cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6168110.v1
title: Additional file 1: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

description: Sequencing Quality Control. Data shows Illumina quality control metrics. PF = Passing chastity filter. Q30 = Phred quality score of 30 or above. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6167906.v2
title: Implementing Harmonically Mapped Averaging Methods on Popular Molecular Simulation Platforms

description: Mapped averaging is a new framework for statistical mechanics that prescribes ways to compute properties with high precision. Our project aims to implement these methods on popular molecular simulation codes so that the larger community of molecular modelers can make use of this advance.<br>
DOI: 10.6084/m9.figshare.6167747
title: Improved protocol for simultaneous analysis of leukocyte subsets and epithelial cells from murine and human lung

description: <b>Purpose</b>: To study and isolate lung cells by flow cytometry, enzymatic digestion and generation of single cell suspensions is required. This significantly influences expression of cellular epitopes and protocols need to be adapted for the best isolation and subsequent analysis of specific cellular subsets. <b>Materials and Methods</b>: We optimized protocols for the simultaneous isolation and characterization of specific human and murine lung cell types. For alveolar epithelial cells (AEC), a primarily dispase based digestion method and for leukocytes, a primarily collagenase based technique was adapted. Protocols were applied in parallel in either single experimental mice or human lung specimens. <b>Results</b>: Optimized dispase/DNase digestion yielded a high percentage of Epcam+CD45-CD31- AEC as assessed by flow cytometry. Epcam+CD45-CD3-CD11b-CD11c-CD16/32-CD19-CD31-F4/80- AEC were readily sortable with high purity and typical morphology and function upon <i>in vitro</i> stimulation with lipopolysaccharide or respiratory-syncytial-virus (RSV) infection. To analyze lung leukocytes, specimens were digested with an adapted collagenase/DNase protocol yielding high percentages of viable leukocytes with typical morphology, function, and preserved subset specific leukocyte markers. Both protocols could be applied simultaneously in a single experimental mouse post mortem. Application of both digestion methods in primary human lung specimens yielded similar results with high proportions of Epcam+CD45- human AEC after dispase/DNase digestion and preservation of human T cell epitopes after collagenase/DNase digestion. <b>Conclusion</b>: The here described protocols were optimized for the simple and efficient isolation of murine and human lung cells. In contrast to previously described techniques, they permit simultaneous in-depth characterization of pulmonary epithelial cells and leukocyte subsets such as T helper, cytotoxic T, and B cells from one sample. As such, they may help to comprehensively and sustainably characterize murine and human lung specimens and facilitate studies on the role of lung immune cells in different respiratory pathologies.
DOI: 10.6084/m9.figshare.6167747.v1
title: Improved protocol for simultaneous analysis of leukocyte subsets and epithelial cells from murine and human lung

description: <b>Purpose</b>: To study and isolate lung cells by flow cytometry, enzymatic digestion and generation of single cell suspensions is required. This significantly influences expression of cellular epitopes and protocols need to be adapted for the best isolation and subsequent analysis of specific cellular subsets. <b>Materials and Methods</b>: We optimized protocols for the simultaneous isolation and characterization of specific human and murine lung cell types. For alveolar epithelial cells (AEC), a primarily dispase based digestion method and for leukocytes, a primarily collagenase based technique was adapted. Protocols were applied in parallel in either single experimental mice or human lung specimens. <b>Results</b>: Optimized dispase/DNase digestion yielded a high percentage of Epcam+CD45-CD31- AEC as assessed by flow cytometry. Epcam+CD45-CD3-CD11b-CD11c-CD16/32-CD19-CD31-F4/80- AEC were readily sortable with high purity and typical morphology and function upon <i>in vitro</i> stimulation with lipopolysaccharide or respiratory-syncytial-virus (RSV) infection. To analyze lung leukocytes, specimens were digested with an adapted collagenase/DNase protocol yielding high percentages of viable leukocytes with typical morphology, function, and preserved subset specific leukocyte markers. Both protocols could be applied simultaneously in a single experimental mouse post mortem. Application of both digestion methods in primary human lung specimens yielded similar results with high proportions of Epcam+CD45- human AEC after dispase/DNase digestion and preservation of human T cell epitopes after collagenase/DNase digestion. <b>Conclusion</b>: The here described protocols were optimized for the simple and efficient isolation of murine and human lung cells. In contrast to previously described techniques, they permit simultaneous in-depth characterization of pulmonary epithelial cells and leukocyte subsets such as T helper, cytotoxic T, and B cells from one sample. As such, they may help to comprehensively and sustainably characterize murine and human lung specimens and facilitate studies on the role of lung immune cells in different respiratory pathologies.
DOI: 10.6084/m9.figshare.6167735
title: Redescription of the oldest crown clade penguin: cranial osteology, jaw myology, neuroanatomy, and phylogenetic affinities of <i>Madrynornis mirandus</i>

