cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15143892
title: Data of "Effects of microplastics on onion nutrition in fertile soils and interaction with arbuscular mycorrhizal fungi"

description: Primary data of the paper "Effects of microplastics on crop nutrition in fertile soils and interaction with arbuscular mycorrhizal fungi"
DOI: 10.6084/m9.figshare.16764217
title: The traits of 'trait ecologists'

description: Supporting Information and a data set from Dawson, SK, CP Carmona, M González-Suárez, M Jönsson, F de Carvalho, M Mallen-Cooper, Y Melero, H Moor, J Simaika, and AB Duthie. 2021 "The traits of 'trait ecologists': an analysis of the use of trait and functional trait terminology". Ecology and Evolution. http://doi.org/10.1002/ece3.8321<br>SUMMARY OF FILES INCLUDED<br>- Supporting Information 1: Includes two tables of survey questions used in data collection. Table S1.1: Questions asked in online survey and response options where a limited number were selected. Table S1.2: Details asked of survey respondents for classification into fields<br>- Supporting Information 2: Anonymous survey data including data collected on participant opinions and participant traits. <br>- Supporting Information 3: Supporting figures summarising survey data collection, and data collected from a literature review on traits from 16 journals where functional trait-based studies are often published: American Naturalist, AREES, Ecography, Ecology, Ecology Letters, Ecological Monographs, Global Ecology and Biogeography, Functional Ecology, Journal of Animal Ecology, Journal of Applied Ecology, Journal of Ecology, Nature Ecology and Evolution, Oecologia, Oikos, PNAS and TREE. All papers used were published in 2018, and included the term ‘trait*’ in the title, abstract and/or keywords. <br>- Supporting Information 4: An analysis of the agreement among eight authors for the literature review analysis. Each author reviewed a similar number of papers from the a total of 712. This supporting information includes the reviewer methodology and a summary of Cohen's Kappa across reviewers, with code illustrating how the analysis was produced.<br>- A CSV file ('lit_review_data.csv') that includes all of the data collected in the literature review. This includes 712 papers published in 2018 on traits.<br>- A CSV file ('extra_10.csv') that includes all of the data collected from co-authors for the analysis performed in Supporting Information 4.<br>
DOI: 10.5281/zenodo.5720492
title: Long reads training material for 'Quality Control' tutorial (Galaxy Training Material)

description: The data provided here are part of a Galaxy Training Network tutorial for reads Quality Control. PacBio HiFi reads were provided by PacBio - GIAB sample HG002 (https://www.pacb.com/smrt-science/smrt-resources/datasets/) and was downsampled using seqtk (https://github.com/lh3/seqtk) Nanopore reads were provided by Tim Kahlke as part of "Long-Read, long reach Bioinformatics Tutorials" (https://timkahlke.github.io/LongRead_tutorials/) and was basecalled using Guppy v5.0.2 (dna_r9.4.1_450bps_sup.cfg).
DOI: 10.5281/zenodo.5720430
title: PC338 major elements and Sr-Nd isotopes

description: Major elements and Sr-Nd isotopes data for the core PC338 from South China Sea.
DOI: 10.15468/xnt8ss
title: Manidae

description: This dataset contains the digitized treatments in Plazi based on the original book chapter Don E. Wilson, Russell A. Mittermeier (2011): Manidae. In: Handbook of the Mammals of the World – Volume 2 Hoofed Mammals. Barcelona: Lynx Edicions: 95-103, DOI: http://doi.org/10.5281/zenodo.5720458
DOI: 10.5281/zenodo.5720486
title: Phase optimization of thermally actuated piezoresistive resonant MEMS cantilever sensors (Data)

description: Origin projects, figures and COMSOL simulation used for the article "Phase optimization of thermally actuated piezoresistive resonant MEMS cantilever sensors", published in <em>Journal of Sensors and Sensor Systems </em>on 14 Jan 2019.
description: This project has received funding from the EMPIR program co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation program under no. 17IND05 MicroProbes.
DOI: 10.5281/zenodo.5720485
title: Phase optimization of thermally actuated piezoresistive resonant MEMS cantilever sensors (Data)

