cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3168997
title: Proteomic changes in response to crystal formation in <i>Drosophila</i> Malpighian tubules

description: Kidney stone disease is a major health burden with a complex and poorly understood pathophysiology. <i>Drosophila</i> Malpighian tubules have been shown to resemble human renal tubules in their physiological function. Herein, we have used <i>Drosophila</i> as a model to study the proteomic response to crystal formation induced by dietary manipulation in Malpighian tubules. Wild-type male flies were reared in parallel groups on standard medium supplemented with lithogenic agents: control, Sodium Oxalate (NaOx) and Ethylene Glycol (EG). Malpighian tubules were dissected after 2 weeks to visualize crystals with polarized light microscopy. The parallel group was dissected for protein extraction. A new method of Gel Assisted Sample Preparation (GASP) was used for protein extraction. Differentially abundant proteins (<i>p&lt;0.05</i>) were identified by label-free quantitative proteomic analysis in flies fed with NaOx and EG diet compared with control. Their molecular functions were further screened for transmembrane ion transporter, calcium or zinc ion binder. Among these, 11 candidate proteins were shortlisted in NaOx diet and 16 proteins in EG diet. We concluded that GASP is a proteomic sample preparation method that can be applied to individual <i>Drosophila</i> Malpighian tubules. Our results may further increase the understanding of the pathophysiology of human kidney stone disease.
DOI: 10.6084/m9.figshare.3168997.v1
title: Proteomic changes in response to crystal formation in <i>Drosophila</i> Malpighian tubules

description: Kidney stone disease is a major health burden with a complex and poorly understood pathophysiology. <i>Drosophila</i> Malpighian tubules have been shown to resemble human renal tubules in their physiological function. Herein, we have used <i>Drosophila</i> as a model to study the proteomic response to crystal formation induced by dietary manipulation in Malpighian tubules. Wild-type male flies were reared in parallel groups on standard medium supplemented with lithogenic agents: control, Sodium Oxalate (NaOx) and Ethylene Glycol (EG). Malpighian tubules were dissected after 2 weeks to visualize crystals with polarized light microscopy. The parallel group was dissected for protein extraction. A new method of Gel Assisted Sample Preparation (GASP) was used for protein extraction. Differentially abundant proteins (<i>p&lt;0.05</i>) were identified by label-free quantitative proteomic analysis in flies fed with NaOx and EG diet compared with control. Their molecular functions were further screened for transmembrane ion transporter, calcium or zinc ion binder. Among these, 11 candidate proteins were shortlisted in NaOx diet and 16 proteins in EG diet. We concluded that GASP is a proteomic sample preparation method that can be applied to individual <i>Drosophila</i> Malpighian tubules. Our results may further increase the understanding of the pathophysiology of human kidney stone disease.
DOI: 10.6084/m9.figshare.3169000.v1
title: Increased ribosome density associated to positively charged residues is evident in ribosome profiling experiments performed in the absence of translation inhibitors

description: It has been proposed that polybasic peptides cause slower movement of ribosomes through an electrostatic interaction with the highly negative ribosome exit tunnel. Ribosome profiling data—the sequencing of short ribosome-bound fragments of mRNA—is a powerful tool for the analysis of mRNA translation. Using the yeast <i>Saccharomyces cerevisiae</i> as a model, we showed that reduced translation efficiency associated with polybasic protein sequences could be inferred from ribosome profiling. However, an increase in ribosome density at polybasic sequences was evident only when the commonly used translational inhibitors cycloheximide and anisomycin were omitted during mRNA isolation. Since ribosome profiling performed without inhibitors agrees with experimental evidence obtained by other methods, we conclude that cycloheximide and anisomycin must be avoided in ribosome profiling experiments.
DOI: 10.6084/m9.figshare.3171472.v9
title: EventWiki: A knowledge base of major events

description: <pre>EventWiki is a knowledge base of major events happening throughout mankind history. It contains 21,229 events of 95 types. The details of event entries can be found in our paper submission and documentation file. Data in the knowledge base is mainly harvested from Wikipedia.</pre><pre>As Wikipedia, this resource can be distributed and shared under CC-BY 3.0 license.</pre>
DOI: 10.6084/m9.figshare.3168874
title: NARA_Research_Communism.xlsx

description: Research Project
DOI: 10.6084/m9.figshare.3168871
title: Research_Communism.xlsx