description: <i>Madrynornis mirandus</i>, one of the few fossil penguins known from a nearly complete articulated skeleton, represents a key taxon for understanding the stem-crown transition in penguins. Despite the wealth of morphological character data preserved in the holotype specimen, the phylogenetic placement of this early late Miocene taxon has remained controversial. Reexamination of the <i>Madrynornis mirandus</i> holotype provides support for placement within the penguin crown clade. However, this placement is highly sensitive to the molecular signal and <i>Madrynornis</i> falls just outside the crown clade when molecular data are excluded. The neuroanatomy of <i>Madrynornis</i> shares many derived features with extant penguins, including an airencephalic brain shape, highly reduced bulbus olfactorius, and absence of an interaural pathway. However, the brain endocast differs from all surveyed extant species in that the eminentia sagittalis (wulst) is less caudally expanded, the tectum opticus is relatively less developed, and the flocculus is stouter and more laterally disposed. The cranial osteology and reconstructed jaw myology of <i>Madrynornis</i> suggest a primarily piscivorous diet, which likely characterizes the clade uniting <i>Madrynornis, Inguza, Eudyptula</i>, and <i>Spheniscus</i>. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Degrange, F. J., D. T. Ksepka, and C. P. Tambussi. 2018. Redescription of the oldest crown clade penguin: cranial osteology, jaw myology, neuroanatomy, and phylogenetic affinities of <i>Madrynornis mirandus</i>. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2018.1445636.
DOI: 10.6084/m9.figshare.6167735.v1
title: Redescription of the oldest crown clade penguin: cranial osteology, jaw myology, neuroanatomy, and phylogenetic affinities of <i>Madrynornis mirandus</i>

description: <i>Madrynornis mirandus</i>, one of the few fossil penguins known from a nearly complete articulated skeleton, represents a key taxon for understanding the stem-crown transition in penguins. Despite the wealth of morphological character data preserved in the holotype specimen, the phylogenetic placement of this early late Miocene taxon has remained controversial. Reexamination of the <i>Madrynornis mirandus</i> holotype provides support for placement within the penguin crown clade. However, this placement is highly sensitive to the molecular signal and <i>Madrynornis</i> falls just outside the crown clade when molecular data are excluded. The neuroanatomy of <i>Madrynornis</i> shares many derived features with extant penguins, including an airencephalic brain shape, highly reduced bulbus olfactorius, and absence of an interaural pathway. However, the brain endocast differs from all surveyed extant species in that the eminentia sagittalis (wulst) is less caudally expanded, the tectum opticus is relatively less developed, and the flocculus is stouter and more laterally disposed. The cranial osteology and reconstructed jaw myology of <i>Madrynornis</i> suggest a primarily piscivorous diet, which likely characterizes the clade uniting <i>Madrynornis, Inguza, Eudyptula</i>, and <i>Spheniscus</i>. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Degrange, F. J., D. T. Ksepka, and C. P. Tambussi. 2018. Redescription of the oldest crown clade penguin: cranial osteology, jaw myology, neuroanatomy, and phylogenetic affinities of <i>Madrynornis mirandus</i>. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2018.1445636.
DOI: 10.6084/m9.figshare.6167726
title: Mandibular CT Dataset Collection

