cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3443402.v1
title: Comparative anatomy, phylogeny, and systematics of the Miocene giraffid <i>Decennatherium pachecoi</i> Crusafont, 1952 (Mammalia, Ruminantia, Pecora): state of the art

description: <i>Decennatherium pachecoi</i> Crusafont, 1952, is one of two giraffid species described from the Miocene of the Iberian Peninsula. This species is recovered exclusively from Vallesian faunas (MN9–10, late Miocene, 10–11 Ma). Despite being relatively well represented in the fossil record, except for the skull and ossicones, the complete vertebral column, and part of the upper dentition, its systematics and phylogenetic position among giraffids are the subject of debate. We update our knowledge of <i>D. pachecoi</i>, revising all Spanish material assigned to this species, as well as previously undescribed fossils. We reassess the systematics of <i>Decennatherium</i>, including its potential relationship with the second Iberian giraffid, the early Turolian <i>Birgerbohlinia</i> Crusafont, 1952, by means of the first cladistic analysis of the Giraffidae that includes <i>Decennatherium</i> together with the most relevant African and Eurasian taxa, both fossil and extant. Our results link <i>Decennatherium</i> with a ‘samothere’ clade, whereas <i>Birgerbohlinia</i> is nested within a ‘sivathere’ clade, thus refuting a previously assumed direct relationship between the two Spanish forms. Finally, we discuss some other possible finds of the genus <i>Decennatherium</i> in Greece, Turkey, and Iran. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Rios, M., I. M. Sánchez, and J. Morales. 2016. Comparative anatomy, phylogeny, and systematics of the Miocene giraffid <i>Decennatherium pachecoi</i> Crusafont, 1952 (Mammalia, Ruminantia, Pecora): State of the art. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1187624.
DOI: 10.6084/m9.figshare.3443381
title: p53 directly regulates the glycosidase FUCA1 to promote chemotherapy-induced cell death

description: p53 is a central factor in tumor suppression as exemplified by its frequent loss in human cancer. p53 exerts its tumor suppressive effects in multiple ways, but the ability to invoke the eradication of damaged cells by programmed cell death is considered a key factor. The ways in which p53 promotes cell death can involve direct activation or engagement of the cell death machinery, or can be via indirect mechanisms, for example though regulation of ER stress and autophagy. We present here another level of control in p53-mediated tumor suppression by showing that p53 activates the glycosidase, FUCA1, a modulator of N-linked glycosylation. We show that p53 transcriptionally activates <i>FUCA1</i> and that p53 modulates fucosidase activity via FUCA1 up-regulation. Importantly, we also report that chemotherapeutic drugs induce FUCA1 and fucosidase activity in a p53-dependent manner. In this context, while we found that over-expression of FUCA1 does not induce cell death, RNAi-mediated knockdown of endogenous FUCA1 significantly attenuates p53-dependent, chemotherapy-induced apoptotic death. In summary, these findings add an additional component to p53s tumor suppressive response and highlight another mechanism by which the tumor suppressor controls programmed cell death that could potentially be exploited for cancer therapy.
DOI: 10.6084/m9.figshare.3443381.v1
title: p53 directly regulates the glycosidase FUCA1 to promote chemotherapy-induced cell death

description: p53 is a central factor in tumor suppression as exemplified by its frequent loss in human cancer. p53 exerts its tumor suppressive effects in multiple ways, but the ability to invoke the eradication of damaged cells by programmed cell death is considered a key factor. The ways in which p53 promotes cell death can involve direct activation or engagement of the cell death machinery, or can be via indirect mechanisms, for example though regulation of ER stress and autophagy. We present here another level of control in p53-mediated tumor suppression by showing that p53 activates the glycosidase, FUCA1, a modulator of N-linked glycosylation. We show that p53 transcriptionally activates <i>FUCA1</i> and that p53 modulates fucosidase activity via FUCA1 up-regulation. Importantly, we also report that chemotherapeutic drugs induce FUCA1 and fucosidase activity in a p53-dependent manner. In this context, while we found that over-expression of FUCA1 does not induce cell death, RNAi-mediated knockdown of endogenous FUCA1 significantly attenuates p53-dependent, chemotherapy-induced apoptotic death. In summary, these findings add an additional component to p53s tumor suppressive response and highlight another mechanism by which the tumor suppressor controls programmed cell death that could potentially be exploited for cancer therapy.
DOI: 10.5258/soton/d1506
title: Dataset for: Reptile-like physiology in Early Jurassic stem mammals

