cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3103057.v1
title: The metadata record, ststistics and supporting information of MiasDB

description: The construction of MiasDB and all results of manuscript were obtained from this file(Miasdb.xlsx). All results of manuscript can be viewed by accessing the MiasDB(http://47.88.84.236/Miasdb).
DOI: 10.6084/m9.figshare.3103027
title: Preservice teachers’ perceptions of heroes and teaching individual development and identity

description: This is a short paper presented at the International Society for the Social Studies Conference in Orlando, FL, February 2016.<br>We also included our initial research outline and the beginning of our first draft for the research report.
DOI: 10.6084/m9.figshare.3103069.v2
title: Reconstruction narratives in Mississippi history text books 1887-1976

description: The goal of this study was to identify and analyze Lost Cause myths in Reconstruction narratives and identify themes that helped maintain the existing social structure/ hierarchy. This was done through analyzing the Reconstruction accounts in Mississippi history textbooks. The texts were the Mississippi history textbooks available in a large university library. The 1887 text was the earliest text I could find and the latest text was 2013. The texts were primarily published by companies in the South. Only two texts that are described in this analysis were published in the North: Lowry and McCardle (1892) in New York and Sansing (1981) in Minnesota.<br> I employed content analysis to analyze the texts. My initial analysis used an inductive approach to identify the themes that emerged from an initial text (Berg, 2007). An initial review of one text (Riley, 1915) identified a base set of themes from the Reconstruction narrative to be used as a starting point for analysis of the other texts. The initial set of themes was derived from the texts, because the goal was to identify themes that emerged from the texts and then see how these themes were presented overtime. I then shifted to a combination of deductive and inductive approaches with the remaining texts. I used the initial set of themes to guide my analysis, but was open to the introduction of new themes that emerged in the other texts. <br>The short version paper was published in the International Society of the Social Studies Conference Proceedings (2014).<br>Anthony, K. (2014). Pedagogy of oppression: Reconstruction narratives in Mississippi history text books 1887-1976. in <i>The International Society for the Social Studies Annual Conference Proceedings</i>, Russell, W. (Ed.). Orlando, FL: The International Society for the Social Studies.<i></i>
DOI: 10.6084/m9.figshare.3103021
title: Harnessing the power of immersive innovative environmental experiences

description: This is a book chapter describing an immersive learning experience for teacher candidates at Tremont Environmental Education Center in the Smoky Mountains, TN.
DOI: 10.6084/m9.figshare.3103036.v2
title: Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk

description: Full details on this study can be found in our preprint: http://biorxiv.org/content/early/2015/11/04/027318<br>
DOI: 10.6084/m9.figshare.3103021.v1
title: Harnessing the power of immersive innovative environmental experiences

description: This is a book chapter describing an immersive learning experience for teacher candidates at Tremont Environmental Education Center in the Smoky Mountains, TN.
DOI: 10.6084/m9.figshare.3103069.v1
title: Reconstruction narratives in Mississippi history text books 1887-1976

description: The goal of this study was to identify and analyze Lost Cause myths in Reconstruction narratives and identify themes that helped maintain the existing social structure/ hierarchy. This was done through analyzing the Reconstruction accounts in Mississippi history textbooks. The texts were the Mississippi history textbooks available in a large university library. The 1887 text was the earliest text I could find and the latest text was 2013. The texts were primarily published by companies in the South. Only two texts that are described in this analysis were published in the North: Lowry and McCardle (1892) in New York and Sansing (1981) in Minnesota.<br> I employed content analysis to analyze the texts. My initial analysis used an inductive approach to identify the themes that emerged from an initial text (Berg, 2007). An initial review of one text (Riley, 1915) identified a base set of themes from the Reconstruction narrative to be used as a starting point for analysis of the other texts. The initial set of themes was derived from the texts, because the goal was to identify themes that emerged from the texts and then see how these themes were presented overtime. I then shifted to a combination of deductive and inductive approaches with the remaining texts. I used the initial set of themes to guide my analysis, but was open to the introduction of new themes that emerged in the other texts. <br>The short version paper was published in the International Society of the Social Studies Conference Proceedings (2014).<br>Anthony, K. (2014). Pedagogy of oppression: Reconstruction narratives in Mississippi history text books 1887-1976. in <i>The International Society for the Social Studies Annual Conference Proceedings</i>, Russell, W. (Ed.). Orlando, FL: The International Society for the Social Studies.<i></i>
DOI: 10.6084/m9.figshare.3103036.v1
title: Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk

