulnerable to these perturbations due to their canopy exposure and lack of underground storage organs and seed banks. <b>Aims</b>: We evaluated the effects of Hurricane Ivan on the population of the endemic epiphytic orchid <i>Encyclia bocourtii</i> to propose a management strategy. <b>Methods</b>: Using a pre- and post-hurricane dataset (2003–2013), we assessed the population asymptotic and transient dynamics. We also identified the individual size-stages that maximise population inertia and <i>E. bocourtii</i>’s spatial arrangement relative to phorophytes and other epiphytes. <b>Results</b>: Hurricane Ivan severely affected the survival and growth of individuals of <i>E. bocourtii</i>, and caused an immediate decline of the population growth rate from λ = 1.05 to λ = 0.32, which was buffered by a population reactivity of ρ<sub>1</sub> = 1.42. Our stochastic model predicted an annual population decrease of 14%. We found an aggregated spatial pattern between <i>E. bocourtii</i> and its host trees, and a random pattern relative to other epiphytes. <b>Conclusion</b>: Our findings suggest that <i>E. bocourtii</i> is not safe from local extinction. We propose the propagation and reintroduction of reproductive specimens, the relocation of surviving individuals, and the establishment of new plantations of phorophytes.
DOI: 10.6084/m9.figshare.9995873.v1
title: Tala 2. Codificación y análisis de contenido

description: Content analysis.
DOI: 10.6084/m9.figshare.9995810.v1
title: Spatiotemporal effects of Hurricane Ivan on an endemic epiphytic orchid: 10 years of follow-up

description: <b>Background</b>: Hurricanes have a strong influence on the ecological dynamics and structure of tropical forests. Orchid populations are especially vulnerable to these perturbations due to their canopy exposure and lack of underground storage organs and seed banks. <b>Aims</b>: We evaluated the effects of Hurricane Ivan on the population of the endemic epiphytic orchid <i>Encyclia bocourtii</i> to propose a management strategy. <b>Methods</b>: Using a pre- and post-hurricane dataset (2003–2013), we assessed the population asymptotic and transient dynamics. We also identified the individual size-stages that maximise population inertia and <i>E. bocourtii</i>’s spatial arrangement relative to phorophytes and other epiphytes. <b>Results</b>: Hurricane Ivan severely affected the survival and growth of individuals of <i>E. bocourtii</i>, and caused an immediate decline of the population growth rate from λ = 1.05 to λ = 0.32, which was buffered by a population reactivity of ρ<sub>1</sub> = 1.42. Our stochastic model predicted an annual population decrease of 14%. We found an aggregated spatial pattern between <i>E. bocourtii</i> and its host trees, and a random pattern relative to other epiphytes. <b>Conclusion</b>: Our findings suggest that <i>E. bocourtii</i> is not safe from local extinction. We propose the propagation and reintroduction of reproductive specimens, the relocation of surviving individuals, and the establishment of new plantations of phorophytes.
DOI: 10.6084/m9.figshare.9995771
title: Mapping_1.zip

description: BAM files for Hendrikson et. al. 2017, provided as input for TOBIAS tool (https://github.com/loosolab/TOBIAS/)<br>
DOI: 10.6084/m9.figshare.9995873.v2
title: Tala 2. Codificación y análisis de contenido

description: Content analysis.
DOI: 10.6084/m9.figshare.9995873.v4
title: Table 2. Coding Table

description: Content analysis.
DOI: 10.6084/m9.figshare.9995873.v3
title: Tala 2. Codificación y análisis de contenido

description: Content analysis.
DOI: 10.6084/m9.figshare.9995732
title: wilson.zip

description: Folder with dataset analyzed via TOBIAS software and prepared for WILSON webapp (https://github.molgen.mpg.de/loosolab/wilson-apps/)<br>
DOI: 10.6084/m9.figshare.9995660
title: Oligocene <i>Limnobiophyllum</i> (Araceae) from the central Tibetan Plateau and its evolutionary and palaeoenvironmental implications