description: Research Project NARA
DOI: 10.6084/m9.figshare.3168868
title: NARA_Research_Communism (1).xlsx

description: Research project for klasdfj;sdkajgsldkajs;gld
DOI: 10.6084/m9.figshare.3168871.v1
title: Research_Communism.xlsx

description: Research Project NARA
DOI: 10.6084/m9.figshare.3168868.v1
title: NARA_Research_Communism (1).xlsx

description: Research project for klasdfj;sdkajgsldkajs;gld
DOI: 10.6084/m9.figshare.3171472.v11
title: EventWiki: A knowledge base of major events

description: <pre>EventWiki is a knowledge base of major events happening throughout mankind history. It contains 21,229 events of 95 types. The details of event entries can be found in our paper submission and documentation file. Data in the knowledge base is mainly harvested from Wikipedia.</pre><pre>As Wikipedia, this resource can be distributed and shared under CC-BY 3.0 license.</pre>
DOI: 10.6084/m9.figshare.3168763
title: Data outcomes mapping exercise

description: This exercise is used in various workshops and trainings to help students, particularly graduate students, think through the ways in which their research design will affect data collection, data management, analysis, write-up/reporting, and reuse. <br>
DOI: 10.6084/m9.figshare.3168682
title: Physiological and Subjective Control Measures for All Analysed (n=124) Subjects

description: Physiological Subjective Control Measures for 124 subjects analysed in Marshall et al.<br>Drug Group 1 = PlaceboDrug Group 2 = DA- (Haloperidol)Drug Group 3 = ACh- (Biperiden)Drug Group 4 = NA- (Prazosin)<br>Note that the data for the Visual Analogue Scales (VAS) for alertness, calmness and contentedness (Bond and Lader 1974) have been rearranged in alertnessflipped, calmnessflipped and contentednessflipped so that 0 is always minimum, and 100 always maximum, alertness/calmness/contentedness.<br>Where repeated measures were taken (i.e. for VAS, BP and HR):Column 1 = baselineColumn 2 = post-drug, immediately before starting the RT taskColumn 3 = post-drug, after completing the RT task<br>Where differences from baseline were calculated (i.e. for VAS, BP and HR):Column 1 = post-drug (before task) - baselineColumn 2 = post-drug (after task) - baseline<br><br>
DOI: 10.6084/m9.figshare.3168679
title: Physiological and Subjective Control Measures (all 128 subjects)

description: Physiological Subjective Control Measures for all 128 subjects in Uncertainty/Pharmacology Experiment<br>Group 1 = PlaceboGroup 2 = DA- (Haloperidol)Group 3 = ACh- (Biperiden)Group 4 = NA- (Prazosin)<br>Note that the data for the Visual Analogue Scales (VAS) for alertness, calmness and contentedness (Bond and Lader 1974) have been rearranged in alertnessflipped, calmnessflipped and contentednessflipped so that 0 is always minimum, and 100 always maximum, alertness/calmness/contentedness.<br>Where repeated measures were taken (i.e. for VAS, BP and HR):Column 1 = baselineColumn 2 = post-drug, immediately before starting the RT taskColumn 3 = post-drug, after completing the RT task<br>Where differences from baseline were calculated (i.e. for VAS, BP and HR):Column 1 = post-drug (before task) - baselineColumn 2 = post-drug (after task) - baseline
DOI: 10.6084/m9.figshare.3168763.v1
title: Data outcomes mapping exercise

description: This exercise is used in various workshops and trainings to help students, particularly graduate students, think through the ways in which their research design will affect data collection, data management, analysis, write-up/reporting, and reuse. <br>
DOI: 10.6084/m9.figshare.3168682.v1
title: Physiological and Subjective Control Measures for All Analysed (n=124) Subjects