description: Dataset supports: Newham, E. et al. (2020). Reptile-like physiology in Early Jurassic stem-mammals. Nature Communications. Virtual thin sections through tooth roots of Jurassic mammals, showing cementum increments.
DOI: 10.6084/m9.figshare.3443318
title: Identification of miRNomes associated with adult neurogenesis after stroke using Argonaute 2-based RNA sequencing

description: Neurogenesis is associated with functional recovery after stroke. However, the underlying molecular mechanisms have not been fully investigated. Using an Ago2-based RNA immunoprecipitation to immunoprecipated Ago2-RNA complexes followed by RNA sequencing (Ago2 RIP-seq) approach, we profiled the miRNomes in neural progenitor cells (NPCs) harvested from the subventricular zone (SVZ) of the lateral ventricles of young adult rats. We identified more than 7 and 15 million reads in normal and ischemic NPC libraries, respectively. We found that stroke substantially changed Ago2-associated miRNA profiles in NPCs compared to those in non-ischemic NPCs. We also discovered a new complex repertoire of isomiRs and multiple miRNA-miRNA* pairs and numerous novel miRNAs in the non-ischemic and ischemic NPCs. Among them, pc-3p-17172 significantly regulated NPC proliferation and neuronal differentiation. Collectively, the present study reveals profiles of Ago2-associated miRNomes in non-ischemic and ischemic NPCs, which provide a molecular basis to further investigate the role of miRNAs in mediating adult neurogenesis under physiological and ischemic conditions.
DOI: 10.6084/m9.figshare.3443318.v1
title: Identification of miRNomes associated with adult neurogenesis after stroke using Argonaute 2-based RNA sequencing

description: Neurogenesis is associated with functional recovery after stroke. However, the underlying molecular mechanisms have not been fully investigated. Using an Ago2-based RNA immunoprecipitation to immunoprecipated Ago2-RNA complexes followed by RNA sequencing (Ago2 RIP-seq) approach, we profiled the miRNomes in neural progenitor cells (NPCs) harvested from the subventricular zone (SVZ) of the lateral ventricles of young adult rats. We identified more than 7 and 15 million reads in normal and ischemic NPC libraries, respectively. We found that stroke substantially changed Ago2-associated miRNA profiles in NPCs compared to those in non-ischemic NPCs. We also discovered a new complex repertoire of isomiRs and multiple miRNA-miRNA* pairs and numerous novel miRNAs in the non-ischemic and ischemic NPCs. Among them, pc-3p-17172 significantly regulated NPC proliferation and neuronal differentiation. Collectively, the present study reveals profiles of Ago2-associated miRNomes in non-ischemic and ischemic NPCs, which provide a molecular basis to further investigate the role of miRNAs in mediating adult neurogenesis under physiological and ischemic conditions.
DOI: 10.6084/m9.figshare.3443315
title: A multicenter retrospective survey of poisoning after consumption of products containing novel psychoactive substances from 2013 to 2014 in Japan

