cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6179219.v1
title: Code and metadata: Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

description: Understanding the genetic basis of phenotypic adaptation to changing environments is an essential goal of population and quantitative genetics. While technological advances now allow interrogation of genome-wide genotyping data in large panels, our theoretical understanding of the process of polygenic adaptation is still quite limited. To address this limitation, we use extensive forward-time simulation to explore the impacts of variation in demography, trait genetics, and selection on the rate and mode of adaptation and the resulting genetic architecture. We simulate a population adapting to an optimum shift, modeling sequence variation for 20 QTL for each of 12 different demographies for 100 different traits varying in the effect size distribution of new mutations, the strength of stabilizing selection, and the contribution of the genomic background. We then use random forest regression approaches to learn the relative importance of input parameters for statistics of interest such as the speed of adaptation, the relative frequency of hard sweeps and sweeps from standing variation, or the final genetic architecture of the trait. We find that selective sweeps occur even for traits under relatively weak selection and where the genetic background explains most of the variation. Though most sweeps occur from variation segregating in the ancestral population, new mutations can be important for traits under strong stabilizing selection that undergo a large optimum shift. Additionally, we find that deleterious mutations are more strongly influenced by the strength of stabilizing selection. We also show that population bottlenecks and expansion impact overall genetic variation as well as the relative importance of sweeps from standing variation and the speed with which adaptation can occur. We then use the matrix of effect sizes and allele frequencies in each population as a target for machine learning and find that demography and the effect size of new mutations have the largest influence on present day genetic architecture. Because a variety of parameter combinations can result in relatively similar genetic architectures, we conclude that it is not straightforward to infer much about the process of adaptation from the genetic architecture alone. Overall, our results underscore the complex population genetics of individual loci in even relatively simple quantitative trait models but provide a glimpse into the factors that drive this complexity.
DOI: 10.6084/m9.figshare.6179216.v1
title: Pereque.csv

description: O Parque Ecológico de Perequê é caracterizado pela presença de árvores de grande porte e dossel contínuo, com grande abundância de epífitas. Entretanto, trabalhos publicados acerca da flora do parque são poucos, destacando-se apenas o levantamento realizado para produção do plano de manejo do Parque. Assim, pretende-se contribuir um pouco com o conhecimento acerca da vegetação encontrada no Parque.
DOI: 10.6084/m9.figshare.6179210
title: A Corpus of Rich Metaphor Annotation

description: This corpus and its creation is described in the following publication:<br>Jonathan Gordon, Jerry R. Hobbs, Jonathan May, Michael Mohler, Fabrizio Morbini, Bryan Rink, Marc Tomlinson, and Suzanne Wertheim. 2015. “A Corpus of Rich Metaphor Annotation”. In <i>Proceedings of the Third Workshop on Metaphor in NLP</i>.<br><br>When linking to this data, please use the URL http://purl.org/net/metaphor-corpus, which will point to its current location.<br><b>Data Attribution Requirement</b><br>Please insert the following statement in any product, report, publication, presentation and/or document that includes or references the data:<br><i>This effort contains or makes use of the the IARPA-funded Metaphor Program USC/ISI annotated metaphorical language collection, release iarpa_metaphor_isi.edu_metaphor_corpus_2015-04-03.</i>
DOI: 10.6084/m9.figshare.6179210.v1
title: A Corpus of Rich Metaphor Annotation

description: This corpus and its creation is described in the following publication:<br>Jonathan Gordon, Jerry R. Hobbs, Jonathan May, Michael Mohler, Fabrizio Morbini, Bryan Rink, Marc Tomlinson, and Suzanne Wertheim. 2015. “A Corpus of Rich Metaphor Annotation”. In Proceedings of the Third Workshop on Metaphor in NLP.<br><br>When linking to this data, please use the URL http://purl.org/net/metaphor-corpus, which will point to its current location.<br><br>## Data Attribution Requirement<br>Please insert the following statement in any product, report, publication, presentation and/or document that includes or references the data:<br>This effort contains or makes use of the the IARPA-funded Metaphor Program USC/ISI annotated metaphorical language collection, release iarpa_metaphor_isi.edu_metaphor_corpus_2015-04-03.<br><br>## Acknowledgments<br>This work was supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Defense US Army Research Laboratory contract number W911NF-12-C-0025. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon. Disclaimer: The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of IARPA, DoD/ARL, or the U.S. Government.<br>
DOI: 10.6084/m9.figshare.6179144
title: Open Source Malaria compound master list 24 April 2018