description: Physiological Subjective Control Measures for 124 subjects analysed in Marshall et al.<br>Drug Group 1 = PlaceboDrug Group 2 = DA- (Haloperidol)Drug Group 3 = ACh- (Biperiden)Drug Group 4 = NA- (Prazosin)<br>Note that the data for the Visual Analogue Scales (VAS) for alertness, calmness and contentedness (Bond and Lader 1974) have been rearranged in alertnessflipped, calmnessflipped and contentednessflipped so that 0 is always minimum, and 100 always maximum, alertness/calmness/contentedness.<br>Where repeated measures were taken (i.e. for VAS, BP and HR):Column 1 = baselineColumn 2 = post-drug, immediately before starting the RT taskColumn 3 = post-drug, after completing the RT task<br>Where differences from baseline were calculated (i.e. for VAS, BP and HR):Column 1 = post-drug (before task) - baselineColumn 2 = post-drug (after task) - baseline<br><br>
DOI: 10.6084/m9.figshare.3168571
title: Using an unbaited stationary video system to investigate the behaviour and interactions of bull sharks <i>Carcharhinus leucas</i> under an aquaculture farm

description: Bull sharks <i>Carcharhinus leucas</i> are common along the coast of Reunion Island (South-West Indian Ocean) and were suspected to aggregate in the vicinity of an aquaculture farm in Saint-Paul Bay on the west coast. In order to understand the behaviour and interaction of bull sharks near aquaculture cages at Saint-Paul Bay, we deployed an experimental unbaited stationary video camera. From 175 hours of recording during daylight hours from March to April 2012, eight individual female bull sharks (seven adults and one immature) were identified based on their natural markings. These sharks were resighted between 3 and 45 times. Residency analysis revealed site attachment under the aquaculture cages for at least three individuals over the course of the study. Recorded behaviours included intraspecific social interactions such as synchronised swimming. Social interactions and relatively strong paired associations for two pairs of females suggest some level of sociality among bull sharks around Reunion Island. Overall, our results demonstrate the utility of unbaited video systems to monitor the behaviour of adult coastal sharks.
DOI: 10.6084/m9.figshare.3168571.v1
title: Using an unbaited stationary video system to investigate the behaviour and interactions of bull sharks <i>Carcharhinus leucas</i> under an aquaculture farm

description: Bull sharks <i>Carcharhinus leucas</i> are common along the coast of Reunion Island (South-West Indian Ocean) and were suspected to aggregate in the vicinity of an aquaculture farm in Saint-Paul Bay on the west coast. In order to understand the behaviour and interaction of bull sharks near aquaculture cages at Saint-Paul Bay, we deployed an experimental unbaited stationary video camera. From 175 hours of recording during daylight hours from March to April 2012, eight individual female bull sharks (seven adults and one immature) were identified based on their natural markings. These sharks were resighted between 3 and 45 times. Residency analysis revealed site attachment under the aquaculture cages for at least three individuals over the course of the study. Recorded behaviours included intraspecific social interactions such as synchronised swimming. Social interactions and relatively strong paired associations for two pairs of females suggest some level of sociality among bull sharks around Reunion Island. Overall, our results demonstrate the utility of unbaited video systems to monitor the behaviour of adult coastal sharks.
DOI: 10.6084/m9.figshare.3168679.v2
title: Physiological and Subjective Control Measures (all 128 subjects)

description: Physiological Subjective Control Measures for all 128 subjects in Uncertainty/Pharmacology Experiment<br>Group 1 = PlaceboGroup 2 = DA- (Haloperidol)Group 3 = ACh- (Biperiden)Group 4 = NA- (Prazosin)<br>Note that the data for the Visual Analogue Scales (VAS) for alertness, calmness and contentedness (Bond and Lader 1974) have been rearranged in alertnessflipped, calmnessflipped and contentednessflipped so that 0 is always minimum, and 100 always maximum, alertness/calmness/contentedness.<br>Where repeated measures were taken (i.e. for VAS, BP and HR):Column 1 = baselineColumn 2 = post-drug, immediately before starting the RT taskColumn 3 = post-drug, after completing the RT task<br>Where differences from baseline were calculated (i.e. for VAS, BP and HR):Column 1 = post-drug (before task) - baselineColumn 2 = post-drug (after task) - baseline
DOI: 10.6084/m9.figshare.3168562
title: DBpedia property analyis

description: DBpedia property analyis
DOI: 10.6084/m9.figshare.3168673.v1
title: DataMatrix128.mat