description: <i>Background</i>: In Japan, fatalities among patients who experienced an acute reaction following self-administration of novel psychoactive substances (NPS) have been more frequently reported since June 2014. <i>Objective</i>: This survey aimed to document and analyze trends in NPS consumption in emergency patients. <i>Methods</i>: We conducted a multicenter retrospective survey of patients who were transported to emergency facilities after consuming NPS-containing products between January 2013 and December 2014. Letters requesting participation were sent to 467 emergency facilities, and questionnaires were mailed to facilities that agreed to participate. <i>Results</i>: We surveyed 589 patients from 85 (18.2%) facilities. Most patients were male (89.6%) and young (median age, 30 years), and inhaled (88%) NPS contained in herbal products (80.5%). Harmful behavior was observed at the scene of acute reaction, including violence (6.9%), traffic accidents (4.9%), and self-injury or suicidal attempts (1.1%). Other than neuropsychiatric and physical symptoms, many patients also had physical complications such as rhabdomyolysis (17.5%), liver injury (12.4%), acute kidney injury (9%), and physical injury (1.9%). Of the 256 patients (43.5%) admitted to hospitals, 35 (5.9%) were hospitalized for seven or more days. Most patients (93.2%) completely recovered, although a few (1.4%) died. However, synthetic cannabinoids and synthetic cathinones were only detected in the blood of five patients. <i>Conclusion</i>: Consumption of NPS-containing products have been associated with harmful behaviors such as violence and traffic accidents, physical complications (e.g., rhabdomyolysis, liver injury), death, or physical and neuropsychiatric symptoms. Compared to a previous survey (2006–2012), the present survey revealed more severe toxicity.
DOI: 10.6084/m9.figshare.3443315.v1
title: A multicenter retrospective survey of poisoning after consumption of products containing novel psychoactive substances from 2013 to 2014 in Japan

description: <i>Background</i>: In Japan, fatalities among patients who experienced an acute reaction following self-administration of novel psychoactive substances (NPS) have been more frequently reported since June 2014. <i>Objective</i>: This survey aimed to document and analyze trends in NPS consumption in emergency patients. <i>Methods</i>: We conducted a multicenter retrospective survey of patients who were transported to emergency facilities after consuming NPS-containing products between January 2013 and December 2014. Letters requesting participation were sent to 467 emergency facilities, and questionnaires were mailed to facilities that agreed to participate. <i>Results</i>: We surveyed 589 patients from 85 (18.2%) facilities. Most patients were male (89.6%) and young (median age, 30 years), and inhaled (88%) NPS contained in herbal products (80.5%). Harmful behavior was observed at the scene of acute reaction, including violence (6.9%), traffic accidents (4.9%), and self-injury or suicidal attempts (1.1%). Other than neuropsychiatric and physical symptoms, many patients also had physical complications such as rhabdomyolysis (17.5%), liver injury (12.4%), acute kidney injury (9%), and physical injury (1.9%). Of the 256 patients (43.5%) admitted to hospitals, 35 (5.9%) were hospitalized for seven or more days. Most patients (93.2%) completely recovered, although a few (1.4%) died. However, synthetic cannabinoids and synthetic cathinones were only detected in the blood of five patients. <i>Conclusion</i>: Consumption of NPS-containing products have been associated with harmful behaviors such as violence and traffic accidents, physical complications (e.g., rhabdomyolysis, liver injury), death, or physical and neuropsychiatric symptoms. Compared to a previous survey (2006–2012), the present survey revealed more severe toxicity.
DOI: 10.6084/m9.figshare.3443312
title: Functional conservation of the lncRNA NEAT1 in the ancestrally diverged marsupial lineage: Evidence for NEAT1 expression and associated paraspeckle assembly during late gestation in the opossum <i>Monodelphis domestica</i>

description: Long non-coding RNAs (lncRNAs) are widely expressed and play various roles in cell homeostasis. However, because of their low conservation at the sequence level, recapitulating lncRNA evolutionary history is often challenging. While performing an ultrastructural analysis of viral particles present in uterine glands of gestating opossum females, we serendipitously noticed the presence of numerous structures similar to paraspeckles, nuclear bodies which in human and mouse cells are assembled around an architectural NEAT1/MENϵ/β lncRNA. Here, using an opossum kidney (OK) cell line, we confirmed by immuno-electron microscopy the presence of paraspeckles in marsupials. We then identified the orthologous opossum <i>NEAT1</i> gene which, although poorly conserved at the sequence level, displays NEAT1 characteristic features such as short and long isoforms expressed from a unique promoter and for the latter an RNase P cleavage site at its 3′-end. Combining tissue-specific qRT-PCR, <i>in situ</i> hybridization at the optical and electron microscopic levels, we show that (i) NEAT1 is paraspeckle-associated in opossum (ii) NEAT1 expression is strongly induced in late gestation in uterine/placental extracts (iii) NEAT1 induction occurs in the uterine gland nuclei in which paraspeckles were detected. Finally, treatment of OK cells with proteasome inhibitors induces paraspeckle assembly, as previously observed in human cells. Altogether, these results demonstrate that paraspeckles are tissue-specific, stress-responding nuclear bodies in marsupials, illustrating their structural and functional continuity over 200 My of evolution throughout the mammalian lineage. In contrast, the rapid evolution of the NEAT1 transcripts highlights the relaxed constraint that, despite functional conservation, is exerted on this lncRNA.
DOI: 10.6084/m9.figshare.3443312.v1
title: Functional conservation of the lncRNA NEAT1 in the ancestrally diverged marsupial lineage: evidence for NEAT1 expression and associated paraspeckle assembly during late gestation in the opossum <i>Monodelphis domestica</i>.

