cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1502679.v2
title: Spawning behavior of garden eels, <i>Gorgasia preclara</i> and <i>Heteroconger hassi</i> (Heterocongrinae), observed in captivity

description: The behavior and reproductive ecology of typically nocturnal marine eels is poorly known but garden eels (Congridae, Heterocongrinae) are familiar tropical marine eels. They live in colonies and protrude their bodies from burrows during the daytime to feed on zooplankton. Apparent daytime courtship/spawning-like behavior has been observed within the colonies but actual spawning and fertilized egg production has not been confirmed. This study describes observations of splendid garden eels (<i>Gorgasia preclara</i>) and spotted garden eels (<i>Heteroconger hassi</i>) spawning in low light at night and producing fertilized eggs in a large multispecies public-display tank in the Sumida Aquarium. Video recordings of 5 of 17 detected spawning or egg or sperm release events documented the spawning behavior of <i>G. preclara</i>, and positively buoyant fertilized eggs of both species were collected. Their spawning behavior while protruding from widely spaced burrows confirms that garden eels likely spawn within their colonies with their pelagic eggs drifting away with currents.
DOI: 10.6084/m9.figshare.1502667.v1
title: Edge Length and Surface Area of a Blank: Experimental Assessment of Measures, Size Predictions and Utility

description: Blank size and form represent one of the main sources of variation in lithic assemblages. They reflect economic properties of blanks and factors such as efficiency and use life. These properties require reliable measures of size, namely edge length and surface area.These measures, however, are not easily captured with calipers. Most attempts to quantify these features employ estimates; however, the efficacy of these estimations for measuring critical features such as blank surface area and edge length has never been properly evaluated. In addition, these parameters are even more difficult to acquire for retouched implements as their original size and hence indication of their previous utility have been lost. It has been suggested, in controlled experimental conditions, that two platform variables, platform thickness and exterior platform angle, are crucial in determining blank size and shape meaning that knappers can control the interaction between size and efficiency by selecting specific core angles and controlling where fracture is initiated. The robustness of these models hasrarely been tested and confirmed in context other than controlled experiments. In this paper, we evaluate which currently employed caliper measurement methods result in the highest accuracy of size estimations of blanks, and we evaluate how platform variables can be used to indirectly infer aspects of size on retouched artifacts. Furthermore, we investigate measures of different platform management strategies that control the shape and size of artifacts. To investigate these questions, we created an experimental lithic assemblage, we digitized images to calculate 2D surface area and edge length, which are used as a point of comparison for the caliper measurements and additional analyses. The analysis of aspects of size determinations and the utility of blanks contributes to our understanding of the technological strategies of prehistoric knappers and what economic decisions they made during process of blank production.
DOI: 10.6084/m9.figshare.1512834.v195
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.1502676.v2
title: Results of RT-PCR microarray validation following treatment with alternative plasticizers in immortilized TM4 sertoli cell line

description: Validation of microarray studies in TM4 sertoli cell line.
DOI: 10.6084/m9.figshare.1502665
title: Supplementary tables with discovered virus sequences

description: Supplementary tables S1-5
DOI: 10.6084/m9.figshare.1502679.v3
title: Spawning behavior of garden eels, <i>Gorgasia preclara</i> and <i>Heteroconger hassi</i> (Heterocongrinae), observed in captivity

description: The behavior and reproductive ecology of typically nocturnal marine eels is poorly known but garden eels (Congridae, Heterocongrinae) are familiar tropical marine eels. They live in colonies and protrude their bodies from burrows during the daytime to feed on zooplankton. Apparent daytime courtship/spawning-like behavior has been observed within the colonies but actual spawning and fertilized egg production has not been confirmed. This study describes observations of splendid garden eels (<i>Gorgasia preclara</i>) and spotted garden eels (<i>Heteroconger hassi</i>) spawning in low light at night and producing fertilized eggs in a large multispecies public-display tank in the Sumida Aquarium. Video recordings of 5 of 17 detected spawning or egg or sperm release events documented the spawning behavior of <i>G. preclara</i>, and positively buoyant fertilized eggs of both species were collected. Their spawning behavior while protruding from widely spaced burrows confirms that garden eels likely spawn within their colonies with their pelagic eggs drifting away with currents.
DOI: 10.6084/m9.figshare.1512834.v196
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.1502662
title: The European distribution of Sus scrofa. Model outputs from the project described within the poster - Where are all the boars? An attempt to gain a continental perspective.

