cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1501496.v1
title: PeerJ cited journal data

description: List of journals cited in PeerJ sampled articles as reported in: Burns, C. S. (2015). Characteristics of a megajournal: A bibliometric case study. <em>Journal of Information Science Theory and Practice, 3</em>(2), 16-30.
DOI: 10.6084/m9.figshare.1501497.v1
title: PeerJ article data

description: Main data set for: Burns, C. S. (2015). Characteristics of a megajournal: A bibliometric case study. <em>Journal of Information Science Theory and Practice, 3</em>(2), 16-30.
DOI: 10.6084/m9.figshare.1512834.v208
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.1501493
title: Simulation: Additional Analyses Bayes Assymmetrical

description: Unpublished additional analyses with a prior variance of .01 for the reference group and a prior variance of 5 (S50_5_0.01) or 10 (S50_10_0.01) in the exceptional group.
DOI: 10.6084/m9.figshare.1501493.v1
title: Simulation: Additional Analyses Bayes Assymmetrical

description: Unpublished additional analyses with a prior variance of .01 for the reference group and a prior variance of 5 (S50_5_0.01) or 10 (S50_10_0.01) in the exceptional group.
DOI: 10.6084/m9.figshare.1501454
title: Biocontrol of <i>Ailanthus altissima</i>: inoculation protocol and risk assessment for <i>Verticillium nonalfalfae</i> (Plectosphaerellaceae: Phyllachorales)

description: <i>Verticillium nonalfalfae</i> has been proposed as a biocontrol for invasive <i>Ailanthus altissima</i> (tree-of-heaven) in Ohio, Pennsylvania and Virginia. However, previous studies evaluating this potential biocontrol utilised a conidial suspension with a short shelf life as inoculum. Anticipating future expanded use of <i>V. nonalfalfae</i>, we evaluated other inoculum formulations, inoculation protocols and sensitivity of non-target (non-<i>Ailanthus</i>) plant species within Pennsylvania. The most effective inoculum formulation, with an extended shelf life, was prepared by mixing water with stored, refrigerated soil containing <i>V. nonalfalfae</i>. Less successful, but positive infections were obtained by simply using infected <i>Ailanthus</i> wood and leaves as inoculum. Monthly inoculation of <i>Ailanthus</i> trees demonstrated that the optimal time for successful inoculations was April to May, but limited infections were achieved during all months, including the winter. The health of <i>Ailanthus</i> and non-target species was evaluated within a decade-old natural Verticillium wilt epicentre, where all mature <i>Ailanthus</i> trees had been killed by <i>V. nonalfalfae</i>. Verticillium wilt was observed on a few small <i>Ailanthus</i> trees, likely newly established seedlings, whereas non-target species were asymptomatic. Our findings reveal that soil formulated and natural inocula are effective biocontrols against <i>Ailanthus</i>, and <i>V. nonalfalfae</i> appears to pose little threat to non-target plants.
DOI: 10.6084/m9.figshare.1512834.v209
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.1501452
title: Seed germination and risks of using the invasive plant <i>Eichhornia crassipes</i> (Mart.) Solms-Laub. (water hyacinth) for composting, ovine feeding and biogas production

description: Water hyacinth (<i>Eichhornia crassipes</i> (Mart.) Solms-Laub.) is an invasive aquatic weed that has one of the highest growth indices of vascular plants, producing large amounts of biomass. Its use for composting, livestock feed and biogas production has been proposed as a management strategy for its control. The work presented here is an assessment of the potential spread of water hyacinth due to the release of seeds from the by-products of some of these manufacturing processes. We tested experimentally if the seeds were destroyed or did not lose germinability when they had passed through the gut of sheep, remained in compost piles or been used in biogas bioreactors. We made optical and electronic microscopic observations, and calculated retrieval and germination percentages of the seeds subjected to these treatments. After having passed through the gut of sheep, the anatomical organization of the seed was completely destroyed, only 30.50 ± 5.83% of the seeds were retrieved and the germinability was null (0 ± 0%). The biogas production and compost-treated seeds both had retrieval percentages of 100 ± 0% and germination values of 1.00 ± 0.57 and 3.50 ± 0.96% respectively, with several anatomical damages. The use for compost or biogas production as a management strategy to control this pest is not completely safe from an environmental perspective and the selected management option should focus on sheep fodder production.
DOI: 10.6084/m9.figshare.1501454.v1
title: Biocontrol of <i>Ailanthus altissima</i>: inoculation protocol and risk assessment for <i>Verticillium nonalfalfae</i> (Plectosphaerellaceae: Phyllachorales)

