cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1512834.v27
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.1510980.v1
title: Long-term sediment oxygen demand and net N2 fluxes in Narragansett Bay, RI (USA)

description: Since 2005 I have been measuring sediment oxygen demand and sediment net N2 fluxes at two stations in Narragansett Bay. The first station is at the head of the Providence River Estuary and the second is located in mid-Narragansett Bay. Sediments are collected by divers at the mid-Narragansett Bay site and with pull corer in the Providence River estuary. At least triplicate cores are collected. Cores are 10 cm i.d. and 30.5 cm long. At the time of core collection filtered (0.2 micron) site water is also collected for use in the incubations. All incubations are conducted in batch mode in the dark and the overlying water is gently stirred (~ 40 rpm) with a magnetic stir bar. O2 and N2 fluxes are measured using the N2/Ar technique and a membrane inlet mass spectrometer. For further details please see the references associated with these data. Questions? please email: rwf@bu.edu. Units are: O2 micromoles per meter squared per hour N2-N micromoles per meter squared per hour Site Names: Prov = Providence River Estuary (PRE mean sampling depth: 3 m) Mid Bay = Mid Narragansett Bay (MNB mean sampling depth: 8 m) Overtime these values have been published in various places. The links below include all places where these data have been published. Many people have helped along the way from teaching me the ways of the mass spectrometer to helping collect sediment cores and analyze data. Special thanks to: J. Cornwell, P. Dimilla, S. Donovan, L. Fields, S. Foster, A. Giblin, S. Granger, K. Hanks, A. Hanson, E. Heiss, J. Iccano, M. Horn, T. Kana, J. Krumholz, C. McManus, J. Mercer, C. Mueller, M. Owens, A. Pimenta, MK Rogener, R. Schweiker, M. Traber, and J.Tucker. I thank Boston University for providing laboratory space and equipment for the most recent measurements.
DOI: 10.6084/m9.figshare.1512834.v28
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.1510947
title: Microsatellite data : Saccorhiza polyschides

description: Microsatellite data used for genetic analysis in the study "Deep reefs are climatic refugia for genetic diversity of marine forests" published in Journal of Biogeography.<br> When using this dataset please use the following citation: Assis, J., Coelho, N.C., Lamy, L., Valero, M., Alberto, F., Serrão, E.A. (2016) Deep reefs are climatic refugia for genetic diversity of marine forests. Journal of Biogeography. 43:833–44.
DOI: 10.6084/m9.figshare.1512834.v29
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.1510946
title: Ecoinformatics next 100 years - ESA 2015

description: Slides from talk in Friday morning session on BIEN Botanical Information and Ecological Network
DOI: 10.6084/m9.figshare.1510980.v2
title: Long-term sediment oxygen demand and net N2 fluxes in Narragansett Bay, RI (USA)

description: Since 2005 I have been measuring sediment oxygen demand and sediment net N2 fluxes at two stations in Narragansett Bay. The first station is at the head of the Providence River Estuary and the second is located in mid-Narragansett Bay. Sediments are collected by divers at the mid-Narragansett Bay site and with pull corer in the Providence River estuary. At least triplicate cores are collected. Cores are 10 cm i.d. and 30.5 cm long. At the time of core collection filtered (0.2 micron) site water is also collected for use in the incubations. All incubations are conducted in batch mode in the dark and the overlying water is gently stirred (~ 40 rpm) with a magnetic stir bar. O2 and N2 fluxes are measured using the N2/Ar technique and a membrane inlet mass spectrometer. For further details please see the references associated with these data. Questions? please email: rwf@bu.edu. Units are: O2 micromoles per meter squared per hour N2-N micromoles per meter squared per hour Site Names: Prov = Providence River Estuary (PRE mean sampling depth: 3 m) Mid Bay = Mid Narragansett Bay (MNB mean sampling depth: 8 m) Overtime these values have been published in various places. The links below include all places where these data have been published. Many people have helped along the way from teaching me the ways of the mass spectrometer to helping collect sediment cores and analyze data. Special thanks to: J. Cornwell, P. Dimilla, S. Donovan, L. Fields, S. Foster, A. Giblin, S. Granger, K. Hanks, A. Hanson, E. Heiss, J. Iccano, M. Horn, T. Kana, J. Krumholz, C. McManus, J. Mercer, C. Mueller, M. Owens, A. Pimenta, MK Rogener, R. Schweiker, M. Traber, and J.Tucker. I thank Boston University for providing laboratory space and equipment for the most recent measurements.
DOI: 10.6084/m9.figshare.1510945
title: Data for Figs. 3-6