description: Origin projects, figures and COMSOL simulation used for the article "Phase optimization of thermally actuated piezoresistive resonant MEMS cantilever sensors", published in <em>Journal of Sensors and Sensor Systems </em>on 14 Jan 2019.
description: This project has received funding from the EMPIR program co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation program under no. 17IND05 MicroProbes.
DOI: 10.5281/zenodo.5720501
title: Obligate mutualistic cooperation limits evolvability

description: Cooperative mutualisms are widespread and play fundamental roles in many ecosystems. Given that these interactions are often obligate, the Darwinian fitness of the participating individuals is not only determined by the information encoded in their own genomes, but also the traits and capabilities of their corresponding interaction partners. Thus, a major outstanding question is how obligate cooperative mutualisms affect the ability of organisms to adapt evolutionarily to changing environmental conditions. Here we address this issue using a mutualistic cooperation between two auxotrophic genotypes of Escherichia coli that reciprocally exchanged costly amino acids. Amino acid-supplemented monocultures and unsupplemented cocultures were exposed to stepwise increasing concentrations of different antibiotics. This selection experiment reveals that metabolically interdependent bacteria are generally less able to adapt to environmental stress than autonomously growing strains. Moreover, obligate cooperative mutualists frequently regain metabolic autonomy, resulting in a collapse of the mutualistic interaction.
DOI: 10.5281/zenodo.5720500
title: Obligate mutualistic cooperation limits evolvability

description: Cooperative mutualisms are widespread and play fundamental roles in many ecosystems. Given that these interactions are often obligate, the Darwinian fitness of the participating individuals is not only determined by the information encoded in their own genomes, but also the traits and capabilities of their corresponding interaction partners. Thus, a major outstanding question is how obligate cooperative mutualisms affect the ability of organisms to adapt evolutionarily to changing environmental conditions. Here we address this issue using a mutualistic cooperation between two auxotrophic genotypes of Escherichia coli that reciprocally exchanged costly amino acids. Amino acid-supplemented monocultures and unsupplemented cocultures were exposed to stepwise increasing concentrations of different antibiotics. This selection experiment reveals that metabolically interdependent bacteria are generally less able to adapt to environmental stress than autonomously growing strains. Moreover, obligate cooperative mutualists frequently regain metabolic autonomy, resulting in a collapse of the mutualistic interaction.
DOI: 10.5281/zenodo.5217997
title: Raw data : Observation of two-mode squeezing in a traveling wave parametric amplifier

description: The raw data used to generate figures presented in the articles is available as qcodes datasets. Fig 2<br> The 100 million quadrature points used to construct statistics in figure 2 are stored at 10 datasets with ids 1 to 10, each containing 10 million points. The data was split in multiple databases to ease storage and processing. Fig 3<br> The pump phase sweep in figure 2 was recorded at 25 points from 0 to pi. Each sweep step is stored as a dataset in the database starting from run id 11 to 35, corresponding to 0 to pi in order. Fig 4<br> The quadratures recorded at delta values 20, 50, 100, 150 and 200 are stored with run id 36 to 40, respectively. Fig SNTJ gain calibration<br> The noise spectrum as a function of voltage applied to SNTJ is stored for frequencies corresponding to the delta values 20, 50, 100, 150 and 200, from run id 41 to 45, respectively.
DOI: 10.5281/zenodo.5217996
title: Raw data : Observation of two-mode squeezing in a traveling wave parametric amplifier

description: The raw data used to generate figures presented in the articles is available as qcodes datasets. Fig 2<br> The 100 million quadrature points used to construct statistics in figure 2 are stored at 10 datasets with ids 1 to 10, each containing 10 million points. The data was split in multiple databases to ease storage and processing. Fig 3<br> The pump phase sweep in figure 2 was recorded at 25 points from 0 to pi. Each sweep step is stored as a dataset in the database starting from run id 11 to 35, corresponding to 0 to pi in order. Fig 4<br> The quadratures recorded at delta values 20, 50, 100, 150 and 200 are stored with run id 36 to 40, respectively. Fig SNTJ gain calibration<br> The noise spectrum as a function of voltage applied to SNTJ is stored for frequencies corresponding to the delta values 20, 50, 100, 150 and 200, from run id 41 to 45, respectively.
DOI: 10.25550/a-qvng
title: Single cell analysis of tooth morphogenesis