description: Mandibular CT Datasets. Please use the following citations if you use them in your work:<br><br>J. Wallner, J. Egger. Mandibular CT Dataset Collection. Figshare, 2018<br><br>and<br><br>J. Wallner, K. Hochegger, X. Chen, I. Mischak, K. Reinbacher, M. Pau, T. Zrnc, K. Schwenzer-Zimmerer, W. Zemann, D. Schmalstieg, J. Egger. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action. PLOS One, 2018.<br>Usage notes:<br>The data files attached with this manuscript can be opened in ImageJ with good results and can be displayed at full quality. The files can also be opened in Irfanview, but then the data do not display at full quality.<br><br>
DOI: 10.6084/m9.figshare.6167726.v1
title: Mandibular CT Dataset Collection

description: Mandibular CT Datasets. Please use the following citations if you use them in your work:<br><br>J. Wallner, J. Egger. Mandibular CT Dataset Collection. Figshare, 2018<br><br>and<br><br>J. Wallner, K. Hochegger, X. Chen, I. Mischak, K. Reinbacher, M. Pau, T. Zrnc, K. Schwenzer-Zimmerer, W. Zemann, D. Schmalstieg, J. Egger. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action. PLOS One, 2018.<br><br>
DOI: 10.6084/m9.figshare.6167726.v3
title: Mandibular CT Dataset Collection

description: Mandibular CT Datasets. Please use the following citations if you use them in your work:<br><br>J. Wallner, J. Egger. Mandibular CT Dataset Collection. Figshare, 2018<br><br>and<br><br>J. Wallner, K. Hochegger, X. Chen, I. Mischak, K. Reinbacher, M. Pau, T. Zrnc, K. Schwenzer-Zimmerer, W. Zemann, D. Schmalstieg, J. Egger. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action. PLOS One, 2018.<br><br>
DOI: 10.6084/m9.figshare.6167726.v4
title: Mandibular CT Dataset Collection

description: Mandibular CT Datasets. Please use the following citations if you use them in your work:<br><br>J. Wallner, J. Egger. Mandibular CT Dataset Collection. Figshare, 2018<br><br>and<br><br>J. Wallner, K. Hochegger, X. Chen, I. Mischak, K. Reinbacher, M. Pau, T. Zrnc, K. Schwenzer-Zimmerer, W. Zemann, D. Schmalstieg, J. Egger. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action. PLOS One, 2018.<br><br>
DOI: 10.6084/m9.figshare.6167723
title: The impact of the public transport commute on the mental health of the working people: A systematic review..pdf

description: Extracted aims/methods and outcomes from a systematic review from 1972 on the mental health impact of the public transport commute.
DOI: 10.6084/m9.figshare.6167717
title: A model to predict the elastic properties of gas hydrate-bearing sediments

description: A simple and accurate model for predicting the elastic properties of gas hydrate-bearing sediment (GHBS) is proposed and validated against experimental data. It is developed on the basis of the homogenization theory for multi-phases composite. Unlike the classical homogenization techniques those fix a homogenization scheme (<i>e.g.</i> self-consistent, Mori-Tanaka, DEM, <i>etc</i>.) for a given microstructure, the proposed model considers a flexible homogenization scheme that adapts with the change of the microstructure of the material. The idea is to modify the elastic properties of the reference matrix with respect to the microstructure change of the mixture. Such modification is ensured by adapting the theoretical method to available experimental data. The derived method is proved to be very powerful as it can fit laboratory measured data on gas hydrate-bearing sand formed by different methods including excess gas and excess water methods and log data taken from various sites. Such feature cannot be satisfied by the existent models those consider the hydrate phase as a cement phase or a pore-filling phase. A very good agreement between the proposed method and experimental data offer a simple and accurate ways to predict the saturation of gas hydrate using sonic log data or 3D seismic data.
DOI: 10.6084/m9.figshare.6167717.v1
title: A model to predict the elastic properties of gas hydrate-bearing sediments

