cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1496624.v4
title: Disruption in the autophagic process underlies the sensory neuropathy in <i>dystonia musculorum</i> mice

description: A homozygous mutation in the <i>DST</i> (dystonin) gene causes a newly identified lethal form of hereditary sensory and autonomic neuropathy in humans (HSAN-VI). DST loss of function similarly leads to sensory neuron degeneration and severe ataxia in <i>dystonia musculorum</i> (<i>Dst</i><sup><i>dt</i></sup>) mice. DST is involved in maintaining cytoskeletal integrity and intracellular transport. As autophagy is highly reliant upon stable microtubules and motor proteins, we assessed the influence of DST loss of function on autophagy using the <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model. Electron microscopy (EM) revealed an accumulation of autophagosomes in sensory neurons from these mice. Furthermore, we demonstrated that the autophagic flux was impaired. Levels of LC3-II, a marker of autophagosomes, were elevated. Consequently, <i>Dst</i><sup><i>dt-Tg4</i></sup> sensory neurons displayed impaired protein turnover of autophagosome substrate SQTSM1/p62 and of polyubiquitinated proteins. Interestingly, in a previously described <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model that is partially rescued by neuronal specific expression of the DST-A2 isoform, autophagosomes, autolysosomes, and damaged organelles were reduced when compared to <i>Dst</i><sup><i>dt-Tg4</i></sup> mutant mice. LC3-II, SQTSM1, polyubiquitinated proteins and autophagic flux were also restored to wild-type levels in the rescued mice. Finally, a significant decrease in DNAIC1 (dynein, axonemal, intermediate chain 1; the mouse ortholog of human DNAI1), a member of the DMC (dynein/dynactin motor complex), was noted in <i>Dst</i><sup><i>dt-Tg4</i></sup> dorsal root ganglia and sensory neurons. Thus, DST-A2 loss of function perturbs late stages of autophagy, and dysfunctional autophagy at least partially underlies <i>Dst</i><sup><i>dt</i></sup> pathogenesis. We therefore conclude that the DST-A2 isoform normally facilitates autophagy within sensory neurons to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1496624.v6
title: Disruption in the autophagic process underlies the sensory neuropathy in <i>dystonia musculorum</i> mice

description: A homozygous mutation in the <i>DST</i> (dystonin) gene causes a newly identified lethal form of hereditary sensory and autonomic neuropathy in humans (HSAN-VI). DST loss of function similarly leads to sensory neuron degeneration and severe ataxia in <i>dystonia musculorum</i> (<i>Dst</i><sup><i>dt</i></sup>) mice. DST is involved in maintaining cytoskeletal integrity and intracellular transport. As autophagy is highly reliant upon stable microtubules and motor proteins, we assessed the influence of DST loss of function on autophagy using the <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model. Electron microscopy (EM) revealed an accumulation of autophagosomes in sensory neurons from these mice. Furthermore, we demonstrated that the autophagic flux was impaired. Levels of LC3-II, a marker of autophagosomes, were elevated. Consequently, <i>Dst</i><sup><i>dt-Tg4</i></sup> sensory neurons displayed impaired protein turnover of autophagosome substrate SQTSM1/p62 and of polyubiquitinated proteins. Interestingly, in a previously described <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model that is partially rescued by neuronal specific expression of the DST-A2 isoform, autophagosomes, autolysosomes, and damaged organelles were reduced when compared to <i>Dst</i><sup><i>dt-Tg4</i></sup> mutant mice. LC3-II, SQTSM1, polyubiquitinated proteins and autophagic flux were also restored to wild-type levels in the rescued mice. Finally, a significant decrease in DNAIC1 (dynein, axonemal, intermediate chain 1; the mouse ortholog of human DNAI1), a member of the DMC (dynein/dynactin motor complex), was noted in <i>Dst</i><sup><i>dt-Tg4</i></sup> dorsal root ganglia and sensory neurons. Thus, DST-A2 loss of function perturbs late stages of autophagy, and dysfunctional autophagy at least partially underlies <i>Dst</i><sup><i>dt</i></sup> pathogenesis. We therefore conclude that the DST-A2 isoform normally facilitates autophagy within sensory neurons to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1497888.v7
title: Toward Closing the Loop between Infrastructure Investments and Societal and Economic Impacts

description: The long-term value proposition of transportation infrastructure investments can be significantly distorted if the short-term effects of spatial externalities on land use patterns, economic expansions, and migration patterns are not properly included in the analysis. Some of these effects occur over a short period of time and soon after the investment materializes, whereas others take longer and follow more steady patterns. In this article, we develop a novel dynamical model of a primal society with constructs that are specifically geared toward transportation infrastructure expansions and investments. The model quantifies the impact of these expansions on some key performance indicators and on the overall utility and production capacity of the society. We argue that traditional analytical models that work on the premises of stationary behavior and a static response of society to changes in infrastructure do not correctly capture these effects. The land use patterns and spatial expansion computed from the model are validated against existing theory on land use. Preliminary results on how to use the model for value proposition analysis are also presented using simple case studies.
DOI: 10.6084/m9.figshare.1512834.v280
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1496624.v5
title: Disruption in the autophagic process underlies the sensory neuropathy in <i>dystonia musculorum</i> mice

