cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4008614
title: Leaf Vein Network CNN Images

description: This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu <em>et al.</em>, (2020) and Blonder <em>et al.,</em> (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. <strong>References</strong> <strong>Software GUI:</strong> Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. <strong>New Phytol</strong>. (In press). <strong>Analysis of trait data:</strong> Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. <strong>New Phytol</strong>. (In press). <strong>Original image data set and ground truths</strong> Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand‐traced segmentations. <strong>Ecology </strong>100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3
description: Additional funding from: Human Frontier Science Program (RGP0053/2012), Leverhulme Trust (RPG-2015-437), NSF: DEB-2025282 and RoL:FELS:RAISE DEB-1840209
description: {"references": ["Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press).", "Blonder, B., S. Both, M. Jodra, N. Majalap, D. Burslem, Y. A. Teh and Y. Malhi (2019). \"Leaf venation networks of Bornean trees: images and hand-traced segmentations.\" Ecology 100: e02844.", "Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. . New Phytol. (In press)."]}
DOI: 10.5281/zenodo.4008613
title: Leaf Vein Network CNN Images

description: This download site contains the CNN vein network predictions and set of Matlab programs that were used for the analyses in Xu <em>et al.</em>, (2020) and Blonder <em>et al.,</em> (2020). These require Matlab 2020a or later. They may work on earlier versions of MatLab, but this has not been tested and cannot be guaranteed. The files are as follows: Zip files (e.g. BEL_downsampled_images.zip) containing a complete set of images of leaf vein predictions from a fully trained convolutional neural network (CNN), along with the ground truth data. Each folder in the unzipped file contains a sample represented by a CODE with format X-TY-BZ. X represents the name of a plot in the Global Ecosystems Monitoring network database (e.g. 'BEL'). Tree (T) Y indicates the number of a tree within a plot (e.g. '101') and Z represents the light stratum of the canopy where the leaf was collected (either 'S' for 'sunlit' or 'SH' for 'shaded'). A set of Matlab programs (Matlab files.zip) to compare the CNN predictions against other vein extraction approaches. A Matlab Readme file with instructions on how to run the analyses. <strong>References</strong> <strong>Software GUI:</strong> Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. <strong>New Phytol</strong>. (In press). <strong>Analysis of trait data:</strong> Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. <strong>New Phytol</strong>. (In press). <strong>Original image data set and ground truths</strong> Blonder, B., Both, S., Jodra, M., Majalap, N., Burslem, D., Teh, Y. A., and Malhi, Y. (2019) Leaf venation networks of Bornean trees: images and hand‐traced segmentations. <strong>Ecology </strong>100: e02844.10.1002/ecy.2844. Available from: https://ora.ox.ac.uk/objects/uuid:de65fc07-4b8f-4277-a6c4-82836afbdeb3
description: Additional funding from: Human Frontier Science Program (RGP0053/2012), Leverhulme Trust (RPG-2015-437), NSF: DEB-2025282 and RoL:FELS:RAISE DEB-1840209
description: {"references": ["Blonder, B., S. Both, M. Jodra, H. Xu, M. Fricker, I. S. Matos, N. Majalap, D. F. R. P. Burslem, Y. Teh and Y. Malhi (2020) Linking functional traits to multiscale statistics of leaf venation networks. New Phytol. (In press).", "Blonder, B., S. Both, M. Jodra, N. Majalap, D. Burslem, Y. A. Teh and Y. Malhi (2019). \"Leaf venation networks of Bornean trees: images and hand-traced segmentations.\" Ecology 100: e02844.", "Xu, H., Blonder, B., Jodra, M., Malhi, Y. and Fricker, M.D. (2020) Automated and accurate segmentation of leaf venation networks via deep learning. . New Phytol. (In press)."]}
DOI: 10.6084/m9.figshare.4299662.v1
title: motivation worksheet data(Fig.1).xls

description: Data of Figure 1.
DOI: 10.6084/m9.figshare.4299629
title: Metadata - 97% OTU abundance table and OTU taxonomy - EMP Sweden

