cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5834484.v1
title: Additional file 2: of Are CONSORT checklists submitted by authors adequately reflecting what information is actually reported in published papers?

description: Summary of evaluations. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.5834481
title: Additional file 2: of Saving Lives at Birth; development of a retrospective theory of change, impact framework and prioritised metrics

description: Prioritised Metrics Toolkit. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.5834481.v1
title: Additional file 2: of Saving Lives at Birth; development of a retrospective theory of change, impact framework and prioritised metrics

description: Prioritised Metrics Toolkit. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.5834274
title: Quantifying esophageal motion during free-breathing and breath-holding using fiducial markers in patients with early-stage esophageal cancer

description: we quantified the esophageal motion during free-breathing and using breath-hold.
DOI: 10.6084/m9.figshare.5834274.v1
title: Quantifying esophageal motion during free-breathing and breath-holding using fiducial markers in patients with early-stage esophageal cancer

description: we quantified the esophageal motion during free-breathing and using breath-hold.
DOI: 10.6084/m9.figshare.5834268
title: Example Package to Test Unattended Deployment to 'figshare' For 'tic'

description: Deploys all builds as a new article on FigShare.nnn Deploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnn
DOI: 10.6084/m9.figshare.5834268.v1
title: Example Package to Test Unattended Deployment to 'figshare' For 'tic'

description: Deploys all builds as a new article on FigShare.nnn Deploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnnDeploys all builds as a new article on FigShare.nnn
DOI: 10.6084/m9.figshare.5834193
title: Title

description: description
DOI: 10.6084/m9.figshare.5834193.v1
title: Title

description: description
DOI: 10.6084/m9.figshare.5833983
title: Systematic review of geographic biases in the collection of at-sea distribution data for seabirds

description: The distribution of wildlife informs conservation planning. In marine systems, spatial information for seabirds is acquired primarily using vessel-based at-sea survey, aerial survey or animal-borne tracking devices. Many factors contribute to geographic biases in marine spatial research and we use a structured database search to review global patterns resulting from these biases. Although survey effort has been substantial, many large marine sectors were poorly represented. Poor representation often coincided spatially with hotspots of seabird species richness or areas experiencing high cumulative human impact, particularly in southern hemisphere and equatorial regions. Therefore, future seabird research priorities should reflect high species-richness areas including the south-west Pacific, particularly waters surrounding New Zealand. Furthermore, under-represented areas of Asia, and the Atlantic coasts of South America and Africa require greater research effort because of high cumulative human impacts in these areas. National gross domestic product (GDP) was positively related to the number of papers a country produced (determined by the first author’s address). This is indicative of constraints imposed by inherent costs of marine research. We recommend international collaboration between scientists from high-GDP nations with those in developing countries to address this. Further uptake of platforms of opportunity may also reduce this imbalance.
DOI: 10.6084/m9.figshare.5833983.v1
title: Systematic review of geographic biases in the collection of at-sea distribution data for seabirds

description: The distribution of wildlife informs conservation planning. In marine systems, spatial information for seabirds is acquired primarily using vessel-based at-sea survey, aerial survey or animal-borne tracking devices. Many factors contribute to geographic biases in marine spatial research and we use a structured database search to review global patterns resulting from these biases. Although survey effort has been substantial, many large marine sectors were poorly represented. Poor representation often coincided spatially with hotspots of seabird species richness or areas experiencing high cumulative human impact, particularly in southern hemisphere and equatorial regions. Therefore, future seabird research priorities should reflect high species-richness areas including the south-west Pacific, particularly waters surrounding New Zealand. Furthermore, under-represented areas of Asia, and the Atlantic coasts of South America and Africa require greater research effort because of high cumulative human impacts in these areas. National gross domestic product (GDP) was positively related to the number of papers a country produced (determined by the first author’s address). This is indicative of constraints imposed by inherent costs of marine research. We recommend international collaboration between scientists from high-GDP nations with those in developing countries to address this. Further uptake of platforms of opportunity may also reduce this imbalance.
DOI: 10.6084/m9.figshare.5833938
title: Other data

description: Other data for:<br>Emily B. Graham, Rachel S. Gabor, Shon Schooler, Diane M. McKnight, Diana R. Nemergut, and Joseph E. Knelman. 2018. Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PeerJ<br>
DOI: 10.6084/m9.figshare.5833938.v1
title: Other data

description: Other data for:<br>Emily B. Graham, Rachel S. Gabor, Shon Schooler, Diane M. McKnight, Diana R. Nemergut, and Joseph E. Knelman. 2018. Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PeerJ<br>
DOI: 10.6084/m9.figshare.5833935
title: Sequences

description: Raw Sequences and Mapping File:<br>Emily B. Graham, Rachel S. Gabor, Shon Schooler, Diane M. McKnight, Diana R. Nemergut, and Joseph E. Knelman. 2018. Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PeerJ<br>
DOI: 10.6084/m9.figshare.5833926
title: Eosophilic Esophagitis mRNA Shotgun Reads

