cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1495351.v1
title: Supplementary figures S1-S3

description: Supplementary Figure 1. Results of permutation tests of population differentiation between the sequences of viruses taken from different categories of host: (a) between arthropods and vertebrates, (b) between arthropods and plants and (c) between plants and vertebrates. Red lines show the degree of differentiation, measured using Hudson’s Fstestimator, and grey histograms show the Fst values from 1000 unique random permutations of host categories over viral sequences. We found significant differentiation between each pair of categories (Fst values: a=0.07, b=0.35, c=0.48) with none of the 1000 permutations resulting in as high an Fst value as the data (P&lt;0.001 for all). Supplementary Figure 2. Correlation of the evolutionary distances between rhabdovirueses and the evolutionary distances between their arthropod hosts. Figure shows the results of a permutation test of this relationship (measured by Pearson’s correlation coefficient). The red line shows the true correlation coefficient (0.36), and the grey histogram shows the correlation coefficients returned from 1000 unique random permutations of host genera over viral sequences (see Methods). We found a significant association between viral and host phylogenies with none of the 1000 permutations resulting in as strong a correlation as the data (P&lt;0.001). Supplementary Figure 3. Results of the permutation test of population differentiation between the sequences of viruses taken from land and aquatic arthropod and vertebrate hosts. Only arthropod and vertebrate hosts were included in the test, since aquatic hosts only included arthropods and vertebrates. The red line shows the true degree of differentiation, measured using Hudson’s Fstestimator, and the grey histogram shows the Fst values returned from 1000 unique random permutations of host categories over viral sequences. Viruses from terrestrial and aquatic hosts were found to have significant population differentiation (with only 7 of the 1000 permutations resulted in as high an Fst value as the data (Fst =0.07, P=0.007).
DOI: 10.6084/m9.figshare.1512834.v320
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.1495333
title: Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system

description: Proteins must fold into their native structures in the crowded cellular environment, to perform their functions. Although such macromolecular crowding has been considered to affect the folding properties of proteins, large-scale experimental data have so far been lacking. Here, we individually translated 142 <em>Escherichia coli</em> cytoplasmic proteins using a reconstituted cell-free translation system in the presence of macromolecular crowding reagents (MCRs), Ficoll 70 or dextran 70, and evaluated the aggregation propensities of 142 proteins. The results showed that the MCR effects varied depending on the proteins, although the degree of these effects was modest. Statistical analyses suggested that structural parameters were involved in the effects of the MCRs. Our dataset provides a valuable resource to understand protein folding and aggregation inside cells. Table 1 shows the data obtained from this analysis and several properties of tested proteins. Table 2 shows the predicted classification of the Structural Classification of Proteins (SCOP) for the structural analysis. Table 3 shows the templates for constructing the structural models for 41 proteins and several structural features obtained from the calculation with the constructed model.
DOI: 10.6084/m9.figshare.1495326
title: Implementation of a cloud-based electronic medical record to reduce gaps in the HIV treatment continuum in rural Kenya

description: Implementation of a cloud-based electronic medical record to reduce gaps in the HIV treatment continuum in rural Kenya
DOI: 10.6084/m9.figshare.1495333.v1
title: Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system

description: Proteins must fold into their native structures in the crowded cellular environment, to perform their functions. Although such macromolecular crowding has been considered to affect the folding properties of proteins, large-scale experimental data have so far been lacking. Here, we individually translated 142 <em>Escherichia coli</em> cytoplasmic proteins using a reconstituted cell-free translation system in the presence of macromolecular crowding reagents (MCRs), Ficoll 70 or dextran 70, and evaluated the aggregation propensities of 142 proteins. The results showed that the MCR effects varied depending on the proteins, although the degree of these effects was modest. Statistical analyses suggested that structural parameters were involved in the effects of the MCRs. Our dataset provides a valuable resource to understand protein folding and aggregation inside cells. Table 1 shows the data obtained from this analysis and several properties of tested proteins. Table 2 shows the predicted classification of the Structural Classification of Proteins (SCOP) for the structural analysis. Table 3 shows the templates for constructing the structural models for 41 proteins and several structural features obtained from the calculation with the constructed model.
DOI: 10.6084/m9.figshare.1495316
title: Use of mobile information technology during a polio campaign in South Sudan