description: Wild boar is a host of a number of arthropod-vectored diseases and its numbers are on the rise in mainland Europe. The first of the three models provide a European map presenting the probability of presence of Sus scrofa, which can be used to describe the likely geographical distribution of the species. The second and third models provide indices to help describe the likely abundance across the continent. The two indices include “the proportion of suitable habitat where presence is estimated” and a simple classification of boar abundance across Europe using quantiles of existing abundance data and proxies.
DOI: 10.6084/m9.figshare.1502665.v1
title: Supplementary tables with discovered virus sequences

description: Supplementary tables S1-5
DOI: 10.6084/m9.figshare.1502661
title: URINE NMR BIOMARKERS OF SEPSIS IN THE ICU

description: We aimed to identify metabolomic biomarkers of sepsis in urine by 1H-NMR spectroscopy to assess the severity and to predict outcomes. Urine samples were collected from 64 patients with severe sepsis or septic shock in the ICU for a 1H NMR spectra acquisition. A supervised analysis was performed on the processed spectra, and a predictive model for prognosis (30-days mortality/survival) of sepsis was constructed using partial least-squares discriminant analysis (PLS-DA). In addition, we compared the prediction power of metabolomics data with the Sequential Organ Failure Assessment (SOFA) score. Supervised multivariate analysis afforded a good predictive model to distinguish the patient groups and detect specific metabolic patterns. Negative prognosis patients presented higher values of ethanol, glucose and hippurate, and on the contrary, lower levels of methionine, glutamine, arginine and phenylalanine. These metabolites could be part of a composite biopattern of the human metabolic response to sepsis shock and its mortality in ICU patients. The internal cross-validation showed robustness of the metabolic predictive model obtained and a better predictive ability in comparison with SOFA values. Our results indicate that NMR metabolic profiling might be helpful for determining the metabolomic phenotype of worst-prognosis septic patients in an early stage. A predictive model for the evolution of septic patients using these metabolites was able to classify cases with more sensitivity and specificity than the well-established organ dysfunction score SOFA.
DOI: 10.6084/m9.figshare.1512834.v197
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.1502537
title: GPS data for RideLondon 100

description: GPS readings throughout Ride London Surrey 100 2015
DOI: 10.6084/m9.figshare.1502661.v1
title: URINE NMR BIOMARKERS OF SEPSIS IN THE ICU

description: We aimed to identify metabolomic biomarkers of sepsis in urine by 1H-NMR spectroscopy to assess the severity and to predict outcomes. Urine samples were collected from 64 patients with severe sepsis or septic shock in the ICU for a 1H NMR spectra acquisition. A supervised analysis was performed on the processed spectra, and a predictive model for prognosis (30-days mortality/survival) of sepsis was constructed using partial least-squares discriminant analysis (PLS-DA). In addition, we compared the prediction power of metabolomics data with the Sequential Organ Failure Assessment (SOFA) score. Supervised multivariate analysis afforded a good predictive model to distinguish the patient groups and detect specific metabolic patterns. Negative prognosis patients presented higher values of ethanol, glucose and hippurate, and on the contrary, lower levels of methionine, glutamine, arginine and phenylalanine. These metabolites could be part of a composite biopattern of the human metabolic response to sepsis shock and its mortality in ICU patients. The internal cross-validation showed robustness of the metabolic predictive model obtained and a better predictive ability in comparison with SOFA values. Our results indicate that NMR metabolic profiling might be helpful for determining the metabolomic phenotype of worst-prognosis septic patients in an early stage. A predictive model for the evolution of septic patients using these metabolites was able to classify cases with more sensitivity and specificity than the well-established organ dysfunction score SOFA.
DOI: 10.6084/m9.figshare.1502478
title: S1 Example

description: S1 Example from the ReproPhylo paper, showing git integration in ReproPhylo
DOI: 10.6084/m9.figshare.1502480
title: Parameters of malnutrition and diagnostic measures of sarcopenia

description: Data corresponding to the following article: Reijnierse et al. 2015. The association between parameters of malnutrition and diagnostic measures of sarcopenia in geriatric outpatients. PLOSONE 2015. doi: 10.1371/journal.pone.0135933
DOI: 10.6084/m9.figshare.1502537.v2
title: GPS data for RideLondon 100