description: Full details on this study can be found in our preprint: http://biorxiv.org/content/early/2015/11/04/027318<br>
DOI: 10.6084/m9.figshare.3103015
title: PANGEA-HIV methods comparison exercise: simulations

description: PANGEA-HIV (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) is a major new initiative funded by the Bill and Melinda Gates Foundation to generate a large amount of next generation sequence data and to provide phylogenetic tools to measure the impact of HIV prevention efforts in generalized epidemics in sub-Saharan Africa. Research groups were invited to participate in a blinded methods comparison exercise on simulated HIV sequence data sets to test the performance of current phylogenetic methods before their application on real data. This file set provides the simulation data sets that were used in the exercise. Please see the README files for further information.
DOI: 10.6084/m9.figshare.3103027.v2
title: Preservice teachers’ perceptions of heroes and teaching individual development and identity

description: This is a short paper presented at the International Society for the Social Studies Conference in Orlando, FL, February 2016.<br>We also included our initial research outline.
DOI: 10.6084/m9.figshare.3103012.v2
title: Inter-comparison of low-cost sensors for measuring the mass concentration of occupational aerosols

description: Low-cost sensors are effective for measuring the mass concentration of ambient aerosols and second-hand smoke in homes, but their use at concentrations relevant to occupational settings has not been demonstrated. We measured the concentrations of four aerosols (salt, Arizona road dust, welding fume, and diesel exhaust) with three types of low-cost sensors (a DC1700 from Dylos and two commodity sensors from Sharp), an aerosol photometer, and reference instruments at concentrations up to 6500 µg/m<sup>3</sup>. Raw output was used to assess sensor precision and develop equations to compute mass concentrations. EPA and NIOSH protocols were used to assess the mass concentrations estimated with low-cost sensors compared to reference instruments. The detection efficiency of the DC1700 ranged from 0.04% at 0.1 µm to 108% at 5 µm, as expected, although misclassification of fine and coarse particles was observed. The raw output of the DC1700 had higher precision (lower coefficient of variation, CV = 7.4%) than that of the two sharp devices (CV = 25% and 17%), a finding attributed to differences in manufacturer calibration. Aerosol type strongly influenced sensor response, indicating the need for on-site calibration to convert sensor output to mass concentration. Once calibrated, however, the mass concentration estimated with low-cost sensors was highly correlated with that of reference instruments (<i>R</i><sup>2</sup>= 0.99). These results suggest that the DC1700 and Sharp sensors are useful in estimating aerosol mass concentration for aerosols at concentrations relevant to the workplace. © 2016 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.3103015.v1
title: PANGEA-HIV methods comparison exercise: simulations

description: PANGEA-HIV (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) is a major new initiative funded by the Bill and Melinda Gates Foundation to generate a large amount of next generation sequence data and to provide phylogenetic tools to measure the impact of HIV prevention efforts in generalized epidemics in sub-Saharan Africa. Research groups were invited to participate in a blinded methods comparison exercise on simulated HIV sequence data sets to test the performance of current phylogenetic methods before their application on real data. This file set provides the simulation data sets that were used in the exercise. Please see the README files for further information.
DOI: 10.6084/m9.figshare.3103015.v3
title: PANGEA-HIV methods comparison exercise: simulations