description: Use of mobile information technology during a polio campaign in South Sudan
DOI: 10.6084/m9.figshare.1495316.v1
title: Use of mobile information technology during a polio campaign in South Sudan

description: Use of mobile information technology during a polio campaign in South Sudan
DOI: 10.6084/m9.figshare.1495326.v1
title: Implementation of a cloud-based electronic medical record to reduce gaps in the HIV treatment continuum in rural Kenya

description: Implementation of a cloud-based electronic medical record to reduce gaps in the HIV treatment continuum in rural Kenya
DOI: 10.6084/m9.figshare.1512834.v321
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.1495314
title: The data and code for ILGM model

description: The data and code for ILGM model
DOI: 10.6084/m9.figshare.1495292
title: The data for ILGM model

description: This is the dataset for the ILGM model
DOI: 10.6084/m9.figshare.1495292.v1
title: The data for ILGM model

description: This is the dataset for the ILGM model
DOI: 10.6084/m9.figshare.1494849
title: Basic statistical analysis of Team Work Survey

description: Aggregated responses of the 9-point post-course team-work questionnaire that was sent out to the students in this gamification pilot study. The dataset is divided into the two teams game-based and instructor-section based teams. A Mann Whitney U Test was performed on the dataset.
DOI: 10.6084/m9.figshare.1512834.v322
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.1494849.v1
title: Basic statistical analysis of Team Work Survey

description: Aggregated responses of the 9-point post-course team-work questionnaire that was sent out to the students in this gamification pilot study. The dataset is divided into the two teams game-based and instructor-section based teams. A Mann Whitney U Test was performed on the dataset.
DOI: 10.6084/m9.figshare.1494839
title: Lake Victoria Shapefiles

description: A digital GIS map of Lake Victoria with Bathymetry
DOI: 10.6084/m9.figshare.1494841
title: The summary data for a review of the relationship with pollen limitation of plant reproduction

description: Recent work on the ecosystem service of biodiversity suggests that higher pollinator diversity could lower pollen limitation, but these two aspects of plant–pollinator communities have only rarely been causally connected. Here we present a review of studies that produced quantitative assessments of both pollinator diversity and evenness as well as pollen limita- tion of focal plant species. Although pollen limitation is expected to be lower when pollinator diversity is high, our analysis suggests this relationship is weak. The relationship may be obscured when features of the plant species (e.g., average level of specialization) are confounded with features of the plant communities (e.g., habitat). We encourage researchers investigat- ing pollen limitation to consider including measures of diversity of the floral visitors, and their effectiveness. These data would permit a more powerful test of the relationships among these variables and improve our understanding of the critical elements of stable plant–pollinator networks.
DOI: 10.6084/m9.figshare.1512834.v323
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.v324
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.1494841.v1
title: The summary data for a review of the relationship with pollen limitation of plant reproduction

description: Recent work on the ecosystem service of biodiversity suggests that higher pollinator diversity could lower pollen limitation, but these two aspects of plant–pollinator communities have only rarely been causally connected. Here we present a review of studies that produced quantitative assessments of both pollinator diversity and evenness as well as pollen limita- tion of focal plant species. Although pollen limitation is expected to be lower when pollinator diversity is high, our analysis suggests this relationship is weak. The relationship may be obscured when features of the plant species (e.g., average level of specialization) are confounded with features of the plant communities (e.g., habitat). We encourage researchers investigat- ing pollen limitation to consider including measures of diversity of the floral visitors, and their effectiveness. These data would permit a more powerful test of the relationships among these variables and improve our understanding of the critical elements of stable plant–pollinator networks.
DOI: 10.6084/m9.figshare.1494831
title: Anesthesiology PB data.xlsx

description: Data from Hedin et al study
DOI: 10.6084/m9.figshare.1494831.v1
title: Anesthesiology PB data.xlsx