description: The metadata that belongs to the 97% OTU abundance table and OTU taxonomy - EMP Sweden - Greengenes taxonomy, OTUs clustered with average neighbour clustering at 97 % with mothur.
DOI: 10.6084/m9.figshare.4299587
title: Supplementary Material for: Positive Traits in the Bipolar Spectrum: The Space between Madness and Genius

description: Bipolar disorder is a severe, lifelong mood disorder for which little is currently understood of the genetic mechanisms underlying risk. By examining related dimensional phenotypes, we may further our understanding of the disorder. Creativity has a historical connection with the bipolar spectrum and is particularly enhanced among unaffected first-degree relatives and those with bipolar spectrum traits. This suggests that some aspects of the bipolar spectrum may confer advantages, while more severe expressions of symptoms negatively influence creative accomplishment. Creativity is a complex, multidimensional construct with both cognitive and affective components, many of which appear to reflect a shared genetic vulnerability with bipolar disorder. It is suggested that a subset of bipolar risk variants confer advantages as positive traits according to an inverted-U-shaped curve with clinically unaffected allele carriers benefitting from the positive traits and serving to maintain the risk alleles in the population. The association of risk genes with creativity in healthy individuals (e.g., NRG1), as well as an overall sharing of common genetic variation between bipolar patients and creative individuals, provides support for this model. Current findings are summarized from a multidisciplinary perspective to demonstrate the feasibility of research in this area to reveal the mechanisms underlying illness.
DOI: 10.6084/m9.figshare.4299587.v1
title: Supplementary Material for: Positive Traits in the Bipolar Spectrum: The Space between Madness and Genius

description: Bipolar disorder is a severe, lifelong mood disorder for which little is currently understood of the genetic mechanisms underlying risk. By examining related dimensional phenotypes, we may further our understanding of the disorder. Creativity has a historical connection with the bipolar spectrum and is particularly enhanced among unaffected first-degree relatives and those with bipolar spectrum traits. This suggests that some aspects of the bipolar spectrum may confer advantages, while more severe expressions of symptoms negatively influence creative accomplishment. Creativity is a complex, multidimensional construct with both cognitive and affective components, many of which appear to reflect a shared genetic vulnerability with bipolar disorder. It is suggested that a subset of bipolar risk variants confer advantages as positive traits according to an inverted-U-shaped curve with clinically unaffected allele carriers benefitting from the positive traits and serving to maintain the risk alleles in the population. The association of risk genes with creativity in healthy individuals (e.g., NRG1), as well as an overall sharing of common genetic variation between bipolar patients and creative individuals, provides support for this model. Current findings are summarized from a multidisciplinary perspective to demonstrate the feasibility of research in this area to reveal the mechanisms underlying illness.
DOI: 10.6084/m9.figshare.4299524
title: Supplementary Material for: Diabetic Phenotype in the Small Intestine of Zucker Diabetic Fatty Rats

description: <b><i>Background/Aims:</i></b> In contrast to streptozotocin (STZ)-induced rodent models of diabetes, there are no thorough characterizations of the intestinal phenotype and the underlying changes in the global gene-expression of genetic models of diabetes, such as the Zucker diabetic fatty (ZDF) rat. The aim of the present study was to characterize the intestine in the ZDF rat. <b><i>Methods:</i></b> The intestine of ZDF rats and lean controls was examined macroscopically and histologically, and ribonucleic acid sequencing (RNAseq) was performed in samples of jejunal mucosa. <b><i>Results:</i></b> We observed an increased mass and length of the small and large intestines in ZDF rats. RNAseq showed an increased expression of <i>Pdk2</i> and <i>Pdk4</i>, which are involved in the regulation of glucose and fatty acid metabolism, and increased expression of genes involved in gluconeogenesis and peroxisomal beta-oxidation in jejunal mucosa. <b><i>Conclusion:</i></b> Intestinal enlargement in ZDF rats is likely driven by increased food intake, since (i) it also occurs in obese and normoglycemic Zucker fatty rats, and (ii) insulin treatment of STZ-induced diabetic rats reduced the food intake and mass of the small intestine. Results from RNAseq indicate that small intestinal epithelial cells in ZDF rats have developed insulin resistance, and support that a normal physiological effect of insulin in the enterocytes is the regulation of glucose metabolism.
DOI: 10.6084/m9.figshare.4299521
title: Shapelet Ensembles source code and results

