cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1497942
title: MULTI-SITE EVALUATION OF A DATA QUALITY TOOL FOR BIG DATA IN HEALTHCARE

description: Evaluation of data quality in large healthcare datasets. abstract: Data quality and fitness for analysis are crucial if outputs of big data analyses should be trusted by the public and the research community. Here we analyze the output from a data quality tool called Achilles Heel as it was applied to 24 datasets across seven different organizations. We highlight 12 data quality rules that identified issues in at least 10 of the 24 datasets and provide a full set of 71 rules identified in at least one dataset. Achilles Heel is developed by Observational Health Data Sciences and Informatics (OHDSI) community and is a freely available software that provides a useful starter set of data quality rules. Our analysis represents the first data quality comparison of multiple datasets across several countries in America, Europe and Asia.
DOI: 10.6084/m9.figshare.1497978.v4
title: Absence of vitamin K-dependent y-carboxylation in human periostin extracted from fibrotic lung or secreted from a cell line engineered to optimize y- carboxylation

description: Identifying the presence and absence of gamma-carboxylation of periostin and coagulation factor VII proteins
DOI: 10.6084/m9.figshare.1497939
title: A Phytogeographical Metaanalysis of the Semiarid Caatinga Domain in Brazil - Supplementary Files

description: These files comprise the database in CSV format used for the analyses described in the paper “A phytogeographical metaanalysis of the semiarid Caatinga Domain in Brazil” published by Moro et al (2016) in The Botanical Review (http://dx.doi.org/10.1007/s12229-016-9164-z). The bibliographical reference for each floristic survey included in our study is given in the file “Appendix 1” and in the Appendix 1 of our paper. The Raunkiaerian life-form spectra analysed in our article and the bibliographical references for those studies are provided here in the file “Appendix 2” with additional data which do not appear in the paper. File 1 represents the initial dataset, with all occurrence data for all species at all sites. File 2 is the full list of species compiled with the habit attributed to each species. Files 3.1, 3.2 and 3.3 are presence-absence matrices showing the occurrence of each species at each site subdivided as follows: 3.1 - occurrence of species in surveys presenting data on the general flora (woody and non woody plants reported in the same floristic survey) 3.2 - occurrence of species in surveys presenting only data on the woody flora (trees, shrubs and woody climbers) 3.3 - occurrence of species in surveys presenting only data on the non woody flora (subshrubs, herbs and non woody climbers).<br>For more information about the Caatinga Phytogeographical Domain, please, consult our paper.<br>
DOI: 10.6084/m9.figshare.1512834.v263
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.1497978.v5
title: Absence of vitamin K-dependent y-carboxylation in human periostin extracted from fibrotic lung or secreted from a cell line engineered to optimize y- carboxylation

description: Identifying the presence and absence of gamma-carboxylation of periostin and coagulation factor VII proteins
DOI: 10.6084/m9.figshare.1497942.v1
title: Data Quality

description: Evaluation of data quality in large healthcare datasets
DOI: 10.6084/m9.figshare.1497926
title: Kap108 Microarray Code

description: All custom code used in the analysis of wild-type vs <em>kap108</em> mutant <em>Saccharomyces cerevisiae</em> microarray data. All code was implemented in R.
DOI: 10.6084/m9.figshare.1512834.v264
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.1497942.v2
title: MULTI-SITE EVALUATION OF A DATA QUALITY TOOL FOR BIG DATA IN HEALTHCARE

description: Evaluation of data quality in large healthcare datasets. abstract: Data quality and fitness for analysis are crucial if outputs of big data analyses should be trusted by the public and the research community. Here we analyze the output from a data quality tool called Achilles Heel as it was applied to 24 datasets across seven different organizations. We highlight 12 data quality rules that identified issues in at least 10 of the 24 datasets and provide a full set of 71 rules identified in at least one dataset. Achilles Heel is developed by Observational Health Data Sciences and Informatics (OHDSI) community and is a freely available software that provides a useful starter set of data quality rules. Our analysis represents the first data quality comparison of multiple datasets across several countries in America, Europe and Asia.
DOI: 10.6084/m9.figshare.1512834.v265
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.1497942.v4
title: MULTI-SITE EVALUATION OF A DATA QUALITY TOOL FOR BIG DATA IN HEALTHCARE

