cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1497917.v3
title: Current conservation status of the Blue Swallow <i>Hirundo atrocaerulea</i> Sundevall 1850 in Africa

description: <b>The global Blue Swallow <i>Hirundo atrocaerulea</i> was classified as Vulnerable in 2010 on account of its small and rapidly declining population estimated at less than 1 500 pairs. We undertook this study to gain a better understanding of the current status and threats facing this migratory species. Three previously unknown areas that might be part of the species' non-breeding range were identified in Kenya and northern Tanzania. Within its breeding range we identified three previously unknown areas of potentially suitable habitat, one in Tanzania and two in Malawi, which require further exploration. Population viability assessment predicted that the Blue Swallow population will decline by 8% in 10 years. The overall probability of extinction of the species in the wild is 3%. Minimum viable population size analysis suggests that a goal for the long-term conservation of the Blue Swallow should be to mitigate current threats that are driving declines such that the population increases to a minimum of 3 600 individuals. This should consist of at least 900 individuals in each of the four clusters identified, along with a minimum of 500 individuals in at least one of the meta-populations per cluster. The four clusters are located in (1) the southeasten Democratic Republic of the Congo, (2) highlands of southern Tanzania and northern Malawi, (3) eastern highlands of Zimbabwe and (4) South Africa and Swaziland. The current proportions of the Blue Swallow population in strictly protected and unprotected areas on their breeding grounds are 53% and 47%, respectively, whereas on their non-breeding grounds the corresponding percentages are 25% and 75%, respectively. Our reassessment of the Blue Swallow's risk of extinction indicates that it continues to qualify as Vulnerable according to the IUCN/SSC criteria C2a(i).</b>
DOI: 10.6084/m9.figshare.1497919.v2
title: multispectral imaging and CSCR

description: Sensitivity and Specificity of Multispectral Imaging in Detecting Central Serous Chorioretinopathy
DOI: 10.6084/m9.figshare.1497910
title: Carbohydrate-binding modules influence substrate specificity of an endoglucanase from <i>Clostridium thermocellum</i>

description: Most cellulases contain carbohydrate-binding modules (CBMs) that largely contribute to their activity for insoluble substrates. <i>Clostridium thermocellum</i> Cel5E is an endoglucanase having xylanolytic activity. The Cel5E originally has a family 11 CBM preferentially binding to β-1,4- and β-1,3-1,4-mixed linkage glucans. In this study, we replaced the CBM with a different type of CBM, either a family 3 microcrystalline cellulose-directed CBM from <i>Clostridium josui</i> scaffoldin, or a family 6 xylan-directed CBM from <i>Clostridium stercorarium</i> xylanase 11A. Chimeric endoglucanases showed enhanced activity that was affected by CBM binding specificity. These chimeric enzymes could efficiently degrade milled lignocellulosic materials, such as corn hulls, because of heterologous components in the plant cell wall, indicating that diverse CBMs play roles in degradation of lignocellulosic materials. Substrate specificities of an endoglucanase, Cel5E from <i>Clostridium thermocellum</i> were affected by fusion of different type CBMs.
DOI: 10.6084/m9.figshare.1497917.v2
title: Current conservation status of the Blue Swallow <i>Hirundo atrocaerulea</i> Sundevall 1850 in Africa

description: <b>The global Blue Swallow <i>Hirundo atrocaerulea</i> was classified as Vulnerable in 2010 on account of its small and rapidly declining population estimated at less than 1 500 pairs. We undertook this study to gain a better understanding of the current status and threats facing this migratory species. Three previously unknown areas that might be part of the species' non-breeding range were identified in Kenya and northern Tanzania. Within its breeding range we identified three previously unknown areas of potentially suitable habitat, one in Tanzania and two in Malawi, which require further exploration. Population viability assessment predicted that the Blue Swallow population will decline by 8% in 10 years. The overall probability of extinction of the species in the wild is 3%. Minimum viable population size analysis suggests that a goal for the long-term conservation of the Blue Swallow should be to mitigate current threats that are driving declines such that the population increases to a minimum of 3 600 individuals. This should consist of at least 900 individuals in each of the four clusters identified, along with a minimum of 500 individuals in at least one of the meta-populations per cluster. The four clusters are located in (1) the southeasten Democratic Republic of the Congo, (2) highlands of southern Tanzania and northern Malawi, (3) eastern highlands of Zimbabwe and (4) South Africa and Swaziland. The current proportions of the Blue Swallow population in strictly protected and unprotected areas on their breeding grounds are 53% and 47%, respectively, whereas on their non-breeding grounds the corresponding percentages are 25% and 75%, respectively. Our reassessment of the Blue Swallow's risk of extinction indicates that it continues to qualify as Vulnerable according to the IUCN/SSC criteria C2a(i).</b>
DOI: 10.6084/m9.figshare.1512834.v270
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.1497907
title: How van der Waals interactions determine the unique properties of water