description: This file contains the Java source code for the Shapelet Ensembles.The file also contains the CSV data from the experiments.A Python script is provided to create figures from the raw experimental results.
DOI: 10.6084/m9.figshare.4299524.v1
title: Supplementary Material for: Diabetic Phenotype in the Small Intestine of Zucker Diabetic Fatty Rats

description: <b><i>Background/Aims:</i></b> In contrast to streptozotocin (STZ)-induced rodent models of diabetes, there are no thorough characterizations of the intestinal phenotype and the underlying changes in the global gene-expression of genetic models of diabetes, such as the Zucker diabetic fatty (ZDF) rat. The aim of the present study was to characterize the intestine in the ZDF rat. <b><i>Methods:</i></b> The intestine of ZDF rats and lean controls was examined macroscopically and histologically, and ribonucleic acid sequencing (RNAseq) was performed in samples of jejunal mucosa. <b><i>Results:</i></b> We observed an increased mass and length of the small and large intestines in ZDF rats. RNAseq showed an increased expression of <i>Pdk2</i> and <i>Pdk4</i>, which are involved in the regulation of glucose and fatty acid metabolism, and increased expression of genes involved in gluconeogenesis and peroxisomal beta-oxidation in jejunal mucosa. <b><i>Conclusion:</i></b> Intestinal enlargement in ZDF rats is likely driven by increased food intake, since (i) it also occurs in obese and normoglycemic Zucker fatty rats, and (ii) insulin treatment of STZ-induced diabetic rats reduced the food intake and mass of the small intestine. Results from RNAseq indicate that small intestinal epithelial cells in ZDF rats have developed insulin resistance, and support that a normal physiological effect of insulin in the enterocytes is the regulation of glucose metabolism.
DOI: 10.6084/m9.figshare.4299521.v2
title: Shapelet Ensembles source code and results

description: This file contains the Java source code for the Shapelet Ensembles.The file also contains the CSV data from the experiments.A Python script is provided to create figures from the raw experimental results.
DOI: 10.6084/m9.figshare.4299479
title: Shapelet Ensambles Figures

description: Contains the figures for HPC and Standalone system runs using Fixed and Tuned parameters
DOI: 10.6084/m9.figshare.4299479.v3
title: Shapelet Ensambles Figures

description: Contains the figures for HPC and Standalone system runs using Fixed and Tuned parameters
DOI: 10.6084/m9.figshare.4299446.v1
title: OAへの転換シナリオ概略表（日本語）－ハーバード大学の報告書『Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences』(2016)より

description: ハーバード大学図書館学術コミュニケーション室が公開した報告書『学術雑誌をオープンアクセスに： アプローチと事例のレビュー (Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences)』(2016)の以下の部分について、簡略に日本語で表にまとめたもの。<br><br>・OAへの転換を促進する要素を紹介している、6.1および6.2の各節の特徴およびSWOT分析を記載したテキストボックス部分<br>・OAへの転換のシナリオを紹介している、7および8の各節の特徴およびSWOT分析を記載したテキストボックス部分<br><br><br>詳細な記述や具体的な事例については報告書本文をご覧ください。<br><br>------------------------<br>報告書本文のURL：<br>http://nrs.harvard.edu/urn-3:HUL.InstRepos:27803834<br><br><br><br><br>
DOI: 10.6084/m9.figshare.4299386
title: DrDRFukaSandbox

description: A Sandbox for Playing
DOI: 10.6084/m9.figshare.4299386.v1
title: DrDRFukaSandbox

description: A Sandbox for Playing
DOI: 10.6084/m9.figshare.4299386.v2
title: DrDRFukaSandbox

description: A Sandbox for Playing
DOI: 10.6084/m9.figshare.4299386.v4
title: DrDRFukaSandbox

description: A Sandbox for Playing
DOI: 10.6084/m9.figshare.4299386.v3
title: DrDRFukaSandbox

description: A Sandbox for Playing
DOI: 10.6084/m9.figshare.4299329
title: Pesquisa LED (2).xlsx