description: <i>Verticillium nonalfalfae</i> has been proposed as a biocontrol for invasive <i>Ailanthus altissima</i> (tree-of-heaven) in Ohio, Pennsylvania and Virginia. However, previous studies evaluating this potential biocontrol utilised a conidial suspension with a short shelf life as inoculum. Anticipating future expanded use of <i>V. nonalfalfae</i>, we evaluated other inoculum formulations, inoculation protocols and sensitivity of non-target (non-<i>Ailanthus</i>) plant species within Pennsylvania. The most effective inoculum formulation, with an extended shelf life, was prepared by mixing water with stored, refrigerated soil containing <i>V. nonalfalfae</i>. Less successful, but positive infections were obtained by simply using infected <i>Ailanthus</i> wood and leaves as inoculum. Monthly inoculation of <i>Ailanthus</i> trees demonstrated that the optimal time for successful inoculations was April to May, but limited infections were achieved during all months, including the winter. The health of <i>Ailanthus</i> and non-target species was evaluated within a decade-old natural Verticillium wilt epicentre, where all mature <i>Ailanthus</i> trees had been killed by <i>V. nonalfalfae</i>. Verticillium wilt was observed on a few small <i>Ailanthus</i> trees, likely newly established seedlings, whereas non-target species were asymptomatic. Our findings reveal that soil formulated and natural inocula are effective biocontrols against <i>Ailanthus</i>, and <i>V. nonalfalfae</i> appears to pose little threat to non-target plants.
DOI: 10.6084/m9.figshare.1501452.v1
title: Seed germination and risks of using the invasive plant <i>Eichhornia crassipes</i> (Mart.) Solms-Laub. (water hyacinth) for composting, ovine feeding and biogas production

description: Water hyacinth (<i>Eichhornia crassipes</i> (Mart.) Solms-Laub.) is an invasive aquatic weed that has one of the highest growth indices of vascular plants, producing large amounts of biomass. Its use for composting, livestock feed and biogas production has been proposed as a management strategy for its control. The work presented here is an assessment of the potential spread of water hyacinth due to the release of seeds from the by-products of some of these manufacturing processes. We tested experimentally if the seeds were destroyed or did not lose germinability when they had passed through the gut of sheep, remained in compost piles or been used in biogas bioreactors. We made optical and electronic microscopic observations, and calculated retrieval and germination percentages of the seeds subjected to these treatments. After having passed through the gut of sheep, the anatomical organization of the seed was completely destroyed, only 30.50 ± 5.83% of the seeds were retrieved and the germinability was null (0 ± 0%). The biogas production and compost-treated seeds both had retrieval percentages of 100 ± 0% and germination values of 1.00 ± 0.57 and 3.50 ± 0.96% respectively, with several anatomical damages. The use for compost or biogas production as a management strategy to control this pest is not completely safe from an environmental perspective and the selected management option should focus on sheep fodder production.
DOI: 10.6084/m9.figshare.1501448
title: Swansea University APC Data January-June 2015

description: This dataset provides a record of publications that have been funded from the RCUK Gold Open Access block grant for Swansea University 2015. Sheet 1 Data for the period January - June 2015 Sheet 2 Contact information Released with the permission of Swansea University, Information Services & Systems (ISS). Note: v.2 edit to amend Wiley prepay data
DOI: 10.6084/m9.figshare.1512834.v210
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.1501448.v2
title: Swansea University APC Data January-June 2015