description: 3-D data with acoustic behavior of bat-moth predator-prey interactions from nature
DOI: 10.6084/m9.figshare.1512834.v30
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.1510945.v1
title: Data for Figs. 3-6

description: 3-D data with acoustic behavior of bat-moth predator-prey interactions from nature
DOI: 10.6084/m9.figshare.1510947.v1
title: Microsatellite data of Saccorhiza polyschides used for genetic analysis

description: Microsatellite data of Saccorhiza polyschides used for genetic analysis in the study "Deep reefs are climatic refugia for genetic diversity of marine forests" published in Journal of Biogeography. When using this dataset please use the following citation: Assis, J., Coelho, N.C., Lamy, L., Valero, M., Alberto, F., Serrão, E.A. (in press) Deep reefs are climatic refugia for genetic diversity of marine forests. Journal of Biogeography
DOI: 10.6084/m9.figshare.1510980.v3
title: Long-term sediment oxygen demand and net N2 fluxes in Narragansett Bay, RI (USA)

description: Since 2005 I have been measuring sediment oxygen demand and sediment net N2 fluxes at two stations in Narragansett Bay. The first station is at the head of the Providence River Estuary and the second is located in mid-Narragansett Bay. Sediments are collected by divers at the mid-Narragansett Bay site and with pull corer in the Providence River estuary. At least triplicate cores are collected. Cores are 10 cm i.d. and 30.5 cm long. At the time of core collection filtered (0.2 micron) site water is also collected for use in the incubations. All incubations are conducted in batch mode in the dark and the overlying water is gently stirred (~ 40 rpm) with a magnetic stir bar. O2 and N2 fluxes are measured using the N2/Ar technique and a membrane inlet mass spectrometer. For further details please see the references associated with these data. Questions? please email: rwf@bu.edu. Units are: O2 micromoles per meter squared per hour N2-N micromoles per meter squared per hour Site Names: Prov = Providence River Estuary (PRE mean sampling depth: 3 m) Mid Bay = Mid Narragansett Bay (MNB mean sampling depth: 8 m) Overtime these values have been published in various places. The links below include all places where these data have been published. Many people have helped along the way from teaching me the ways of the mass spectrometer to helping collect sediment cores and analyze data. Special thanks to: J. Cornwell, P. Dimilla, S. Donovan, L. Fields, S. Foster, A. Giblin, S. Granger, K. Hanks, A. Hanson, E. Heiss, J. Iccano, M. Horn, T. Kana, J. Krumholz, C. McManus, J. Mercer, C. Mueller, M. Owens, A. Pimenta, MK Rogener, R. Schweiker, M. Traber, and J.Tucker. I thank Boston University for providing laboratory space and equipment for the most recent measurements.
DOI: 10.6084/m9.figshare.1510941
title: Chapter 4- Supplemental Table 1

description: UCSC genomic coordinates and zebrafish gene IDs (Ensembl) of intronic PFEs identified in genome-wide analysis
DOI: 10.6084/m9.figshare.1510947.v3
title: Microsatellite data : Saccorhiza polyschides