description: The extinct genus <i>Limnobiophyllum</i> (Araceae) has been considered a tentative link between the Aroideae and Lemnoideae subfamilies of Araceae. General understanding of morphological character evolution among these subfamilies has been limited due to the lack of preserved key structures in fossils such as infructescences. In this study, a new fossil species, <i>Limnobiophyllum pedunculatum</i> Low, Su & Xing sp. nov., is reported based on unusually complete specimens with intact leaves, stolon and attached infructescence and seeds from the late Oligocene of central Tibet, China. It represents the first convincing <i>Limnobiophyllum</i> fossil from the Tibetan Plateau and the first well-documented occurrence from east Asia. Its phylogenetic position was inferred using a matrix of 56 morphological characters and 5226 gene sequences of 41 taxa. Phylogenetic inference based on the matrix suggests that <i>Limnobiophyllum</i> is sister to <i>Cobbania</i>, as well as to the remaining extinct and living genera within the Araceae subfamily Lemnoideae. Reconstruction of vegetative and reproductive character evolution confirms that <i>Limnobiophyllum</i> possessed intermediate characters, especially for infructescences, between the subfamilies Lemnoideae and Aroideae. Within Lemnoideae, both vegetative and reproductive characters show clear reduction and simplification from extinct genera to living lemnoids. These findings shed new light on the evolutionary history of the family Araceae. In addition, the discovery of this species, in association with the surrounding plant megafossil assemblage, suggests a warm, humid lowland environment in the central Tibetan Plateau during the late Oligocene, contradicting previous studies that indicated high elevation of the plateau since the early Palaeogene. However, the extinction of <i>Limnobiophyllum</i> might have been due to both global cooling and orogenesis.
DOI: 10.6084/m9.figshare.9995660.v1
title: Oligocene <i>Limnobiophyllum</i> (Araceae) from the central Tibetan Plateau and its evolutionary and palaeoenvironmental implications

description: The extinct genus <i>Limnobiophyllum</i> (Araceae) has been considered a tentative link between the Aroideae and Lemnoideae subfamilies of Araceae. General understanding of morphological character evolution among these subfamilies has been limited due to the lack of preserved key structures in fossils such as infructescences. In this study, a new fossil species, <i>Limnobiophyllum pedunculatum</i> Low, Su & Xing sp. nov., is reported based on unusually complete specimens with intact leaves, stolon and attached infructescence and seeds from the late Oligocene of central Tibet, China. It represents the first convincing <i>Limnobiophyllum</i> fossil from the Tibetan Plateau and the first well-documented occurrence from east Asia. Its phylogenetic position was inferred using a matrix of 56 morphological characters and 5226 gene sequences of 41 taxa. Phylogenetic inference based on the matrix suggests that <i>Limnobiophyllum</i> is sister to <i>Cobbania</i>, as well as to the remaining extinct and living genera within the Araceae subfamily Lemnoideae. Reconstruction of vegetative and reproductive character evolution confirms that <i>Limnobiophyllum</i> possessed intermediate characters, especially for infructescences, between the subfamilies Lemnoideae and Aroideae. Within Lemnoideae, both vegetative and reproductive characters show clear reduction and simplification from extinct genera to living lemnoids. These findings shed new light on the evolutionary history of the family Araceae. In addition, the discovery of this species, in association with the surrounding plant megafossil assemblage, suggests a warm, humid lowland environment in the central Tibetan Plateau during the late Oligocene, contradicting previous studies that indicated high elevation of the plateau since the early Palaeogene. However, the extinction of <i>Limnobiophyllum</i> might have been due to both global cooling and orogenesis.
DOI: 10.6084/m9.figshare.9995516
title: EMBOJ-2019-102817

description: SILAC immunopurification output (protein lists) of duplicate experiments.<br>SILAC complexomic data MT-CYB mutant vs. WT <br>
DOI: 10.6084/m9.figshare.9995516.v1
title: EMBOJ-2019-102817

description: SILAC immunopurification output (protein lists) of duplicate experiments.<br>SILAC complexomic data MT-CYB mutant vs. WT <br>
DOI: 10.6084/m9.figshare.9995393
title: Mangrove Extent maps for the Klang Islands, Malaysia

description: <b>Mangrove Extent maps for the Klang Islands, Malaysia</b><br>Satellite derived maps of mangrove extent in the Klang Islands, Malaysia for use within a GIS.<br>Using the 2010 Global Mangrove Watch (GMW) map downloaded from https://data.unep-wcmc.org/datasets/45 as a baseline, a refined local area product was generated by manually editing the GMW polygons in QGIS to match satellite data from 2010.<br>This refined map was then used as a baseline and manually edited to reflect changes when comparing to satellite data for a given year. The output is a map of mangrove extent for each year.<br>Due to the difficulty in obtaining cloud free satellite data for the entire area multiple scenes were used for many years.<br>Data are supplied as polygons in ESRI shapefile format with a separate shapefile for each year.<br><br>
DOI: 10.6084/m9.figshare.9995399
title: Dataset, neplatny