description: We transcriptionally profiled single cells from mouse molars at several critical developmental stages and identified the landscape of cellular heterogeneity within the dental mesenchyme across mouse molar development from embryonic to postnatal stages. We defined the cellular domains through newly identified signature genes in the dental mesenchyme as the molar develops and found that each one makes a specific contribution to mouse molar formation.
DOI: 10.13135/ela-417
title: Honours for Euphron of Sikyon
DOI: 10.5281/zenodo.5720505
title: Phase characteristic optimization of resonant MEMS environmental sensors (Data)

description: Origin projects and figures used for the article "Phase characteristic optimization of resonant MEMS environmental sensors", published in the proceedings of Sensoren und Messsysteme 2018, 19. ITG/GMA-Fachtagung; 26.06.2018 to 27.06.2018; Nürnberg, Germany.
DOI: 10.5281/zenodo.5720504
title: Phase characteristic optimization of resonant MEMS environmental sensors (Data)

description: Origin projects and figures used for the article "Phase characteristic optimization of resonant MEMS environmental sensors", published in the proceedings of Sensoren und Messsysteme 2018, 19. ITG/GMA-Fachtagung; 26.06.2018 to 27.06.2018; Nürnberg, Germany.
DOI: 10.5523/bris.1omzijcjqo8j820wlv6gvy86nr
title: Data for 2021 RetracTip

description: Inlcuded here are data to support the paper: Qiukai Q, Chaoqun Xiang, Van Anh Ho, Jonathan Rossiter, A Sea-Anemone-Inspired, Multifunctional, Bistable Gripper. Soft Robotics (2021).
DOI: 10.48420/16573880
title: Magnetic data

description: SQUID data for compound 1 in paper
DOI: 10.48420/16573880.v1
title: Magnetic data

description: SQUID data for compound 1 in paper
DOI: 10.48420/16573874
title: CASSCF output files

description: MOLCAS output files
DOI: 10.48420/16573874.v1
title: CASSCF output files

description: MOLCAS output files
DOI: 10.6084/m9.figshare.14852359
title: Patient-specific fluid–structure interaction model of bile flow: comparison between 1-way and 2-way algorithms

description: Gallbladder disease is one of the most spread pathologies in the world. Despite the number of operations dealing with biliary surgery increases, the number of postoperative complications is also high. The aim of this study is to show the influence of the biliary system pathology on bile flow character and to numerically assess the effect of surgical operation (cholecystectomy) on the fluid dynamics in the extrahepatic biliary tree, and also to reveal the difference between 1-way and 2-way FSI algorithms on the results. Moreover, the bile viscosity and biliary tree geometry influence on the choledynamics were evaluated. Bile velocity, pressure, wall shear stress (WSS), displacements and von Mises stress distributions in the extrahepatic biliary tree are presented, and comparison is made between a healthy and a lithogenic bile. The patient-specific biliary tree model is created using magnetic resonance imaging (MRI) and imported in a commercial finite element analysis software. It is found that in the case of lithogenic bile, velocities have lower magnitude while pressures are higher. Furthermore, stress analysis of the bile ducts shows that the WSS distribution is found mostly prevailing in the common hepatic duct and common bile duct areas. It is shown that when it is necessary to evaluate the bile flow dynamics in urgent medical situations, 1-way analysis is acceptable. Nevertheless, 2-way FSI provides more accurate data, if necessary to evaluate the stress–strain state of bile ducts. The proposed model can be applied to medical practice to reduce the number of post-operative complications.
DOI: 10.6084/m9.figshare.14852359.v2
title: Patient-specific fluid–structure interaction model of bile flow: comparison between 1-way and 2-way algorithms