description: Evaluation of data quality in large healthcare datasets. abstract: Data quality and fitness for analysis are crucial if outputs of big data analyses should be trusted by the public and the research community. Here we analyze the output from a data quality tool called Achilles Heel as it was applied to 24 datasets across seven different organizations. We highlight 12 data quality rules that identified issues in at least 10 of the 24 datasets and provide a full set of 71 rules identified in at least one dataset. Achilles Heel is developed by Observational Health Data Sciences and Informatics (OHDSI) community and is a freely available software that provides a useful starter set of data quality rules. Our analysis represents the first data quality comparison of multiple datasets across several countries in America, Europe and Asia.
DOI: 10.6084/m9.figshare.1497926.v1
title: kap_108

description: All custom code used in the analysis of wild-type vs <em>kap108</em> mutant <em>Saccharomyces cerevisiae</em> microarray data. All code was implemented in R.
DOI: 10.6084/m9.figshare.1497942.v3
title: MULTI-SITE EVALUATION OF A DATA QUALITY TOOL FOR BIG DATA IN HEALTHCARE

description: Evaluation of data quality in large healthcare datasets. abstract: Data quality and fitness for analysis are crucial if outputs of big data analyses should be trusted by the public and the research community. Here we analyze the output from a data quality tool called Achilles Heel as it was applied to 24 datasets across seven different organizations. We highlight 12 data quality rules that identified issues in at least 10 of the 24 datasets and provide a full set of 71 rules identified in at least one dataset. Achilles Heel is developed by Observational Health Data Sciences and Informatics (OHDSI) community and is a freely available software that provides a useful starter set of data quality rules. Our analysis represents the first data quality comparison of multiple datasets across several countries in America, Europe and Asia.
DOI: 10.6084/m9.figshare.1497926.v3
title: Kap108 Microarray Code

description: All custom code used in the analysis of wild-type vs <em>kap108</em> mutant <em>Saccharomyces cerevisiae</em> microarray data. All code was implemented in R.
DOI: 10.6084/m9.figshare.1512834.v266
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.1497919
title: MSI and CSCR 1

description: Multispectral Imaging in Detecting Central Serous Chorioretinopathy
DOI: 10.6084/m9.figshare.1497926.v2
title: Kap108 Microarray Code

description: All custom code used in the analysis of wild-type vs <em>kap108</em> mutant <em>Saccharomyces cerevisiae</em> microarray data. All code was implemented in R.
DOI: 10.6084/m9.figshare.1497917
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.v267
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.1497914
title: Pollen morphology in <i>Athenaea</i> Sendtn. and <i>Aureliana</i> Sendtn. (Solanaceae)

description: <i>Aureliana</i> and <i>Athenaea</i> (Withaniinae, Solanaceae) are two genera of shrubs or small trees with centres of diversity in the Brazilian Atlantic Rain Forest. They are difficult to distinguish using gross morphology, and are traditionally segregated based on differences in fruiting calyx size. Pollen grains of all taxa were acetolysed, treated and examined with light and scanning electron microscopy, with the aim of identifying diagnostic characters. Microphotographs and illustrations of pollen grains are presented. The species analysed present small- to medium-sized monad pollen grains of varying morphology with long to extremely long colpi, and lalongate endoapertures. The analysis showed that the pollen grains of both genera are very similar, differing in size-related characters. These data contributed to the synonymisation of <i>Athenaea</i> within <i>Aureliana</i>.
DOI: 10.6084/m9.figshare.1512834.v268
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.1497914.v1
title: Pollen morphology in <i>Athenaea</i> Sendtn. and <i>Aureliana</i> Sendtn. (Solanaceae)

description: <i>Aureliana</i> and <i>Athenaea</i> (Withaniinae, Solanaceae) are two genera of shrubs or small trees with centres of diversity in the Brazilian Atlantic Rain Forest. They are difficult to distinguish using gross morphology, and are traditionally segregated based on differences in fruiting calyx size. Pollen grains of all taxa were acetolysed, treated and examined with light and scanning electron microscopy, with the aim of identifying diagnostic characters. Microphotographs and illustrations of pollen grains are presented. The species analysed present small- to medium-sized monad pollen grains of varying morphology with long to extremely long colpi, and lalongate endoapertures. The analysis showed that the pollen grains of both genera are very similar, differing in size-related characters. These data contributed to the synonymisation of <i>Athenaea</i> within <i>Aureliana</i>.
DOI: 10.6084/m9.figshare.1497919.v1
title: plos one

description: Sensitivity and Specificity of Multispectral Imaging in Detecting Central Serous Chorioretinopathy
DOI: 10.6084/m9.figshare.1497917.v1
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.v269
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
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.