description: In honour of Malaria Day a version of the project compound master list was uploaded from <br>https://docs.google.com/spreadsheets/d/1Rvy6OiM291d1GN_cyT6eSw_C3lSuJ1jaR7AJa8hgGsc/edit#gid=510297618<br>
DOI: 10.6084/m9.figshare.6179144.v1
title: Open Source Malaria compound master list 24 April 2018

description: In honour of Malaria Day a version of the project compound master list was uploaded from <br>https://docs.google.com/spreadsheets/d/1Rvy6OiM291d1GN_cyT6eSw_C3lSuJ1jaR7AJa8hgGsc/edit#gid=510297618<br>
DOI: 10.6084/m9.figshare.6179138
title: Acanthomorphs: 2,628 baits targeting 1,314 conserved loci (Acanthomorphs-UCE-1Kv1.fasta.zip)

description: A target enrichment probe set designed from 2,628 baits targeting 1,314 conserved loci identified among Acanthomorphs. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.6084/m9.figshare.6179069.v1
title: Elevated CO2 impacts on vitamins, minerals, and protein (nitrogen) in rice grains

description: This is a supplemental data file for the following 2018 Science Advances article:<br>Chunwu Zhu, Kazuhiko Kobayashi, Irakli Loladze, Jianguo Zhu, Qian Jiang, Xi Xu, Gang Liu, Saman Seneweera, Kristie L. Ebi, Adam Drewnowski, Naomi Fukagawa, Lewis H. Ziska (2018) Carbon dioxide (CO2) levels this century will alter the protein, micronutrients, and vitamin content of rice grains with potential health consequences for the poorest rice-dependent countries, <i>Science Advances, </i>DOI:<i> </i>10.1126/sciadv.aaq1012
DOI: 10.6084/m9.figshare.6179069.v2
title: Elevated CO2 impacts on vitamins, minerals, and protein (nitrogen) in rice grains

description: This is a supplemental data file for the following 2018 Science Advances article:<br>Chunwu Zhu, Kazuhiko Kobayashi, Irakli Loladze, Jianguo Zhu, Qian Jiang, Xi Xu, Gang Liu, Saman Seneweera, Kristie L. Ebi, Adam Drewnowski, Naomi Fukagawa, Lewis H. Ziska (2018) Carbon dioxide (CO2) levels this century will alter the protein, micronutrients, and vitamin content of rice grains with potential health consequences for the poorest rice-dependent countries, <i>Science Advances, </i>DOI:<i> </i>10.1126/sciadv.aaq1012
DOI: 10.6084/m9.figshare.6179060
title: Data & analysis script for "Reward associations do not explain transitive inference performance in monkeys" preprint

description: Event counts for Experiments 1 and 2, as well as the R script that analyzes the data using Stan.
DOI: 10.6084/m9.figshare.6179060.v1
title: Data & analysis script for "Reward associations do not explain transitive inference performance in monkeys" preprint

description: Event counts for Experiments 1 and 2, as well as the R script that analyzes the data using Stan.
DOI: 10.6084/m9.figshare.6179060.v2
title: Data & analysis script for "Reward associations do not explain transitive inference performance in monkeys" preprint

description: Event counts for Experiments 1 and 2, as well as the R script that analyzes the data using Stan.
DOI: 10.6084/m9.figshare.6179054
title: Aegolius vcf, reference, and script files

description: Variant call format genomic data, reference sequence, and unique dadi scripts from a study of divergence in Aegolius acadicus, Northern Saw-whet Owl. Manuscript by K. Winker et al. is entitled "<b>Speciation despite gene flow in two owls (<i>Aegolius </i>ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs)."</b>
DOI: 10.6084/m9.figshare.6179054.v1
title: Aegolius vcf files

description: Variant call format genomic data from a study of divergence in Aegolius acadicus, Northern Saw-whet Owl. Manuscript by K. Winker et al. is entitled "<b>Speciation despite gene flow in two owls (<i>Aegolius </i>ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs)."</b>
DOI: 10.6084/m9.figshare.6179054.v3
title: Aegolius vcf, reference, and script files

description: Variant call format genomic data, reference sequence, and unique dadi scripts from a study of divergence in Aegolius acadicus, Northern Saw-whet Owl. Manuscript by K. Winker et al. is entitled "<b>Speciation despite gene flow in two owls (<i>Aegolius </i>ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs)."</b>
DOI: 10.6084/m9.figshare.6179054.v2
title: Aegolius vcf, reference, and script files

