cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11889804
title: Supplementary Material for: Investigation of the Effect of Secreted Factors from Mesenchymal Stem Cells on Disc Cells from Degenerated Discs

description: Low back pain is experienced by a large number of people in western countries and may be caused and influenced by many different pathologies and psychosocial factors including disc degeneration. Disc degeneration involves the increased expression of proinflammatory cytokines and matrix metalloproteinases (MMPs) in the disc environment, which leads to the loss of extracellular matrix (ECM) and the viability of the native disc cells (DCs). Treatment approaches using growth factors and cell therapy have been proposed due to the compelling results that growth factors and mesenchymal stem cells (MSCs) can influence the degenerated discs. The aim of this study was to investigate the effects of conditioned media (CM) from human MSCs (hMSCs) and connective tissue growth factor (CTGF) and TGF-β on disc cells, and hMSCs isolated from patients with degenerative discs and severe low back pain. The aim was also to examine the constituents of CM in order to study the peptides that could bring about intervertebral disc (IVD) regeneration. DCs and hMSC pellets (approx.. 200,000 cells) were cultured and stimulated with hMSC-derived CM or CTGF and TGF-β over 28 days. The effects of CM and CTGF on DCs and hMSCs were assessed via cell viability, proteoglycan production, the expression of ECM proteins, and chondrogenesis in 3D pellet culture. To identify the constituents of CM, CM was analyzed with tandem mass spectrometry. The findings indicate that CM enhanced the cellular viability and ECM production of DCs while CTGF and the control exhibited nonsignificant differences. The same was observed in the hMSC group. Mass spectrometry analysis of CM identified &gt;700 peptides, 129 of which showed a relative abundance of ≥2 (CTGF among them). The results suggest that CM holds potential to counter the progression of disc degeneration, likely resulting from the combination of all the substances released by the hMSCs. The soluble factors released belong to different peptide families. The precise mechanism underlying the regenerative effect needs to be investigated further, prior to incorporating peptides in the development of new treatment strategies for low back pain that is potentially caused by IVD degeneration.
DOI: 10.6084/m9.figshare.11889825.v1
title: Áreas de Atuação profissional - Docentes

description: Conjunto de dados referente a atuação profissional dos docentes dos PPG brasileiros, extraídos da plataforma Lattes.
DOI: 10.6084/m9.figshare.11889771
title: Data for Schmitz et al. 2020

description: Data generated for the paper by Schmitz et al. 2020. GTF, expression data, transcript ages.<br>
DOI: 10.6084/m9.figshare.11889642
title: Supplementary Material for: microRNA-422a Inhibits DCC Expression in a Manner Dependent on SNP rs12607853

description: DCC netrin 1 receptor (DCC) affects the structure and function of the dopamine circuitry, which in turn affects the susceptibility to developing addiction. In a previous study, we found that single nucleotide polymorphism (SNP) rs12607853 in the 3′ untranslated region (3′-UTR) of <i>DCC</i> was significantly associated with heroin addiction. In the current study, we first used bioinformatics prediction to identify the <i>DCC</i> rs12607853 C allele as a potential hsa-miR-422a and hsa-miR-378c target site. We then used vector construction and dual-luciferase reporter assays to investigate the targeting relationship of <i>DCC</i> rs12607853 with hsa-miR-422a and hsa-miR-378c. The dual-luciferase reporter gene assay confirmed that the C allele of rs12607853 in combination with hsa-miR-422a led to repressed dual-luciferase gene expression. Moreover, gene expression assays disclosed that hsa-miR-422a inhibited DCC expression at both the mRNA and protein levels. We also found that morphine inhibited the expression of hsa-miR-422a but increased the expression of <i>DCC</i> mRNA, and this change in the expression of hsa-miR-422a could not be reversed by naloxone, which suggested that the role of DCC in opioid addiction might be regulated by hsa-miR-422a. In summary, this study improves our understanding of the role of hsa-miR-422a and identifies the genetic basis of rs12607853, which might contribute to the discovery of new biomarkers or therapeutic targets for opioid addiction.
DOI: 10.6084/m9.figshare.11889642.v1
title: Supplementary Material for: microRNA-422a Inhibits DCC Expression in a Manner Dependent on SNP rs12607853