description: Data from Hedin et al study
DOI: 10.6084/m9.figshare.1512834.v325
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.1494829
title: Computational analysis of pediatric ventricular assist device implantation to decrease cerebral particulate embolization

description: Stroke is the most devastating complication after ventricular assist device (VAD) implantation with a 19% incidence and 65% mortality in the pediatric population. Current pediatric VAD technology and anticoagulation strategies alone are suboptimal. VAD implantation assisted by computational methods (CFD) may contribute reducing the risk of cerebral embolization. Representative three-dimensional aortic arch models of an infant and a child were generated. An 8 mm VAD outflow-graft (VAD-OG) anastomosed to the aorta was rendered and CFD was applied to study blood flow patterns. Particle tracks, originating in the VAD, were computed with a Lagrangian phase model and the percentage of particles entering the cerebral vessels was calculated. Eight implantation configurations (infant = 5 and child = 3) and 5 particle sizes (0.5, 1, 2, 3, and 4 mm) were considered. For the infant model, percentage of particles entering the cerebral vessels ranged from 15% for a VAD-OG anastomosed at 90° to the aorta, to 31% for 30° VAD-OG anastomosis (overall percentages: <i>X</i><sup>2</sup> = 10,852, <i>p</i> 2 = 10,323, <i>p</i>
DOI: 10.6084/m9.figshare.1512834.v326
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.1494829.v1
title: Computational analysis of pediatric ventricular assist device implantation to decrease cerebral particulate embolization

description: Stroke is the most devastating complication after ventricular assist device (VAD) implantation with a 19% incidence and 65% mortality in the pediatric population. Current pediatric VAD technology and anticoagulation strategies alone are suboptimal. VAD implantation assisted by computational methods (CFD) may contribute reducing the risk of cerebral embolization. Representative three-dimensional aortic arch models of an infant and a child were generated. An 8 mm VAD outflow-graft (VAD-OG) anastomosed to the aorta was rendered and CFD was applied to study blood flow patterns. Particle tracks, originating in the VAD, were computed with a Lagrangian phase model and the percentage of particles entering the cerebral vessels was calculated. Eight implantation configurations (infant = 5 and child = 3) and 5 particle sizes (0.5, 1, 2, 3, and 4 mm) were considered. For the infant model, percentage of particles entering the cerebral vessels ranged from 15% for a VAD-OG anastomosed at 90° to the aorta, to 31% for 30° VAD-OG anastomosis (overall percentages: <i>X</i><sup>2</sup> = 10,852, <i>p</i> 2 = 10,323, <i>p</i>
DOI: 10.6084/m9.figshare.1494822
title: (Jaekl et al., 2015) Audiovisual delay as a novel cue to distance: Exp. 1 data

description: Five subjects, for Left and Right cluster being closer (L & R variables) Each row is a different sound delay: 0 20, 40, 60, 80, 100 ms Each column is a different adjustment measurement
DOI: 10.6084/m9.figshare.1494821
title: (Jaekl et al., 2015) Audiovisual delay as a novel cue to distance: Exp. 2 data

description: Each row is an individual subject Each value is proportion of "distance increase responses" (out of 20 trials) Each column is a different AV asynchrony (as shown in xdata)
DOI: 10.6084/m9.figshare.1512834.v327
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.1494821.v1
title: (Jaekl et al., 2015) Audiovisual delay as a novel cue to distance: Exp. 2 data

description: Each row is an individual subject Each value is proportion of "distance increase responses" (out of 20 trials) Each column is a different AV asynchrony (as shown in xdata)
DOI: 10.6084/m9.figshare.1494822.v1
title: (Jaekl et al., 2015) Audiovisual delay as a novel cue to distance: Exp. 1 data

description: Five subjects, for Left and Right cluster being closer (L & R variables) Each row is a different sound delay: 0 20, 40, 60, 80, 100 ms Each column is a different adjustment measurement
DOI: 10.6084/m9.figshare.1512834.v328
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.