description: Gallbladder disease is one of the most spread pathologies in the world. Despite the number of operations dealing with biliary surgery increases, the number of postoperative complications is also high. The aim of this study is to show the influence of the biliary system pathology on bile flow character and to numerically assess the effect of surgical operation (cholecystectomy) on the fluid dynamics in the extrahepatic biliary tree, and also to reveal the difference between 1-way and 2-way FSI algorithms on the results. Moreover, the bile viscosity and biliary tree geometry influence on the choledynamics were evaluated. Bile velocity, pressure, wall shear stress (WSS), displacements and von Mises stress distributions in the extrahepatic biliary tree are presented, and comparison is made between a healthy and a lithogenic bile. The patient-specific biliary tree model is created using magnetic resonance imaging (MRI) and imported in a commercial finite element analysis software. It is found that in the case of lithogenic bile, velocities have lower magnitude while pressures are higher. Furthermore, stress analysis of the bile ducts shows that the WSS distribution is found mostly prevailing in the common hepatic duct and common bile duct areas. It is shown that when it is necessary to evaluate the bile flow dynamics in urgent medical situations, 1-way analysis is acceptable. Nevertheless, 2-way FSI provides more accurate data, if necessary to evaluate the stress–strain state of bile ducts. The proposed model can be applied to medical practice to reduce the number of post-operative complications.
DOI: 10.6084/m9.figshare.14852359.v1
title: Patient-specific fluid–structure interaction model of bile flow: comparison between 1-way and 2-way algorithms

description: Gallbladder disease is one of the most spread pathologies in the world. Despite the number of operations dealing with biliary surgery increases, the number of postoperative complications is also high. The aim of this study is to show the influence of the biliary system pathology on bile flow character and to numerically assess the effect of surgical operation (cholecystectomy) on the fluid dynamics in the extrahepatic biliary tree, and also to reveal the difference between 1-way and 2-way FSI algorithms on the results. Moreover, the bile viscosity and biliary tree geometry influence on the choledynamics were evaluated. Bile velocity, pressure, wall shear stress (WSS), displacements and von Mises stress distributions in the extrahepatic biliary tree are presented, and comparison is made between a healthy and a lithogenic bile. The patient-specific biliary tree model is created using magnetic resonance imaging (MRI) and imported in a commercial finite element analysis software. It is found that in the case of lithogenic bile, velocities have lower magnitude while pressures are higher. Furthermore, stress analysis of the bile ducts shows that the WSS distribution is found mostly prevailing in the common hepatic duct and common bile duct areas. It is shown that when it is necessary to evaluate the bile flow dynamics in urgent medical situations, 1-way analysis is acceptable. Nevertheless, 2-way FSI provides more accurate data, if necessary to evaluate the stress–strain state of bile ducts. The proposed model can be applied to medical practice to reduce the number of post-operative complications.
DOI: 10.48420/17061680
title: Pre-defined Gene Co-expression Modules in Rheumatoid Arthritis Transition towards Molecular Health following Anti-TNF Therapy

description: Patient cohort Two prospectively followed RA patient cohorts were studied, in addition to 10 disease-free controls. The first cohort (adalimumab cohort; n = 70) were recruited from UK centres to the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS), previously described by Oliver et al. [15] All selected patients were white adults with a clinician diagnosis of RA, and about to begin treatment with adalimumab for the first time for their RA symptoms. Patients were categorised as either good- or non-responders to treatment following 3-months of therapy using established EULAR response criteria.[16] Good responders (n = 50) were patients who achieved a &lt;2.6 Disease Activity Score of 28-joints (DAS28) (i.e. DAS28 clinical remission) and a DAS28 improvement of &gt;1.2 at the 3-month follow-up. Non-responders (n = 20) were defined as patients that had a 3-month DAS28 score of &gt;5.1 (i.e. high disease activity) and an improvement of &lt;0.6. Non-responders were excluded from analysis if they reported non-adherence to treatment or if anti-drug antibodies were detected in their blood samples. Ethics was approved by the North West 6 Central Manchester South Research Ethics Committee (COREC 04/Q1403/37) and all patients provided written consent.[15]The second patient cohort (MTX cohort; n = 85) were recruited from the Rheumatoid Arthritis Medication Study (RAMS), a UK multicentre longitudinal observational study that enrols new-onset RA patients who are about to commence therapy with MTX. Response to treatment was assessed 6-months after treatment using the EULAR response criteria. Patients were then categorised as good (n = 42) or non-responders (n = 43) to MTX. RAMS was approved by the Central Manchester NHS Research Ethics Committee (reference 08/H1008/25) and all patients provided written informed consent.[17]The disease-free controls were recruited under the National Repository for Healthy Volunteers (NRHV) study within the Versus Arthritis Centre for Genetics and Genomics at the University of Manchester. Ethical approval was obtained (reference REC 99/8/84) and all volunteers gave written informed consent in compliance with Good Clinical Practice and the Declaration of Helsinki. Summary demographic information on both patient cohorts and disease-free controls are provided in Supplementary Table 1.Transcriptome measurement Whole blood gene expression profiles were captured using the Affymetrix Human Transcriptome Array 2.0 (HTA) at pre-treatment and following 3-months of treatment with adalimumab, and using the Illumina HumanHT-12 v3 Array at pre-treatment and following 4-weeks of treatment with MTX, in the adalimumab cohort and MTX cohort respectively. <br>
DOI: 10.48420/17061680.v1
title: Pre-defined Gene Co-expression Modules in Rheumatoid Arthritis Transition towards Molecular Health following Anti-TNF Therapy