description: Variant call format genomic data, reference sequence, and unique dadi script from a study of divergence in Aegolius acadicus, Northern Saw-whet Owl. Manuscript by K. Winker et al. is entitled "<b>Speciation despite gene flow in two owls (<i>Aegolius </i>ssp.): Evidence from 2,517 loci with ultraconserved elements (UCEs)."</b>
DOI: 10.6084/m9.figshare.6179003
title: Elucidating differential nano-bio interactions of multi-walled andsingle-walled carbon nanotubes using subcellular proteomics

description: Understanding the relationship between adverse exposure events and specific material properties will facilitate predictive classification of carbon nanotubes (CNTs) according to their mechanisms of action, and a safe-by-design approach for the next generation of CNTs. Mass-spectrometry-based proteomics is a reliable tool to uncover the molecular dynamics of hazardous exposures, yet challenges persist with regards to its limited dynamic range when sampling whole organisms, tissues or cell lysates. Here, the simplicity of the sub-cellular proteome was harnessed to unravel distinctive adverse exposure outcomes at the molecular level, between two CNT subtypes. A549, MRC9 and human macrophage cells, were exposed for 24h to non-cytotoxic doses of single-walled or multi-walled CNTs (swCNTs or mwCNTs). Label-free proteomics on enriched cytoplasmic fractions was complemented with analyses of reactive oxygen species (ROS) production and mitochondrial integrity. The extent/number of modulated proteoforms indicated the single-walled variant was more bioactive. Greater enrichment of pathways corresponding to oxido-reductive activity was consistent with greater intracellular ROS induction and mitochondrial dysfunction capacities of swCNTs. Other compromised cellular functions, as revealed by pathway analysis were; ribosome, spliceosome and DNA repair. Highly upregulated proteins (fold change in abundance &gt;6) such as, APOC3, RBP4 and INS are also highlighted as potential markers of hazardous CNT exposure. We conclude that, changes in cytosolic proteome abundance resulting from nano-bio interactions, elucidate adverse response pathways and their distinctive molecular components. Our results indicate that CNT-protein interactions might have a thus far unappreciated significance for protein trafficking, and this warrants further investigation.
DOI: 10.6084/m9.figshare.6177275
title: Interspecific variation in diurnal photo-protective strategies of Thalassia testudinum and Halophila johnsonii

description: PAM fluorometer data of diurnal changes in 2013 + 2014HPLC diurnal photopigment data in 2014Trolox equivalent antioxidant capacity (TEAC) diurnal data for 2013Physical water quality data 2013 + 2014
DOI: 10.6084/m9.figshare.6177275.v1
title: Interspecific variation in diurnal photo-protective strategies of Thalassia testudinum and Halophila johnsonii

description: PAM fluorometer data of diurnal changes in 2013 + 2014HPLC diurnal photopigment data in 2014Trolox equivalent antioxidant capacity (TEAC) diurnal data for 2013Physical water quality data 2013 + 2014
DOI: 10.6084/m9.figshare.6177269
title: supporting data.mat

description: data is the supplementary information for this article " Robust desynchronization of Parkinson's disease pathological oscillations by frequency modulation of delayed feedback deep brain stimulation".
DOI: 10.6084/m9.figshare.6177269.v1
title: supporting data.mat

description: data is the supplementary information for this article " Robust desynchronization of Parkinson's disease pathological oscillations by frequency modulation of delayed feedback deep brain stimulation".
DOI: 10.6084/m9.figshare.6177191
title: mcmcglmm_script_Temperature Host shift Data

description: R script for running the MCMCGlmm models for the temperature effects on viral host shifts
DOI: 10.6084/m9.figshare.6177191.v1
title: mcmcglmm_script_Temperature Host shift Data

description: R script for running the MCMCGlmm models for the temperature effects on viral host shifts
DOI: 10.6084/m9.figshare.6177173
title: The Efficiency of Escherichia coli Disinfection

description: The Efficiency of Ecoli disinfection by a single water flow through an asymmetrically compound parabolic solar concentrator
DOI: 10.6084/m9.figshare.6177173.v1
title: The Efficiency of Escherichia coli Disinfection

description: The Efficiency of Ecoli disinfection by a single water flow through an asymmetrically compound parabolic solar concentrator
DOI: 10.6084/m9.figshare.6177155
title: 2D-G-KIN.DATA.ZIP

description: Supplementary data associated to the paper:<br>"Chemical Heterogeneities in the Mantle: Progress Towards a Large Scale Quantitative Description"<br>by Max Tirone<br>(Solid Earth, se-2018-67)
DOI: 10.6084/m9.figshare.6177155.v1
title: 2D-G-KIN.DATA.ZIP