description: PANGEA-HIV (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) is a major new initiative funded by the Bill and Melinda Gates Foundation to generate a large amount of next generation sequence data and to provide phylogenetic tools to measure the impact of HIV prevention efforts in generalized epidemics in sub-Saharan Africa. Research groups were invited to participate in a blinded methods comparison exercise on simulated HIV sequence data sets to test the performance of current phylogenetic methods before their application on real data. This file set provides the simulation data sets that were used in the exercise. Please see the README files for further information.
DOI: 10.6084/m9.figshare.3102994
title: The first karenitid (Therapsida, Therocephalia) from the upper Permian of Gondwana and the biogeography of Permo-Triassic therocephalians

description: Therocephalians were an ecologically diverse group of therapsids whose long stratigraphic record and widespread distribution during Permian and Triassic times make them important for understanding biogeographic patterns during a major faunal transition. Here, we describe a new therocephalian, <i>Mupashi migrator</i> gen. et sp. nov., from the upper Madumabisa Mudstone Formation (upper Permian) of Zambia's Luangwa Basin. The specimen has a long snout with a maxilla–vomerine contact on the hard palate, a high antecanine tooth count and numerous postcanines, and a conspicuous boss on the dentary angle whose structure is identical to that of the Russian baurioid <i>Karenites</i>. Additional endocranial anatomy, including palatal and braincase features, are revealed by high-resolution X-ray computed tomography and described in detail in light of the growing availability of tomographic data for therapsids. A phylogenetic analysis of 56 therapsid taxa and 136 cranial and postcranial characters recovers <i>Mupashi</i> as the sister taxon to <i>Karenites</i>, placing the pair between basal ictidosuchid-grade baurioids and the later Triassic bauriamorphs. Parsimony optimizations of geographic occurrences are ambiguous regarding the origination centers of therocephalian subclades. However, the patterns are suggestive of either (1) rapid, early dispersal events of Eutherocephalia and its major subgroups from a Laurasian center during the early–late Permian or, more likely, (2) within-province diversifications with occasional dispersal events occurring between provinces. Regardless, these associations strengthen the hypothesis that unknown but effective dispersal routes to high latitudes were available to therapsids and other tetrapods at least until early–late Permian times. http://zoobank.org/urn:lsid:zoobank.org:pub:B1E95B00-85BC-45E3-A823-841AD701A3F3 SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Huttenlocker, A. K., and C. A. Sidor. 2016. The first karenitid (Therapsida, Therocephalia) from the upper Permian of Gondwana and the biogeography of Permo-Triassic therocephalians. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111897.
DOI: 10.6084/m9.figshare.3103015.v2
title: PANGEA-HIV methods comparison exercise: simulations

description: PANGEA-HIV (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) is a major new initiative funded by the Bill and Melinda Gates Foundation to generate a large amount of next generation sequence data and to provide phylogenetic tools to measure the impact of HIV prevention efforts in generalized epidemics in sub-Saharan Africa. Research groups were invited to participate in a blinded methods comparison exercise on simulated HIV sequence data sets to test the performance of current phylogenetic methods before their application on real data. This file set provides the simulation data sets that were used in the exercise. Please see the README files for further information.
DOI: 10.6084/m9.figshare.3102994.v1
title: The first karenitid (Therapsida, Therocephalia) from the upper Permian of Gondwana and the biogeography of Permo-Triassic therocephalians