description: This dataset provides a record of publications that have been funded from the RCUK Gold Open Access block grant for Swansea University 2015. Sheet 1 Data for the period January - June 2015 Sheet 2 Contact information Released with the permission of Swansea University, Information Services & Systems (ISS). Note: v.2 edit to amend Wiley prepay data
DOI: 10.6084/m9.figshare.1512834.v211
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.1501448.v1
title: Swansea University APC Data January-June 2015

description: This dataset provides a record of publications that have been funded from the RCUK Gold Open Access block grant for Swansea University 2015. Sheet 1 Data for the period January - June 2015 Sheet 2 Contact information Released with the permission of Swansea University, Information Services & Systems (ISS).
DOI: 10.6084/m9.figshare.1501373
title: Twitter archive from Future of Libraries Summit, #Fol15 held at The Michael Fowler Centre, Wellington, New Zealand, 31 July 2015

description: This file contains a data set of 1800 tweets (1136 unique tweets) tagged with #Fol15 (case not sensitive) that were published on Twitter between 26/07/2015 23:21:06 and 04/08/2015 03:12:21 GMT. This file was created and shared by Sarah Gallagher @sarahlibrarina (University of Otago, Dunedin, New Zealand) with a Creative Commons Attribution license (CC-BY) to encourage research in scholarly communication and for educational purposes. The Tweets contained in this file were collected using Martin Hawksey’s [@mhawksey] TAGS 6.0 http://tags.hawksey.info/ An automatic deduplication has been performed and spam tweets have been manually reoved. Despite this intervention data may require further refining. The contents of each Tweet are responsibility of the original authors. This data set has been shared “as is”, for educational and research purposes. As noted by Priego (2014) “both research and experience show that the Twitter search API isn't 100% reliable. Large tweet volumes affect the search collection process. The API might "over-represent the more central users", not offering "an accurate picture of peripheral activity" (González-Bailón, Sandra, et al. 2012).” Therefore there is no guarantee that this file all Tweets tagged with (#Fol15) during the indicated period. This dataset is shared to encourage open research into scholarly activity on Twitter. If you use or refer to this data in any way please cite using the preferred citation above. Contact: @sarahlibrarina
DOI: 10.6084/m9.figshare.1512834.v212
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.1501125
title: Inhibition of polo like kinase 1 in sarcomas induces apoptosis that is dependent on Mcl-1 suppression

description: Sarcomas are rare cancers and the current treatments in inoperable or metastatic disease have not been shown to prolong survival. In order to develop novel targeted therapies, we tested the efficacy of polo-like kinase 1 (PLK-1) inhibitor (TAK-960) in sarcoma. All the sarcoma cell lines were sensitive to TAK-960 with IC50s in the low nanomolar range. We chose MPNST, CHP100 and LS141 for our studies and of which MPNST cells exclusively underwent polyploidy after a delay in mitosis for about 18 hours; CHP100 cells, after a 24h mitotic delay, died of apoptosis; LS141, after a delay in mitosis stayed at 4N with mild apoptosis. Apoptosis induced by TAK-960 in CHP100 was associated with down-regulation of Mcl-1 and the effect was recapitulated by down-regulating PLK1 by siRNA, confirming that the effect of TAK-960 on Mcl-1 expression is target specific. With suppression of Mcl-1 by siRNA, TAK-960 induced apoptosis in MPNST cells as well. These effects were confirmed <i>in vivo</i>, such that TAK-960 more effectively inhibited CHP100 than MPNST xenografts. In the setting of PLK-1 inhibition, Mcl-1 down regulation is shown to be an important determinant of apoptosis. Collectively, the net effect of this is to drive cells to apoptosis, resulting in a greater anti-tumor effect <i>in vivo</i>. Therefore, targeting PLK-1 should have a greater impact in treating sarcomas provided there is concomitant suppression of Mcl-1. These results further indicate that Mcl-1 could be an important biomarker to predict sensitivity to the induction of apoptosis by PLK-1 targeted therapy in sarcoma.
DOI: 10.6084/m9.figshare.1501373.v1
title: Twitter archive from Future of Libraries Summit, #Fol15 held at The Michael Fowler Centre, Wellington, New Zealand, 31 July 2015