description: This file contains data for an article entitled: "<i>Sedentary behavior patterns and adiposity in children: a study based on compositional data analysis</i>" published in XXXXXX.<br>
DOI: 10.6084/m9.figshare.9995366
title: EJN-mERa & sex diff-Dataset.xlsx

description: Initial behavioral characterization of the ERalpha-C451A mouse model (first described in Adlanmerini et al., 2014). This dataset also contain data relative to the analysis of the number of neurons immunoractive for kisspeptin (Kp) in the anteroventral periventricular nucleus (AVPv) and for calbindin neurons of the sexual dimorphic nucleus of the preoptic area (SDN-POA) in the mice and the effect of early post-natal (P0-P5) treatment with estradiol benzoate.<br>
DOI: 10.6084/m9.figshare.9995399.v2
title: Dataset, neplatny

description: This file contains data for an article entitled: "<i>Sedentary behavior patterns and adiposity in children: a study based on compositional data analysis</i>" published in XXXXXX.<br>
DOI: 10.6084/m9.figshare.9995399.v1
title: Dataset.sav

description: This file contains data for an article entitled: "XXXXXX" published in XXXXXX.<br>
DOI: 10.6084/m9.figshare.9995366.v1
title: EJN-mERa & sex diff-Dataset.xlsx

description: Initial behavioral characterization of the ERalpha-C451A mouse model (first described in Adlanmerini et al., 2014). This dataset also contain data relative to the analysis of the number of neurons immunoractive for kisspeptin (Kp) in the anteroventral periventricular nucleus (AVPv) and for calbindin neurons of the sexual dimorphic nucleus of the preoptic area (SDN-POA) in the mice and the effect of early post-natal (P0-P5) treatment with estradiol benzoate.<br>
DOI: 10.6084/m9.figshare.9995315
title: A new specimen of <i>Stenorhynchosaurus munozi</i> Páramo-Fonseca et al., 2016 (Plesiosauria, Pliosauridae), from the Barremian of Colombia: new morphological features and ontogenetic implications

description: A new specimen of <i>Stenorhynchosaurus munozi</i> Páramo-Fonseca et al., 2016 (Plesiosauria, Pliosauridae), found at Sáchica (Boyacá, Colombia) in upper Barremian beds of the Arcillolitas Abigarradas Member of the Paja Formation, is described herein. It consists of a complete skull and 10 cervical vertebrae of an adult individual and provides valuable new morphological information on the species: the presence of nasals covering a subsurface circular cavity where salt glands were probably lodged (new autapomorphy), the presence of a high sagittal crest on the parietal, a very elongated pineal foramen enclosed entirely within the parietals, and unfused neural arches in the cervical vertebrae. A phylogenetic analysis supports the inclusion of <i>Stenorhynchosaurus munozi</i> within the pliosaurid clade Brachaucheninae. A morphological comparison between the juvenile and adult stages of <i>S. munozi</i> shows that in the adult stage, the margins of the internal nares and the anterior part of the anterior interpterygoid vacuity are well ossified, the medial joints of the pterygoids and the mandibular symphysis are closed, and the atlas and the axis are fused, but the cervical neural arches remain unfused to the centra. The growth pattern of the skull dorsal bones differs from that of the palatal elements, but the relative distance between the external and internal nares remains the same. A greater longitudinal growth in the skull and a negative allometric orbital growth pattern results in a proportionally longer skull and relatively smaller orbits in the adult.
DOI: 10.6084/m9.figshare.9995315.v1
title: A new specimen of <i>Stenorhynchosaurus munozi</i> Páramo-Fonseca et al., 2016 (Plesiosauria, Pliosauridae), from the Barremian of Colombia: new morphological features and ontogenetic implications