description: Microsatellite data used for genetic analysis in the study "Deep reefs are climatic refugia for genetic diversity of marine forests" published in Journal of Biogeography.<br> When using this dataset please use the following citation: Assis, J., Coelho, N.C., Lamy, L., Valero, M., Alberto, F., Serrão, E.A. (2016) Deep reefs are climatic refugia for genetic diversity of marine forests. Journal of Biogeography. 43:833–44.
DOI: 10.6084/m9.figshare.1510940
title: Chapter 4- Supplemental Table 6

description: RNA-seq reads mapping to PFEs and controls identified in pathway-focussed analysis
DOI: 10.6084/m9.figshare.1510941.v1
title: Chapter 4- Supplemental Table 1

description: UCSC genomic coordinates and zebrafish gene IDs (Ensembl) of intronic PFEs identified in genome-wide analysis
DOI: 10.6084/m9.figshare.1510980.v4
title: Long-term sediment oxygen demand and net N2 fluxes in Narragansett Bay, RI (USA)

description: Since 2005 I have been measuring sediment oxygen demand and sediment net N2 fluxes at two stations in Narragansett Bay. The first station is at the head of the Providence River Estuary and the second is located in mid-Narragansett Bay. Sediments are collected by divers at the mid-Narragansett Bay site and with pull corer in the Providence River estuary. At least triplicate cores are collected. Cores are 10 cm i.d. and 30.5 cm long. At the time of core collection filtered (0.2 micron) site water is also collected for use in the incubations. All incubations are conducted in batch mode in the dark and the overlying water is gently stirred (~ 40 rpm) with a magnetic stir bar. O2 and N2 fluxes are measured using the N2/Ar technique and a membrane inlet mass spectrometer. For further details please see the references associated with these data. Questions? please email: rwf@bu.edu. Units are: O2 micromoles per meter squared per hour N2-N micromoles per meter squared per hour Site Names: Prov = Providence River Estuary (PRE mean sampling depth: 3 m) Mid Bay = Mid Narragansett Bay (MNB mean sampling depth: 8 m) Overtime these values have been published in various places. The links below include all places where these data have been published. Many people have helped along the way from teaching me the ways of the mass spectrometer to helping collect sediment cores and analyze data. Special thanks to: J. Cornwell, P. Dimilla, S. Donovan, L. Fields, S. Foster, A. Giblin, S. Granger, K. Hanks, A. Hanson, E. Heiss, J. Iccano, M. Horn, T. Kana, J. Krumholz, C. McManus, J. Mercer, C. Mueller, M. Owens, A. Pimenta, MK Rogener, R. Schweiker, M. Traber, and J.Tucker. I thank Boston University for providing laboratory space and equipment for the most recent measurements.
DOI: 10.6084/m9.figshare.1512834.v31
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.1510939
title: Chapter 4- Supplemental Table 5

description: Validating PFEs identified in pathway-focussed analysis using other functional evidence
DOI: 10.6084/m9.figshare.1510947.v2
title: Microsatellite data of Saccorhiza polyschides used for genetic analysis

description: Microsatellite data of Saccorhiza polyschides used for genetic analysis in the study "Deep reefs are climatic refugia for genetic diversity of marine forests" published in Journal of Biogeography. When using this dataset please use the following citation: Assis, J., Coelho, N.C., Lamy, L., Valero, M., Alberto, F., Serrão, E.A. (in press) Deep reefs are climatic refugia for genetic diversity of marine forests. Journal of Biogeography
DOI: 10.6084/m9.figshare.1510938
title: Chapter 4- Supplemental Table 4

description: Intergenic PFEs identified in genome-wide analysis
DOI: 10.6084/m9.figshare.1510939.v1
title: Chapter 4- Supplemental Table 5

description: Validating PFEs identified in pathway-focussed analysis using other functional evidence
DOI: 10.6084/m9.figshare.1510936
title: Chapter 4- Supplemental Table 2

description: Validating intronic PFEs identified in genome-wide analysis using other functional evidence
DOI: 10.6084/m9.figshare.1510937
title: Chapter 4- Supplemental Table 3

description: Genes with PFEs classified as transcription factors
DOI: 10.6084/m9.figshare.1510938.v1
title: Chapter 4- Supplemental Table 4