description: Supplementary data associated to the paper:<br>"Chemical Heterogeneities in the Mantle: Progress Towards a Large Scale Quantitative Description"<br>by Max Tirone<br>(Solid Earth, se-2018-67)
DOI: 10.6084/m9.figshare.6177110
title: Carotenoid presence is associated with the Or gene in domesticated carrot

description: Supplementary data sets, tables, and figures for the manuscript "Carotenoid presence is associated with the Or gene in domesticated carrot."<br>
DOI: 10.6084/m9.figshare.6177074
title: Supplementary Material for: IL-33 and Its Receptor ST2 after Inhaled Allergen Challenge in Allergic Asthmatics

description: <b><i>Background:</i></b> Previous murine models have demonstrated interleukin (IL)-33 to be an important mediator of type-2 inflammation and to promote airway hyperresponsiveness in allergic asthma. A number of inflammatory cells produce IL-33 and eosinophils express ST2 mRNA. The relationship between IL-33 and eosinophils in allergic asthma, however, remains unclear. <b><i>Objective:</i></b> The aim of this work was to evaluate in vitro the effect of allergen inhalation on IL-33 levels and expression of its receptor (ST2L) on eosinophils in allergic asthmatics, and the effect of IL-33 stimulation on eosinophil activity. <b><i>Methods:</i></b> Plasma and sputum IL-33, soluble ST2 (sST2) levels, and ST2L expression on eosinophils were measured in 10 healthy controls and 10 allergic asthmatics. Asthmatics underwent allergen and diluent inhalation challenges. Blood and sputum samples were collected to measure IL-33, sST2, and ST2L eosinophil expression before and 24 h after allergen inhalation. Purified blood eosinophils from allergic asthmatics were incubated overnight with IL-33 to assess ST2 and intracellular IL-5 expression. <b><i>Results:</i></b> Baseline levels of IL-33 in sputum and sST2 in plasma and sputum were similar in allergic asthmatics compared to healthy controls. In addition, there was no difference in blood or sputum eosinophil ST2L expression in healthy controls versus allergic asthmatics. Eosinophil ST2L expression was significantly increased 24 h postallergen inhalation in allergic asthmatics. In vitro stimulation of human eosinophils with IL-33 and LPS significantly increased eosinophil ST2L expression and IL-33 stimulation increased intracellular IL-5 expression, which was attenuated by treatment with sST2 and ST2 blockade. <b><i>Conclusion and Clinical Relevance:</i></b> In mild asthmatics, there was a significant upregulation of ST2 surface expression on eosinophils from blood and sputum following allergen inhalation challenge. In vitro, IL-33 stimulation of eosinophils increases both ST2 membrane expression and IL-5 production. These results support a role for IL-33 in causing allergen-induced eosinophilia. Blockade of IL-33 and ST2 signaling may present a novel therapeutic avenue for asthma treatment.
DOI: 10.6084/m9.figshare.6177044
title: Equilibrium study of dried orange peel for its efficiency in removal of cupric ions from water

description: Excess of copper ion (&gt;2 mg/L) in water is toxic to human beings and the ecosystem. Various water treatment technologies for copper remediation have been investigated in the past. Along with industrial effluents, Bordeaux mixture is also a noteworthy copper contamination source in the agricultural ecosystem. In our study, the biosorbent efficiency of dried orange peel was investigated through an environment-friendly process for the removal of cupric ions. Effects of pH, adsorbate concentration, adsorbent dosage, and temperature for the removal of Cu (II) were studied. Slightly acidic environment (pH = 6) was found to be optimum for removal of copper. The equilibrium data were well fitted with the Langmuir and Freundlich isotherms. The surface morphology of the adsorbent was studied using scanning electron microscope. Crystalline nonhomogenous surface was observed after copper adsorption. Desorption study indicated that 0.1N H<sub>2</sub>SO<sub>4</sub> is the best eluent for the removal of adsorbed copper from the powdered dried orange peel.
DOI: 10.6084/m9.figshare.6177044.v1
title: Equilibrium study of dried orange peel for its efficiency in removal of cupric ions from water