description: A simple and accurate model for predicting the elastic properties of gas hydrate-bearing sediment (GHBS) is proposed and validated against experimental data. It is developed on the basis of the homogenization theory for multi-phases composite. Unlike the classical homogenization techniques those fix a homogenization scheme (<i>e.g.</i> self-consistent, Mori-Tanaka, DEM, <i>etc</i>.) for a given microstructure, the proposed model considers a flexible homogenization scheme that adapts with the change of the microstructure of the material. The idea is to modify the elastic properties of the reference matrix with respect to the microstructure change of the mixture. Such modification is ensured by adapting the theoretical method to available experimental data. The derived method is proved to be very powerful as it can fit laboratory measured data on gas hydrate-bearing sand formed by different methods including excess gas and excess water methods and log data taken from various sites. Such feature cannot be satisfied by the existent models those consider the hydrate phase as a cement phase or a pore-filling phase. A very good agreement between the proposed method and experimental data offer a simple and accurate ways to predict the saturation of gas hydrate using sonic log data or 3D seismic data.
DOI: 10.6084/m9.figshare.6167711
title: Supplementary Table Metabolite Levels.xlsx

description: Raw data for metabolic profiles<br>Nature Cell Biology: <b>Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumors</b>
DOI: 10.5281/zenodo.4007589
title: GHTraffic: A Dataset for Reproducible Research in Service-Oriented Computing

description: This is the latest version of the GHTraffic project. The main aim is to model a variety of transaction sequences to reflect more complex service behaviour. It has two editions: Small (S) and Large (L) where the records were created by selecting the same repositories as the original Small and Large datasets. The newest S dataset contains records from google/guava repository. The L dataset contains records from eight repositories (i.e., twbs/bootstrap, symfony/symfony, docker/docker, Homebrew/homebrew, rust-lang/rust, kubernetes/kubernetes, rails/rails, and angular/angular.js). The entire data generation process is quite similar to the original GHTraffic design. But it incorporates minor changes to the process of synthetic data generation where it uses a random date after successfully posting a resource to make up the request and response for all of the HTTP methods. It also adds yet another subset of unsuccessful transactions by stipulating requests before resource creation is successful. This results in a far more dynamic series of transactions to named resources. Scripts used for datasets construction are accessible from the repository.
description: Due to the use of random data generation, the GHTraffic scripts will produce slightly different datasets at each execution.
DOI: 10.5281/zenodo.1034572
title: GHTraffic: A Dataset for Reproducible Research in Service-Oriented Computing

description: This is the latest version of the GHTraffic project. The main aim is to model a variety of transaction sequences to reflect more complex service behaviour. It has two editions: Small (S) and Large (L) where the records were created by selecting the same repositories as the original Small and Large datasets. The newest S dataset contains records from google/guava repository. The L dataset contains records from eight repositories (i.e., twbs/bootstrap, symfony/symfony, docker/docker, Homebrew/homebrew, rust-lang/rust, kubernetes/kubernetes, rails/rails, and angular/angular.js). The entire data generation process is quite similar to the original GHTraffic design. But it incorporates minor changes to the process of synthetic data generation where it uses a random date after successfully posting a resource to make up the request and response for all of the HTTP methods. It also adds yet another subset of unsuccessful transactions by stipulating requests before resource creation is successful. This results in a far more dynamic series of transactions to named resources. Scripts used for datasets construction are accessible from the repository.
description: Due to the use of random data generation, the GHTraffic scripts will produce slightly different datasets at each execution.
DOI: 10.6084/m9.figshare.6167594
title: Data set for Cartwright and Singh (2018)

description: Data set for paper on 'observation and contagion effects in cooperation: An experimental investigation'. Published in Journal of Behavioral and Experimental Economics.
DOI: 10.6084/m9.figshare.6167594.v1
title: Data set for Cartwright and Singh (2018)

description: Data set for paper on 'observation and contagion effects in cooperation: An experimental investigation'. Published in Journal of Behavioral and Experimental Economics.
DOI: 10.6084/m9.figshare.6166208
title: Motivational decline and recovery in higher education STEM courses