description: A new specimen of <i>Stenorhynchosaurus munozi</i> Páramo-Fonseca et al., 2016 (Plesiosauria, Pliosauridae), found at Sáchica (Boyacá, Colombia) in upper Barremian beds of the Arcillolitas Abigarradas Member of the Paja Formation, is described herein. It consists of a complete skull and 10 cervical vertebrae of an adult individual and provides valuable new morphological information on the species: the presence of nasals covering a subsurface circular cavity where salt glands were probably lodged (new autapomorphy), the presence of a high sagittal crest on the parietal, a very elongated pineal foramen enclosed entirely within the parietals, and unfused neural arches in the cervical vertebrae. A phylogenetic analysis supports the inclusion of <i>Stenorhynchosaurus munozi</i> within the pliosaurid clade Brachaucheninae. A morphological comparison between the juvenile and adult stages of <i>S. munozi</i> shows that in the adult stage, the margins of the internal nares and the anterior part of the anterior interpterygoid vacuity are well ossified, the medial joints of the pterygoids and the mandibular symphysis are closed, and the atlas and the axis are fused, but the cervical neural arches remain unfused to the centra. The growth pattern of the skull dorsal bones differs from that of the palatal elements, but the relative distance between the external and internal nares remains the same. A greater longitudinal growth in the skull and a negative allometric orbital growth pattern results in a proportionally longer skull and relatively smaller orbits in the adult.
DOI: 10.6084/m9.figshare.9995087
title: HRT/LRT Gastroc LFQ profiling

description: HDMSE label-free quantitation of soluble proteins in gastrocnemius of rats selectively bred as either high- or low-responders to endurance exercise training.
DOI: 10.6084/m9.figshare.9995087.v1
title: HRT/LRT Gastroc LFQ profiling

description: HDMSE label-free quantitation of soluble proteins in gastrocnemius of rats selectively bred as either high- or low-responders to endurance exercise training.
DOI: 10.6084/m9.figshare.9994961
title: Model data for article submitted to JGR-Oceans (Feng Tian, Rong-Hua Zhang, Xiujun Wang)

description: Upload are model data submitted to JGR-Oceans， but not been accpted.
DOI: 10.6084/m9.figshare.9994952
title: Community structure of zooplankton across environmental variables in a high-altitude lake of central Himalayas, India

description: We determined seasonal and spatial variation of zooplankton and their correlation with environment variables in a subtropical lake of the Himalayas. Thirty-eight species of zooplankton were identified, of which, 38.0% belonged to rotifera, 26.3% to cladocera, and 15.7% to copepoda. Nitrogen nutrients, total organic matter (TOM), and clay particles significantly influenced on the distribution pattern of zooplankton. Non-metric multidimensional scaling analysis showed homogeneous assemblages of dominant zooplankton species except <i>Chydorus gibbus</i> which has wider range of niche partitioning. Turbidity formed by suspended materials facilitated better avoidance of larger zooplankton like <i>Daphnia similis</i> from predators. Sedimentary silt particles influenced on the assemblages of sensitive species such as <i>Tropocyclops prasinus</i>, <i>Asplanchna priodonta</i> and <i>Colurella obtuse</i>. Changes within the land-use pattern in the catchment of the central Himalayan lakes either directly or indirectly impact on the distribution of zooplankton community.
DOI: 10.6084/m9.figshare.9994952.v1
title: Community structure of zooplankton across environmental variables in a high-altitude lake of central Himalayas, India

description: We determined seasonal and spatial variation of zooplankton and their correlation with environment variables in a subtropical lake of the Himalayas. Thirty-eight species of zooplankton were identified, of which, 38.0% belonged to rotifera, 26.3% to cladocera, and 15.7% to copepoda. Nitrogen nutrients, total organic matter (TOM), and clay particles significantly influenced on the distribution pattern of zooplankton. Non-metric multidimensional scaling analysis showed homogeneous assemblages of dominant zooplankton species except <i>Chydorus gibbus</i> which has wider range of niche partitioning. Turbidity formed by suspended materials facilitated better avoidance of larger zooplankton like <i>Daphnia similis</i> from predators. Sedimentary silt particles influenced on the assemblages of sensitive species such as <i>Tropocyclops prasinus</i>, <i>Asplanchna priodonta</i> and <i>Colurella obtuse</i>. Changes within the land-use pattern in the catchment of the central Himalayan lakes either directly or indirectly impact on the distribution of zooplankton community.
DOI: 10.6084/m9.figshare.9994961.v1
title: Model data for article submitted to JGR-Oceans (Feng Tian, Rong-Hua Zhang, Xiujun Wang)

description: Upload are model data submitted to JGR-Oceans