description: Excess of copper ion (&gt;2 mg/L) in water is toxic to human beings and the ecosystem. Various water treatment technologies for copper remediation have been investigated in the past. Along with industrial effluents, Bordeaux mixture is also a noteworthy copper contamination source in the agricultural ecosystem. In our study, the biosorbent efficiency of dried orange peel was investigated through an environment-friendly process for the removal of cupric ions. Effects of pH, adsorbate concentration, adsorbent dosage, and temperature for the removal of Cu (II) were studied. Slightly acidic environment (pH = 6) was found to be optimum for removal of copper. The equilibrium data were well fitted with the Langmuir and Freundlich isotherms. The surface morphology of the adsorbent was studied using scanning electron microscope. Crystalline nonhomogenous surface was observed after copper adsorption. Desorption study indicated that 0.1N H<sub>2</sub>SO<sub>4</sub> is the best eluent for the removal of adsorbed copper from the powdered dried orange peel.
DOI: 10.6084/m9.figshare.6177017
title: Supplementary Material for: Interim Results of a Phase II Study of Hypofractionated Radiotherapy with Concurrent Temozolomide Followed by Adjuvant Temozolomide in Patients over 70 Years Old with Newly Diagnosed Glioblastoma

description: <b><i>Objective:</i></b> In this phase II study, we investigate clinical outcomes and tolerability of hypofractionated radiotherapy (HRT) combined with temozolomide (TMZ) to treat elderly patients with glioblastoma (GBM). <b><i>Methods:</i></b> Patients 70 years of age or older with newly diagnosed GBM received HRT to a dose of 34 Gy given in ten fractions over 2 weeks, delivered with concurrent and adjuvant TMZ. <b><i>Results:</i></b> In this interim analysis, ten patients were enrolled on trial from 12/1/2015 to 4/5/2017. With a median follow-up of 9 months (range 3–12 months), median progression-free survival (PFS) was 6 months. The median overall survival (OS) has not been reached. Estimated 1-year OS and PFS rates were 53.3 and 44.4%, respectively. All patients completed the full course of RT, with no patients developing grade 3 or higher adverse events from treatment. <b><i>Conclusions:</i></b> The preliminary results of our phase II trial suggest HRT delivered over 2 weeks with concurrent and adjuvant TMZ is well tolerated in elderly patients with GBM without compromising clinical outcomes.
DOI: 10.6084/m9.figshare.6177017.v1
title: Supplementary Material for: Interim Results of a Phase II Study of Hypofractionated Radiotherapy with Concurrent Temozolomide Followed by Adjuvant Temozolomide in Patients over 70 Years Old with Newly Diagnosed Glioblastoma

description: <b><i>Objective:</i></b> In this phase II study, we investigate clinical outcomes and tolerability of hypofractionated radiotherapy (HRT) combined with temozolomide (TMZ) to treat elderly patients with glioblastoma (GBM). <b><i>Methods:</i></b> Patients 70 years of age or older with newly diagnosed GBM received HRT to a dose of 34 Gy given in ten fractions over 2 weeks, delivered with concurrent and adjuvant TMZ. <b><i>Results:</i></b> In this interim analysis, ten patients were enrolled on trial from 12/1/2015 to 4/5/2017. With a median follow-up of 9 months (range 3–12 months), median progression-free survival (PFS) was 6 months. The median overall survival (OS) has not been reached. Estimated 1-year OS and PFS rates were 53.3 and 44.4%, respectively. All patients completed the full course of RT, with no patients developing grade 3 or higher adverse events from treatment. <b><i>Conclusions:</i></b> The preliminary results of our phase II trial suggest HRT delivered over 2 weeks with concurrent and adjuvant TMZ is well tolerated in elderly patients with GBM without compromising clinical outcomes.
DOI: 10.6084/m9.figshare.6177014.v3
title: RetractoBot: a protocol for a randomised controlled trial to assess the impact of notifying authors that they have cited a retracted paper

description: This is description of an software tool notifying authors that they cited a retracted paper and a protocol for a proposed randomised trial investigating the impact of notifying authors that they have cited a retracted paper.
DOI: 10.6084/m9.figshare.6177011
title: Supplementary Material for: A Rare Cause of Juvenile Stroke: Extracranial Carotid Artery Aneurysm with Venous Complete Reconstruction of the Carotid Bifurcation

description: Extracranial carotid artery aneurysms (ECAA) are a rare cause of embolic stroke. The underlying etiology is variable, with atherosclerosis being the most common entity in older subjects. Several treatments have been developed over the last 20 years, but the preferred method remains unknown. Notwithstanding the widespread use of endovascular techniques, surgical reconstruction by means of a bifurcated venous bypass graft should be applied in younger patients. In this way, it is possible to avoid major concerns about the development of long-term intrastent restenosis, and also to spare the external carotid artery which represents the main branch for the ipsilateral cerebral and facial perfusion. We propose ECAA resection and interposition of the inverted great saphenous vein to both the internal and external carotid artery by means the use of a tributary, i.e., the Giacomini vein.