description: Samples used for case study of mRNA shotgun read metataxonomic analysis. Submitted for publishing in Bioinformatics, "On the problem of metataxonomy analysis using metagenome databases contaminated with human sequences: case study of Eosinophilic esophagitis RNA-seq data"
DOI: 10.6084/m9.figshare.5833926.v2
title: Eosophilic Esophagitis mRNA Shotgun Reads

description: Samples used for case study of mRNA shotgun read metataxonomic analysis. Submitted for publishing in Bioinformatics, "On the problem of metataxonomy analysis using metagenome databases contaminated with human sequences: case study of Eosinophilic esophagitis RNA-seq data"
DOI: 10.6084/m9.figshare.5833926.v1
title: Eosophilic Esophagitis mRNA Shotgun Reads

description: Samples used for case study of mRNA shotgun read metataxonomic analysis. Submitted for publishing in Bioinformatics, "On the problem of metataxonomy analysis using metagenome databases contaminated with human sequences: case study of Eosinophilic esophagitis RNA-seq data"
DOI: 10.6084/m9.figshare.5833824
title: EGFRvIII expression triggers a metabolic dependency and therapeutic vulnerability sensitive to autophagy inhibition

description: Expression of EGFRvIII is frequently observed in glioblastoma and is associated with increased cellular proliferation, enhanced tolerance to metabolic stresses, accelerated tumor growth, therapy resistance and poor prognosis. We observed that expression of EGFRvIII elevates the activation of macroautophagy/autophagy during starvation and hypoxia and explored the underlying mechanism and consequence. Autophagy was inhibited (genetically or pharmacologically) and its consequence for tolerance to metabolic stress and its therapeutic potential in (EGFRvIII<sup>+</sup>) glioblastoma was assessed in cellular systems, (patient derived) tumor xenopgrafts and glioblastoma patients. Autophagy inhibition abrogated the enhanced proliferation and survival advantage of EGFRvIII<sup>+</sup> cells during stress conditions, decreased tumor hypoxia and delayed tumor growth in EGFRvIII<sup>+</sup> tumors. These effects can be attributed to the supporting role of autophagy in meeting the high metabolic demand of EGFRvIII<sup>+</sup> cells. As hypoxic tumor cells greatly contribute to therapy resistance, autophagy inhibition revokes the radioresistant phenotype of EGFRvIII<sup>+</sup> tumors in (patient derived) xenograft tumors. In line with these findings, retrospective analysis of glioblastoma patients indicated that chloroquine treatment improves survival of all glioblastoma patients, but patients with EGFRvIII<sup>+</sup> glioblastoma benefited most. Our findings disclose the unique autophagy dependency of EGFRvIII<sup>+</sup> glioblastoma as a therapeutic opportunity. Chloroquine treatment may therefore be considered as an additional treatment strategy for glioblastoma patients and can reverse the worse prognosis of patients with EGFRvIII<sup>+</sup> glioblastoma.
DOI: 10.6084/m9.figshare.5833824.v1
title: EGFRvIII expression triggers a metabolic dependency and therapeutic vulnerability sensitive to autophagy inhibition

description: Expression of EGFRvIII is frequently observed in glioblastoma and is associated with increased cellular proliferation, enhanced tolerance to metabolic stresses, accelerated tumor growth, therapy resistance and poor prognosis. We observed that expression of EGFRvIII elevates the activation of macroautophagy/autophagy during starvation and hypoxia and explored the underlying mechanism and consequence. Autophagy was inhibited (genetically or pharmacologically) and its consequence for tolerance to metabolic stress and its therapeutic potential in (EGFRvIII<sup>+</sup>) glioblastoma was assessed in cellular systems, (patient derived) tumor xenopgrafts and glioblastoma patients. Autophagy inhibition abrogated the enhanced proliferation and survival advantage of EGFRvIII<sup>+</sup> cells during stress conditions, decreased tumor hypoxia and delayed tumor growth in EGFRvIII<sup>+</sup> tumors. These effects can be attributed to the supporting role of autophagy in meeting the high metabolic demand of EGFRvIII<sup>+</sup> cells. As hypoxic tumor cells greatly contribute to therapy resistance, autophagy inhibition revokes the radioresistant phenotype of EGFRvIII<sup>+</sup> tumors in (patient derived) xenograft tumors. In line with these findings, retrospective analysis of glioblastoma patients indicated that chloroquine treatment improves survival of all glioblastoma patients, but patients with EGFRvIII<sup>+</sup> glioblastoma benefited most. Our findings disclose the unique autophagy dependency of EGFRvIII<sup>+</sup> glioblastoma as a therapeutic opportunity. Chloroquine treatment may therefore be considered as an additional treatment strategy for glioblastoma patients and can reverse the worse prognosis of patients with EGFRvIII<sup>+</sup> glioblastoma.
DOI: 10.6084/m9.figshare.5833821.v2
title: Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