description: Long non-coding RNAs (lncRNAs) are widely expressed and play various roles in cell homeostasis. However, because of their low conservation at the sequence level, recapitulating lncRNA evolutionary history is often challenging. While performing an ultrastructural analysis of viral particles present in uterine glands of gestating opossum females, we serendipitously noticed the presence of numerous structures similar to paraspeckles, nuclear bodies which in human and mouse cells are assembled around an architectural NEAT1/MENϵ/β lncRNA. Here, using an opossum kidney (OK) cell line, we confirmed by immuno-electron microscopy the presence of paraspeckles in marsupials. We then identified the orthologous opossum <i>NEAT1</i> gene which, although poorly conserved at the sequence level, displays NEAT1 characteristic features such as short and long isoforms expressed from a unique promoter and for the latter an RNase P cleavage site at its 3′-end. Combining tissue-specific qRT-PCR, <i>in situ</i> hybridization at the optical and electron microscopic levels, we show that (i) NEAT1 is paraspeckle-associated in opossum (ii) NEAT1 expression is strongly induced in late gestation in uterine/placental extracts (iii) NEAT1 induction occurs in the uterine gland nuclei in which paraspeckles were detected. Finally, treatment of OK cells with proteasome inhibitors induces paraspeckle assembly, as previously observed in human cells. Altogether, these results demonstrate that paraspeckles are tissue-specific, stress-responding nuclear bodies in marsupials, illustrating their structural and functional continuity over 200 My of evolution throughout the mammalian lineage. In contrast, the rapid evolution of the NEAT1 transcripts highlights the relaxed constraint that, despite functional conservation, is exerted on this lncRNA.
DOI: 10.6084/m9.figshare.3443291
title: Distribution of thyroid hormone and thyrotropin receptors in reproductive tissues of adult female rabbits

description: <b>Purpose</b>: Thyroid dysfunctions are related to anovulation, miscarriages, and infertility in women and laboratory animals. Mechanisms associated with these effects are unknown, although indirect or direct actions of thyroid hormones and thyrotropin could be assumed. The present study aimed to identify the distribution of thyroid hormones (TRs) and thyrotropin (TSHR) receptors in reproductive organs of female rabbits. <b>Material and Methods</b>: Ovary of virgin and pregnant rabbits, as well as the oviduct, uterus, and vagina of virgin rabbits were excised, histologically processed, and cut. Slices from these organs were used for immunohistochemical studies for TRα1-2, TRß1, and TSHR. <b>Results</b>: The presence of TRs and TSHR was found in the primordial, primary, secondary, tertiary, and Graafian follicles of virgin rabbits, as well as in the corpora lutea, corpora albicans, and wall of hemorrhagic cysts of pregnant rabbits. Oviductal regions (fimbria-infundibulum, ampulla, isthmus, and utero-tubal junction), uterus (endometrium and myometrium), and vagina (abdominal, pelvic, and perineal portions) of virgin rabbits showed anti-TRs and anti-TSHR immunoreactivity. Additionally, the distal urethra, paravaginal ganglia, levator ani and iliococcygeus muscles, dorsal nerve and body of the clitoris, perigenital skin, and prostate had TRs and TSHR. <b>Conclusions</b>: The wide presence of TRs and TSHR in female reproductive organs suggests varied effects of thyroid hormones and thyrotropin in reproduction.
DOI: 10.6084/m9.figshare.3443291.v1
title: Distribution of thyroid hormone and thyrotropin receptors in reproductive tissues of adult female rabbits