description: A homozygous mutation in the <i>DST</i> (dystonin) gene causes a newly identified lethal form of hereditary sensory and autonomic neuropathy in humans (HSAN-VI). DST loss of function similarly leads to sensory neuron degeneration and severe ataxia in <i>dystonia musculorum</i> (<i>Dst</i><sup><i>dt</i></sup>) mice. DST is involved in maintaining cytoskeletal integrity and intracellular transport. As autophagy is highly reliant upon stable microtubules and motor proteins, we assessed the influence of DST loss of function on autophagy using the <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model. Electron microscopy (EM) revealed an accumulation of autophagosomes in sensory neurons from these mice. Furthermore, we demonstrated that the autophagic flux was impaired. Levels of LC3-II, a marker of autophagosomes, were elevated. Consequently, <i>Dst</i><sup><i>dt-Tg4</i></sup> sensory neurons displayed impaired protein turnover of autophagosome substrate SQTSM1/p62 and of polyubiquitinated proteins. Interestingly, in a previously described <i>Dst</i><sup><i>dt-Tg4</i></sup> mouse model that is partially rescued by neuronal specific expression of the DST-A2 isoform, autophagosomes, autolysosomes, and damaged organelles were reduced when compared to <i>Dst</i><sup><i>dt-Tg4</i></sup> mutant mice. LC3-II, SQTSM1, polyubiquitinated proteins and autophagic flux were also restored to wild-type levels in the rescued mice. Finally, a significant decrease in DNAIC1 (dynein, axonemal, intermediate chain 1; the mouse ortholog of human DNAI1), a member of the DMC (dynein/dynactin motor complex), was noted in <i>Dst</i><sup><i>dt-Tg4</i></sup> dorsal root ganglia and sensory neurons. Thus, DST-A2 loss of function perturbs late stages of autophagy, and dysfunctional autophagy at least partially underlies <i>Dst</i><sup><i>dt</i></sup> pathogenesis. We therefore conclude that the DST-A2 isoform normally facilitates autophagy within sensory neurons to maintain cellular homeostasis.
DOI: 10.6084/m9.figshare.1497888.v6
title: Toward Closing the Loop between Infrastructure Investments and Societal and Economic Impacts

description: The long-term value proposition of transportation infrastructure investments can be significantly distorted if the short-term effects of spatial externalities on land use patterns, economic expansions, and migration patterns are not properly included in the analysis. Some of these effects occur over a short period of time and soon after the investment materializes, whereas others take longer and follow more steady patterns. In this article, we develop a novel dynamical model of a primal society with constructs that are specifically geared toward transportation infrastructure expansions and investments. The model quantifies the impact of these expansions on some key performance indicators and on the overall utility and production capacity of the society. We argue that traditional analytical models that work on the premises of stationary behavior and a static response of society to changes in infrastructure do not correctly capture these effects. The land use patterns and spatial expansion computed from the model are validated against existing theory on land use. Preliminary results on how to use the model for value proposition analysis are also presented using simple case studies.
DOI: 10.6084/m9.figshare.1512834.v281
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1512834.v282
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1496613
title: SAS code: HDX and HealthMap Ebola case and mortality correlation analysis (March 14 - August 27, 2014)

description: Collinearity assessment, regression analysis, and model creation for comparitive analysis of Ebola HealthMap news curated articles (March 14 - August 27, 2014) and HDX WHO/MOH official Ebola estimates (March 24 - August 27, 2014).<br><br>Data (HealthMap), data cleaning (HDX & HealthMap) referenced below.
DOI: 10.6084/m9.figshare.1496611
title: SAS code: HDX subnational timeseries data cleaning (March 24 - August 27, 2014)

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014. <br><br>SAS code for data cleaning for Humanitarian Data Exchange (HDX) "Sub-national time series data on Ebola cases and deaths in Guinea, Liberia, Sierra Leone, Nigeria, Senegal and Mali since March 2014" at https://data.hdx.rwlabs.org/dataset/rowca-ebola-cases
DOI: 10.6084/m9.figshare.1512834.v283
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1496612
title: SAS code: Ebola HealthMap data cleaning (March 14 - August 27, 2014)