description: Parameter sets for neural network potentials (NNPs) for bulk water based on BLYP and RPBE density-functionals with and without van der Waals (vdW) corrections. These files represent supplementary material for the manuscript: 'How van der Waals interactions determine the properties of water' by<br>Tobias Morawietz, Andreas Singraber, Christoph Dellago, and Jörg Behler Electronic Mail:<br>tobias.morawietz@theochem.ruhr-uni-bochum.de<br>joerg.behler@theochem.ruhr-uni-bochum.de
DOI: 10.6084/m9.figshare.1497911.v1
title: Evaluating habitat suitability curves for predicting variation in macroinvertebrate biomass with weighted usable area in braided rivers in New Zealand

description: We investigated changes in seasonal biomass of benthic macroinvertebrates over whole floodplain transects upstream and downstream of existing flow diversions in the Wilberforce and South Ashburton Rivers, Canterbury, New Zealand. We tested the predictive performance of a 1-dimensional hydraulic-habitat model informed with existing general habitat suitability curves (HSC), as well as river- and channel-specific HSC developed from the studied rivers. Diversions resulted in significant declines in wetted width, habitat complexity, and resulting declines in benthic biomass, but community composition was unchanged. Weighted usable area (WUA) predictions based on general HSC were often poorly correlated with cross-sectional macroinvertebrate biomass. River- and channel-type-specific HSC greatly improved the accuracy of predictions; however, all HSC generally under-predicted the total proportional change in cross-sectional macroinvertebrate biomass associated with flow change. We conclude that WUA was an insensitive indicator of flow-related macroinvertebrate biomass change. We encourage development of HSC categorised by river hydrology, size and channel form.
DOI: 10.6084/m9.figshare.1512834.v271
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.1497910.v1
title: Carbohydrate-binding modules influence substrate specificity of an endoglucanase from <i>Clostridium thermocellum</i>

description: Most cellulases contain carbohydrate-binding modules (CBMs) that largely contribute to their activity for insoluble substrates. <i>Clostridium thermocellum</i> Cel5E is an endoglucanase having xylanolytic activity. The Cel5E originally has a family 11 CBM preferentially binding to β-1,4- and β-1,3-1,4-mixed linkage glucans. In this study, we replaced the CBM with a different type of CBM, either a family 3 microcrystalline cellulose-directed CBM from <i>Clostridium josui</i> scaffoldin, or a family 6 xylan-directed CBM from <i>Clostridium stercorarium</i> xylanase 11A. Chimeric endoglucanases showed enhanced activity that was affected by CBM binding specificity. These chimeric enzymes could efficiently degrade milled lignocellulosic materials, such as corn hulls, because of heterologous components in the plant cell wall, indicating that diverse CBMs play roles in degradation of lignocellulosic materials.
DOI: 10.6084/m9.figshare.1497910.v3
title: Carbohydrate-binding modules influence substrate specificity of an endoglucanase from <i>Clostridium thermocellum</i>

description: Most cellulases contain carbohydrate-binding modules (CBMs) that largely contribute to their activity for insoluble substrates. <i>Clostridium thermocellum</i> Cel5E is an endoglucanase having xylanolytic activity. The Cel5E originally has a family 11 CBM preferentially binding to β-1,4- and β-1,3-1,4-mixed linkage glucans. In this study, we replaced the CBM with a different type of CBM, either a family 3 microcrystalline cellulose-directed CBM from <i>Clostridium josui</i> scaffoldin, or a family 6 xylan-directed CBM from <i>Clostridium stercorarium</i> xylanase 11A. Chimeric endoglucanases showed enhanced activity that was affected by CBM binding specificity. These chimeric enzymes could efficiently degrade milled lignocellulosic materials, such as corn hulls, because of heterologous components in the plant cell wall, indicating that diverse CBMs play roles in degradation of lignocellulosic materials. Substrate specificities of an endoglucanase, Cel5E from <i>Clostridium thermocellum</i> were affected by fusion of different type CBMs.
DOI: 10.6084/m9.figshare.1497911.v2
title: Evaluating habitat suitability curves for predicting variation in macroinvertebrate biomass with weighted usable area in braided rivers in New Zealand

description: We investigated changes in seasonal biomass of benthic macroinvertebrates over whole floodplain transects upstream and downstream of existing flow diversions in the Wilberforce and South Ashburton Rivers, Canterbury, New Zealand. We tested the predictive performance of a 1-dimensional hydraulic-habitat model informed with existing general habitat suitability curves (HSC), as well as river- and channel-specific HSC developed from the studied rivers. Diversions resulted in significant declines in wetted width, habitat complexity, and resulting declines in benthic biomass, but community composition was unchanged. Weighted usable area (WUA) predictions based on general HSC were often poorly correlated with cross-sectional macroinvertebrate biomass. River- and channel-type-specific HSC greatly improved the accuracy of predictions; however, all HSC generally under-predicted the total proportional change in cross-sectional macroinvertebrate biomass associated with flow change. We conclude that WUA was an insensitive indicator of flow-related macroinvertebrate biomass change. We encourage development of HSC categorised by river hydrology, size and channel form.
DOI: 10.6084/m9.figshare.1512834.v272
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.1497910.v2
title: Carbohydrate-binding modules influence substrate specificity of an endoglucanase from <i>Clostridium thermocellum</i>