description: Decline in student motivation is a concern for STEM education, especially for underrepresented groups in the sciences. Using the Science Motivation Questionnaire II, 41 foundational STEM courses were surveyed at the beginning and end of each semester in an academic year at a small primarily undergraduate university. Significant pre- to post-semester declines were observed in each of five measured motivational factors (<i>Intrinsic motivation, Career motivation, Self determination, Self-efficacy,</i> and <i>Grade motivation</i>), with effect sizes ranging from 0.21 to 0.41. However, in the second semester pre-survey, four motivational factors rebounded, including three returning to initial levels, suggesting that the observed motivational decline is not long-lasting. Analysis suggests that declines are not related to survey fatigue or student demographics, but rather to grades and, in the case of one motivational factor, to academic field. These findings suggest that a refocus on grading practices across STEM fields may influence student motivation and persistence in STEM.
DOI: 10.6084/m9.figshare.6166208.v1
title: Motivational decline and recovery in higher education STEM courses

description: Decline in student motivation is a concern for STEM education, especially for underrepresented groups in the sciences. Using the Science Motivation Questionnaire II, 41 foundational STEM courses were surveyed at the beginning and end of each semester in an academic year at a small primarily undergraduate university. Significant pre- to post-semester declines were observed in each of five measured motivational factors (<i>Intrinsic motivation, Career motivation, Self determination, Self-efficacy,</i> and <i>Grade motivation</i>), with effect sizes ranging from 0.21 to 0.41. However, in the second semester pre-survey, four motivational factors rebounded, including three returning to initial levels, suggesting that the observed motivational decline is not long-lasting. Analysis suggests that declines are not related to survey fatigue or student demographics, but rather to grades and, in the case of one motivational factor, to academic field. These findings suggest that a refocus on grading practices across STEM fields may influence student motivation and persistence in STEM.
DOI: 10.17028/rd.lboro.6166103
title: RAW DATASET _Cultural influences on perception of disability and disabled people: A comparison of opinions from students in the United Kingdom (UK) and Pakistan (PAK) about a generic wheelchair, using a semantic differential scale.

description: The raw dataset provides the details of questionnaire data, being processed in this study by employing appropriate statistical tests. The data files have been developed in accordance to the questionnaire designed for the survey. In MS Excel 2010, the main spreadsheet is segregated into four sub-sheets viz.; personal and demographics, first SD scale (PAK), second SD scale and personal evaluation. The response data was invaded into those spreadsheets and basic descriptive statistical tests were performed in this raw dataset. In addition to the responses for comparing data of both cultural groups, this raw data provides details of responses for the comparison based on gender and evaluation based on previous experience of using wheelchair, which was separately processed. However, to provide a protection against disclosure of participant’s information, the access to those raw data files remains restricted and can be obtained by contacting the author of this research. Openly published results are available at https://doi.org/10.17028/rd.lboro.6200228.<br>The compiled version of the dataset have been published in the journal paper having following DOI: https://doi.org/10.1080/17483107.2019.1568595
DOI: 10.17028/rd.lboro.6166103.v2
title: RAW DATASET _Cultural influences on perception of disability and disabled people: A comparison of opinions from students in the United Kingdom (UK) and Pakistan (PAK) about a generic wheelchair, using a semantic differential scale.

description: The raw dataset provides the details of questionnaire data, being processed in this study by employing appropriate statistical tests. The data files have been developed in accordance to the questionnaire designed for the survey. In MS Excel 2010, the main spreadsheet is segregated into four sub-sheets viz.; personal and demographics, first SD scale (PAK), second SD scale and personal evaluation. The response data was invaded into those spreadsheets and basic descriptive statistical tests were performed in this raw dataset. In addition to the responses for comparing data of both cultural groups, this raw data provides details of responses for the comparison based on gender and evaluation based on previous experience of using wheelchair, which was separately processed. However, to provide a protection against disclosure of participant’s information, the access to those raw data files remains restricted and can be obtained by contacting the author of this research. Openly published results are available at https://doi.org/10.17028/rd.lboro.6200228.<br>The compiled version of the dataset have been published in the journal paper having following DOI: https://doi.org/10.1080/17483107.2019.1568595