description: <b>Effects of Light-Emitting Diode Therapy on Time to Exhaustion at Maximal Aerobic Speed</b>
DOI: 10.6084/m9.figshare.4299329.v1
title: Pesquisa LED (2).xlsx

description: <b>Effects of Light-Emitting Diode Therapy on Time to Exhaustion at Maximal Aerobic Speed</b>
DOI: 10.6084/m9.figshare.4299326
title: Vortex Cannons

description: A few methods to create your own vortex cannon
DOI: 10.6084/m9.figshare.4299326.v2
title: Vortex Cannons

description: A few methods to create your own vortex cannon
DOI: 10.6084/m9.figshare.4299326.v1
title: Vortex Cannons

description: A few methods to create your own vortex cannon
DOI: 10.6084/m9.figshare.4299266
title: Data repository - Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses

description: Data repository and analysis scripts for pre-print version of paper "Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses."<br>
DOI: 10.6084/m9.figshare.4299230
title: Growth Rate Data

description: The multivariable response of Trichodesmium IMS101 growth rates to varying CO2, light and temperature
DOI: 10.6084/m9.figshare.4299266.v1
title: Data repository - Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses

description: Data repository and analysis scripts for pre-print version of paper "Effects of Historical Coinfection on Host Shift Abilities of Exploitative and Competitive Viruses."<br>
DOI: 10.6084/m9.figshare.4299215
title: Autophagic homeostasis is required for the pluripotency of cancer stem cells

description: Pluripotency is an important feature of cancer stem cells (CSCs) that contributes to self-renewal and chemoresistance. The maintenance of pluripotency of CSCs under various pathophysiological conditions requires a complex interaction between various cellular pathways including those involved in homeostasis and energy metabolism. However, the exact mechanisms that maintain the CSC pluripotency remain poorly understood. In this report, using both human and murine models of CSCs, we demonstrate that basal levels of autophagy are required to maintain the pluripotency of CSCs, and that this process is differentially regulated by the rate-limiting enzyme in the NAD<sup>+</sup> synthesis pathway NAMPT (nicotinamide phosphoribosyltransferase) and the transcription factor POU5F1/OCT4 (POU class 5 homeobox 1). First, our data show that the pharmacological inhibition and knockdown (K<sub>D</sub>) of NAMPT or the K<sub>D</sub> of POU5F1 in human CSCs significantly decreased the expression of pluripotency markers POU5F1, NANOG (Nanog homeobox) and SOX2 (SRY-box 2), and upregulated the differentiation markers TUBB3 (tubulin β 3 class III), CSN2 (casein β), SPP1 (secreted phosphoprotein 1), GATA6 (GATA binding protein 6), T (T brachyury transcription factor) and CDX2 (caudal type homeobox 2). Interestingly, these pluripotency-regulating effects of NAMPT and POU5F1 were accompanied by contrasting levels of autophagy, wherein NAMPT K<sub>D</sub> promoted while POU5F1 K<sub>D</sub> inhibited the autophagy machinery. Most importantly, any deviation from the basal level of autophagy, either increase (via rapamycin, serum starvation or Tat-beclin 1 [Tat-BECN1] peptide) or decrease (via ATG7 or ATG12 K<sub>D</sub>), strongly decreased the pluripotency and promoted the differentiation and/or senescence of CSCs. Collectively, these results uncover the link between the NAD<sup>+</sup> biosynthesis pathway, CSC transcription factor POU5F1 and pluripotency, and further identify autophagy as a novel regulator of pluripotency of CSCs.
DOI: 10.6084/m9.figshare.4299215.v1
title: Autophagic homeostasis is required for the pluripotency of cancer stem cells