description: <b>Purpose</b>: Thyroid dysfunctions are related to anovulation, miscarriages, and infertility in women and laboratory animals. Mechanisms associated with these effects are unknown, although indirect or direct actions of thyroid hormones and thyrotropin could be assumed. The present study aimed to identify the distribution of thyroid hormones (TRs) and thyrotropin (TSHR) receptors in reproductive organs of female rabbits. <b>Material and Methods</b>: Ovary of virgin and pregnant rabbits, as well as the oviduct, uterus, and vagina of virgin rabbits were excised, histologically processed, and cut. Slices from these organs were used for immunohistochemical studies for TRα1-2, TRß1, and TSHR. <b>Results</b>: The presence of TRs and TSHR was found in the primordial, primary, secondary, tertiary, and Graafian follicles of virgin rabbits, as well as in the corpora lutea, corpora albicans, and wall of hemorrhagic cysts of pregnant rabbits. Oviductal regions (fimbria-infundibulum, ampulla, isthmus, and utero-tubal junction), uterus (endometrium and myometrium), and vagina (abdominal, pelvic, and perineal portions) of virgin rabbits showed anti-TRs and anti-TSHR immunoreactivity. Additionally, the distal urethra, paravaginal ganglia, levator ani and iliococcygeus muscles, dorsal nerve and body of the clitoris, perigenital skin, and prostate had TRs and TSHR. <b>Conclusions</b>: The wide presence of TRs and TSHR in female reproductive organs suggests varied effects of thyroid hormones and thyrotropin in reproduction.
DOI: 10.6084/m9.figshare.3443267
title: NEON Data Institute 2016 - Remote Sensing Data Subsets

description: This collections contains a remote sensing data subset for NEON field sites in Domain 01 & 03 (Florida, Georgia, Massachusetts). This data supports teaching materials for the 2016 Data Institute. More information can be found here: http://neondataskills.org/workshop-event/NEON-Work-With-Data-Insitute-2016
DOI: 10.6084/m9.figshare.3443267.v1
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 17 - California Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v2
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 03 - Florida Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v3
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachusettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v4
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v5
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v6
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v7
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v8
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443267.v10
title: NEON Data Institute 2016 - Remote Sensing Data Subsets

description: This collections contains a remote sensing data subset for NEON field sites in Domain 01 & 03 (Florida, Georgia, Massachusetts). This data supports teaching materials for the 2016 Data Institute. More information can be found here: http://neondataskills.org/workshop-event/NEON-Work-With-Data-Insitute-2016
DOI: 10.6084/m9.figshare.3443267.v9
title: NEON Data Institute 2016 - Remote Sensing Data Subsets - Domain 01, 03, - Florida, Georgia, Massachussettes Field Sites

description: This repo contains a data subset for the NEON Ordway Swisher Biological Station Field Site located in Domain 03 - Florida.<br>
DOI: 10.6084/m9.figshare.3443210
title: Multi-interaction network involving different types of mutualism (animal pollination, seed-dispersal by frugivorous birds, and anti-herbivore defense by protective ants) sampled in a coastal tropical environment in Mexico.

description: Interaction matrix A, in which elements aij = 1 represent the presence of an interaction between the plant species i and the animal species j, and zero for no observed interaction
DOI: 10.6084/m9.figshare.3443210.v1
title: Interaction matrix A, in which elements aij = 1 represent the presence of an interaction between the plant species i and the animal species j, and zero for no observed interaction

description: Multi-interaction network involving different types of mutualism (animal pollination, seed-dispersal by frugivorous birds, and anti-herbivore defense by protective ants) sampled in a coastal tropical environment in Mexico
DOI: 10.6084/m9.figshare.3443165
title: Supplement 2 - Sex-related factor loadings

description: Supplement 2 - Sex-related factor loadings<br><br>(from the article "The relation of Toxoplasma infection and sexual attraction to fear, danger, pain and submissiveness")