cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1512834.v341
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.1494648
title: Random Forest Population Mapping Complexity Reduction Algorithm, Data and Code

description: These files represent the source code and technical fitting details of the Random Forest-based population mapping algorithm as descrbed in Stevens, et al. (2015). Though the randomForest R package provides the functionality to fit a model with an arbitrarily large number of covariates and observations (limited only by memory and disk space) a limiting feature of our approach is the time spent during the prediction phase. This code and sample data provides the details of a data reduction method that greatly increases the prediction-phase for new data, necessitated by running per-pixel predictions on large countries for WorldPop population mapping products.
DOI: 10.6084/m9.figshare.1494649
title: The dataset for a systematic review of the attractant-decoy and repellent- plant hypotheses: do plants with heterospecific neighbours escape herbivory?

description: Aims This systematic review highlights the relative support and implica- tions of the attractant-decoy and repellent-plant hypotheses, discuss- ing important linkages between these theories and the opportunity for novel integration into ecological and applied research. Methods An extensive systematic review of the current literature on the attract- ant-decoy and repellent-plant hypotheses was done to describe the following attributes of the research to date: (i) the geographic extent (country and biome) of studies on this topic, (ii) the scope of experi- mental designs used, (iii) the level of support for these hypotheses with respect to the breadth of ecological niches tested, (iv) the level of support for these hypotheses with respect to the classes of herbi- vores examined and, lastly, (v) the ecological impact or purpose of these studies. Herein, we summarize important research gaps in the empirical literature on this topic and identify novel opportunities for critical linkages between ecological and applied theories.
DOI: 10.6084/m9.figshare.1494650
title: The relative success of studies of plant facilitation 2009

description: Competition and facilitation are extensively studied in plant ecology and are central to ecological theory. However, these processes do not occur in isolation from each other and should be studied concurrently and synthetically. Here, we compare the relative citation success of studies that focus on either side of the same interaction coin in terms of number of publications and citations per publication in six of the following major themes in plant ecology: biogeography, populations, communities, ecosystems, evolu- tion and conservation. There were eight times more publications on plant competition than on facilitation but this is not surprising given its long history of comprehensive and relatively exclusive study in plant ecology. Although studies of facilitation comprised a smaller body of literature, the mean citation rate for each publication was equivalent to that of competition studies. Thus, facilitation studies are being used as much as com- petition. These patterns of use by the ecological community clearly indicate that both aspects of plant interactions address broad themes and that studies on plant interactions should now strive to either test both simultaneously or at the very minimum include interpretations and relevant literature from both sets of ideas. Importantly, these broad trends illustrate the old axiom that quality and not quantity of studies may be a consid- eration in the success of a sub-discipline.
DOI: 10.6084/m9.figshare.1512834.v342
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.1494640
title: Random Forest Population Mapping Supplementary Metadata and KML Visualizations

description: These files are supplementary information to illustrate the metadata reports and default visualizations provided as end-user products for WorldPop Random Forest-based population mapping. This collection contains those reports outlining all ancillary covariates and model fitting, as well as KML for each case-stady country outlined in Stevens, et al. (2015) which describes the methods to produce these data in detail. Stevens FR, Gaughan AE, Linard C, Tatem AJ (2015) Disaggregating Census Data for Population Mapping Using Random Forests with Remotely-Sensed and Ancillary Data. PLoS ONE 10(2): e0107042. doi:10.1371/journal.pone.0107042
DOI: 10.6084/m9.figshare.1494650.v1
title: The relative success of studies of plant facilitation 2009

description: Competition and facilitation are extensively studied in plant ecology and are central to ecological theory. However, these processes do not occur in isolation from each other and should be studied concurrently and synthetically. Here, we compare the relative citation success of studies that focus on either side of the same interaction coin in terms of number of publications and citations per publication in six of the following major themes in plant ecology: biogeography, populations, communities, ecosystems, evolu- tion and conservation. There were eight times more publications on plant competition than on facilitation but this is not surprising given its long history of comprehensive and relatively exclusive study in plant ecology. Although studies of facilitation comprised a smaller body of literature, the mean citation rate for each publication was equivalent to that of competition studies. Thus, facilitation studies are being used as much as com- petition. These patterns of use by the ecological community clearly indicate that both aspects of plant interactions address broad themes and that studies on plant interactions should now strive to either test both simultaneously or at the very minimum include interpretations and relevant literature from both sets of ideas. Importantly, these broad trends illustrate the old axiom that quality and not quantity of studies may be a consid- eration in the success of a sub-discipline.
DOI: 10.6084/m9.figshare.1494648.v1
title: Random Forest Population Mapping Complexity Reduction Algorithm, Data and Code

description: These files represent the source code and technical fitting details of the Random Forest-based population mapping algorithm as descrbed in Stevens, et al. (2015). Though the randomForest R package provides the functionality to fit a model with an arbitrarily large number of covariates and observations (limited only by memory and disk space) a limiting feature of our approach is the time spent during the prediction phase. This code and sample data provides the details of a data reduction method that greatly increases the prediction-phase for new data, necessitated by running per-pixel predictions on large countries for WorldPop population mapping products.
DOI: 10.6084/m9.figshare.1512834.v343
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.v344
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.1494600
title: EcoImpactMapper (outdated version)

description: Please get the newest version from the link below.
DOI: 10.6084/m9.figshare.1512834.v345
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.1494600.v1
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1512834.v346
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.1494600.v2
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1494600.v3
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1512834.v347
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.1494600.v4
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1512834.v348
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.1494600.v5
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1512834.v349
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.1494600.v6
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008).
DOI: 10.6084/m9.figshare.1512834.v350
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.v351
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.1494600.v7
title: ImpactMapper (v1.0)

description: The ImpactMapper is an easy-to use open source software tool for mapping human impacts on marine ecosystems. It is based on the additive human impact model suggested by Halpern et al. ("A global map of human impact on marine ecosystems", <em>Science</em>, 2008). The source code will soon be available on GitHub.
DOI: 10.6084/m9.figshare.1494590
title: Activation of new replication foci under conditions of replication stress

description: DNA damage, binding of drugs to DNA or a shortage of nucleotides can decrease the rate or completely halt the progress of replication forks. Although the global rate of replication decreases, mammalian cells can respond to replication stress by activating new replication origins. We demonstrate that a moderate level of stress induced by inhibitors of topoisomerase I, commencing in early, mid or late S-phase, induces activation of new sites of replication located within or in the immediate vicinity of the original replication factories; only in early S some of these new sites are also activated at a distance greater than 300 nm. Under high stress levels very few new replication sites are activated; such sites are located within the original replication regions. There is a large variation in cellular response to stress – while in some cells the number of replication sites increases even threefold, it decreases almost twofold in other cells. Replication stress results in a loss of PCNA from replication factories and a twofold increase in nuclear volume. These observations suggest that activation of new replication origins from the pool of dormant origins within replication cluster under conditions of mild stress is generally restricted to the original replication clusters (factories) active at a time of stress initiation, while activation of distant origins and new replication factories is suppressed.