description: Pluripotency is an important feature of cancer stem cells (CSCs) that contributes to self-renewal and chemoresistance. The maintenance of pluripotency of CSCs under various pathophysiological conditions requires a complex interaction between various cellular pathways including those involved in homeostasis and energy metabolism. However, the exact mechanisms that maintain the CSC pluripotency remain poorly understood. In this report, using both human and murine models of CSCs, we demonstrate that basal levels of autophagy are required to maintain the pluripotency of CSCs, and that this process is differentially regulated by the rate-limiting enzyme in the NAD<sup>+</sup> synthesis pathway NAMPT (nicotinamide phosphoribosyltransferase) and the transcription factor POU5F1/OCT4 (POU class 5 homeobox 1). First, our data show that the pharmacological inhibition and knockdown (K<sub>D</sub>) of NAMPT or the K<sub>D</sub> of POU5F1 in human CSCs significantly decreased the expression of pluripotency markers POU5F1, NANOG (Nanog homeobox) and SOX2 (SRY-box 2), and upregulated the differentiation markers TUBB3 (tubulin β 3 class III), CSN2 (casein β), SPP1 (secreted phosphoprotein 1), GATA6 (GATA binding protein 6), T (T brachyury transcription factor) and CDX2 (caudal type homeobox 2). Interestingly, these pluripotency-regulating effects of NAMPT and POU5F1 were accompanied by contrasting levels of autophagy, wherein NAMPT K<sub>D</sub> promoted while POU5F1 K<sub>D</sub> inhibited the autophagy machinery. Most importantly, any deviation from the basal level of autophagy, either increase (via rapamycin, serum starvation or Tat-beclin 1 [Tat-BECN1] peptide) or decrease (via ATG7 or ATG12 K<sub>D</sub>), strongly decreased the pluripotency and promoted the differentiation and/or senescence of CSCs. Collectively, these results uncover the link between the NAD<sup>+</sup> biosynthesis pathway, CSC transcription factor POU5F1 and pluripotency, and further identify autophagy as a novel regulator of pluripotency of CSCs.
DOI: 10.6084/m9.figshare.4299230.v1
title: Growth Rate Data

description: The multivariable response of Trichodesmium IMS101 growth rates to varying CO2, light and temperature
DOI: 10.6084/m9.figshare.4299230.v3
title: Growth Rate Data

description: The multivariable response of Trichodesmium IMS101 growth rates to varying CO2, light and temperature
DOI: 10.6084/m9.figshare.4299230.v2
title: Growth Rate Data

description: The multivariable response of Trichodesmium IMS101 growth rates to varying CO2, light and temperature
DOI: 10.6084/m9.figshare.4299206
title: FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules

description: Ribonucleoprotein (RNP) granules play a major role in compartmentalizing cytoplasmic RNA regulation. Haploid round spermatids that have exceptionally diverse transcriptomes are characterized by a unique germ cell-specific RNP granule, the chromatoid body (CB). The CB shares many characteristics with somatic RNP granules but also has germline-specific features. The CB appears to be a central structure in PIWI-interacting RNA (piRNA)-targeted RNA regulation. Here, we identified a novel CB component, FYCO1, which is involved in the intracellular transport of autophagic vesicles in somatic cells. We demonstrated that the CB is associated with autophagic activity. Induction of autophagy leads to the recruitment of lysosomal vesicles onto the CB in a FYCO1-dependent manner as demonstrated by the analysis of a germ cell-specific <i>Fyco1</i> conditional knockout mouse model. Furthermore, in the absence of FYCO1, the integrity of the CB was affected and the CB was fragmented. Our results suggest that RNP granule homeostasis is regulated by FYCO1-mediated autophagy.
DOI: 10.6084/m9.figshare.4299206.v1
title: FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules

description: Ribonucleoprotein (RNP) granules play a major role in compartmentalizing cytoplasmic RNA regulation. Haploid round spermatids that have exceptionally diverse transcriptomes are characterized by a unique germ cell-specific RNP granule, the chromatoid body (CB). The CB shares many characteristics with somatic RNP granules but also has germline-specific features. The CB appears to be a central structure in PIWI-interacting RNA (piRNA)-targeted RNA regulation. Here, we identified a novel CB component, FYCO1, which is involved in the intracellular transport of autophagic vesicles in somatic cells. We demonstrated that the CB is associated with autophagic activity. Induction of autophagy leads to the recruitment of lysosomal vesicles onto the CB in a FYCO1-dependent manner as demonstrated by the analysis of a germ cell-specific <i>Fyco1</i> conditional knockout mouse model. Furthermore, in the absence of FYCO1, the integrity of the CB was affected and the CB was fragmented. Our results suggest that RNP granule homeostasis is regulated by FYCO1-mediated autophagy.