description: Intergenic PFEs identified in genome-wide analysis
DOI: 10.6084/m9.figshare.1510940.v1
title: Chapter 4- Supplemental Table 6

description: RNA-seq reads mapping to PFEs and controls identified in pathway-focussed analysis
DOI: 10.6084/m9.figshare.1510932
title: Table 6.SOC stocks contained in the 0-1 m soil layer measured at 0-0.1, 0.1-0.2, 0.2-0.4, 0.4-0.6, and 0.6-1 m soil depths under reforestation and secondary coniferous forest

description: SOC stocks contained in the 0-1 m soil layer measured at 0-0.1, 0.1-0.2, 0.2-0.4, 0.4-0.6, and 0.6-1 m soil depths under reforestation and secondary coniferous forest
DOI: 10.6084/m9.figshare.1510936.v1
title: Chapter 4- Supplemental Table 2

description: Validating intronic PFEs identified in genome-wide analysis using other functional evidence
DOI: 10.6084/m9.figshare.1512834.v32
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.1510930
title: Table 4. Carbon stock allocation of all components of the trees, herbs and litter in the plantations and the secondary coniferous forest

description: Carbon stock allocation of all components of the trees, herbs and litter in the plantations and the secondary coniferous forest
DOI: 10.6084/m9.figshare.1510931
title: Table 5. Accumulation rates of standing biomass carbon stocks in different stand stages of Pinus kesiya var. langbianensis plantations

description: Accumulation rates of standing biomass carbon stocks in different stand stages of Pinus kesiya var. langbianensis plantations
DOI: 10.6084/m9.figshare.1510932.v1
title: Table 6.SOC stocks contained in the 0-1 m soil layer measured at 0-0.1, 0.1-0.2, 0.2-0.4, 0.4-0.6, and 0.6-1 m soil depths under reforestation and secondary coniferous forest

description: SOC stocks contained in the 0-1 m soil layer measured at 0-0.1, 0.1-0.2, 0.2-0.4, 0.4-0.6, and 0.6-1 m soil depths under reforestation and secondary coniferous forest
DOI: 10.6084/m9.figshare.1510937.v1
title: Chapter 4- Supplemental Table 3

description: Genes with PFEs classified as transcription factors
DOI: 10.6084/m9.figshare.1510930.v1
title: Table 4. Carbon stock allocation of all components of the trees, herbs and litter in the plantations and the secondary coniferous forest

description: Carbon stock allocation of all components of the trees, herbs and litter in the plantations and the secondary coniferous forest
DOI: 10.6084/m9.figshare.1510928
title: Table 1. Stand characteristics of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest

description: Stand characteristics of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest
DOI: 10.6084/m9.figshare.1510929
title: Table 2. Allometric equations and carbon concentrations of each component of Pinus kesiya var. langbianensis and other broad leaf species

description: Allometric equations and carbon concentrations of each component of Pinus kesiya var. langbianensis and other broad leaf species
DOI: 10.6084/m9.figshare.1512834.v33
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.1510931.v1
title: Table 5. Accumulation rates of standing biomass carbon stocks in different stand stages of Pinus kesiya var. langbianensis plantations

description: Accumulation rates of standing biomass carbon stocks in different stand stages of Pinus kesiya var. langbianensis plantations
DOI: 10.6084/m9.figshare.1510927
title: Table 3. SOC contents of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest

description: SOC contents of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest
DOI: 10.6084/m9.figshare.1510928.v1
title: Table 1. Stand characteristics of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest

description: Stand characteristics of Pinus kesiya var. langbianensis plantations along stand age chronosequence and secondary coniferous forest
DOI: 10.6084/m9.figshare.1510929.v1
title: Table 2. Allometric equations and carbon concentrations of each component of Pinus kesiya var. langbianensis and other broad leaf species

description: Allometric equations and carbon concentrations of each component of Pinus kesiya var. langbianensis and other broad leaf species