description: DCC netrin 1 receptor (DCC) affects the structure and function of the dopamine circuitry, which in turn affects the susceptibility to developing addiction. In a previous study, we found that single nucleotide polymorphism (SNP) rs12607853 in the 3′ untranslated region (3′-UTR) of <i>DCC</i> was significantly associated with heroin addiction. In the current study, we first used bioinformatics prediction to identify the <i>DCC</i> rs12607853 C allele as a potential hsa-miR-422a and hsa-miR-378c target site. We then used vector construction and dual-luciferase reporter assays to investigate the targeting relationship of <i>DCC</i> rs12607853 with hsa-miR-422a and hsa-miR-378c. The dual-luciferase reporter gene assay confirmed that the C allele of rs12607853 in combination with hsa-miR-422a led to repressed dual-luciferase gene expression. Moreover, gene expression assays disclosed that hsa-miR-422a inhibited DCC expression at both the mRNA and protein levels. We also found that morphine inhibited the expression of hsa-miR-422a but increased the expression of <i>DCC</i> mRNA, and this change in the expression of hsa-miR-422a could not be reversed by naloxone, which suggested that the role of DCC in opioid addiction might be regulated by hsa-miR-422a. In summary, this study improves our understanding of the role of hsa-miR-422a and identifies the genetic basis of rs12607853, which might contribute to the discovery of new biomarkers or therapeutic targets for opioid addiction.
DOI: 10.6084/m9.figshare.11889609
title: Data Experiment 3

description: Raw data of third experiment.
DOI: 10.6084/m9.figshare.11889564
title: Data Experiment 1

description: Raw data of the first experiment. Including all relevant participants, i.e. not the data of the two excluded participants.
DOI: 10.6084/m9.figshare.11889606
title: Data Experiment 2

description: Raw data files of the second experiment.
DOI: 10.6084/m9.figshare.11889609.v2
title: Data Experiment 3

description: Raw data of third experiment.
DOI: 10.6084/m9.figshare.11889564.v1
title: Data Experiment 1

description: Raw data of the first experiment. Including all relevant participants, i.e. not the data of the two excluded participants.
DOI: 10.6084/m9.figshare.11889606.v2
title: Data Experiment 2

description: Raw data files of the second experiment.
DOI: 10.6084/m9.figshare.11889609.v1
title: Data Experiment 3

description: Raw data of third experiment.
DOI: 10.6084/m9.figshare.11889564.v3
title: Data Experiment 1

description: Raw data of the first experiment. Including all relevant participants, i.e. not the data of the two excluded participants.
DOI: 10.6084/m9.figshare.11889606.v1
title: Data Experiment 2

description: Raw data files of the second experiment.
DOI: 10.6084/m9.figshare.11889564.v2
title: Data Experiment 1

description: Raw data of the first experiment. Including all relevant participants, i.e. not the data of the two excluded participants.
DOI: 10.6084/m9.figshare.11889483
title: Supplementary Material for: Immunmodulation bei chronisch-obstruktiver Lungenerkrankung: Aktuelle Konzepte und zukünftige Strategien

description: Die chronisch-obstruktive Lungenerkrankung (chronic obstructive pulmonary disease, COPD) wird durch das langjährige aktive oder passive Einatmen schädlicher Partikel und Gase (vor allem, aber nicht nur, Zigarettenrauch) verursacht, wodurch es zu einer anhaltenden angeborenen und adaptiven Immunantwort in der Lunge kommt. Diese Immunantwort ist mit einer Störung der Gewebereparatur- und Remodelingprozesse verbunden und führt zu einer chronischen Entzündung mit übermäßiger Schleimproduktion in den zentralen Atemwegen und zu einer dauerhaften Zerstörung der kleinen Atemwege sowie der Gasaustausch-Oberfläche in der peripheren Lunge. Derzeit bestehen die Hauptziele der Behandlung bei COPD in einer Bronchodilatation zur Symptomkontrolle (durch inhalative kurz und lang wirksame β-Agonisten- und antimuskarinische Wirkstoffe) sowie in der Gabe unspezifischer breit wirksamer Entzündungshemmer (wie inhalative und orale Kortikosteroide, Phosphordiesterase-Hemmer und Makrolide). Diese bewirken eine symptomatische Linderung, haben jedoch, wenn überhaupt, nur einen sehr geringen Einfluss auf das Fortschreiten der Erkrankung oder die Mortalität. Mit zunehmendem Verständnis der Immunpathogenese der COPD wurden Immunmodulationstherapien verfügbar, die in der Lage sind, schädliche Immunmechanismen zu verändern oder zu stören, wodurch das unaufhaltsame Fortschreiten der Lungengewebezerstörung verlangsamt wird. In der vorliegenden kurzen Übersichtsarbeit sollen das aktuelle Wissen über die Immunpathogenese sowohl der Atemwegs- als auch der Parenchymschädigung sowie die gestörten Gewebereparaturprozesse erörtert werden, und es werden immunmodulierende Interventionen vorgeschlagen, die versuchen, die pathologischen Veränderungen zu stabilisieren oder in ihren Normalzustand zurückzuversetzen. Ziel der Immunmodulationstherapie ist es letztendlich, die mit der COPD verbundene Morbidität und Mortalität zu senken.
DOI: 10.6084/m9.figshare.11889486
title: A new Miocene turtle from Colombia sheds light on the evolutionary history of the extant genus <i>Mesoclemmys</i> Gray, 1873