description: Therocephalians were an ecologically diverse group of therapsids whose long stratigraphic record and widespread distribution during Permian and Triassic times make them important for understanding biogeographic patterns during a major faunal transition. Here, we describe a new therocephalian, <i>Mupashi migrator</i> gen. et sp. nov., from the upper Madumabisa Mudstone Formation (upper Permian) of Zambia's Luangwa Basin. The specimen has a long snout with a maxilla–vomerine contact on the hard palate, a high antecanine tooth count and numerous postcanines, and a conspicuous boss on the dentary angle whose structure is identical to that of the Russian baurioid <i>Karenites</i>. Additional endocranial anatomy, including palatal and braincase features, are revealed by high-resolution X-ray computed tomography and described in detail in light of the growing availability of tomographic data for therapsids. A phylogenetic analysis of 56 therapsid taxa and 136 cranial and postcranial characters recovers <i>Mupashi</i> as the sister taxon to <i>Karenites</i>, placing the pair between basal ictidosuchid-grade baurioids and the later Triassic bauriamorphs. Parsimony optimizations of geographic occurrences are ambiguous regarding the origination centers of therocephalian subclades. However, the patterns are suggestive of either (1) rapid, early dispersal events of Eutherocephalia and its major subgroups from a Laurasian center during the early–late Permian or, more likely, (2) within-province diversifications with occasional dispersal events occurring between provinces. Regardless, these associations strengthen the hypothesis that unknown but effective dispersal routes to high latitudes were available to therapsids and other tetrapods at least until early–late Permian times. http://zoobank.org/urn:lsid:zoobank.org:pub:B1E95B00-85BC-45E3-A823-841AD701A3F3 SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Huttenlocker, A. K., and C. A. Sidor. 2016. The first karenitid (Therapsida, Therocephalia) from the upper Permian of Gondwana and the biogeography of Permo-Triassic therocephalians. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111897.
DOI: 10.6084/m9.figshare.3102988.v2
title: Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis

description: Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.
DOI: 10.6084/m9.figshare.3102970
title: Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells

description: Spermatogonial stem cells (SSCs), which are unipotent stem cells in the testes that give rise to sperm, can be converted into germline-derived pluripotent stem (gPS) by self-induction. The androgenetic imprinting pattern of SSCs is maintained even after their reprogramming into gPS cells. In this study, we used an <i>in vitro</i> neural differentiation model to investigate whether the imprinting patterns are maintained or altered during differentiation. The androgenetic patterns of <i>H19, Snrpn</i>, and <i>Mest</i> were maintained even after differentiation of gPS cells into NSCs (gPS-NSCs), whereas the fully unmethylated status of <i>Ndn</i> in SSCs was altered to somatic patterns in gPS cells and gPS-NSCs. Thus, our study demonstrates epigenetic alteration of genomic imprinting during the induction of pluripotency in SSCs and neural differentiation, suggesting that gPS-NSCs can be a useful model to study the roles of imprinted genes in brain development and human neurodevelopmental disorders.
DOI: 10.6084/m9.figshare.3102988.v1
title: Combining geometric morphometrics and finite element analysis with evolutionary modeling: toward a synthesis

description: Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.
DOI: 10.6084/m9.figshare.3102967
title: Insulin-degrading enzyme secretion from astrocytes is mediated by an autophagy-based unconventional secretory pathway in Alzheimer disease

description: The secretion of proteins that lack a signal sequence to the extracellular milieu is regulated by their transition through the unconventional secretory pathway. IDE (insulin-degrading enzyme) is one of the major proteases of amyloid beta peptide (Aβ), a presumed causative molecule in Alzheimer disease (AD) pathogenesis. IDE acts in the extracellular space despite having no signal sequence, but the underlying mechanism of IDE secretion extracellularly is still unknown. In this study, we found that IDE levels were reduced in the cerebrospinal fluid (CSF) of patients with AD and in pathology-bearing AD-model mice. Since astrocytes are the main cell types for IDE secretion, astrocytes were treated with Aβ. Aβ increased the IDE levels in a time- and concentration-dependent manner. Moreover, IDE secretion was associated with an autophagy-based unconventional secretory pathway, and depended on the activity of RAB8A and GORASP (Golgi reassembly stacking protein). Finally, mice with global haploinsufficiency of an essential autophagy gene, showed decreased IDE levels in the CSF in response to an intracerebroventricular (i.c.v.) injection of Aβ. These results indicate that IDE is secreted from astrocytes through an autophagy-based unconventional secretory pathway in AD conditions, and that the regulation of autophagy is a potential therapeutic target in addressing Aβ pathology.