description: Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call ‘homeostatic tolerance,’ is involved in amino acid signaling in <i>Arabidopsis</i>. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in <i>atg5</i>, <i>atg7</i>, and <i>gcn2</i> single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in <i>atg5 gcn2</i> and <i>atg7 gcn2</i> double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced <i>TOR</i> RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.
DOI: 10.6084/m9.figshare.5833821.v1
title: Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

description: Sulfonylurea (SU) herbicides inhibit branched-chain amino acid (BCAA) biosynthesis by targeting acetolactate synthase. Plants have evolved target-site resistance and metabolic tolerance to SU herbicides; the GCN2 (general control non-repressible 2) pathway is also involved in SU tolerance. Here, we report a novel SU tolerance mechanism, autophagy, which we call ‘homeostatic tolerance,’ is involved in amino acid signaling in <i>Arabidopsis</i>. The activation and reversion of autophagy and GCN2 by the SU herbicide tribenuron-methyl (TM) and exogenous BCAA, respectively, confirmed that TM-induced BCAA starvation is responsible for the activation of autophagy and GCN2. Genetic and biochemical analyses revealed a lower proportion of free BCAA and more sensitive phenotypes in <i>atg5</i>, <i>atg7</i>, and <i>gcn2</i> single mutants than in wild-type seedlings after TM treatment; the lowest proportion of free BCAA and the most sensitive phenotypes were found in <i>atg5 gcn2</i> and <i>atg7 gcn2</i> double mutants. Immunoblotting and microscopy revealed that TM-induced activation of autophagy and GCN2 signaling do not depend on the presence of each other, and these 2 pathways may serve as mutually compensatory mechanisms against TM. TM inhibited the TOR (target of rapamycin), and activated autophagy in an estradiol-induced <i>TOR</i> RNAi line, suggesting that TM-induced BCAA starvation activates autophagy, probably via TOR inactivation. Autophagy and GCN2 were also activated, and independently contributed to TM tolerance in plants conferring metabolic tolerance. Together, these data suggest that autophagy is a proteolytic process for amino acid recycling and contributes to GCN2-independent SU tolerance, probably by its ability to replenish fresh BCAA.
DOI: 10.6084/m9.figshare.5833818
title: Environmental Sensor Metadata Survey.csv.zip

description: The following dataset is a collection of twelve anonymously gathered responses from scientists and technicians working with Environmental Science Sensor Networks Collecting in-situ time Series data. Specifically, the survey which produced this dataset was distributed to two working groups associated with the organization of Earth Science Information Partners: the Envirosensing Cluster and the Documentation Cluster.<br>This survey was crafted to hopefully provide a picture of what metadata management and creation looks like for professionals working with environmental sensor data.
DOI: 10.6084/m9.figshare.5833797
title: Figure 6

description: Data corresponding to figure 6
DOI: 10.6084/m9.figshare.5833794
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5833794.v1
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5833794.v2
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5833794.v3
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5833794.v5
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5833794.v4
title: Project 19.1: Pediatric FN Definition 2012 Bern (NCT01683370): Prospective clinical observation of 39 pediatric patients treated with chemotherapy for cancer, with 43 episodes of fever in neutropenia

description: The Pediatric FN Definition 2012 Bern (NCT01683370) study recruited patients from August 2012 to May 2013 in a single Center, the Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.39 patients were observed during 289 months of cumulative chemotherapy exposure time. 43 episodes of fever in chemotherapy-induced neutropenia (FN) were diagnosed in 20 of the 39 patients.Information on FN episodes diagnosed is published here, based on &gt;8000 temperature measurements and &gt;1800 CBCs, together with exact relative time data.Data are irreversibly anonymized. In order not to compromise anonymization in this small sample of patients, information on gender, age, and malignancy diagnosis is not given.A key-file explains all variables.39 further files contain the data of the single patients.
DOI: 10.6084/m9.figshare.5832054
title: Computed Retrosynthetic Routes with MCTS and Heuristic Best First Search

description: mcts_examples.pdf contains routes found by the 3N-MCTS algorithm. <br> heuristicBFS_examples.pdf contains routes found by heuristic best first search without policy network and in-scope filter.
DOI: 10.6084/m9.figshare.5832054.v1
title: Computed Retrosynthetic Routes with MCTS and Heuristic Best First Search

description: mcts_examples.pdf contains routes found by the 3N-MCTS algorithm. <br> heuristicBFS_examples.pdf contains routes found by heuristic best first search without policy network and in-scope filter.
DOI: 10.6084/m9.figshare.5831982
title: Crop production data in Senegal (2010-2016) at department level

description: Crop production, area and yield data in Senegal (1997-2016) at department level.Data source: Direction de l'Analyse, de la Prévision et des Statistiques Agricoles (DAPSA) http://www.dapsa.gouv.sn/
DOI: 10.6084/m9.figshare.5831982.v1
title: Crop production data in Senegal (2010-2016) at department level

description: Crop production, area and yield data in Senegal (1997-2016) at department level.Data source: Direction de l'Analyse, de la Prévision et des Statistiques Agricoles (DAPSA) http://www.dapsa.gouv.sn/