description: <i>Mesoclemmys</i> is the most diverse extant genus of South American pleurodires or side-necked turtles, with at least 10 species inhabiting fluvial to littoral environments. Despite this high extant diversity and extensive geographic distribution, the evolutionary history and fossil record of this genus are completely unknown. Here, we describe the first fossil record of this genus, which supports a previous molecular-based hypothesis that indicates a minimum split time of 13.5 Ma between this and other genera of South American chelids. <i>Mesoclemmys vanegasorum</i>, sp. nov., is represented by a nearly complete shell (carapace and plastron) and some postcranial bones found in the middle Miocene (13.6 ± 0.2 Ma), La Victoria Formation, Tatacoa Desert, Colombia, increasing the turtle paleodiversity of La Venta Fauna. It differs from all extant species of <i>Mesoclemmys</i> by vertebral scute 1 reaching the sutural boundary between peripherals 1 and 2; shorter cervical and marginal scutes 1 to 3; pleurals 1 very advanced over the peripherals; pygal bone with a posteromedial shallow notch; vertebral 5 covering half of the pygal bone; small extragulars reaching only half of the epiplastra length; and a fine microvermiculation of the shell. Our phylogenetic results show a close relationship between <i>M. vanegasorum</i>, sp. nov., and the extant <i>M. hogei</i>. The overall morphology and size of <i>Mesoclemmys</i> genus have remained relatively constant for at least the last 13.6 million years. However, its geographic distribution has decreased drastically in northwestern South America, being restricted today to the lower region of the Magdalena River Basin.
DOI: 10.6084/m9.figshare.11889486.v1
title: A new Miocene turtle from Colombia sheds light on the evolutionary history of the extant genus <i>Mesoclemmys</i> Gray, 1873

description: <i>Mesoclemmys</i> is the most diverse extant genus of South American pleurodires or side-necked turtles, with at least 10 species inhabiting fluvial to littoral environments. Despite this high extant diversity and extensive geographic distribution, the evolutionary history and fossil record of this genus are completely unknown. Here, we describe the first fossil record of this genus, which supports a previous molecular-based hypothesis that indicates a minimum split time of 13.5 Ma between this and other genera of South American chelids. <i>Mesoclemmys vanegasorum</i>, sp. nov., is represented by a nearly complete shell (carapace and plastron) and some postcranial bones found in the middle Miocene (13.6 ± 0.2 Ma), La Victoria Formation, Tatacoa Desert, Colombia, increasing the turtle paleodiversity of La Venta Fauna. It differs from all extant species of <i>Mesoclemmys</i> by vertebral scute 1 reaching the sutural boundary between peripherals 1 and 2; shorter cervical and marginal scutes 1 to 3; pleurals 1 very advanced over the peripherals; pygal bone with a posteromedial shallow notch; vertebral 5 covering half of the pygal bone; small extragulars reaching only half of the epiplastra length; and a fine microvermiculation of the shell. Our phylogenetic results show a close relationship between <i>M. vanegasorum</i>, sp. nov., and the extant <i>M. hogei</i>. The overall morphology and size of <i>Mesoclemmys</i> genus have remained relatively constant for at least the last 13.6 million years. However, its geographic distribution has decreased drastically in northwestern South America, being restricted today to the lower region of the Magdalena River Basin.
DOI: 10.6084/m9.figshare.11889474
title: RNA-seq gene expression data of S. venezuelae ATCC 15439

description: RNA-seq gene expression data of S. venezuelae ATCC 15439
DOI: 10.6084/m9.figshare.11889468
title: Ribosome profiling gene expression data of S. venezuelae ATCC 15439

description: Ribosome profiling gene expression data of S. venezuelae ATCC 15439
DOI: 10.6084/m9.figshare.11889471
title: RNA-seq gene expression data of S. tsukubaensis NRRL 18488

description: RNA-seq gene expression data of S. tsukubaensis NRRL 18488
DOI: 10.6084/m9.figshare.11889468.v1
title: Ribosome profiling gene expression data of S. venezuelae ATCC 15439