description: This file contains a data set of 1800 tweets (1136 unique tweets) tagged with #Fol15 (case not sensitive) that were published on Twitter between 26/07/2015 23:21:06 and 04/08/2015 03:12:21 GMT. This file was created and shared by Sarah Gallagher @sarahlibrarina (University of Otago, Dunedin, New Zealand) with a Creative Commons Attribution license (CC-BY) to encourage research in scholarly communication and for educational purposes. The Tweets contained in this file were collected using Martin Hawksey’s [@mhawksey] TAGS 6.0 http://tags.hawksey.info/ An automatic deduplication has been performed and spam tweets have been manually reoved. Despite this intervention data may require further refining. The contents of each Tweet are responsibility of the original authors. This data set has been shared “as is”, for educational and research purposes. As noted by Priego (2014) “both research and experience show that the Twitter search API isn't 100% reliable. Large tweet volumes affect the search collection process. The API might "over-represent the more central users", not offering "an accurate picture of peripheral activity" (González-Bailón, Sandra, et al. 2012).” Therefore there is no guarantee that this file all Tweets tagged with (#Fol15) during the indicated period. This dataset is shared to encourage open research into scholarly activity on Twitter. If you use or refer to this data in any way please cite using the preferred citation above. Contact: @sarahlibrarina
DOI: 10.6084/m9.figshare.1512834.v213
title: Localized Protein Quantification of Blood Brain Barrier Vasculature in Brightfield IHC Images

description: In this paper, we present an objective method for locally quantifying proteins in blood brain barrier (BBB) vasculature using standard immunohistochemistry (IHC) techniques and bright-field microscopy. Images from the hippocampal region at the BBB are acquired using bright-field microscopy and subjected to our immunohistochemistry quantification (IQ) algorithm which is designed to automatically identify and segment microvessels containing the protein glucose transporter 1 (GLUT1). Gabor filtering and k-means clustering are employed to isolate potential vascular structures within cryopsectioned slabs of the hippocampus, which are subsequently subjected to feature extraction followed by classification via decision forest. The false positive rate (FPR) of microvessel classification is characterized using synthetic and non-synthetic IHC image data for image entropies ranging between 3 and 8 bits. The average FPR for synthetic and non-synthetic IHC image data was found to be 5.48% and 5.04%, respectively.
DOI: 10.6084/m9.figshare.1512834.v214
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.1501125.v2
title: Inhibition of polo like kinase 1 in sarcomas induces apoptosis that is dependent on Mcl-1 suppression

description: Sarcomas are rare cancers and the current treatments in inoperable or metastatic disease have not been shown to prolong survival. In order to develop novel targeted therapies, we tested the efficacy of polo-like kinase 1 (PLK-1) inhibitor (TAK-960) in sarcoma. All the sarcoma cell lines were sensitive to TAK-960 with IC50s in the low nanomolar range. We chose MPNST, CHP100 and LS141 for our studies and of which MPNST cells exclusively underwent polyploidy after a delay in mitosis for about 18 hours; CHP100 cells, after a 24h mitotic delay, died of apoptosis; LS141, after a delay in mitosis stayed at 4N with mild apoptosis. Apoptosis induced by TAK-960 in CHP100 was associated with down-regulation of Mcl-1 and the effect was recapitulated by down-regulating PLK1 by siRNA, confirming that the effect of TAK-960 on Mcl-1 expression is target specific. With suppression of Mcl-1 by siRNA, TAK-960 induced apoptosis in MPNST cells as well. These effects were confirmed <i>in vivo</i>, such that TAK-960 more effectively inhibited CHP100 than MPNST xenografts. In the setting of PLK-1 inhibition, Mcl-1 down regulation is shown to be an important determinant of apoptosis. Collectively, the net effect of this is to drive cells to apoptosis, resulting in a greater anti-tumor effect <i>in vivo</i>. Therefore, targeting PLK-1 should have a greater impact in treating sarcomas provided there is concomitant suppression of Mcl-1. These results further indicate that Mcl-1 could be an important biomarker to predict sensitivity to the induction of apoptosis by PLK-1 targeted therapy in sarcoma.