description: Reaction time (RT) data for 128 healthy human volunteers.<br>Group 1 = Placebo groupGroup 2 = DA- group (Haloperidol)Group 3 = ACh- group (Biperiden)Group 4 = NA- group (Prazosin)<br>Each data structure contains data for 1200 trials (rows) for an individual participantColumn 1 = RT (ms); NaN = missed responseColumn 2 = Correct (1) or Incorrect (0) responseColumn 3 = Trial-wise stimulus typeColumn 4 = Transition Matrix typeColumn 5 = Trial count (within context)Column 6 = Total trial countColumn 7 = Post-error trial (1), Non-post-error trial (0)Column 8 = Post-infrequent trial (1), Non-post-infrequent trial (0)<br>The data contained in data.druggroup.CorrectRTs.matrix is as above, but RTs for incorrect responses have been replaced with NaN.<br>Note that in Marshall et al. four participants were excluded from analyses:Group 3: Participants 19, 21 and 23Group 4: Participant 23<br>
DOI: 10.6084/m9.figshare.3168679.v1
title: Physiological and Subjective Control Measures (all subjects)

description: Physiological Subjective Control Measures for all 128 subjects in Uncertainty/Pharmacology Experiment<br>Group 1 = PlaceboGroup 2 = DA- (Haloperidol)Group 3 = ACh- (Biperiden)Group 4 = NA- (Prazosin)
DOI: 10.6084/m9.figshare.3168562.v1
title: DBpedia property analyis

description: DBpedia property analyis
DOI: 10.6084/m9.figshare.3168529
title: Tweet geolocation 5m

description: Tweet-geolocation-5m is a dataset with more than 5 million geolocated tweets with detailed geolocation information associated. Each geolocated tweet is associated with its fine-grained location information, collected from OpenStreetMap [1] using the reverse geocoding feature in Nominatim [2]. It was originally created for country-level classification of tweets, but finer-grained classification is also provided with the dataset. The country codes are provided using the ISO 3166-1 alpha-2 standard [3].<br>The dataset was collected in two different week long periods: TC2014, collected in October 2014, and TC2015, collected in October 2015.<br>Two files are provided here:* tweet-geolocation-5m.tar.bz2, which is the actual datasets, providing the tweet IDs and ground truth country IDs that enable conducting further experiments.* vectors-and-folds.tar.bz2, which is provided for the purposes of reproducibility. With the information provided in this file, you should be able to reproduce the results we presented in the paper.
DOI: 10.6084/m9.figshare.3168391
title: Incidence and patterns of cardiomyopathy in carbon monoxide-poisoned patients with myocardial injury

description: <b>Objectives</b>: Sustained myocardial injury is a significant predictor of mortality in carbon monoxide (CO) poisoning. There are few reports in the literature regarding the presence of CO-induced cardiomyopathy from early stages in the emergency department (ED). We prospectively investigated the early incidence of CO-induced cardiomyopathy and its patterns in patients with cardiomyopathy. <b>Materials and methods</b>: During a 10-month period, transthoracic echocardiography (TTE) was performed in 43 consecutive patients with CO poisoning and myocardial injury, which was defined as elevated high-sensitive troponin I within 24 h after ED arrival. Measurements of left ventricular ejection fraction and wall motion abnormalities were performed to evaluate cardiac function. If a patient had CO-induced cardiomyopathy, we measured cardiac function at the time of patient admission, day 1, day 2, and once within seven days of hospitalization. <b>Results</b>: The incidence of cardiomyopathy was as high as 74.4% (32 of 43 patients) in CO-poisoned patients with myocardial injury based on initial ED results. Echocardiographic patterns included non-cardiomyopathy (25.6%), global dysfunction (51.2%), and Takotsubo-like cardiomyopathy (23.2%). Patients in the global dysfunction group had significantly more normalized cardiac dysfunction within 72 h than did those in the Takotsubo-like cardiomyopathy group (81.8% vs. 22.2%, <i>p</i> = 0.001). <b>Discussion and conclusion</b>: Patients with CO poisoning and myocardial injury experienced cardiomyopathy, including reversible global dysfunction and a Takotsubo-like pattern. Investigation of cardiomyopathy needs to be considered in patients with CO poisoning and myocardial injury.
DOI: 10.6084/m9.figshare.3168529.v1
title: Tweet geolocation 5m

description: Tweet-geolocation-5m is a dataset with more than 5 million geolocated tweets with detailed geolocation information associated. Each geolocated tweet is associated with its fine-grained location information, collected from OpenStreetMap [1] using the reverse geocoding feature in Nominatim [2]. It was originally created for country-level classification of tweets, but finer-grained classification is also provided with the dataset. The country codes are provided using the ISO 3166-1 alpha-2 standard [3].<br>The dataset was collected in two different week long periods: TC2014, collected in October 2014, and TC2015, collected in October 2015.
DOI: 10.6084/m9.figshare.3168382
title: Kirkegaard2016 - Metagenomes from AD at Damhusaaen WWTP