description: Ribosome profiling gene expression data of S. venezuelae ATCC 15439
DOI: 10.6084/m9.figshare.11889474.v1
title: RNA-seq gene expression data of S. venezuelae ATCC 15439

description: RNA-seq gene expression data of S. venezuelae ATCC 15439
DOI: 10.6084/m9.figshare.11889465
title: Ribosome profiling gene expression data of S. tsukubaensis NRRL 18488

description: Ribosome profiling gene expression data of S. tsukubaensis NRRL 18488
DOI: 10.6084/m9.figshare.11889471.v1
title: RNA-seq gene expression data of S. tsukubaensis NRRL 18488

description: RNA-seq gene expression data of S. tsukubaensis NRRL 18488
DOI: 10.6084/m9.figshare.11889462
title: RNA-seq gene expression data of S. clavuligerus ATCC 27064

description: RNA-seq gene expression data of S. clavuligerus ATCC 27064
DOI: 10.6084/m9.figshare.11889465.v1
title: Ribosome profiling gene expression data of S. tsukubaensis NRRL 18488

description: Ribosome profiling gene expression data of S. tsukubaensis NRRL 18488
DOI: 10.6084/m9.figshare.11889456
title: Ribosome profiling gene expression data of S. avermitilis MA-4680

description: Ribosome profiling gene expression data of S. avermitilis MA-4680
DOI: 10.6084/m9.figshare.11889459
title: Ribosome profiling gene expression data of S. clavuligerus ATCC 27064

description: Ribosome profiling gene expression data of S. clavuligerus ATCC 27064
DOI: 10.6084/m9.figshare.11889462.v1
title: RNA-seq gene expression data of S. clavuligerus ATCC 27064

description: RNA-seq gene expression data of S. clavuligerus ATCC 27064
DOI: 10.6084/m9.figshare.11889453
title: Ribosome profiling gene expression data of S. lividans TK24

description: Ribosome profiling gene expression data of S. lividans TK24
DOI: 10.6084/m9.figshare.11889456.v1
title: Ribosome profiling gene expression data of S. avermitilis MA-4680

description: Ribosome profiling gene expression data of S. avermitilis MA-4680
DOI: 10.6084/m9.figshare.11889450
title: RNA-Seq gene expression data of S. avermitilis MA-4680

description: RNA-Seq gene expression data of S. avermitilis MA-4680
DOI: 10.6084/m9.figshare.11889453.v1
title: Ribosome profiling gene expression data of S. lividans TK24

description: Ribosome profiling gene expression data of S. lividans TK24
DOI: 10.6084/m9.figshare.11889447
title: RNA-Seq gene expression data of S. lividans TK24

description: RNA-Seq gene expression data of S. lividans TK24
DOI: 10.6084/m9.figshare.11889450.v1
title: RNA-Seq gene expression data of S. avermitilis MA-4680

description: RNA-Seq gene expression data of S. avermitilis MA-4680
DOI: 10.6084/m9.figshare.11889459.v1
title: Ribosome profiling gene expression data of S. clavuligerus ATCC 27064

description: Ribosome profiling gene expression data of S. clavuligerus ATCC 27064
DOI: 10.6084/m9.figshare.11889447.v1
title: RNA-Seq gene expression data of S. lividans TK24

description: RNA-Seq gene expression data of S. lividans TK24
DOI: 10.6084/m9.figshare.11889405
title: Data from "Demographic biases in engagement with nature in a tropical Asian city"

description: Data for the manuscript (under review) " Demographic biases in engagement with nature in a tropical Asian city".
DOI: 10.6084/m9.figshare.11889405.v1
title: Data from "Demographic biases in engagement with nature in a tropical Asian city"

description: Data for the manuscript (under review) " Demographic biases in engagement with nature in a tropical Asian city".
DOI: 10.6084/m9.figshare.11889366
title: ESM 3 Nestling from Autumn freeze–thaw events carry over to depress late-winter reproductive performance in Canada jays

description: Evidence suggests that range-edge populations are highly vulnerable to the impacts of climate change, but few studies have examined the specific mechanisms that are driving observed declines. Species that store perishable food for extended periods of time may be particularly susceptible to environmental change because shifts in climatic conditions could accelerate the natural degradation of their cached food. Here, we use 40 years of breeding data from a marked population of Canada jays (<i>Perisoreus canadensis</i>) located at the southern edge of their range in Algonquin Provincial Park, Ontario, to examine whether climatic conditions prior to breeding carry over to influence reproductive performance. We found that multiple measures of Canada jay reproductive performance (brood size, nest success and nestling condition) in the late winter were negatively correlated with the number of freeze–thaw events the previous autumn. Our results suggest that freeze–thaw events have a significant detrimental impact on the quality and/or quantity of cached food available to Canada jays. Future increases in such events, caused by climate change, could pose a serious threat to Canada jays and other food caching species that store perishable foods for long periods of time.
DOI: 10.6084/m9.figshare.11889363
title: ESM 2 from Autumn freeze–thaw events carry over to depress late-winter reproductive performance in Canada jays