description: GPS readings throughout Ride London Surrey 100 2015
DOI: 10.6084/m9.figshare.1512834.v198
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.1502478.v1
title: S1 Example

description: S1 Example from the ReproPhylo paper, showing git integration in ReproPhylo
DOI: 10.6084/m9.figshare.1502480.v1
title: Parameters of malnutrition and diagnostic measures of sarcopenia

description: Data corresponding to the following article: Reijnierse et al. 2015. The association between parameters of malnutrition and diagnostic measures of sarcopenia in geriatric outpatients. PLOSONE 2015. doi: 10.1371/journal.pone.0135933
DOI: 10.6084/m9.figshare.1502537.v1
title: GPS data for RideLondon 100

description: GPS readings throughout Ride London Surrey 100 2015
DOI: 10.6084/m9.figshare.1502477
title: S1 Methods

description: ReproPhylo code examples. The snippets are numbered accprding to the steps in Figure 1 in the ReproPhylo paper
DOI: 10.6084/m9.figshare.1512834.v199
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.1502432
title: Absence of hybridisation between <i>Fuscospora</i> species at a site in Arthur's Pass National Park, New Zealand

description: We analysed simple sequence repeat markers for a selection of red beech (<i>Fuscospora fusca</i>) and mountain beech (<i>Fuscospora cliffortioides</i>) trees growing together and for seeds collected from them. Our analysis detected neither hybrid trees nor hybrid seeds within our sample. We suggest pre-zygotic reproductive isolating mechanisms such as differences in flowering time may be important in maintaining boundaries between <i>Fuscospora</i> species despite extensive sympatry.
DOI: 10.6084/m9.figshare.1502435
title: Cranfield University APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by Cranfield University during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1502433
title: University of Sussex APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Sussex during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/). Caveats regarding this data are that it does not include APCs which are paid for out of non-central funds within the university, and the figures likely include APCs for articles not yet published.
DOI: 10.6084/m9.figshare.1502435.v1
title: Cranfield University APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by Cranfield University during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1502477.v1
title: S1 Methods

description: ReproPhylo code examples. The snippets are numbered accprding to the steps in Figure 1 in the ReproPhylo paper
DOI: 10.6084/m9.figshare.1502433.v1
title: University of Sussex APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by the University of Sussex during January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/). Caveats regarding this data are that it does not include APCs which are paid for out of non-central funds within the university, and the figures likely include APCs for articles not yet published.
DOI: 10.6084/m9.figshare.1512834.v200
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.1502429
title: Royal Holloway APCs 2015 (Jan-June)

description: This spreadsheet contains details of article processing charges (APCs) paid by Royal Holloway, University of London January-June 2015. The data is being collected as part of Jisc's APC data collection project to address the Total Cost of Ownership of scholarly communication (https://www.jisc-collections.ac.uk/Jisc-Monitor/APC-data-collection/).
DOI: 10.6084/m9.figshare.1502428
title: PrePex Pilot Study PHRU-PSI

description: PrePex Device Medical Male Circumcision Field Study - Pilot in South Africa
DOI: 10.6084/m9.figshare.1512834.v201
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: 10.6073/pasta/580c5326940a16982cbcf3c97e86f2ee
title: Calling activity of Birds in the White Mountain National Forest: Audio Recordings (2016 and 2018)

description: We collected 410 10-minute sound recordings of birds in and near the Hubbard Brook Experimental Forest in New Hampshire. Recordings, which encompassed most of the bird breeding season in each of two years, included 130,776 vocalizations from 46 taxa. In the associated publication, we report species lists, rarefaction curves, and vocalization descriptions. We also provide analyses of habitat associations, phenology, and spatial patterning in vocalization activity. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
DOI: 10.6084/m9.figshare.1502432.v1
title: Absence of hybridisation between <i>Fuscospora</i> species at a site in Arthur's Pass National Park, New Zealand

description: We analysed simple sequence repeat markers for a selection of red beech (<i>Fuscospora fusca</i>) and mountain beech (<i>Fuscospora cliffortioides</i>) trees growing together and for seeds collected from them. Our analysis detected neither hybrid trees nor hybrid seeds within our sample. We suggest pre-zygotic reproductive isolating mechanisms such as differences in flowering time may be important in maintaining boundaries between <i>Fuscospora</i> species despite extensive sympatry.