description: Most cellulases contain carbohydrate-binding modules (CBMs) that largely contribute to their activity for insoluble substrates. <i>Clostridium thermocellum</i> Cel5E is an endoglucanase having xylanolytic activity. The Cel5E originally has a family 11 CBM preferentially binding to β-1,4- and β-1,3-1,4-mixed linkage glucans. In this study, we replaced the CBM with a different type of CBM, either a family 3 microcrystalline cellulose-directed CBM from <i>Clostridium josui</i> scaffoldin, or a family 6 xylan-directed CBM from <i>Clostridium stercorarium</i> xylanase 11A. Chimeric endoglucanases showed enhanced activity that was affected by CBM binding specificity. These chimeric enzymes could efficiently degrade milled lignocellulosic materials, such as corn hulls, because of heterologous components in the plant cell wall, indicating that diverse CBMs play roles in degradation of lignocellulosic materials.
DOI: 10.6084/m9.figshare.1497911.v4
title: Evaluating habitat suitability curves for predicting variation in macroinvertebrate biomass with weighted usable area in braided rivers in New Zealand

description: We investigated changes in seasonal biomass of benthic macroinvertebrates over whole floodplain transects upstream and downstream of existing flow diversions in the Wilberforce and South Ashburton Rivers, Canterbury, New Zealand. We tested the predictive performance of a 1-dimensional hydraulic-habitat model informed with existing general habitat suitability curves (HSC), as well as river- and channel-specific HSC developed from the studied rivers. Diversions resulted in significant declines in wetted width, habitat complexity, and resulting declines in benthic biomass, but community composition was unchanged. Weighted usable area (WUA) predictions based on general HSC were often poorly correlated with cross-sectional macroinvertebrate biomass. River- and channel-type-specific HSC greatly improved the accuracy of predictions; however, all HSC generally under-predicted the total proportional change in cross-sectional macroinvertebrate biomass associated with flow change. We conclude that WUA was an insensitive indicator of flow-related macroinvertebrate biomass change. We encourage development of HSC categorised by river hydrology, size and channel form.
DOI: 10.6084/m9.figshare.1512834.v273
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.1497911.v3
title: Evaluating habitat suitability curves for predicting variation in macroinvertebrate biomass with weighted usable area in braided rivers in New Zealand

description: We investigated changes in seasonal biomass of benthic macroinvertebrates over whole floodplain transects upstream and downstream of existing flow diversions in the Wilberforce and South Ashburton Rivers, Canterbury, New Zealand. We tested the predictive performance of a 1-dimensional hydraulic-habitat model informed with existing general habitat suitability curves (HSC), as well as river- and channel-specific HSC developed from the studied rivers. Diversions resulted in significant declines in wetted width, habitat complexity, and resulting declines in benthic biomass, but community composition was unchanged. Weighted usable area (WUA) predictions based on general HSC were often poorly correlated with cross-sectional macroinvertebrate biomass. River- and channel-type-specific HSC greatly improved the accuracy of predictions; however, all HSC generally under-predicted the total proportional change in cross-sectional macroinvertebrate biomass associated with flow change. We conclude that WUA was an insensitive indicator of flow-related macroinvertebrate biomass change. We encourage development of HSC categorised by river hydrology, size and channel form.
DOI: 10.6084/m9.figshare.1497888
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.1497894
title: Leaf Area index field measurements, forest and woodland in Tanzania

description: This dataset shows estimates of Leaf Area Index (LAI), fraction of vegetation cover (fCover) and fraction of absorbed photsynthetically active radiation (fAPAR) for moist forest and miombo woodlands from Hanang district in Tanzania, using hemipsherical photography. For more dataset from other biomes in Africa see http://www.york.ac.uk/environment/research/kite/resources/#tab-2.
DOI: 10.6084/m9.figshare.1497894.v1
title: Leaf Area index field measurements, forest and woodland in Tanzania

description: This dataset shows estimates of Leaf Area Index (LAI), fraction of vegetation cover (fCover) and fraction of absorbed photsynthetically active radiation (fAPAR) for moist forest and miombo woodlands from Hanang district in Tanzania, using hemipsherical photography. For more dataset from other biomes in Africa see http://www.york.ac.uk/environment/research/kite/resources/#tab-2.
DOI: 10.6084/m9.figshare.1512834.v274
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.