description: Patient cohort Two prospectively followed RA patient cohorts were studied, in addition to 10 disease-free controls. The first cohort (adalimumab cohort; n = 70) were recruited from UK centres to the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS), previously described by Oliver et al. [15] All selected patients were white adults with a clinician diagnosis of RA, and about to begin treatment with adalimumab for the first time for their RA symptoms. Patients were categorised as either good- or non-responders to treatment following 3-months of therapy using established EULAR response criteria.[16] Good responders (n = 50) were patients who achieved a &lt;2.6 Disease Activity Score of 28-joints (DAS28) (i.e. DAS28 clinical remission) and a DAS28 improvement of &gt;1.2 at the 3-month follow-up. Non-responders (n = 20) were defined as patients that had a 3-month DAS28 score of &gt;5.1 (i.e. high disease activity) and an improvement of &lt;0.6. Non-responders were excluded from analysis if they reported non-adherence to treatment or if anti-drug antibodies were detected in their blood samples. Ethics was approved by the North West 6 Central Manchester South Research Ethics Committee (COREC 04/Q1403/37) and all patients provided written consent.[15]The second patient cohort (MTX cohort; n = 85) were recruited from the Rheumatoid Arthritis Medication Study (RAMS), a UK multicentre longitudinal observational study that enrols new-onset RA patients who are about to commence therapy with MTX. Response to treatment was assessed 6-months after treatment using the EULAR response criteria. Patients were then categorised as good (n = 42) or non-responders (n = 43) to MTX. RAMS was approved by the Central Manchester NHS Research Ethics Committee (reference 08/H1008/25) and all patients provided written informed consent.[17]The disease-free controls were recruited under the National Repository for Healthy Volunteers (NRHV) study within the Versus Arthritis Centre for Genetics and Genomics at the University of Manchester. Ethical approval was obtained (reference REC 99/8/84) and all volunteers gave written informed consent in compliance with Good Clinical Practice and the Declaration of Helsinki. Summary demographic information on both patient cohorts and disease-free controls are provided in Supplementary Table 1.Transcriptome measurement Whole blood gene expression profiles were captured using the Affymetrix Human Transcriptome Array 2.0 (HTA) at pre-treatment and following 3-months of treatment with adalimumab, and using the Illumina HumanHT-12 v3 Array at pre-treatment and following 4-weeks of treatment with MTX, in the adalimumab cohort and MTX cohort respectively. <br>
DOI: 10.13135/ela-325
title: Honours for Eudemos of Plataia
DOI: 10.6084/m9.figshare.12848147.v1
title: The unit extended Weibull families of distributions and its applications

description: In this paper, two new general families of distributions supported on the unit interval are introduced. The proposed families include several known models as special cases and define at least twenty (each one) new special models. Since the list of well-being indicators may include several double bounded random variables, the applicability for modeling those is the major practical motivation for introducing the distributions on those families. We propose a parametrization of the new families in terms of the median and develop a shiny application to provide interactive density shape illustrations for some special cases. Various properties of the introduced families are studied. Some special models in the new families are discussed. In particular, the complementary unit Weibull distribution is studied in some detail. The method of maximum likelihood for estimating the model parameters is discussed. An extensive Monte Carlo experiment is conducted to evaluate the performances of these estimators in finite samples. Applications to the literacy rate in Brazilian and Colombian municipalities illustrate the usefulness of the two new families for modeling well-being indicators.