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014.<br> SAS code for data cleaning for Ebola HealthMap articles (3/14-8/27/2014) at http://figshare.com/articles/Ebola_HealthMap_article_data_3_14_8_27_2014/1496610
DOI: 10.6084/m9.figshare.1496613.v2
title: SAS code: HDX and HealthMap Ebola case and mortality correlation analysis (March 14 - August 27, 2014)

description: Collinearity assessment, regression analysis, and model creation for comparitive analysis of Ebola HealthMap news curated articles (March 14 - August 27, 2014) and HDX WHO/MOH official Ebola estimates (March 24 - August 27, 2014).<br><br>Data (HealthMap), data cleaning (HDX & HealthMap) referenced below.
DOI: 10.6084/m9.figshare.1496613.v1
title: SAS code: Correlation between HDX and HealthMap Ebola case and mortality (March 14 - August 27, 2014)

description: Collinearity assessment, regression analysis, and model creation for comparitive analysis of Ebola HealthMap news curated articles (March 14 - August 27, 2014) and HDX WHO/MOH official Ebola estimates (March 24 - August 27, 2014).
DOI: 10.6084/m9.figshare.1496610
title: Access dataset: Ebola HealthMap articles (March 14 - August 27, 2014)

description: Access Database of HealthMap-curated news articles from March 14 to August 27 2014 identifying thirteen variables, excluding three unique identifiers representing the three data tables (HMID, ReportID, and ValueID). Variables included Date, news agency name (News Agency), news agency reporting location (Location), Notes, reason for missing counts (Reason Missing), URL, Country, type of counts (Category), Value (also known as count), agency providing counts (Reference), whether a person was named in reference of the counts (Named), whether only Guinea, Liberia, and Sierra Leone were estimated in West African totals (Not Adj), or whether the count was approximated (Approx).
DOI: 10.6084/m9.figshare.1512834.v284
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1496609
title: Taxonomic and geographic differentiation of <i>Pinus mugo</i> complex on the needle characteristics

description: The phenotypic differentiation of <i>Pinus mugo</i> complex was verified using 31 populations of <i>P. mugo sensu stricto</i>, 11 of <i>P. uncinata</i>, five of <i>P. uliginosa</i>, one of the potential hybrids <i>P. uliginosa</i> × <i>P. mugo</i> and three of <i>P. sylvestris</i>, the latter as a control. The 22 morphological and anatomical needle characteristics were measured and statistically examined to describe the taxa and the population within the taxa differentiation. All the taxa of the <i>P. mugo</i> complex differed significantly from <i>P. sylvestris</i> in most of the verified needle characteristics. Within <i>P. mugo</i> complex, populations of <i>P. uncinata</i> were clearly distinguished from <i>P. mugo s. s</i>. The population of potential hybrid origin was the most similar to <i>P. uliginosa</i>. Populations of the latter taxon were strongly differentiated; some of them were closer to <i>P. uncinata</i>, and others to <i>P. mugo s. s</i>. Within the whole sampled data, three geographic groups of populations were detected: the first included <i>P. uncinata</i> and two of <i>P. uliginosa</i>, the second contained East and South Carpathian <i>P. mugo s. s</i>. with the presumed hybrid population, and the third contained all the other populations of <i>P. mugo s. s</i>. and <i>P. uliginosa</i>. Within <i>P. mugo s. s</i>., the Sudetan populations formed a separate group. <i>Pinus uncinata</i> from the Pyrenees reflected a high level of differentiation. The marginal populations of this taxon (Cebollera, Gúdar, Massif Central) also differed from those in the Pyrenees. The phenotypic differentiation of taxa and populations appeared similar to that which was detected based on <i>cp</i>DNA markers.
DOI: 10.6084/m9.figshare.1496611.v1
title: SAS code: HDX subnational timeseries data cleaning

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014. <br><br>SAS code for data cleaning for Humanitarian Data Exchange (HDX) "Sub-national time series data on Ebola cases and deaths in Guinea, Liberia, Sierra Leone, Nigeria, Senegal and Mali since March 2014" at https://data.hdx.rwlabs.org/dataset/rowca-ebola-cases
DOI: 10.6084/m9.figshare.1496612.v1
title: SAS code: HealthMap ebola data cleaning

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014.<br> SAS code for data cleaning for Ebola HealthMap articles (3/14-8/27/2014) at http://figshare.com/articles/Ebola_HealthMap_article_data_3_14_8_27_2014/1496610
DOI: 10.6084/m9.figshare.1496612.v3
title: SAS code: Ebola HealthMap data cleaning (March 14 - August 27, 2014)

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014.<br> SAS code for data cleaning for Ebola HealthMap articles (3/14-8/27/2014) at http://figshare.com/articles/Ebola_HealthMap_article_data_3_14_8_27_2014/1496610
DOI: 10.6084/m9.figshare.1496611.v2
title: SAS code: HDX subnational timeseries data cleaning (March 24 - August 27, 2015)

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014. <br><br>SAS code for data cleaning for Humanitarian Data Exchange (HDX) "Sub-national time series data on Ebola cases and deaths in Guinea, Liberia, Sierra Leone, Nigeria, Senegal and Mali since March 2014" at https://data.hdx.rwlabs.org/dataset/rowca-ebola-cases
DOI: 10.6084/m9.figshare.1496612.v2
title: SAS code: Ebola HealthMap data cleaning (March 14 - August 27, 2015)

description: Purpose: comparitive study of HealthMap and HDX (WHO/MOH) ebola case and mortality estimates from March 14 - August 27, 2014.<br> SAS code for data cleaning for Ebola HealthMap articles (3/14-8/27/2014) at http://figshare.com/articles/Ebola_HealthMap_article_data_3_14_8_27_2014/1496610
DOI: 10.6084/m9.figshare.1512834.v285
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.