description: R formatted metagenome dataset: "Kirkegaard2016_Dam.RData" for extracting genomes from metagenomes. This dataset is based on sequencing of DNA from the anaerobic digester at Damhusaaen WWTP.<br><br><br>
DOI: 10.6084/m9.figshare.3168391.v1
title: Incidence and patterns of cardiomyopathy in carbon monoxide-poisoned patients with myocardial injury

description: <b>Objectives</b>: Sustained myocardial injury is a significant predictor of mortality in carbon monoxide (CO) poisoning. There are few reports in the literature regarding the presence of CO-induced cardiomyopathy from early stages in the emergency department (ED). We prospectively investigated the early incidence of CO-induced cardiomyopathy and its patterns in patients with cardiomyopathy. <b>Materials and methods</b>: During a 10-month period, transthoracic echocardiography (TTE) was performed in 43 consecutive patients with CO poisoning and myocardial injury, which was defined as elevated high-sensitive troponin I within 24 h after ED arrival. Measurements of left ventricular ejection fraction and wall motion abnormalities were performed to evaluate cardiac function. If a patient had CO-induced cardiomyopathy, we measured cardiac function at the time of patient admission, day 1, day 2, and once within seven days of hospitalization. <b>Results</b>: The incidence of cardiomyopathy was as high as 74.4% (32 of 43 patients) in CO-poisoned patients with myocardial injury based on initial ED results. Echocardiographic patterns included non-cardiomyopathy (25.6%), global dysfunction (51.2%), and Takotsubo-like cardiomyopathy (23.2%). Patients in the global dysfunction group had significantly more normalized cardiac dysfunction within 72 h than did those in the Takotsubo-like cardiomyopathy group (81.8% vs. 22.2%, <i>p</i> = 0.001). <b>Discussion and conclusion</b>: Patients with CO poisoning and myocardial injury experienced cardiomyopathy, including reversible global dysfunction and a Takotsubo-like pattern. Investigation of cardiomyopathy needs to be considered in patients with CO poisoning and myocardial injury.
DOI: 10.6084/m9.figshare.3168376
title: Kirkegaard2016 - Genome binning of Candidatus Fermentibacter daniensis from AD at Damhusaaen WWTP

description: "Kirkegaard2016_Hyd24-12_Dam_1.html"This html document illustrates the binning of the Dam_1 Hyd24-12 genome that was published in Kirkegaard et al 2016 (https://doi.org/10.1038/ismej.2016.43). The binning was carried out before the development of the mmgenome package (http://madsalbertsen.github.io/mmgenome/) and used the "alphahull" package for selections. As I cannot remember the package version I have not been able to reproduce it since they released an update.
DOI: 10.6084/m9.figshare.3168346
title: University of Birmingham APCs 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Birmingham during 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.3168352
title: University of Manchester APCs 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Manchester during 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.3168343
title: Queen's University Belfast APCs 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by Queen's University Belfast during 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.3168382.v2
title: Kirkegaard2016 - Metagenomes from AD at Damhusaaen WWTP

description: R formatted metagenome dataset: "Kirkegaard2016_Dam.RData" for extracting genomes from metagenomes. This dataset is based on sequencing of DNA from the anaerobic digester at Damhusaaen WWTP.<br><br><br>
DOI: 10.6084/m9.figshare.3168343.v1
title: Queen's University Belfast APCs 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by Queen's University Belfast during 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.3168352.v2
title: University of Manchester APCs 2015

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Manchester during 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.3168376.v1
title: Kirkegaard2016_Hyd24-12_Dam_1.html

description: This html document illustrates the binning of the Dam_1 Hyd24-12 genome that was published in Kirkegaard et al 2016 (https://doi.org/10.1038/ismej.2016.43). The binning was carried out before the development of the mmgenome package (http://madsalbertsen.github.io/mmgenome/) and used the "alphahull" package for selections. As I cannot remember the package version I have not been able to reproduce it since they released an update.
DOI: 10.6084/m9.figshare.3168382.v1
title: Kirkegaard2016_Dam.RData

description: R formatted metagenome dataset.