description: Evidence suggests that range-edge populations are highly vulnerable to the impacts of climate change, but few studies have examined the specific mechanisms that are driving observed declines. Species that store perishable food for extended periods of time may be particularly susceptible to environmental change because shifts in climatic conditions could accelerate the natural degradation of their cached food. Here, we use 40 years of breeding data from a marked population of Canada jays (<i>Perisoreus canadensis</i>) located at the southern edge of their range in Algonquin Provincial Park, Ontario, to examine whether climatic conditions prior to breeding carry over to influence reproductive performance. We found that multiple measures of Canada jay reproductive performance (brood size, nest success and nestling condition) in the late winter were negatively correlated with the number of freeze–thaw events the previous autumn. Our results suggest that freeze–thaw events have a significant detrimental impact on the quality and/or quantity of cached food available to Canada jays. Future increases in such events, caused by climate change, could pose a serious threat to Canada jays and other food caching species that store perishable foods for long periods of time.
DOI: 10.6084/m9.figshare.11889366.v1
title: ESM 3 Nestling from Autumn freeze–thaw events carry over to depress late-winter reproductive performance in Canada jays

description: Evidence suggests that range-edge populations are highly vulnerable to the impacts of climate change, but few studies have examined the specific mechanisms that are driving observed declines. Species that store perishable food for extended periods of time may be particularly susceptible to environmental change because shifts in climatic conditions could accelerate the natural degradation of their cached food. Here, we use 40 years of breeding data from a marked population of Canada jays (<i>Perisoreus canadensis</i>) located at the southern edge of their range in Algonquin Provincial Park, Ontario, to examine whether climatic conditions prior to breeding carry over to influence reproductive performance. We found that multiple measures of Canada jay reproductive performance (brood size, nest success and nestling condition) in the late winter were negatively correlated with the number of freeze–thaw events the previous autumn. Our results suggest that freeze–thaw events have a significant detrimental impact on the quality and/or quantity of cached food available to Canada jays. Future increases in such events, caused by climate change, could pose a serious threat to Canada jays and other food caching species that store perishable foods for long periods of time.
DOI: 10.6084/m9.figshare.11889363.v1
title: ESM 2 from Autumn freeze–thaw events carry over to depress late-winter reproductive performance in Canada jays

description: Evidence suggests that range-edge populations are highly vulnerable to the impacts of climate change, but few studies have examined the specific mechanisms that are driving observed declines. Species that store perishable food for extended periods of time may be particularly susceptible to environmental change because shifts in climatic conditions could accelerate the natural degradation of their cached food. Here, we use 40 years of breeding data from a marked population of Canada jays (<i>Perisoreus canadensis</i>) located at the southern edge of their range in Algonquin Provincial Park, Ontario, to examine whether climatic conditions prior to breeding carry over to influence reproductive performance. We found that multiple measures of Canada jay reproductive performance (brood size, nest success and nestling condition) in the late winter were negatively correlated with the number of freeze–thaw events the previous autumn. Our results suggest that freeze–thaw events have a significant detrimental impact on the quality and/or quantity of cached food available to Canada jays. Future increases in such events, caused by climate change, could pose a serious threat to Canada jays and other food caching species that store perishable foods for long periods of time.
DOI: 10.6084/m9.figshare.11889165
title: Datasets for the impacts of global gasoline and diesel emissions on air quality, climate and human health

description: We quantify the impacts of global gasoline and diesel emissions on air quality, climate change and human health, by employing the NCAR CESM CAM5-Chem model at the horizontal resolution of 0.9 degrees latitude by 1.25 degrees longitude as well as integrated exposure response functions in combinations with the most recent 2017 Global Burden of Disease. We run three sets of CAM5-Chem model simulations: (1) the control model simulation with anthropogenic emissions from IIASA GAINS ECLIPSE V5a for the year 2015 (hereafter referred to as CRL2015); (2) one sensitivity simulation identical to CRL2015 but with global gasoline emissions off (referred to as GSL2015); (3) one sensitivity simulation identical to CRL2015 but with global diesel emissions off (referred to as DS2015). The differences between CRL2015 and GSL2015, and between CRL2015 and DS2015, will be the net impacts of global gasoline and diesel sectors, respectively.<br>